@article {pmid34962958,
year = {2021},
author = {Ren, W and Zhao, J and Ma, X and Wang, X},
title = {Analysis of the spatial differentiation and scale effects of the three-dimensional architectural landscape in Xi'an, China.},
journal = {PloS one},
volume = {16},
number = {12},
pages = {e0261846},
pmid = {34962958},
issn = {1932-6203},
mesh = {*Architecture ; China ; Cities ; *City Planning ; Climate ; Conservation of Natural Resources ; *Ecology ; Ecosystem ; Geographic Information Systems ; Geography ; Models, Theoretical ; Principal Component Analysis ; Software ; Spatial Analysis ; Sustainable Development ; Urban Renewal ; },
abstract = {Three-dimensional landscape patterns are an effective means to study the relationship between landscape pattern evolution and eco-environmental effects. This paper selects six districts in Xi'an as the study area to examine the spatial distribution characteristics of the three-dimensional architectural landscape in the city's main urban area using three-dimensional information on the buildings in 2020 with the support of GIS. In this study, two new architectural landscape indices-landscape height variable coefficient and building rugosity index-were employed in landscape pattern analysis, whilst a system of rigorous and comprehensive three-dimensional architectural landscape metrics was established using principal component analysis. A mathematical model of weighted change of landscape metrics based on the objective weighting method was applied to carry out scale analysis of the landscape patterns. Spatial statistical analysis and spatial autocorrelation analysis were conducted to comprehensively study the differentiation of three-dimensional architectural landscape spatial patterns. The results show that the characteristic scale of the three-dimensional landscape pattern in Xi'an's main urban area is around 8 km. Moreover, the three-dimensional landscape of the buildings in this area is spatially positively correlated, exhibiting a high degree of spatial autocorrelation whilst only showing small spatial differences. The layout of the architectural landscape pattern is disorderly and chaotic within the second ring, whilst the clustering of patch types occurs near the third ring. Moreover, the building density in the Beilin, Lianhu, and Xincheng districts is large, the building height types are rich, and the roughness of the underlying surface is high, such that these are key areas to be improved through urban renewal. The height, volume, density, morphological heterogeneity, and vertical roughness of the architectural landscape vary amongst functional areas within the study area. This paper is the first to apply the study of spatial heterogeneity of three-dimensional landscape patterns to Xi'an. It does so in order to provide a quantitative basis for urban landscape ecological design for urban renewal and the rational planning of built-up areas, which will promote the sustainable development of the city's urban environment.},
}

*Architecture
China
Cities
*City Planning
Climate
Conservation of Natural Resources
*Ecology
Ecosystem
Geographic Information Systems
Geography
Models, Theoretical
Principal Component Analysis
Software
Spatial Analysis
Sustainable Development
Urban Renewal

@article {pmid34396479,
year = {2022},
author = {Karabulut, Aİ and Yazici-Karabulut, B and Derin, P and Yesilnacar, MI and Cullu, MA},
title = {Landfill siting for municipal solid waste using remote sensing and geographic information system integrated analytic hierarchy process and simple additive weighting methods from the point of view of a fast-growing metropolitan area in GAP area of Turkey.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {3},
pages = {4044-4061},
pmid = {34396479},
issn = {1614-7499},
mesh = {Analytic Hierarchy Process ; Geographic Information Systems ; Humans ; *Refuse Disposal ; Remote Sensing Technology ; *Solid Waste ; Turkey ; Waste Disposal Facilities ; },
abstract = {The site selection process for municipal solid wastes (MSW) plays an important role in environmental impact studies by allowing the use of environmental design criteria in city and country planning. This process also includes the subject of urban planning due to its impact on the economy, ecology, and environmental health of the region. Urban growth is a phenomenon that is difficult to stop or limit in line with environmental, social, and economic changes and development. Therefore, the selection of solid waste landfill is of great importance in terms of ensuring a sustainable urban future. In the study, Landsat 5 and Landsat 8 satellite images, base map, soil, and geology maps were used for the integration of geospatial data. Each layer specified in the map has been formed using the spatial analysis potential of the ArcGIS10.5 software. In these digitized layers, weight scoring was made using the comparison matrix and the final suitability map was produced. All digital layers established in the generated maps were arranged according to the analytical hierarchy method (AHP) and subjected to the simple additive weighting (SAW) method. The results indicated that 13.51% of the total area was suitable for a sanitary landfill. As a result of this study, urban growth, population projection, and domestic solid waste volume of Sanliurfa province were determined. According to the 25-year population projection, the population in 2045 was approximately 4,471,938 people, and the cumulative waste volume was 27,415,627 m3. In addition, as a result of accepting the wastes of three metropolitan districts and seven district municipalities to the sanitary landfill, only "first candidate area" is the most and has been deemed appropriate. Given the ecological and environmental challenges (proximity to the city center, etc.) associated with the existing MSW sanitary landfill facility in Sanliurfa, the results of this study show that the geographic information system (GIS) integrated AHP and SAW method is an effective tool to assist decision makers to properly plan towards achieving a sustainable environment.},
}

Analytic Hierarchy Process
Geographic Information Systems
Humans
*Refuse Disposal
Remote Sensing Technology
*Solid Waste
Turkey
Waste Disposal Facilities

@article {pmid35003918,
year = {2021},
author = {La Manna, G and Picciulin, M and Crobu, A and Perretti, F and Ronchetti, F and Manghi, M and Ruiu, A and Ceccherelli, G},
title = {Marine soundscape and fish biophony of a Mediterranean marine protected area.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e12551},
doi = {10.7717/peerj.12551},
pmid = {35003918},
issn = {2167-8359},
abstract = {Background: Marine soundscape is the aggregation of sound sources known as geophony, biophony, and anthrophony. The soundscape analysis, in terms of collection and analysis of acoustic signals, has been proposed as a tool to evaluate the specific features of ecological assemblages and to estimate their acoustic variability over space and time. This study aimed to characterise the Capo Caccia-Isola Piana Marine Protected Area (Italy, Western Mediterranean Sea) soundscape over short temporal (few days) and spatial scales (few km) and to quantify the main anthropogenic and biological components, with a focus on fish biophonies.

Methods: Within the MPA, three sites were chosen each in a different protection zone (A for the integral protection, B as the partial protection, and C as the general protection). In each site, two underwater autonomous acoustic recorders were deployed in July 2020 at a depth of about 10 m on rocky bottoms. To characterise the contribution of both biophonies and anthrophonies, sea ambient noise (SAN) levels were measured as sound pressure level (SPL dB re: 1 μ Pa-rms) at eight 1/3 octave bands, centred from 125 Hz to 16 kHz, and biological and anthropogenic sounds were noted. Fish sounds were classified and counted following a catalogue of known fish sounds from the Mediterranean Sea based on the acoustic characteristic of sound types. A contemporary fish visual census had been carried out at the test sites.

Results: SPL were different by site, time (day vs. night), and hour. SPLs bands centred at 125, 250, and 500 Hz were significantly higher in the daytime, due to the high number of boats per minute whose noise dominated the soundscapes. The loudest man-made noise was found in the A zone, followed by the B and the C zone, confirming that MPA current regulations do not provide protection from acoustic pollution. The dominant biological components of the MPA soundscape were the impulsive sounds generated by some invertebrates, snapping shrimps and fish. The vast majority of fish sounds were recorded at the MPA site characterized by the highest sound richness, abundance, and Shannon-Wiener index, coherently with the results of a fish visual census. Moreover, the acoustic monitoring detected a sound associated with a cryptic species (Ophidion spp.) never reported in the study area before, further demonstrating the usefulness of passive acoustic monitoring as a complementary technique to species census. This study provides baseline data to detect future changes of the marine soundscapes and some suggestions to reduce the impact of noise on marine biodiversity.},
}

@article {pmid34552242,
year = {2021},
author = {Migliavacca, M and Musavi, T and Mahecha, MD and Nelson, JA and Knauer, J and Baldocchi, DD and Perez-Priego, O and Christiansen, R and Peters, J and Anderson, K and Bahn, M and Black, TA and Blanken, PD and Bonal, D and Buchmann, N and Caldararu, S and Carrara, A and Carvalhais, N and Cescatti, A and Chen, J and Cleverly, J and Cremonese, E and Desai, AR and El-Madany, TS and Farella, MM and Fernández-Martínez, M and Filippa, G and Forkel, M and Galvagno, M and Gomarasca, U and Gough, CM and Göckede, M and Ibrom, A and Ikawa, H and Janssens, IA and Jung, M and Kattge, J and Keenan, TF and Knohl, A and Kobayashi, H and Kraemer, G and Law, BE and Liddell, MJ and Ma, X and Mammarella, I and Martini, D and Macfarlane, C and Matteucci, G and Montagnani, L and Pabon-Moreno, DE and Panigada, C and Papale, D and Pendall, E and Penuelas, J and Phillips, RP and Reich, PB and Rossini, M and Rotenberg, E and Scott, RL and Stahl, C and Weber, U and Wohlfahrt, G and Wolf, S and Wright, IJ and Yakir, D and Zaehle, S and Reichstein, M},
title = {The three major axes of terrestrial ecosystem function.},
journal = {Nature},
volume = {598},
number = {7881},
pages = {468-472},
pmid = {34552242},
issn = {1476-4687},
mesh = {*Carbon Cycle ; Carbon Dioxide/metabolism ; Climate ; Datasets as Topic ; *Ecosystem ; Humidity ; Plants/classification/*metabolism ; Principal Component Analysis ; *Water Cycle ; },
abstract = {The leaf economics spectrum1,2 and the global spectrum of plant forms and functions3 revealed fundamental axes of variation in plant traits, which represent different ecological strategies that are shaped by the evolutionary development of plant species2. Ecosystem functions depend on environmental conditions and the traits of species that comprise the ecological communities4. However, the axes of variation of ecosystem functions are largely unknown, which limits our understanding of how ecosystems respond as a whole to anthropogenic drivers, climate and environmental variability4,5. Here we derive a set of ecosystem functions6 from a dataset of surface gas exchange measurements across major terrestrial biomes. We find that most of the variability within ecosystem functions (71.8%) is captured by three key axes. The first axis reflects maximum ecosystem productivity and is mostly explained by vegetation structure. The second axis reflects ecosystem water-use strategies and is jointly explained by variation in vegetation height and climate. The third axis, which represents ecosystem carbon-use efficiency, features a gradient related to aridity, and is explained primarily by variation in vegetation structure. We show that two state-of-the-art land surface models reproduce the first and most important axis of ecosystem functions. However, the models tend to simulate more strongly correlated functions than those observed, which limits their ability to accurately predict the full range of responses to environmental changes in carbon, water and energy cycling in terrestrial ecosystems7,8.},
}

*Carbon Cycle
Carbon Dioxide/metabolism
Climate
Datasets as Topic
*Ecosystem
Humidity
Plants/classification/*metabolism
Principal Component Analysis
*Water Cycle

@article {pmid34234328,
year = {2021},
author = {Queiroz, N and Humphries, NE and Couto, A and Vedor, M and da Costa, I and Sequeira, AMM and Mucientes, G and Santos, AM and Abascal, FJ and Abercrombie, DL and Abrantes, K and Acuña-Marrero, D and Afonso, AS and Afonso, P and Anders, D and Araujo, G and Arauz, R and Bach, P and Barnett, A and Bernal, D and Berumen, ML and Lion, SB and Bezerra, NPA and Blaison, AV and Block, BA and Bond, ME and Bonfil, R and Braun, CD and Brooks, EJ and Brooks, A and Brown, J and Byrne, ME and Campana, SE and Carlisle, AB and Chapman, DD and Chapple, TK and Chisholm, J and Clarke, CR and Clua, EG and Cochran, JEM and Crochelet, EC and Dagorn, L and Daly, R and Cortés, DD and Doyle, TK and Drew, M and Duffy, CAJ and Erikson, T and Espinoza, E and Ferreira, LC and Ferretti, F and Filmalter, JD and Fischer, GC and Fitzpatrick, R and Fontes, J and Forget, F and Fowler, M and Francis, MP and Gallagher, AJ and Gennari, E and Goldsworthy, SD and Gollock, MJ and Green, JR and Gustafson, JA and Guttridge, TL and Guzman, HM and Hammerschlag, N and Harman, L and Hazin, FHV and Heard, M and Hearn, AR and Holdsworth, JC and Holmes, BJ and Howey, LA and Hoyos, M and Hueter, RE and Hussey, NE and Huveneers, C and Irion, DT and Jacoby, DMP and Jewell, OJD and Johnson, R and Jordan, LKB and Joyce, W and Keating Daly, CA and Ketchum, JT and Klimley, AP and Kock, AA and Koen, P and Ladino, F and Lana, FO and Lea, JSE and Llewellyn, F and Lyon, WS and MacDonnell, A and Macena, BCL and Marshall, H and McAllister, JD and Meÿer, MA and Morris, JJ and Nelson, ER and Papastamatiou, YP and Peñaherrera-Palma, C and Pierce, SJ and Poisson, F and Quintero, LM and Richardson, AJ and Rogers, PJ and Rohner, CA and Rowat, DRL and Samoilys, M and Semmens, JM and Sheaves, M and Shillinger, G and Shivji, M and Singh, S and Skomal, GB and Smale, MJ and Snyders, LB and Soler, G and Soria, M and Stehfest, KM and Thorrold, SR and Tolotti, MT and Towner, A and Travassos, P and Tyminski, JP and Vandeperre, F and Vaudo, JJ and Watanabe, YY and Weber, SB and Wetherbee, BM and White, TD and Williams, S and Zárate, PM and Harcourt, R and Hays, GC and Meekan, MG and Thums, M and Irigoien, X and Eguiluz, VM and Duarte, CM and Sousa, LL and Simpson, SJ and Southall, EJ and Sims, DW},
title = {Reply to: Caution over the use of ecological big data for conservation.},
journal = {Nature},
volume = {595},
number = {7866},
pages = {E20-E28},
pmid = {34234328},
issn = {1476-4687},
mesh = {*Big Data ; Conservation of Natural Resources ; *Ecology ; },
}

*Big Data
Conservation of Natural Resources
*Ecology

@article {pmid34234327,
year = {2021},
author = {Harry, AV and Braccini, JM},
title = {Caution over the use of ecological big data for conservation.},
journal = {Nature},
volume = {595},
number = {7866},
pages = {E17-E19},
pmid = {34234327},
issn = {1476-4687},
mesh = {*Big Data ; Conservation of Natural Resources ; *Ecology ; },
}

*Big Data
Conservation of Natural Resources
*Ecology

@article {pmid34857747,
year = {2021},
author = {Yang, X and Baskin, CC and Baskin, JM and Pakeman, RJ and Huang, Z and Gao, R and Cornelissen, JHC},
title = {Global patterns of potential future plant diversity hidden in soil seed banks.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {7023},
pmid = {34857747},
issn = {2041-1723},
mesh = {Altitude ; *Biodiversity ; Databases, Factual ; Ecosystem ; *Models, Statistical ; Plant Dispersal/*physiology ; Plants/classification ; Seed Bank ; Seeds/classification/*physiology ; Soil ; },
abstract = {Soil seed banks represent a critical but hidden stock for potential future plant diversity on Earth. Here we compiled and analyzed a global dataset consisting of 15,698 records of species diversity and density for soil seed banks in natural plant communities worldwide to quantify their environmental determinants and global patterns. Random forest models showed that absolute latitude was an important predictor for diversity of soil seed banks. Further, climate and soil were the major determinants of seed bank diversity, while net primary productivity and soil characteristics were the main predictors of seed bank density. Moreover, global mapping revealed clear spatial patterns for soil seed banks worldwide; for instance, low densities may render currently species-rich low latitude biomes (such as tropical rain-forests) less resilient to major disturbances. Our assessment provides quantitative evidence of how environmental conditions shape the distribution of soil seed banks, which enables a more accurate prediction of the resilience and vulnerabilities of plant communities and biomes under global changes.},
}

Altitude
*Biodiversity
Databases, Factual
Ecosystem
*Models, Statistical
Plant Dispersal/*physiology
Plants/classification
Seed Bank
Seeds/classification/*physiology
Soil

@article {pmid34843472,
year = {2021},
author = {Osone, Y and Hashimoto, S and Kenzo, T},
title = {Verification of our empirical understanding of the physiology and ecology of two contrasting plantation species using a trait database.},
journal = {PloS one},
volume = {16},
number = {11},
pages = {e0254599},
pmid = {34843472},
issn = {1932-6203},
mesh = {Chamaecyparis/*physiology ; Climate Change ; Cryptomeria/*physiology ; Databases, Factual ; *Droughts ; *Ecosystem ; *Forests ; Trees ; },
abstract = {The effects of climate change on forest ecosystems take on increasing importance more than ever. Information on plant traits is a powerful predictor of ecosystem dynamics and functioning. We reviewed the major ecological traits, such as foliar gas exchange and nutrients, xylem morphology and drought tolerance, of Cryptomeria japonica and Chamaecyparis obtusa, which are major timber species in East Asia, especially in Japan, by using a recently developed functional trait database for both species (SugiHinokiDB). Empirically, C. obtusa has been planted under drier conditions, whereas C. japonica, which grows faster but thought to be less drought tolerant, has been planted under wetter conditions. Our analysis generally support the empirical knowledge: The maximum photosynthetic rate, stomatal conductance, foliar nutrient content and soil-to-foliage hydraulic conductance were higher in C. japonica than in C. obtusa. In contrast, the foliar turgor loss point and xylem pressure corresponding to 50% conductivity, which indicate drought tolerance, were lower in C. obtusa and are consistent with the drier habitat of C. obtusa. Ontogenetic shifts were also observed; as the age and height of the trees increased, foliar nutrient concentrations, foliar minimum midday water potential and specific leaf area decreased in C. japonica, suggesting that nutrient and water limitation occurs with the growth. In C. obtusa, the ontogenetic shits of these foliar traits were less pronounced. Among the Cupressaceae worldwide, the drought tolerance of C. obtusa, as well as C. japonica, was not as high. This may be related to the fact that the Japanese archipelago has historically not been subjected to strong dryness. The maximum photosynthetic rate showed intermediate values within the family, indicating that C. japonica and C. obtusa exhibit relatively high growth rates in the Cupressaceae family, and this is thought to be the reason why they have been selected as economically suitable timber species in Japanese forestry. This study clearly demonstrated that the plant trait database provides us a promising opportunity to verify out empirical knowledge of plantation management and helps us to understand effect of climate change on plantation forests by using trait-based modelling.},
}

Chamaecyparis/*physiology
Climate Change
Cryptomeria/*physiology
Databases, Factual
*Droughts
*Ecosystem
*Forests
Trees

@article {pmid34556766,
year = {2021},
author = {Kouba, M and Bartoš, L and Bartošová, J and Hongisto, K and Korpimäki, E},
title = {Long-term trends in the body condition of parents and offspring of Tengmalm's owls under fluctuating food conditions and climate change.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {18893},
pmid = {34556766},
issn = {2045-2322},
mesh = {Animals ; Climate Change ; Datasets as Topic ; Ecological Parameter Monitoring/*statistics & numerical data ; Female ; Finland ; Forests ; Male ; Physical Fitness/*physiology ; Population Dynamics/statistics & numerical data/trends ; Predatory Behavior ; Reproduction ; Seasons ; Strigiformes/*physiology ; },
abstract = {Physical condition is important for the ability to resist various parasites and diseases as well as in escaping predators thus contributing to reproductive success, over-winter survival and possible declines in wildlife populations. However, in-depth research on trends in body condition is rare because decades-long datasets are not available for a majority of species. We analysed the long-term dataset of offspring covering 34 years, male parents (40 years) and female parents (42 years) to find out whether the decline of Tengmalm's owl population in western Finland is attributable to either decreased adult and/or juvenile body condition in interaction with changing weather conditions and density estimates of main foods. We found that body condition of parent owl males and females declined throughout the 40-year study period whereas the body condition of owlets at the fledging stage very slightly increased. The body condition of parent owls increased with augmenting depth of snow cover in late winter (January to March), and that of offspring improved with increasing precipitation in late spring (May to June). We conclude that the decreasing trend of body condition of parent owl males and females is important factor probably inducing reduced adult survival and reduced reproduction success thus contributing to the long-term decline of the Tengmalm's owl study population. The very slightly increasing trend of body condition of offspring is obviously not able to compensate the overall decline of Tengmalm's owl population, because the number of offspring in turn simultaneously decreased considerably in the long-term. The ongoing climate change appeared to work in opposite ways in this case because declining depth of snow cover will make the situation worse but increased precipitation will improve. We suggest that the main reasons for long-term decline of body condition of parent owls are interactive or additive effects of reduced food resources and increased overall predation risk due to habitat degradation (loss and fragmentation of mature and old-growth forests due to clear-felling) subsequently leading to decline of Tengmalm's owl study population.},
}

Animals
Climate Change
Datasets as Topic
Ecological Parameter Monitoring/*statistics & numerical data
Female
Finland
Forests
Male
Physical Fitness/*physiology
Population Dynamics/statistics & numerical data/trends
Predatory Behavior
Reproduction
Seasons
Strigiformes/*physiology

@article {pmid34938590,
year = {2021},
author = {Latombe, G and Richardson, DM and McGeoch, MA and Altwegg, R and Catford, JA and Chase, JM and Courchamp, F and Esler, KJ and Jeschke, JM and Landi, P and Measey, J and Midgley, GF and Minoarivelo, HO and Rodger, JG and Hui, C},
title = {Mechanistic reconciliation of community and invasion ecology.},
journal = {Ecosphere (Washington, D.C)},
volume = {12},
number = {2},
pages = {e03359},
doi = {10.1002/ecs2.3359},
pmid = {34938590},
issn = {2150-8925},
abstract = {Community and invasion ecology have mostly grown independently. There is substantial overlap in the processes captured by different models in the two fields, and various frameworks have been developed to reduce this redundancy and synthesize information content. Despite broad recognition that community and invasion ecology are interconnected, a process-based framework synthesizing models across these two fields is lacking. Here we review 65 representative community and invasion models and propose a common framework articulated around six processes (dispersal, drift, abiotic interactions, within-guild interactions, cross-guild interactions, and genetic changes). The framework is designed to synthesize the content of the two fields, provide a general perspective on their development, and enable their comparison. The application of this framework and of a novel method based on network theory reveals some lack of coherence between the two fields, despite some historical similarities. Community ecology models are characterized by combinations of multiple processes, likely reflecting the search for an overarching theory to explain community assembly and structure, drawing predominantly on interaction processes, but also accounting largely for the other processes. In contrast, most models in invasion ecology invoke fewer processes and focus more on interactions between introduced species and their novel biotic and abiotic environment. The historical dominance of interaction processes and their independent developments in the two fields is also reflected in the lower level of coherence for models involving interactions, compared to models involving dispersal, drift, and genetic changes. It appears that community ecology, with a longer history than invasion ecology, has transitioned from the search for single explanations for patterns observed in nature to investigate how processes may interact mechanistically, thereby generating and testing hypotheses. Our framework paves the way for a similar transition in invasion ecology, to better capture the dynamics of multiple alien species introduced in complex communities. Reciprocally, applying insights from invasion to community ecology will help us understand and predict the future of ecological communities in the Anthropocene, in which human activities are weakening species' natural boundaries. Ultimately, the successful integration of the two fields could advance a predictive ecology that is urgently required in a rapidly changing world.},
}

@article {pmid33367263,
year = {2020},
author = {Cruzan, MB and Hendrickson, EC},
title = {Landscape Genetics of Plants: Challenges and Opportunities.},
journal = {Plant communications},
volume = {1},
number = {6},
pages = {100100},
pmid = {33367263},
issn = {2590-3462},
mesh = {*Ecosystem ; *Gene Flow ; Genetics, Population/*instrumentation ; Geographic Information Systems/*instrumentation ; Plant Dispersal/*genetics ; Plants/*genetics ; },
abstract = {Dispersal is one of the most important but least understood processes in plant ecology and evolutionary biology. Dispersal of seeds maintains and establishes populations, and pollen and seed dispersal are responsible for gene flow within and among populations. Traditional views of dispersal and gene flow assume models that are governed solely by geographic distance and do not account for variation in dispersal vector behavior in response to heterogenous landscapes. Landscape genetics integrates population genetics with Geographic Information Systems (GIS) to evaluate the effects of landscape features on gene flow patterns (effective dispersal). Surprisingly, relatively few landscape genetic studies have been conducted on plants. Plants present advantages because their populations are stationary, allowing more reliable estimates of the effects of landscape features on effective dispersal rates. On the other hand, plant dispersal is intrinsically complex because it depends on the habitat preferences of the plant and its pollen and seed dispersal vectors. We discuss strategies to assess the separate contributions of pollen and seed movement to effective dispersal and to delineate the effects of plant habitat quality from those of landscape features that affect vector behavior. Preliminary analyses of seed dispersal for three species indicate that isolation by landscape resistance is a better predictor of the rates and patterns of dispersal than geographic distance. Rates of effective dispersal are lower in areas of high plant habitat quality, which may be due to the effects of the shape of the dispersal kernel or to movement behaviors of biotic vectors. Landscape genetic studies in plants have the potential to provide novel insights into the process of gene flow among populations and to improve our understanding of the behavior of biotic and abiotic dispersal vectors in response to heterogeneous landscapes.},
}

*Ecosystem
*Gene Flow
Genetics, Population/*instrumentation
Geographic Information Systems/*instrumentation
Plant Dispersal/*genetics
Plants/*genetics

@article {pmid34921678,
year = {2021},
author = {Allen-Perkins, A and Magrach, A and Dainese, M and Garibaldi, LA and Kleijn, D and Rader, R and Reilly, JR and Winfree, R and Lundin, O and McGrady, CM and Brittain, C and Biddinger, DJ and Artz, DR and Elle, E and Hoffman, G and Ellis, JD and Daniels, J and Gibbs, J and Campbell, JW and Brokaw, J and Wilson, JK and Mason, K and Ward, KL and Gundersen, KB and Bobiwash, K and Gut, L and Rowe, LM and Boyle, NK and Williams, NM and Joshi, NK and Rothwell, N and Gillespie, RL and Isaacs, R and Fleischer, SJ and Peterson, SS and Rao, S and Pitts-Singer, TL and Fijen, T and Boreux, V and Rundlöf, M and Viana, BF and Klein, AM and Smith, HG and Bommarco, R and Carvalheiro, LG and Ricketts, TH and Ghazoul, J and Krishnan, S and Benjamin, FE and Loureiro, J and Castro, S and Raine, NE and de Groot, GA and Horgan, FG and Hipólito, J and Smagghe, G and Meeus, I and Eeraerts, M and Potts, SG and Kremen, C and García, D and Miñarro, M and Crowder, DW and Pisanty, G and Mandelik, Y and Vereecken, NJ and Leclercq, N and Weekers, T and Lindstrom, SAM and Stanley, DA and Zaragoza-Trello, C and Nicholson, CC and Scheper, J and Rad, C and Marks, EAN and Mota, L and Danforth, B and Park, M and Bezerra, ADM and Freitas, BM and Mallinger, RE and da Silva, FO and Willcox, B and Ramos, DL and da Silva E Silva, FD and Lázaro, A and Alomar, D and González-Estévez, MA and Taki, H and Cariveau, DP and Garratt, MPD and Nabaes Jodar, DN and Stewart, RIA and Ariza, D and Pisman, M and Lichtenberg, EM and Schüepp, C and Herzog, F and Entling, MH and Dupont, YL and Michener, CD and Daily, GC and Ehrlich, PR and Burns, KLW and Vilà, M and Robson, A and Howlett, B and Blechschmidt, L and Jauker, F and Schwarzbach, F and Nesper, M and Diekötter, T and Wolters, V and Castro, H and Gaspar, H and Nault, BA and Badenhausser, I and Petersen, JD and Tscharntke, T and Bretagnolle, V and Chan, DSW and Chacoff, N and Andersson, GKS and Jha, S and Colville, JF and Veldtman, R and Coutinho, J and Bianchi, FJJA and Sutter, L and Albrecht, M and Jeanneret, P and Zou, Y and Averill, AL and Saez, A and Sciligo, AR and Vergara, CH and Bloom, EH and Oeller, E and Badano, EI and Loeb, GM and Grab, H and Ekroos, J and Gagic, V and Cunningham, SA and Åström, J and Cavigliasso, P and Trillo, A and Classen, A and Mauchline, AL and Montero-Castaño, A and Wilby, A and Woodcock, BA and Sidhu, CS and Steffan-Dewenter, I and Vogiatzakis, IN and Herrera, JM and Otieno, M and Gikungu, MW and Cusser, SJ and Nauss, T and Nilsson, L and Knapp, J and Ortega-Marcos, JJ and González, JA and Osborne, JL and Blanche, R and Shaw, RF and Hevia, V and Stout, J and Arthur, AD and Blochtein, B and Szentgyorgyi, H and Li, J and Mayfield, MM and Woyciechowski, M and Nunes-Silva, P and de Oliveira, RH and Henry, S and Simmons, BI and Dalsgaard, B and Hansen, K and Sritongchuay, T and O'Reilly, AD and García, FJC and Parra, GN and Pigozo, CM and Bartomeus, I},
title = {CropPol: a dynamic, open and global database on crop pollination.},
journal = {Ecology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ecy.3614},
pmid = {34921678},
issn = {1939-9170},
abstract = {Seventy five percent of the world's food crops benefit from insect pollination. Hence, there has been increased interest in how global change drivers impact this critical ecosystem service. Because standardized data on crop pollination are rarely available, we are limited in our capacity to understand the variation in pollination benefits to crop yield, as well as to anticipate changes in this service, develop predictions, and inform management actions. Here, we present CropPol, a dynamic, open and global database on crop pollination. It contains measurements recorded from 202 crop studies, covering 3,394 field observations, 2,552 yield measurements (i.e. berry weight, number of fruits and kg per hectare, among others), and 47,752 insect records from 48 commercial crops distributed around the globe. CropPol comprises 32 of the 87 leading global crops and commodities that are pollinator dependent. Malus domestica is the most represented crop (32 studies), followed by Brassica napus (22 studies), Vaccinium corymbosum (13 studies), and Citrullus lanatus (12 studies). The most abundant pollinator guilds recorded are honey bees (34.22% counts), bumblebees (19.19%), flies other than Syrphidae and Bombyliidae (13.18%), other wild bees (13.13%), beetles (10.97%), Syrphidae (4.87%), and Bombyliidae (0.05%). Locations comprise 34 countries distributed among Europe (76 studies), Northern America (60), Latin America and the Caribbean (29), Asia (20), Oceania (10), and Africa (7). Sampling spans three decades and is concentrated on 2001-05 (21 studies), 2006-10 (40), 2011-15 (88), and 2016-20 (50). This is the most comprehensive open global data set on measurements of crop flower visitors, crop pollinators and pollination to date, and we encourage researchers to add more datasets to this database in the future. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA). This article is protected by copyright. All rights reserved.},
}

@article {pmid34648487,
year = {2021},
author = {Grundler, MC and Rabosky, DL},
title = {Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction.},
journal = {PLoS biology},
volume = {19},
number = {10},
pages = {e3001414},
pmid = {34648487},
issn = {1545-7885},
mesh = {Animals ; *Biodiversity ; Databases as Topic ; *Diet ; *Extinction, Biological ; Models, Biological ; Multivariate Analysis ; Phenotype ; Phylogeny ; Snakes/*physiology ; Time Factors ; },
abstract = {The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs as well as to long-term physiographic changes that created new biogeographic theaters and new habitats. Snakes underwent massive ecological diversification during this period, repeatedly evolving novel dietary adaptations and prey preferences. The evolutionary tempo and mode of these trophic ecological changes remain virtually unknown, especially compared with co-radiating lineages of birds and mammals that are simultaneously predators and prey of snakes. Here, we assemble a dataset on snake diets (34,060 observations on the diets of 882 species) to investigate the history and dynamics of the multidimensional trophic niche during the global radiation of snakes. Our results show that per-lineage dietary niche breadths remained remarkably constant even as snakes diversified to occupy disparate outposts of dietary ecospace. Rapid increases in dietary diversity and complexity occurred in the early Cenozoic, and the overall rate of ecospace expansion has slowed through time, suggesting a potential response to ecological opportunity in the wake of the end-Cretaceous mass extinction. Explosive bursts of trophic innovation followed colonization of the Nearctic and Neotropical realms by a group of snakes that today comprises a majority of living snake diversity. Our results indicate that repeated transformational shifts in dietary ecology are important drivers of adaptive radiation in snakes and provide a framework for analyzing and visualizing the evolution of complex ecological phenotypes on phylogenetic trees.},
}

Animals
*Biodiversity
Databases as Topic
*Diet
*Extinction, Biological
Models, Biological
Multivariate Analysis
Phenotype
Phylogeny
Snakes/*physiology
Time Factors

@article {pmid34593819,
year = {2021},
author = {Falster, D and Gallagher, R and Wenk, EH and Wright, IJ and Indiarto, D and Andrew, SC and Baxter, C and Lawson, J and Allen, S and Fuchs, A and Monro, A and Kar, F and Adams, MA and Ahrens, CW and Alfonzetti, M and Angevin, T and Apgaua, DMG and Arndt, S and Atkin, OK and Atkinson, J and Auld, T and Baker, A and von Balthazar, M and Bean, A and Blackman, CJ and Bloomfield, K and Bowman, DMJS and Bragg, J and Brodribb, TJ and Buckton, G and Burrows, G and Caldwell, E and Camac, J and Carpenter, R and Catford, JA and Cawthray, GR and Cernusak, LA and Chandler, G and Chapman, AR and Cheal, D and Cheesman, AW and Chen, SC and Choat, B and Clinton, B and Clode, PL and Coleman, H and Cornwell, WK and Cosgrove, M and Crisp, M and Cross, E and Crous, KY and Cunningham, S and Curran, T and Curtis, E and Daws, MI and DeGabriel, JL and Denton, MD and Dong, N and Du, P and Duan, H and Duncan, DH and Duncan, RP and Duretto, M and Dwyer, JM and Edwards, C and Esperon-Rodriguez, M and Evans, JR and Everingham, SE and Farrell, C and Firn, J and Fonseca, CR and French, BJ and Frood, D and Funk, JL and Geange, SR and Ghannoum, O and Gleason, SM and Gosper, CR and Gray, E and Groom, PK and Grootemaat, S and Gross, C and Guerin, G and Guja, L and Hahs, AK and Harrison, MT and Hayes, PE and Henery, M and Hochuli, D and Howell, J and Huang, G and Hughes, L and Huisman, J and Ilic, J and Jagdish, A and Jin, D and Jordan, G and Jurado, E and Kanowski, J and Kasel, S and Kellermann, J and Kenny, B and Kohout, M and Kooyman, RM and Kotowska, MM and Lai, HR and Laliberté, E and Lambers, H and Lamont, BB and Lanfear, R and van Langevelde, F and Laughlin, DC and Laugier-Kitchener, BA and Laurance, S and Lehmann, CER and Leigh, A and Leishman, MR and Lenz, T and Lepschi, B and Lewis, JD and Lim, F and Liu, U and Lord, J and Lusk, CH and Macinnis-Ng, C and McPherson, H and Magallón, S and Manea, A and López-Martinez, A and Mayfield, M and McCarthy, JK and Meers, T and van der Merwe, M and Metcalfe, DJ and Milberg, P and Mokany, K and Moles, AT and Moore, BD and Moore, N and Morgan, JW and Morris, W and Muir, A and Munroe, S and Nicholson, Á and Nicolle, D and Nicotra, AB and Niinemets, Ü and North, T and O'Reilly-Nugent, A and O'Sullivan, OS and Oberle, B and Onoda, Y and Ooi, MKJ and Osborne, CP and Paczkowska, G and Pekin, B and Guilherme Pereira, C and Pickering, C and Pickup, M and Pollock, LJ and Poot, P and Powell, JR and Power, SA and Prentice, IC and Prior, L and Prober, SM and Read, J and Reynolds, V and Richards, AE and Richardson, B and Roderick, ML and Rosell, JA and Rossetto, M and Rye, B and Rymer, PD and Sams, MA and Sanson, G and Sauquet, H and Schmidt, S and Schönenberger, J and Schulze, ED and Sendall, K and Sinclair, S and Smith, B and Smith, R and Soper, F and Sparrow, B and Standish, RJ and Staples, TL and Stephens, R and Szota, C and Taseski, G and Tasker, E and Thomas, F and Tissue, DT and Tjoelker, MG and Tng, DYP and de Tombeur, F and Tomlinson, K and Turner, NC and Veneklaas, EJ and Venn, S and Vesk, P and Vlasveld, C and Vorontsova, MS and Warren, CA and Warwick, N and Weerasinghe, LK and Wells, J and Westoby, M and White, M and Williams, NSG and Wills, J and Wilson, PG and Yates, C and Zanne, AE and Zemunik, G and Ziemińska, K},
title = {AusTraits, a curated plant trait database for the Australian flora.},
journal = {Scientific data},
volume = {8},
number = {1},
pages = {254},
pmid = {34593819},
issn = {2052-4463},
support = {FT160100113//Department of Education and Training | Australian Research Council (ARC)/ ; DE170100208//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Australia ; *Databases, Factual ; *Phenotype ; Plant Physiological Phenomena ; *Plants ; },
abstract = {We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.},
}

Australia
*Databases, Factual
*Phenotype
Plant Physiological Phenomena
*Plants

@article {pmid34219394,
year = {2021},
author = {Pauling, CD and Finke, DL and Anderson, DM},
title = {Interrelationship of soil moisture and temperature to sylvatic plague cycle among prairie dogs in the Western United States.},
journal = {Integrative zoology},
volume = {16},
number = {6},
pages = {852-867},
doi = {10.1111/1749-4877.12567},
pmid = {34219394},
issn = {1749-4877},
support = {//University of Missouri Research and Creative Works Program/ ; },
mesh = {Animals ; Climate Change ; Databases, Factual ; Plague/epidemiology/*veterinary ; Rodent Diseases/epidemiology/*microbiology ; Sciuridae/*microbiology ; Soil/*chemistry ; *Temperature ; United States/epidemiology ; Water/*chemistry ; Yersinia pestis/physiology ; },
abstract = {Plague, caused by Yersinia pestis, is a flea-borne disease that is endemic in areas throughout the world due to its successful maintenance in a sylvatic cycle, mainly in areas with temperate climates. Burrowing rodents are thought to play a key role in the enzootic maintenance as well as epizootic outbreaks of plague. In the United States, prairie dogs (Cynomys), rodents (Muridae), and ground squirrels (Spermophilus) are susceptible to infection and are parasitized by fleas that transmit plague. In particular, prairie dogs can experience outbreaks that rapidly spread, which can lead to extirpation of colonies. A number of ecological parameters, including climate, are associated with these epizootics. In this study, we asked whether soil parameters, primarily moisture and temperature, are associated with outbreaks of plague in black-tailed prairie dogs and Gunnison's prairie dogs in the Western United States, and at what depth these associations were apparent. We collected publicly available county-level information on the occurrence of population declines or colony extirpation, while historical soil data was collected from SCAN and USCRN stations in counties and states where prairie dogs have been located. The analysis suggests that soil moisture at lower depths correlates with colony die-offs, in addition to temperature near the surface, with key differences within the landscape ecology that impact the occurrence of plague. Overall, the model suggests that the burrow environment may play a significant role in the epizootic spread of disease amongst black-tailed and Gunnison's prairie dogs.},
}

Animals
Climate Change
Databases, Factual
Plague/epidemiology/*veterinary
Rodent Diseases/epidemiology/*microbiology
Sciuridae/*microbiology
Soil/*chemistry
*Temperature
United States/epidemiology
Water/*chemistry
Yersinia pestis/physiology

@article {pmid33888580,
year = {2021},
author = {Everson, KM and Gray, LN and Jones, AG and Lawrence, NM and Foley, ME and Sovacool, KL and Kratovil, JD and Hotaling, S and Hime, PM and Storfer, A and Parra-Olea, G and Percino-Daniel, R and Aguilar-Miguel, X and O'Neill, EM and Zambrano, L and Shaffer, HB and Weisrock, DW},
title = {Geography is more important than life history in the recent diversification of the tiger salamander complex.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {17},
pages = {},
pmid = {33888580},
issn = {1091-6490},
support = {T32 GM070449/GM/NIGMS NIH HHS/United States ; },
mesh = {Ambystoma/*genetics/*metabolism ; Ambystoma mexicanum/genetics ; Animals ; Databases, Genetic ; Gene Flow ; Genetics, Population/methods ; Geography ; Larva/genetics ; Metamorphosis, Biological/genetics ; North America ; Phylogeny ; },
abstract = {The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.},
}

Ambystoma/*genetics/*metabolism
Ambystoma mexicanum/genetics
Animals
Databases, Genetic
Gene Flow
Genetics, Population/methods
Geography
Larva/genetics
Metamorphosis, Biological/genetics
North America
Phylogeny

@article {pmid33860294,
year = {2021},
author = {Schweizer, RM and Saarman, N and Ramstad, KM and Forester, BR and Kelley, JL and Hand, BK and Malison, RL and Ackiss, AS and Watsa, M and Nelson, TC and Beja-Pereira, A and Waples, RS and Funk, WC and Luikart, G},
title = {Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field.},
journal = {The Journal of heredity},
volume = {112},
number = {4},
pages = {313-327},
doi = {10.1093/jhered/esab019},
pmid = {33860294},
issn = {1465-7333},
support = {DOB-1639014//National Science Foundation/ ; IOS-NSF 1755411//National Science Foundation/ ; },
mesh = {*Big Data ; Biological Evolution ; *Conservation of Natural Resources ; Genetics, Population ; Genomics ; Humans ; },
abstract = {A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.},
}

*Big Data
Biological Evolution
*Conservation of Natural Resources
Genetics, Population
Genomics
Humans

@article {pmid34877561,
year = {2021},
author = {Wang, F and Harindintwali, JD and Yuan, Z and Wang, M and Wang, F and Li, S and Yin, Z and Huang, L and Fu, Y and Li, L and Chang, SX and Zhang, L and Rinklebe, J and Yuan, Z and Zhu, Q and Xiang, L and Tsang, DCW and Xu, L and Jiang, X and Liu, J and Wei, N and Kästner, M and Zou, Y and Ok, YS and Shen, J and Peng, D and Zhang, W and Barceló, D and Zhou, Y and Bai, Z and Li, B and Zhang, B and Wei, K and Cao, H and Tan, Z and Zhao, LB and He, X and Zheng, J and Bolan, N and Liu, X and Huang, C and Dietmann, S and Luo, M and Sun, N and Gong, J and Gong, Y and Brahushi, F and Zhang, T and Xiao, C and Li, X and Chen, W and Jiao, N and Lehmann, J and Zhu, YG and Jin, H and Schäffer, A and Tiedje, JM and Chen, JM},
title = {Technologies and perspectives for achieving carbon neutrality.},
journal = {Innovation (New York, N.Y.)},
volume = {2},
number = {4},
pages = {100180},
doi = {10.1016/j.xinn.2021.100180},
pmid = {34877561},
issn = {2666-6758},
abstract = {Global development has been heavily reliant on the overexploitation of natural resources since the Industrial Revolution. With the extensive use of fossil fuels, deforestation, and other forms of land-use change, anthropogenic activities have contributed to the ever-increasing concentrations of greenhouse gases (GHGs) in the atmosphere, causing global climate change. In response to the worsening global climate change, achieving carbon neutrality by 2050 is the most pressing task on the planet. To this end, it is of utmost importance and a significant challenge to reform the current production systems to reduce GHG emissions and promote the capture of CO2 from the atmosphere. Herein, we review innovative technologies that offer solutions achieving carbon (C) neutrality and sustainable development, including those for renewable energy production, food system transformation, waste valorization, C sink conservation, and C-negative manufacturing. The wealth of knowledge disseminated in this review could inspire the global community and drive the further development of innovative technologies to mitigate climate change and sustainably support human activities.},
}

@article {pmid34834835,
year = {2021},
author = {Love, NLR and Bonnet, P and Goëau, H and Joly, A and Mazer, SJ},
title = {Machine Learning Undercounts Reproductive Organs on Herbarium Specimens but Accurately Derives Their Quantitative Phenological Status: A Case Study of Streptanthus tortuosus.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/plants10112471},
pmid = {34834835},
issn = {2223-7747},
abstract = {Machine learning (ML) can accelerate the extraction of phenological data from herbarium specimens; however, no studies have assessed whether ML-derived phenological data can be used reliably to evaluate ecological patterns. In this study, 709 herbarium specimens representing a widespread annual herb, Streptanthus tortuosus, were scored both manually by human observers and by a mask R-CNN object detection model to (1) evaluate the concordance between ML and manually-derived phenological data and (2) determine whether ML-derived data can be used to reliably assess phenological patterns. The ML model generally underestimated the number of reproductive structures present on each specimen; however, when these counts were used to provide a quantitative estimate of the phenological stage of plants on a given sheet (i.e., the phenological index or PI), the ML and manually-derived PI's were highly concordant. Moreover, herbarium specimen age had no effect on the estimated PI of a given sheet. Finally, including ML-derived PIs as predictor variables in phenological models produced estimates of the phenological sensitivity of this species to climate, temporal shifts in flowering time, and the rate of phenological progression that are indistinguishable from those produced by models based on data provided by human observers. This study demonstrates that phenological data extracted using machine learning can be used reliably to estimate the phenological stage of herbarium specimens and to detect phenological patterns.},
}

@article {pmid34182782,
year = {2021},
author = {Murareanu, BM and Sukhdeo, R and Qu, R and Jiang, J and Reinke, AW},
title = {Generation of a Microsporidia Species Attribute Database and Analysis of the Extensive Ecological and Phenotypic Diversity of Microsporidia.},
journal = {mBio},
volume = {12},
number = {3},
pages = {e0149021},
pmid = {34182782},
issn = {2150-7511},
mesh = {Animals ; *Databases, Factual ; *Ecology ; *Genetic Variation ; Host Specificity ; Humans ; Microsporidia/classification/*genetics ; *Phenotype ; },
abstract = {Microsporidia are a large group of fungus-related obligate intracellular parasites. Though many microsporidia species have been identified over the past 160 years, depiction of the full diversity of this phylum is lacking. To systematically describe the characteristics of these parasites, we created a database of 1,440 species and their attributes, including the hosts they infect and spore characteristics. We find that microsporidia have been reported to infect 16 metazoan and 4 protozoan phyla, with smaller phyla being underrepresented. Most species are reported to infect only a single host, but those that are generalists are also more likely to infect a broader set of host tissues. Strikingly, polar tubes are threefold longer in species that infect tissues besides the intestine, suggesting that polar tube length is a determinant of tissue specificity. Phylogenetic analysis revealed four clades which each contain microsporidia that infect hosts from all major habitats. Although related species are more likely to infect similar hosts, we observe examples of changes in host specificity and convergent evolution. Taken together, our results show that microsporidia display vast diversity in their morphology and the hosts they infect, illustrating the flexibility of these parasites to evolve new traits. IMPORTANCE Microsporidia are a large group of parasites that cause death and disease in humans and many agriculturally important animal species. To fully understand the diverse properties of these parasites, we curated species reports from the last 160 years. Using these data, we describe when and where microsporidia were identified and what types of animals and host tissues these parasites infect. Microsporidia infect hosts using a conserved apparatus known as the polar tube. We observe that the length of this tube is correlated with the tissues that are being infected, suggesting that the polar tube controls where within the animals that the parasite infects. Finally, we show that microsporidia species often exist in multiple environments and are flexible in their ability to evolve new traits. Our study provides insight into the ecology and evolution of microsporidia and provides a useful resource to further understand these fascinating parasites.},
}

Animals
*Databases, Factual
*Ecology
*Genetic Variation
Host Specificity
Humans
Microsporidia/classification/*genetics
*Phenotype

@article {pmid34785977,
year = {2021},
author = {Chamanara, J and Gaikwad, J and Gerlach, R and Algergawy, A and Ostrowski, A and König-Ries, B},
title = {BEXIS2: A FAIR-aligned data management system for biodiversity, ecology and environmental data.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e72901},
doi = {10.3897/BDJ.9.e72901},
pmid = {34785977},
issn = {1314-2828},
abstract = {Background: Obtaining fit-to-use data associated with diverse aspects of biodiversity, ecology and environment is challenging since often it is fragmented, sub-optimally managed and available in heterogeneous formats. Recently, with the universal acceptance of the FAIR data principles, the requirements and standards of data publications have changed substantially. Researchers are encouraged to manage the data as per the FAIR data principles and ensure that the raw data, metadata, processed data, software, codes and associated material are securely stored and the data be made available with the completion of the research.

New information: We have developed BEXIS2 as an open-source community-driven web-based research data management system to support research data management needs of mid to large-scale research projects with multiple sub-projects and up to several hundred researchers. BEXIS2 is a modular and extensible system providing a range of functions to realise the complete data lifecycle from data structure design to data collection, data discovery, dissemination, integration, quality assurance and research planning. It is an extensible and customisable system that allows for the development of new functions and customisation of its various components from database schemas to the user interface layout, elements and look and feel.During the development of BEXIS2, we aimed to incorporate key aspects of what is encoded in FAIR data principles. To investigate the extent to which BEXIS2 conforms to these principles, we conducted the self-assessment using the FAIR indicators, definitions and criteria provided in the FAIR Data Maturity Model. Even though the FAIR data maturity model is developed initially to judge the conformance of datasets, the self-assessment results indicated that BEXIS2 remarkably conforms and supports FAIR indicators. BEXIS2 strongly conforms to the indicators Findability and Accessibility. The indicator Interoperability is moderately supported as of now; however, for many of the lesssupported facets, we have concrete plans for improvement. Reusability (as defined by the FAIR data principles) is partially achieved.This paper also illustrates community deployment examples of the BEXIS2 instances as success stories to exemplify its capacity to meet the biodiversity and ecological data management needs of differently sized projects and serve as an organisational research data management system.},
}

@article {pmid34776776,
year = {2021},
author = {Ambarlı, D and Simons, NK and Wehner, K and Kämper, W and Gossner, MM and Nauss, T and Neff, F and Seibold, S and Weisser, W and Blüthgen, N},
title = {Animal-Mediated Ecosystem Process Rates in Forests and Grasslands are Affected by Climatic Conditions and Land-Use Intensity.},
journal = {Ecosystems (New York, N.Y.)},
volume = {24},
number = {2},
pages = {467-483},
doi = {10.1007/s10021-020-00530-7},
pmid = {34776776},
issn = {1432-9840},
abstract = {Decomposition, vegetation regeneration, and biological control are essential ecosystem functions, and animals are involved in the underlying processes, such as dung removal, seed removal, herbivory, and predation. Despite evidence for declines of animal diversity and abundance due to climate change and land-use intensification, we poorly understand how animal-mediated processes respond to these global change drivers. We experimentally measured rates of four ecosystem processes in 134 grassland and 149 forest plots in Germany and tested their response to climatic conditions and land-use intensity, that is, grazing, mowing, and fertilization in grasslands and the proportion of harvested wood, non-natural trees, and deadwood origin in forests. For both climate and land use, we distinguished between short-term effects during the survey period and medium-term effects during the preceding years. Forests had significantly higher process rates than grasslands. In grasslands, the climatic effects on the process rates were similar or stronger than land-use effects, except for predation; land-use intensity negatively affected several process rates. In forests, the land-use effects were more pronounced than the climatic effects on all processes except for predation. The proportion of non-natural trees had the greatest impact on the process rates in forests. The proportion of harvested wood had negative effects, whereas the proportion of anthropogenic deadwood had positive effects on some processes. The effects of climatic conditions and land-use intensity on process rates mirror climatic and habitat effects on animal abundance, activity, and resource quality. Our study demonstrates that land-use changes and interventions affecting climatic conditions will have substantial impacts on animal-mediated ecosystem processes.},
}

@article {pmid34319970,
year = {2021},
author = {Rubin, IN and Ispolatov, I and Doebeli, M},
title = {Evolution to alternative levels of stable diversity leaves areas of niche space unexplored.},
journal = {PLoS computational biology},
volume = {17},
number = {7},
pages = {e1008650},
pmid = {34319970},
issn = {1553-7358},
mesh = {*Biodiversity ; *Biological Evolution ; Computational Biology ; *Ecosystem ; Genetic Fitness ; *Models, Biological ; Mutation ; },
abstract = {One of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthur's classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lotka-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.},
}

*Biodiversity
*Biological Evolution
Computational Biology
*Ecosystem
Genetic Fitness
*Models, Biological
Mutation

@article {pmid33828196,
year = {2021},
author = {Spiesman, BJ and Gratton, C and Hatfield, RG and Hsu, WH and Jepsen, S and McCornack, B and Patel, K and Wang, G},
title = {Assessing the potential for deep learning and computer vision to identify bumble bee species from images.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7580},
pmid = {33828196},
issn = {2045-2322},
mesh = {Animals ; *Artificial Intelligence ; Bees/*anatomy & histology/*classification ; Conservation of Natural Resources ; Databases, Factual ; *Deep Learning ; Ecosystem ; Image Processing, Computer-Assisted ; Neural Networks, Computer ; North America ; Pigmentation ; Pollination ; Species Specificity ; },
abstract = {Pollinators are undergoing a global decline. Although vital to pollinator conservation and ecological research, species-level identification is expensive, time consuming, and requires specialized taxonomic training. However, deep learning and computer vision are providing ways to open this methodological bottleneck through automated identification from images. Focusing on bumble bees, we compare four convolutional neural network classification models to evaluate prediction speed, accuracy, and the potential of this technology for automated bee identification. We gathered over 89,000 images of bumble bees, representing 36 species in North America, to train the ResNet, Wide ResNet, InceptionV3, and MnasNet models. Among these models, InceptionV3 presented a good balance of accuracy (91.6%) and average speed (3.34 ms). Species-level error rates were generally smaller for species represented by more training images. However, error rates also depended on the level of morphological variability among individuals within a species and similarity to other species. Continued development of this technology for automatic species identification and monitoring has the potential to be transformative for the fields of ecology and conservation. To this end, we present BeeMachine, a web application that allows anyone to use our classification model to identify bumble bees in their own images.},
}

Animals
*Artificial Intelligence
Bees/*anatomy & histology/*classification
Conservation of Natural Resources
Databases, Factual
*Deep Learning
Ecosystem
Image Processing, Computer-Assisted
Neural Networks, Computer
North America
Pigmentation
Pollination
Species Specificity

@article {pmid34638623,
year = {2021},
author = {Hafeez, M and Li, X and Ullah, F and Zhang, Z and Zhang, J and Huang, J and Khan, MM and Chen, L and Ren, X and Zhou, S and Fernández-Grandon, GM and Zalucki, MP and Lu, Y},
title = {Behavioral and Physiological Plasticity Provides Insights into Molecular Based Adaptation Mechanism to Strain Shift in Spodoptera frugiperda.},
journal = {International journal of molecular sciences},
volume = {22},
number = {19},
pages = {},
pmid = {34638623},
issn = {1422-0067},
support = {2020C02003//The Key R&D Program of Zhejiang Province/ ; 233952//China National Postdoctoral Science foundation/ ; },
mesh = {Adaptation, Physiological/genetics ; Animals ; China ; Crops, Agricultural/parasitology ; Digestive System Physiological Phenomena ; Feeding Behavior/physiology ; Female ; Gene Ontology ; Genes, Insect ; Herbivory/genetics/physiology ; Host Adaptation/genetics/physiology ; Host Specificity/genetics/physiology ; Host-Parasite Interactions/genetics/physiology ; Larva/physiology ; Male ; Oryza/parasitology ; Oviposition/physiology ; Spodoptera/*genetics/pathogenicity/*physiology ; Transcriptome ; Zea mays/parasitology ; },
abstract = {How herbivorous insects adapt to host plants is a key question in ecological and evolutionary biology. The fall armyworm, (FAW) Spodoptera frugiperda (J.E. Smith), although polyphagous and a major pest on various crops, has been reported to have a rice and corn (maize) feeding strain in its native range in the Americas. The species is highly invasive and has recently established in China. We compared behavioral changes in larvae and adults of a corn population (Corn) when selected on rice (Rice) and the molecular basis of these adaptational changes in midgut and antennae based on a comparative transcriptome analysis. Larvae of S. frugiperda reared on rice plants continuously for 20 generations exhibited strong feeding preference for with higher larval performance and pupal weight on rice than on maize plants. Similarly, females from the rice selected population laid significantly more eggs on rice as compared to females from maize population. The most highly expressed DEGs were shown in the midgut of Rice vs. Corn. A total of 6430 DEGs were identified between the populations mostly in genes related to digestion and detoxification. These results suggest that potential adaptations for feeding on rice crops, may contribute to the current rapid spread of fall armyworm on rice crops in China and potentially elsewhere. Consistently, highly expressed DEGs were also shown in antennae; a total of 5125 differentially expressed genes (DEGs) s were identified related to the expansions of major chemosensory genes family in Rice compared to the Corn feeding population. These results not only provide valuable insight into the molecular mechanisms in host plants adaptation of S. frugiperda but may provide new gene targets for the management of this pest.},
}

Adaptation, Physiological/genetics
Animals
China
Crops, Agricultural/parasitology
Digestive System Physiological Phenomena
Feeding Behavior/physiology
Female
Gene Ontology
Genes, Insect
Herbivory/genetics/physiology
Host Adaptation/genetics/physiology
Host Specificity/genetics/physiology
Host-Parasite Interactions/genetics/physiology
Larva/physiology
Male
Oryza/parasitology
Oviposition/physiology
Spodoptera/*genetics/pathogenicity/*physiology
Transcriptome
Zea mays/parasitology

@article {pmid33818967,
year = {2021},
author = {Navidpour, S and Jahanifard, E and Hosseini-Vasoukolaei, N},
title = {Species Composition and Spatial Distribution of Scorpions Based on Eco-Environmental Variables in Provinces Along with the Oman Sea and the Persian Gulf in Iran: A GIS-Based Approach.},
journal = {Archives of Razi Institute},
volume = {76},
number = {1},
pages = {149-160},
pmid = {33818967},
issn = {2008-9872},
mesh = {Animals ; *Geographic Information Systems ; Indian Ocean ; Iran/epidemiology ; Oman ; *Scorpions ; Species Specificity ; },
abstract = {Scorpions are venomous arachnids with major medical health importance in Iran, specifically in the Southwest. In total, three families of scorpions, including Scorpionidae, Hemiscorpiidae, and Buthidae were reported in Iran. This study was conducted on scorpion ecology to determine the species composition and the dispersion of scorpions based on the ecological and environmental variables in combination with the Geographic Information System (GIS) in Khuzestan, Hormozgan, and Bushehr Provinces along with the Oman Sea and the Persian Gulf in Iran. Scorpions were collected from Hormozgan, Khuzestan, and Bushehr Provinces, Iran using the Ultra Violet light. The specimens were then identified according to their morphological characters utilizing reliable keys. To determine the relationship between the eco-environmental variables and the spatial distribution of species, the GPS points of the collected scorpions were recorded, and the scorpion shapefile was overlaid on digital elevation model, slope, land use, temperature, rainfall, soil texture, and bioclimatic maps. Totally, 25 specimens were reported in three families of Scorpionidae, Hemiscorpiidae, and Buthidae. Furthermore, Razianus zarudnyi, Androctonus crassicauda, Buthacus macrocentrus, Mesobuthus eupeus phillipsii, Odontobuthus bidentatus, and Hemiscorpius lepturus were the common species collected from Hormozgan, Khuzestan, and Bushehr Provinces, Iran. The results of the current study showed that a large number of species preferred the sand texture due to ecomorphological adaptation. Moreover, the poor rangeland vegetation cover was preferred by the majority of the scorpion species, including S. maurus townsendi. According to the results, the combination of the ecological factors related to the suitable habitat of different species of scorpion and GIS will provide the dispersal areas of each species. Furthermore, such databases can be comprehensive and valuable guides for health authorities to reduce and manage scorpion envenomation.},
}

Animals
*Geographic Information Systems
Indian Ocean
Iran/epidemiology
Oman
*Scorpions
Species Specificity

@article {pmid33662005,
year = {2021},
author = {Jansson, S and Malmqvist, E and Mlacha, Y and Ignell, R and Okumu, F and Killeen, G and Kirkeby, C and Brydegaard, M},
title = {Real-time dispersal of malaria vectors in rural Africa monitored with lidar.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0247803},
pmid = {33662005},
issn = {1932-6203},
mesh = {Africa/epidemiology ; Animals ; Anopheles/*physiology ; Environmental Monitoring/*methods ; Female ; Geographic Information Systems/*standards ; Malaria/*diagnosis/epidemiology/prevention & control/transmission ; Male ; Mosquito Vectors/*parasitology ; Rural Population/*statistics & numerical data ; },
abstract = {Lack of tools for detailed, real-time observation of mosquito behavior with high spatio-temporal resolution limits progress towards improved malaria vector control. We deployed a high-resolution entomological lidar to monitor a half-kilometer static transect positioned over rice fields outside a Tanzanian village. A quarter of a million in situ insect observations were classified, and several insect taxa were identified based on their modulation signatures. We observed distinct range distributions of male and female mosquitoes in relation to the village periphery, and spatio-temporal behavioral features, such as swarming. Furthermore, we observed that the spatial distributions of males and females change independently of each other during the day, and were able to estimate the daily dispersal of mosquitoes towards and away from the village. The findings of this study demonstrate how lidar-based monitoring could dramatically improve our understanding of malaria vector ecology and control options.},
}

Africa/epidemiology
Animals
Anopheles/*physiology
Environmental Monitoring/*methods
Female
Geographic Information Systems/*standards
Malaria/*diagnosis/epidemiology/prevention & control/transmission
Male
Mosquito Vectors/*parasitology
Rural Population/*statistics & numerical data

@article {pmid34634737,
year = {2021},
author = {Wang, X and Zhang, C and Wang, C and Liu, G and Wang, H},
title = {GIS-based for prediction and prevention of environmental geological disaster susceptibility: From a perspective of sustainable development.},
journal = {Ecotoxicology and environmental safety},
volume = {226},
number = {},
pages = {112881},
doi = {10.1016/j.ecoenv.2021.112881},
pmid = {34634737},
issn = {1090-2414},
mesh = {China ; Cities ; *Disasters ; Environment ; *Geographic Information Systems ; Humans ; Sustainable Development ; },
abstract = {Geological disasters seriously threaten the safety of human life, property, ecological resources, and the environment. Effective control of geological disasters is the focus of achieving sustainable social development. The Helong City (Jilin Province, China) was selected as the case study. Combined with GIS technology, a new integrated prediction model of geological disaster susceptibility was developed to improve the accuracy of geological disaster assessment, reduce the cost of geological disaster treatment, and ensure the sustainable development of ecological environment. The research results showed that elevation and normalized difference vegetation index (NDVI) were the key factors affecting susceptibility. Compared with the conventional model, the accuracy of the developing integrated model FR-DT and FR-RF was improved by more than 6%, and the disaster points were more concentrated in the high susceptibility zone. Statistical results of disaster treatment cost estimation and gross domestic product (GDP) value showed that the integrated model can save about 10% of treatment cost, and the ratio of total GDP/disaster governance cost was higher. The performance of the integrated model FR-DT and FR-RF had obvious advantages over the conventional model in terms of prediction accuracy, prevention pertinence, and prevention cost. These research results promote the advancement of geological disaster prevention and control technology, ensure the safety of the geological environment, and are of great significance to the sustainable development of the regional economy.},
}

China
Cities
*Disasters
Environment
*Geographic Information Systems
Humans
Sustainable Development

@article {pmid34608637,
year = {2021},
author = {Freschet, GT and Pagès, L and Iversen, CM and Comas, LH and Rewald, B and Roumet, C and Klimešová, J and Zadworny, M and Poorter, H and Postma, JA and Adams, TS and Bagniewska-Zadworna, A and Bengough, AG and Blancaflor, EB and Brunner, I and Cornelissen, JHC and Garnier, E and Gessler, A and Hobbie, SE and Meier, IC and Mommer, L and Picon-Cochard, C and Rose, L and Ryser, P and Scherer-Lorenzen, M and Soudzilovskaia, NA and Stokes, A and Sun, T and Valverde-Barrantes, OJ and Weemstra, M and Weigelt, A and Wurzburger, N and York, LM and Batterman, SA and Gomes de Moraes, M and Janeček, Š and Lambers, H and Salmon, V and Tharayil, N and McCormack, ML},
title = {A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements.},
journal = {The New phytologist},
volume = {232},
number = {3},
pages = {973-1122},
doi = {10.1111/nph.17572},
pmid = {34608637},
issn = {1469-8137},
mesh = {Databases, Factual ; Ecology ; *Ecosystem ; Phenotype ; *Plants ; },
abstract = {In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.},
}

Databases, Factual
Ecology
*Ecosystem
Phenotype
*Plants

@article {pmid34562356,
year = {2021},
author = {Upham, NS and Poelen, JH and Paul, D and Groom, QJ and Simmons, NB and Vanhove, MPM and Bertolino, S and Reeder, DM and Bastos-Silveira, C and Sen, A and Sterner, B and Franz, NM and Guidoti, M and Penev, L and Agosti, D},
title = {Liberating host-virus knowledge from biological dark data.},
journal = {The Lancet. Planetary health},
volume = {5},
number = {10},
pages = {e746-e750},
doi = {10.1016/S2542-5196(21)00196-0},
pmid = {34562356},
issn = {2542-5196},
support = {R01 AI151144/AI/NIAID NIH HHS/United States ; R21 AI164268/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *COVID-19/epidemiology/virology ; *Host Microbial Interactions ; Humans ; *Information Storage and Retrieval ; SARS-CoV-2 ; Zoonoses ; },
abstract = {Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis. Knowledge of host-to-virus ecological interactions will be biased until this challenge is addressed. In this Viewpoint, we outline two viable solutions: first, in the short term, to interconnect published data about host organisms, viruses, and other pathogens; and second, to shift the publishing framework beyond unstructured text (the so-called PDF prison) to labelled networks of digital knowledge. As the indexing system for biodiversity data, biological taxonomy is foundational to both solutions. Building digitally connected knowledge graphs of host-pathogen interactions will establish the agility needed to quickly identify reservoir hosts of novel zoonoses, allow for more robust predictions of emergence, and thereby strengthen human and planetary health systems.},
}

Animals
*COVID-19/epidemiology/virology
*Host Microbial Interactions
Humans
*Information Storage and Retrieval
SARS-CoV-2
Zoonoses

@article {pmid32391910,
year = {2020},
author = {Escamilla Molgora, JM and Sedda, L and Atkinson, PM},
title = {Biospytial: spatial graph-based computing for ecological Big Data.},
journal = {GigaScience},
volume = {9},
number = {5},
pages = {},
pmid = {32391910},
issn = {2047-217X},
mesh = {*Big Data ; *Databases, Factual ; Ecology ; Geography ; Models, Theoretical ; *Software ; },
abstract = {BACKGROUND: The exponential accumulation of environmental and ecological data together with the adoption of open data initiatives bring opportunities and challenges for integrating and synthesising relevant knowledge that need to be addressed, given the ongoing environmental crises.

FINDINGS: Here we present Biospytial, a modular open source knowledge engine designed to import, organise, analyse and visualise big spatial ecological datasets using the power of graph theory. The engine uses a hybrid graph-relational approach to store and access information. A graph data structure uses linkage relationships to build semantic structures represented as complex data structures stored in a graph database, while tabular and geospatial data are stored in an efficient spatial relational database system. We provide an application using information on species occurrences, their taxonomic classification and climatic datasets. We built a knowledge graph of the Tree of Life embedded in an environmental and geographical grid to perform an analysis on threatened species co-occurring with jaguars (Panthera onca).

CONCLUSIONS: The Biospytial approach reduces the complexity of joining datasets using multiple tabular relations, while its scalable design eases the problem of merging datasets from different sources. Its modular design makes it possible to distribute several instances simultaneously, allowing fast and efficient handling of big ecological datasets. The provided example demonstrates the engine's capabilities in performing basic graph manipulation, analysis and visualizations of taxonomic groups co-occurring in space. The example shows potential avenues for performing novel ecological analyses, biodiversity syntheses and species distribution models aided by a network of taxonomic and spatial relationships.},
}

*Big Data
*Databases, Factual
Ecology
Geography
Models, Theoretical
*Software

@article {pmid34599334,
year = {2021},
author = {Westfall, AK and Telemeco, RS and Grizante, MB and Waits, DS and Clark, AD and Simpson, DY and Klabacka, RL and Sullivan, AP and Perry, GH and Sears, MW and Cox, CL and Cox, RM and Gifford, ME and John-Alder, HB and Langkilde, T and Angilletta, MJ and Leaché, AD and Tollis, M and Kusumi, K and Schwartz, TS},
title = {A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.},
journal = {GigaScience},
volume = {10},
number = {10},
pages = {},
doi = {10.1093/gigascience/giab066},
pmid = {34599334},
issn = {2047-217X},
support = {DGE 1414475//National Science Foundation/ ; //University of Virginia/ ; //Arizona State University/ ; //Auburn University/ ; },
abstract = {BACKGROUND: High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources.

FINDINGS: We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length.

CONCLUSIONS: These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.},
}

@article {pmid34030983,
year = {2021},
author = {Miller, KE and Polaszek, A and Evans, DM},
title = {A dearth of data: fitting parasitoids into ecological networks.},
journal = {Trends in parasitology},
volume = {37},
number = {10},
pages = {863-874},
doi = {10.1016/j.pt.2021.04.012},
pmid = {34030983},
issn = {1471-5007},
mesh = {Animals ; DNA Barcoding, Taxonomic ; Databases, Genetic ; *Ecosystem ; *Host-Parasite Interactions/physiology ; },
abstract = {Studying parasitoids can provide insights into global diversity estimates, climate change impacts, and agroecosystem service provision. However, this potential remains largely untapped due to a lack of data on how parasitoids interact with other organisms. Ecological networks are a useful tool for studying and exploiting the impacts of parasitoids, but their construction is hindered by the magnitude of undescribed parasitoid species, a sparse knowledge of host ranges, and an under-representation of parasitoids within DNA-barcode databases (we estimate <5% have a barcode). Here, we advocate the use of DNA metabarcoding to construct the host-parasitoid component of multilayer networks. While the incorporation of parasitoids into network-based analyses has far ranging applications, we focus on its potential for assessing ecosystem service provision within agroecosystems.},
}

Animals
DNA Barcoding, Taxonomic
Databases, Genetic
*Ecosystem
*Host-Parasite Interactions/physiology

@article {pmid34404811,
year = {2021},
author = {Sabatini, FM and Bluhm, H and Kun, Z and Aksenov, D and Atauri, JA and Buchwald, E and Burrascano, S and Cateau, E and Diku, A and Duarte, IM and Fernández López, ÁB and Garbarino, M and Grigoriadis, N and Horváth, F and Keren, S and Kitenberga, M and Kiš, A and Kraut, A and Ibisch, PL and Larrieu, L and Lombardi, F and Matovic, B and Melu, RN and Meyer, P and Midteng, R and Mikac, S and Mikoláš, M and Mozgeris, G and Panayotov, M and Pisek, R and Nunes, L and Ruete, A and Schickhofer, M and Simovski, B and Stillhard, J and Stojanovic, D and Szwagrzyk, J and Tikkanen, OP and Toromani, E and Volosyanchuk, R and Vrška, T and Waldherr, M and Yermokhin, M and Zlatanov, T and Zagidullina, A and Kuemmerle, T},
title = {European primary forest database v2.0.},
journal = {Scientific data},
volume = {8},
number = {1},
pages = {220},
pmid = {34404811},
issn = {2052-4463},
support = {658876//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ETN-WIE-FZS-001//Zoologische Gesellschaft Frankfurt (Frankfurt Zoological Society)/ ; ETN-WIE-FZS-001//Zoologische Gesellschaft Frankfurt (Frankfurt Zoological Society)/ ; },
mesh = {*Conservation of Natural Resources ; Databases, Factual ; Europe ; *Forests ; },
abstract = {Primary forests, defined here as forests where the signs of human impacts, if any, are strongly blurred due to decades without forest management, are scarce in Europe and continue to disappear. Despite these losses, we know little about where these forests occur. Here, we present a comprehensive geodatabase and map of Europe's known primary forests. Our geodatabase harmonizes 48 different, mostly field-based datasets of primary forests, and contains 18,411 individual patches (41.1 Mha) spread across 33 countries. When available, we provide information on each patch (name, location, naturalness, extent and dominant tree species) and the surrounding landscape (biogeographical regions, protection status, potential natural vegetation, current forest extent). Using Landsat satellite-image time series (1985-2018) we checked each patch for possible disturbance events since primary forests were identified, resulting in 94% of patches free of significant disturbances in the last 30 years. Although knowledge gaps remain, ours is the most comprehensive dataset on primary forests in Europe, and will be useful for ecological studies, and conservation planning to safeguard these unique forests.},
}

*Conservation of Natural Resources
Databases, Factual
Europe
*Forests

@article {pmid33909693,
year = {2021},
author = {Freedman, R and Brown, JA and Caldow, C and Caselle, JE},
title = {Species-specific thermal classification schemes can improve climate related marine resource decisions.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0250792},
pmid = {33909693},
issn = {1932-6203},
mesh = {Animals ; Biota ; California ; Climate Change ; Conservation of Natural Resources/*methods ; Databases, Factual ; Decision Making ; Fishes/*classification ; Humans ; Kelp/*classification ; Species Specificity ; Temperature ; },
abstract = {Global climate change increasingly contributes to large changes in ecosystem structure. Timely management of rapidly changing marine ecosystems must be matched with methods to rapidly quantify and assess climate driven impacts to ecological communities. Here we create a species-specific, classification system for fish thermal affinities, using three quantifiable datasets and expert opinion. Multiple sources of information limit potential data bias and avoid misclassification. Using a temperate kelp forest fish community in California, USA as a test case for this new methodology, we found the majority of species had high classification agreement across all four data sources (n = 78) but also a number of low agreement species (2 sources disagree from the others, n = 47). For species with low agreement, use of just one dataset to classify species, as is commonly done, would lead to high risk of misclassification. Differences in species classification between individual datasets and our composite classification were apparent. Applying different thermal classifications, lead to different conclusions when quantifying 'warm' and 'cool' species density responses to a marine heatwave. Managers can use this classification approach as a tool to generate accurate, timely and simple information for resource management.},
}

Animals
Biota
California
Climate Change
Conservation of Natural Resources/*methods
Databases, Factual
Decision Making
Fishes/*classification
Humans
Kelp/*classification
Species Specificity
Temperature

@article {pmid34586901,
year = {2021},
author = {Fernandes-Martins, MC and Keller, LM and Munro-Ehrlich, M and Zimlich, KR and Mettler, MK and England, AM and Clare, R and Surya, K and Shock, EL and Colman, DR and Boyd, ES},
title = {Ecological dichotomies arise in microbial communities due to mixing of deep hydrothermal waters and atmospheric gas in a circumneutral hot spring.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {AEM0159821},
doi = {10.1128/AEM.01598-21},
pmid = {34586901},
issn = {1098-5336},
abstract = {Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen ∼2.4 Gya. IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral to alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼ 2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.},
}

@article {pmid33861764,
year = {2021},
author = {Fatemi, M and Rezaei-Moghaddam, K and Karami, E and Hayati, D and Wackernagel, M},
title = {An integrated approach of Ecological Footprint (EF) and Analytical Hierarchy Process (AHP) in human ecology: A base for planning toward sustainability.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0250167},
pmid = {33861764},
issn = {1932-6203},
mesh = {Agriculture ; Analytic Hierarchy Process ; Conservation of Natural Resources/*methods ; Ecological and Environmental Phenomena ; Ecology ; Farmers ; Humans ; Iran ; Natural Resources ; Pilot Projects ; Reproducibility of Results ; Surveys and Questionnaires ; Sustainable Development/economics/*trends ; },
abstract = {Environmental challenges to natural resources have been attributed to human behavior and traditional agricultural production techniques. Natural resource degradation in agriculture has always been a prime concern in agro ecological research and sustainability analysis. There are many techniques for assessing environmental performance; one of which, ecological footprint (EF), assesses human pressure on the environment and natural resources. The main purpose of this study was calculation of ecological indices including biocapacity (BC) and EF of rural areas of Fars province of Iran. The study was accomplished using survey and structured interviews consisting of three main questionnaires in two different steps. Different agricultural stakeholders, including farmers (for the first step) as well as the policymakers, extension managers and authorities (for the second step) were interviewed. Based on multi-stage stratified random sampling, 50 villages and 423 farmers were selected. Face validity and reliability of the questionnaires were assessed by a panel of specialists as well as conducting a pilot study, respectively. The paradigmatic perspectives of agricultural policy makers and managers (22 individuals) were also analyzed using another specific questionnaire by Analytical Hierarchy Process (AHP). Findings revealed that most of the studied villages faced a critical environmental condition due to the results of ecological indicator which was calculated in the study. According to the four main components of human ecology (POET model) including Population, Organization, Environment and Technology, village groups that differed in terms of sustainability level also showed significantly differences due to population, social participation, use of green technologies and attitude towards diverse environmental management paradigms. The causal model also revealed that population, green technology, social participation and attitude toward frontier economics, which were in accordance with the elements of human ecology model, were the main factors affecting the ecological index. Finally, AHP results determined the dominant economic perspectives of agricultural authorities. A paradigm shift toward the comprehensive paradigm of eco-development plus consideration of the results of the ecological indicator calculation as the base of agricultural planning at the local level were recommended.},
}

Agriculture
Analytic Hierarchy Process
Conservation of Natural Resources/*methods
Ecological and Environmental Phenomena
Ecology
Farmers
Humans
Iran
Natural Resources
Pilot Projects
Reproducibility of Results
Surveys and Questionnaires
Sustainable Development/economics/*trends

@article {pmid34522345,
year = {2021},
author = {Remeš, V and Remešová, E and Friedman, NR and Matysioková, B and Rubáčová, L},
title = {Functional diversity of avian communities increases with canopy height: From individual behavior to continental-scale patterns.},
journal = {Ecology and evolution},
volume = {11},
number = {17},
pages = {11839-11851},
pmid = {34522345},
issn = {2045-7758},
abstract = {Vegetation complexity is an important predictor of animal species diversity. Specifically, taller vegetation should provide more potential ecological niches and thus harbor communities with higher species richness and functional diversity (FD). Resource use behavior is an especially important functional trait because it links species to their resource base with direct relevance to niche partitioning. However, it is unclear how exactly the diversity of resource use behavior changes with vegetation complexity. To address this question, we studied avian FD in relation to vegetation complexity along a continental-scale vegetation gradient. We quantified foraging behavior of passerine birds in terms of foraging method and substrate use at 21 sites (63 transects) spanning 3,000 km of woodlands and forests in Australia. We also quantified vegetation structure on 630 sampling points at the same sites. Additionally, we measured morphological traits for all 111 observed species in museum collections. We calculated individual-based, abundance-weighted FD in morphology and foraging behavior and related it to species richness and vegetation complexity (indexed by canopy height) using structural equation modeling, rarefaction analyses, and distance-based metrics. FD of morphology and foraging methods was best predicted by species richness. However, FD of substrate use was best predicted by canopy height (ranging 10-30 m), but only when substrates were categorized with fine resolution (17 categories), not when categorized coarsely (8 categories). These results suggest that, first, FD might increase with vegetation complexity independently of species richness, but whether it does so depends on the studied functional trait. Second, patterns found might be shaped by how finely we categorize functional traits. More complex vegetation provided larger "ecological space" with more resources, allowing the coexistence of more species with disproportionately more diverse foraging substrate use. We suggest that the latter pattern was driven by nonrandom accumulation of functionally distinct species with increasing canopy height.},
}

@article {pmid34450871,
year = {2021},
author = {Guo, J and Zhang, M and Shang, Q and Liu, F and Wu, A and Li, X},
title = {River Basin Cyberinfrastructure in the Big Data Era: An Integrated Observational Data Control System in the Heihe River Basin.},
journal = {Sensors (Basel, Switzerland)},
volume = {21},
number = {16},
pages = {},
pmid = {34450871},
issn = {1424-8220},
support = {2016YFC0500105//the National Key R&D Program of China/ ; XDA20060602//The Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {Big Data ; China ; *Conservation of Natural Resources ; Hydrology ; *Rivers ; },
abstract = {River basin cyberinfrastructure with the Internet of Things (IoT) as the core has brought watershed data science into the big data era, greatly improving data acquisition and sharing efficiency. However, challenges in analyzing, processing, and applying very large quantities of observational data remain. Given the observational needs in watershed research, we studied the construction of river basin cyberinfrastructure and developed an integrated observational data control system (IODCS). The IODCS is an important platform for processing large quantities of observational data, including automated collection, storage, analysis, processing, and release. This paper presents various aspects of the IODCS in detail, including the system's overall design, function realization, big data analysis methods, and integrated models. We took the middle reaches of the Heihe River Basin (HRB) as the application research area to show the performance of the developed system. Since the system began operation, it has automatically received, analyzed, and stored more than 1.4 billion observational data records, with an average of more than 14 million observational data records processed per month and up to 21,011 active users. The demonstrated results show that the IODCS can effectively leverage the processing capability of massive observational data and provide a new perspective for facilitating ecological and hydrological scientific research on the HRB.},
}

Big Data
China
*Conservation of Natural Resources
Hydrology
*Rivers

@article {pmid34430295,
year = {2021},
author = {Abdullah, MM and Al-Ali, ZM and Srinivasan, S},
title = {The use of UAV-based remote sensing to estimate biomass and carbon stock for native desert shrubs.},
journal = {MethodsX},
volume = {8},
number = {},
pages = {101399},
pmid = {34430295},
issn = {2215-0161},
abstract = {Unmanned Aerial Vehicles (UAVs) have started to receive more attention in the ecological field in the past 15 years, as they provide very high-resolution imagery that ranges from meters to millimeters. Very high-resolution multispectral imagery obtained from UAVs can help in assessing and monitoring native desert vegetation. Thus, this study use UAVs to develop a method to estimate the biomass and carbon stock of native desert shrubs. The method integrates different techniques and software to monitor native plants' coverage, biomass, and carbon stock. The techniques used in this work are also applicable for other native desert shrubs in the region and could support ecosystem managers in assessing and monitoring arid ecosystems and restoration and revegetation programs. A three-stage image and data management are discussed, including: (1) fieldwork and image acquisition using UAVs, (2) image pre-processing, and (3) image processing using different techniques and software.•Determining shrub biomass is not restricted to multispectral data only but could be applicable for RGB data since it mainly depends on the DSM and DTM.•Allometric parameters could help in estimating desert shrub biomass which could be measured easily and rapidly using UAV imagery.•SVM Supervised classification could help in distinguishing between native shrubs and grasses.},
}

@article {pmid34371221,
year = {2021},
author = {Li, J and Chen, X and Kurban, A and Van de Voorde, T and De Maeyer, P and Zhang, C},
title = {Identification of conservation priorities in the major basins of Central Asia: Using an integrated GIS-based ordered weighted averaging approach.},
journal = {Journal of environmental management},
volume = {298},
number = {},
pages = {113442},
doi = {10.1016/j.jenvman.2021.113442},
pmid = {34371221},
issn = {1095-8630},
mesh = {Asia ; China ; *Conservation of Natural Resources ; *Ecosystem ; Geographic Information Systems ; Humans ; Soil ; },
abstract = {Ecosystem services (ESs) provided by the major basins of Central Asia are critical to human well-being and have attracted the attention of the international community. The identification of conservation priorities is of great significance for the maintenance and protection of key ESs. In this study, we quantified the spatiotemporal changes of net primary productivity (NPP), soil conservation (SC), water yield (WY) and habitat quality (HQ) in the major basins of Central Asia from 1995 to 2015. In addition, a GIS-based ordered weighted averaging (OWA) multi-criterion valuation method was adopted to identify potential conservation areas under 11 scenarios. Conservation priorities were determined by comparing the conservation efficiency under each scenario. Then, a broad range of indicators were considered to distinguish the driving factors affecting ESs in conservation priorities. The results show that the average conservation efficiency in the Issyk-Kul Basin was the highest, followed by the Am Darya Basin, Ili-Balkhash Basin and Syr Darya Basin. We observed that the conservation efficiency of the four ESs declined continuously in the Ili-Balkhash Basin from 1995 to 2015, while it changed steadily in the other three basins. Correlation analysis indicated that natural factors (e.g., precipitation and topography) were the main driving factors of WY, SR and NPP in conservation priorities, while HQ was more affected by socio-economic factors (e.g., population density and both cropland and urban percentages). The identification of conservation priorities and their driving factors plays an important role in ensuring the ecological security of the lower reaches, regulating the regional water balance and stabilizing the climate pattern.},
}

Asia
China
*Conservation of Natural Resources
*Ecosystem
Geographic Information Systems
Humans
Soil

@article {pmid34349739,
year = {2021},
author = {Jones, B and Goodall, T and George, PBL and Gweon, HS and Puissant, J and Read, DS and Emmett, BA and Robinson, DA and Jones, DL and Griffiths, RI},
title = {Beyond Taxonomic Identification: Integration of Ecological Responses to a Soil Bacterial 16S rRNA Gene Database.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {682886},
pmid = {34349739},
issn = {1664-302X},
abstract = {High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalizing syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterize taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth CS) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from survey metadata. Specifically, we modeled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on both the shape of landscape scale pH-abundance responses, and pH optima (pH at which OTU abundance is maximal). We identify that most of the soil OTUs examined exhibited a non-flat relationship with soil pH. Further, the pH optima could not be generalized by broad taxonomy, highlighting the need for tools and databases synthesizing ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER/), and flat files are made available for use in bioinformatic pipelines. The further development of advanced informatics infrastructures incorporating modeled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.},
}

@article {pmid34339067,
year = {2021},
author = {Hagmann, RK and Hessburg, PF and Prichard, SJ and Povak, NA and Brown, PM and Fulé, PZ and Keane, RE and Knapp, EE and Lydersen, JM and Metlen, KL and Reilly, MJ and Sánchez Meador, AJ and Stephens, SL and Stevens, JT and Taylor, AH and Yocom, LL and Battaglia, MA and Churchill, DJ and Daniels, LD and Falk, DA and Henson, P and Johnston, JD and Krawchuk, MA and Levine, CR and Meigs, GW and Merschel, AG and North, MP and Safford, HD and Swetnam, TW and Waltz, AEM},
title = {Evidence for widespread changes in the structure, composition, and fire regimes of western North American forests.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {},
number = {},
pages = {e02431},
doi = {10.1002/eap.2431},
pmid = {34339067},
issn = {1051-0761},
abstract = {Implementation of wildfire- and climate-adaptation strategies in seasonally dry forests of western North America is impeded by numerous constraints and uncertainties. After more than a century of resource and land use change, some question the need for proactive management, particularly given novel social, ecological, and climatic conditions. To address this question, we first provide a framework for assessing changes in landscape conditions and fire regimes. Using this framework, we then evaluate evidence of change and lack of change in contemporary conditions relative to those maintained by active fire regimes, i.e., those uninterrupted by a century or more of human-induced fire exclusion. The cumulative results of more than a century of research document a persistent and substantial fire deficit and widespread alterations to ecological structures and functions. These changes are not necessarily apparent at all spatial scales or in all dimensions of fire regimes and forest and nonforest conditions. Nonetheless, loss of the once abundant influence of low- and moderate-severity fires suggests that while some ecosystems within these landscapes may not be directly altered by fire exclusion, even the least fire-prone among them may be affected by alteration of the surrounding landscape and, consequently, ecosystem functions. Vegetation spatial patterns in fire-excluded forested landscapes no longer reflect the heterogeneity maintained by interacting fires of active fire regimes. Live and dead vegetation (surface and canopy fuels) is generally more abundant and continuous than before European colonization. As a result, current conditions are more vulnerable to the direct and indirect effects of seasonal and episodic increases in drought and fire, especially under a rapidly warming climate. Long-term fire exclusion and contemporaneous social-ecological influences continue to extensively modify seasonally dry forested landscapes. Management that realigns or adapts fire-excluded conditions to the seasonal and episodic increases in drought and fire can moderate ecosystem transitions as forests and human communities adapt to changing climatic and disturbance regimes. As adaptation strategies are developed, evaluated, and implemented, objective scientific evaluation of ongoing research and monitoring can aid differentiation of warranted and unwarranted uncertainties.},
}

@article {pmid34313464,
year = {2021},
author = {Li, YX and Rao, YZ and Qi, YL and Qu, YN and Chen, YT and Jiao, JY and Shu, WS and Jiang, H and Hedlund, BP and Hua, ZS and Li, WJ},
title = {Deciphering Symbiotic Interactions of "Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks.},
journal = {mSystems},
volume = {6},
number = {4},
pages = {e0060621},
pmid = {34313464},
issn = {2379-5077},
support = {91951205//National Natural Science Foundation of China (NSFC)/ ; 91751206//National Natural Science Foundation of China (NSFC)/ ; },
abstract = {"Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota" in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota" in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota contribute substantially to the niche expansion of "Ca. Aenigmarchaeota" via horizontal gene transfer (HGT), especially genes related to virus defense and stress responses. Based on co-occurrence network results and recent genetic exchanges among community members, we conjectured that "Ca. Aenigmarchaeota" may be symbionts associated with one MAG affiliated with the genus Pyrobaculum, though host specificity might be wide and variable across different "Ca. Aenigmarchaeota" organisms. This study provides significant insight into possible DPANN-host interactions and ecological roles of "Ca. Aenigmarchaeota." IMPORTANCE Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community. By integrating horizontal gene transfer (HGT) detection and co-occurrence network analysis on "Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota"), we made one of the first attempts to infer their putative interaction partners and further decipher the potential functional and genetic interactions between the symbionts. We revealed that HGTs contributed by members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota conferred "Ca. Aenigmarchaeota" with the ability to survive under different environmental stresses, such as virus infection, high temperature, and oxidative stress. This study demonstrates that the interaction partners might be inferable by applying informatics analyses on metagenomic sequencing data.},
}

@article {pmid34303237,
year = {2021},
author = {Liu, C and Yang, M and Hou, Y and Xue, X},
title = {Ecosystem service multifunctionality assessment and coupling coordination analysis with land use and land cover change in China's coastal zones.},
journal = {The Science of the total environment},
volume = {797},
number = {},
pages = {149033},
doi = {10.1016/j.scitotenv.2021.149033},
pmid = {34303237},
issn = {1879-1026},
abstract = {Ecosystem services (ESs) have received widespread attention worldwide for their potential to solve sustainability issues. However, extensive land use and land cover change (LUCC) driven by human activities has raised concerns regarding its impacts on ESs, especially in coastal zones. More importantly, spatial-temporal changes, their coupling relationships with LUCC, and their underlying drivers have not been thoroughly analyzed. This study focuses on China's coastal zones to investigate the spatial-temporal changes of ecosystem service multifunctionality (ESM) from 2000 to 2018. Coupling coordination degree (CCD) analysis of the relationship between ESM and comprehensive intensity of land use was applied to identify coastal cities with low-level coordination and their main drivers in 2018. The results show that: (1) the proportion with high levels of ESM decreased by 1.01% from 2000 to 2010 and then increased by 3.29% from 2010 to 2018; (2) the ESM of China's coastal zones present significant spatial heterogeneity, and the low levels of ESM are mainly distributed in the north and urban areas, while most areas in the southern coastal zones have high levels of ESM; (3) forest land is the leading land cover type for ESM, and China's forest conservation policies significantly contribute to the increase in ESM; (4) the CCD of most cities in the southern coastal zones, apart from Shanghai and the Pearl River Delta, is at a relatively high level and experiences no significant changes, while most cities in the northern coastal zones display an improving trend; (5) the land use type, landform type, and leaf area index are the determinants of ESM, and the annual average temperature, population density, and surface elevation are the greatest influences on the CCD. The findings of this study can inform ecological conservation and landscape planning and are beneficial to the sustainable development of coastal zones in China.},
}

@article {pmid34299819,
year = {2021},
author = {Ali, EOM and Babalghith, AO and Bahathig, AOS and Toulah, FHS and Bafaraj, TG and Al-Mahmoudi, SMY and Alhazmi, AMF and Abdel-Latif, ME},
title = {Prevalence of Larval Breeding Sites and Seasonal Variations of Aedes aegypti Mosquitoes (Diptera: Culicidae) in Makkah Al-Mokarramah, Saudi Arabia.},
journal = {International journal of environmental research and public health},
volume = {18},
number = {14},
pages = {},
pmid = {34299819},
issn = {1660-4601},
mesh = {*Aedes ; Animals ; *Dengue/epidemiology ; Larva ; Prevalence ; Saudi Arabia/epidemiology ; Seasons ; },
abstract = {Since 1994, dengue fever (DF) transmission rates have increased significantly in Saudi Arabia (KSA). Climatic, geographic, and demographic conditions make KSA especially suitable for DF's spread. Still, there are insufficient strategies for controlling the Aedes species that transmit DF virus (DENV). To develop effective management strategies, it is necessary to identify Aedes species and the ecological habitat of larvae in Makkah Al-Mokarramah, KSA. We conducted a longitudinal survey of Aedes mosquitoes in 14 localities from January 2015 to December 2015. World Health Organization (WHO) inspection kits for larvae were used to detect and sample larvae, along with pictorial keys. A total of 42,981 potential Aedes larval breeding sites were surveyed. A total of 5403 (12.6%) sites had at least one water source positive for Aedes aegypti (Linnaeus) mosquitoes. Among the total of 15,133 water sources surveyed within the sampled sites, 1815 (12.0%) were positive for Aedes aegypti. Aedes aegypti was the only Aedes species identified in the course of the survey. The presence of such a large immature population may indicate an imminent outbreak of DF in the near future unless proper implementation of control and elimination of Aedes&nbsp;aegypti are undertaken. Additionally, the adaptation of Aedes&nbsp;aegypti to the arid climate of Makkah needs further investigation.},
}

*Aedes
Animals
*Dengue/epidemiology
Larva
Prevalence
Saudi Arabia/epidemiology
Seasons

@article {pmid34286299,
year = {2021},
author = {Coutinho, FH and Zaragoza-Solas, A and López-Pérez, M and Barylski, J and Zielezinski, A and Dutilh, BE and Edwards, R and Rodriguez-Valera, F},
title = {RaFAH: Host prediction for viruses of Bacteria and Archaea based on protein content.},
journal = {Patterns (New York, N.Y.)},
volume = {2},
number = {7},
pages = {100274},
pmid = {34286299},
issn = {2666-3899},
abstract = {Culture-independent approaches have recently shed light on the genomic diversity of viruses of prokaryotes. One fundamental question when trying to understand their ecological roles is: which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), that uses scores to 43,644 protein clusters to assign hosts to complete or fragmented genomes of viruses of Archaea and Bacteria. RaFAH displayed performance comparable with that of other methods for virus-host prediction in three different benchmarks encompassing viruses from RefSeq, single amplified genomes, and metagenomes. RaFAH was applied to assembled metagenomic datasets of uncultured viruses from eight different biomes of medical, biotechnological, and environmental relevance. Our analyses led to the identification of 537 sequences of archaeal viruses representing unknown lineages, whose genomes encode novel auxiliary metabolic genes, shedding light on how these viruses interfere with the host molecular machinery. RaFAH is available at https://sourceforge.net/projects/rafah/.},
}

@article {pmid34262682,
year = {2021},
author = {Rocchini, D and Thouverai, E and Marcantonio, M and Iannacito, M and Da Re, D and Torresani, M and Bacaro, G and Bazzichetto, M and Bernardi, A and Foody, GM and Furrer, R and Kleijn, D and Larsen, S and Lenoir, J and Malavasi, M and Marchetto, E and Messori, F and Montaghi, A and Moudrý, V and Naimi, B and Ricotta, C and Rossini, M and Santi, F and Santos, MJ and Schaepman, ME and Schneider, FD and Schuh, L and Silvestri, S and Ŝímová, P and Skidmore, AK and Tattoni, C and Tordoni, E and Vicario, S and Zannini, P and Wegmann, M},
title = {rasterdiv-An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back.},
journal = {Methods in ecology and evolution},
volume = {12},
number = {6},
pages = {1093-1102},
pmid = {34262682},
issn = {2041-210X},
abstract = {Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow.In this paper, we present a new R package-rasterdiv-to calculate heterogeneity indices based on remotely sensed data. We also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns.The rasterdiv package allows calculating multiple indices, robustly rooted in Information Theory, and based on reproducible open-source algorithms.},
}

@article {pmid34260961,
year = {2021},
author = {Levi, A and Barnett-Itzhaki, Z},
title = {Effects of chronic exposure to ambient air pollutants, demographic, and socioeconomic factors on COVID-19 morbidity: The Israeli case study.},
journal = {Environmental research},
volume = {202},
number = {},
pages = {111673},
doi = {10.1016/j.envres.2021.111673},
pmid = {34260961},
issn = {1096-0953},
abstract = {BACKGROUND: Recent studies conducted in several OECD countries have shown that chronic exposure to elevated levels of air pollutants (especially PM2.5, PM10 and NOx), might negatively impact COVID-19 morbidity and mortality rates. The aim of this study was to examine the association between chronic exposure to air pollution in Israeli cities and towns, their demographic and socioeconomic status, and COVID-19 morbidity, during the three local morbidity waves.

METHODS: We examined the associations between: (a) annual average concentrations of NOx, CO, PM10, PM2.5 and SO2 in 2016-2019, and demographic and socioeconomic parameters, and (b) COVID-19 positive cases in 279 Israeli cities and towns, in the four state-wide morbidity peaks: 1st wave peak: March 31st, 2020; 2nd wave peaks: July 24th and September 27th, 2020, and the 3rd wave peak: January 17th, 2021, which occurred after the beginning of the nationwide vaccination campaign. These associations were calculated using both Spearman correlations and multivariate linear regressions.

RESULTS: We found statistically significant positive correlations between the concentrations of most pollutants in 2016-19 and COVID-19 morbidity rate at the first three timepoints but not the 4th (January 17th, 2021). Population density and city/town total population were also positively associated with the COVID-19 morbidity rates at these three timepoints, but not the 4th, in which socioeconomic parameters were more dominant - we found a statistically significant negative correlation between socioeconomic cluster and COVID-19 morbidity. In addition, all multivariate models including PM2.5 concentrations were statistically significant, and PM2.5 concentrations were positively associated with the COVID-19 morbidity rates in all models.

CONCLUSIONS: We found a nationwide association between population chronic exposure to five main air pollutants in Israeli cities and towns, and COVID-19 morbidity rates during two of the three morbidity waves experienced in Israel. The widespread morbidity that was related to socioeconomic factors during the 3rd wave, emphasizes the need for special attention to morbidity prevention in socioeconomically vulnerable populations and especially in large household communities. Nevertheless, this ecological study has several limitations, such as the inability to draw conclusions about causality or mechanisms of action. The growing body of evidence, regarding association between exacerbated COVID-19 morbidity and mortality rates and long-term chronic exposure to elevated concentrations of air pollutants should serve as a wake-up call to policy makers regarding the urgent need to reduce air pollution and its harmful effects.},
}

@article {pmid34253732,
year = {2021},
author = {Mehrshad, M and Lopez-Fernandez, M and Sundh, J and Bell, E and Simone, D and Buck, M and Bernier-Latmani, R and Bertilsson, S and Dopson, M},
title = {Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {4253},
pmid = {34253732},
issn = {2041-1723},
mesh = {Biodiversity ; Databases, Genetic ; *Energy Metabolism ; Gene Expression Regulation ; Groundwater/*microbiology ; Isoelectric Point ; Metagenome ; *Microbiota/genetics ; Phylogeny ; Transcription, Genetic ; Transcriptome/genetics ; },
abstract = {While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.},
}

Biodiversity
Databases, Genetic
*Energy Metabolism
Gene Expression Regulation
Groundwater/*microbiology
Isoelectric Point
Metagenome
*Microbiota/genetics
Phylogeny
Transcription, Genetic
Transcriptome/genetics

@article {pmid34214077,
year = {2021},
author = {Weinstein, BG and Graves, SJ and Marconi, S and Singh, A and Zare, A and Stewart, D and Bohlman, SA and White, EP},
title = {A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network.},
journal = {PLoS computational biology},
volume = {17},
number = {7},
pages = {e1009180},
pmid = {34214077},
issn = {1553-7358},
abstract = {Broad scale remote sensing promises to build forest inventories at unprecedented scales. A crucial step in this process is to associate sensor data into individual crowns. While dozens of crown detection algorithms have been proposed, their performance is typically not compared based on standard data or evaluation metrics. There is a need for a benchmark dataset to minimize differences in reported results as well as support evaluation of algorithms across a broad range of forest types. Combining RGB, LiDAR and hyperspectral sensor data from the USA National Ecological Observatory Network's Airborne Observation Platform with multiple types of evaluation data, we created a benchmark dataset to assess crown detection and delineation methods for canopy trees covering dominant forest types in the United States. This benchmark dataset includes an R package to standardize evaluation metrics and simplify comparisons between methods. The benchmark dataset contains over 6,000 image-annotated crowns, 400 field-annotated crowns, and 3,000 canopy stem points from a wide range of forest types. In addition, we include over 10,000 training crowns for optional use. We discuss the different evaluation data sources and assess the accuracy of the image-annotated crowns by comparing annotations among multiple annotators as well as overlapping field-annotated crowns. We provide an example submission and score for an open-source algorithm that can serve as a baseline for future methods.},
}

@article {pmid34181792,
year = {2021},
author = {Mairal, M and Chown, SL and Shaw, J and Chala, D and Chau, JH and Hui, C and Kalwij, JM and Münzbergová, Z and Jansen van Vuuren, B and Le Roux, JJ},
title = {Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub-Antarctic.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16045},
pmid = {34181792},
issn = {1365-294X},
support = {110728//South African Agency for Science and Technology Advancement/ ; },
abstract = {The link between the successful establishment of alien species and propagule pressure is well-documented. Less known is how humans influence the post-introduction dynamics of invasive alien populations. The latter requires studying parallel invasions by the same species in habitats that are differently impacted by humans. We analysed microsatellite and genome size variation, and then compared the genetic diversity and structure of invasive Poa annua L. on two sub-Antarctic islands: human-occupied Marion Island and unoccupied Prince Edward Island. We also carried out niche modelling to map the potential distribution of the species on both islands. We found high levels of genetic diversity and evidence for extensive admixture between genetically distinct lineages of P. annua on Marion Island. By contrast, the Prince Edward Island populations showed low genetic diversity, no apparent admixture, and had smaller genomes. On both islands, high genetic diversity was apparent at human landing sites, and on Marion Island, also around human settlements, suggesting that these areas received multiple introductions and/or acted as initial introduction sites and secondary sources (bridgeheads) for invasive populations. More than 70 years of continuous human activity associated with a meteorological station on Marion Island led to a distribution of this species around human settlements and along footpaths, which facilitates ongoing gene flow among geographically separated populations. By contrast, this was not the case for Prince Edward Island, where P. annua populations showed high genetic structure. The high levels of genetic variation and admixture in P. annua facilitated by human activity, coupled with high habitat suitability on both islands, suggest that P. annua is likely to increase its distribution and abundance in the future.},
}

@article {pmid34151345,
year = {2021},
author = {Tanner, RL and Grover, N and Anderson, ML and Crocker, KC and Dutta, S and Horner, AM and Hough, LE and Moore, TY and Rosen, GL and Whitney, KS and Summers, AP},
title = {Examining cultural structures and functions in biology.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icab140},
pmid = {34151345},
issn = {1557-7023},
abstract = {Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods. But our choices are shaped by more than objective curiosity-we are influenced by cultural paradigms reinforced by societal upbringing and scientific indoctrination during training. This extends to the systems and data that we consider to be ethically obtainable or available for study, and who is considered qualified to do research, ask questions, and communicate about research. It is also influenced by the profitability of concepts like open-access-a system designed to improve equity, but which enacts gatekeeping in unintended but foreseeable ways. Creating truly integrative biology programs will require more than intentionally developing departments or institutes that allow overlapping expertise in two or more subfields of biology. Interdisciplinary work requires the expertise of large and diverse teams of scientists working together-this is impossible without an authentic commitment to addressing, not denying, racism when practiced by individuals, institutions, and cultural aspects of academic science. We have identified starting points for remedying how our field has discouraged and caused harm, but we acknowledge there is a long path forward. This path must be paved with field-wide solutions and institutional buy-in: our solutions must match the scale of the problem. Together, we can integrate-not reintegrate-the nuances of biology into our field.},
}

@article {pmid34140494,
year = {2021},
author = {Borko, Š and Trontelj, P and Seehausen, O and Moškrič, A and Fišer, C},
title = {A subterranean adaptive radiation of amphipods in Europe.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3688},
pmid = {34140494},
issn = {2041-1723},
mesh = {*Adaptation, Physiological ; Amphipoda/*anatomy & histology/*genetics/physiology ; Animals ; Biodiversity ; *Biological Evolution ; Databases, Chemical ; Ecosystem ; Europe ; Europe, Eastern ; Evolution, Molecular ; *Genetic Speciation ; Phenotype ; Phylogeny ; },
abstract = {Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.},
}

*Adaptation, Physiological
Amphipoda/*anatomy & histology/*genetics/physiology
Animals
Biodiversity
*Biological Evolution
Databases, Chemical
Ecosystem
Europe
Europe, Eastern
Evolution, Molecular
*Genetic Speciation
Phenotype
Phylogeny

@article {pmid34081744,
year = {2021},
author = {Colella, JP and Bates, J and Burneo, SF and Camacho, MA and Carrion Bonilla, C and Constable, I and D'Elía, G and Dunnum, JL and Greiman, S and Hoberg, EP and Lessa, E and Liphardt, SW and Londoño-Gaviria, M and Losos, E and Lutz, HL and Ordóñez Garza, N and Peterson, AT and Martin, ML and Ribas, CC and Struminger, B and Torres-Pérez, F and Thompson, CW and Weksler, M and Cook, JA},
title = {Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network.},
journal = {PLoS pathogens},
volume = {17},
number = {6},
pages = {e1009583},
pmid = {34081744},
issn = {1553-7374},
mesh = {Animals ; Animals, Wild ; Biodiversity ; Biological Specimen Banks/*organization & administration/standards/supply & distribution/trends ; COVID-19/epidemiology ; *Communicable Disease Control/methods/organization & administration/standards ; Communicable Diseases, Emerging/epidemiology/microbiology/*prevention & control/virology ; Community Networks/*organization & administration/standards/supply & distribution/trends ; Disaster Planning/methods/organization & administration/standards ; Geography ; Global Health/standards/trends ; Humans ; Medical Countermeasures ; Pandemics/prevention & control ; Public Health ; Public Health Surveillance/*methods ; Risk Assessment ; SARS-CoV-2/physiology ; Zoonoses/epidemiology/prevention & control ; },
abstract = {The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO's virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.},
}

Animals
Animals, Wild
Biodiversity
Biological Specimen Banks/*organization & administration/standards/supply & distribution/trends
COVID-19/epidemiology
*Communicable Disease Control/methods/organization & administration/standards
Communicable Diseases, Emerging/epidemiology/microbiology/*prevention & control/virology
Community Networks/*organization & administration/standards/supply & distribution/trends
Disaster Planning/methods/organization & administration/standards
Geography
Global Health/standards/trends
Humans
Medical Countermeasures
Pandemics/prevention & control
Public Health
Public Health Surveillance/*methods
Risk Assessment
SARS-CoV-2/physiology
Zoonoses/epidemiology/prevention & control

@article {pmid34070673,
year = {2021},
author = {Cadar, D and Schmidt-Chanasit, J and Tappe, D},
title = {Genomic and Micro-Evolutionary Features of Mammalian 2 orthobornavirus (Variegated Squirrel Bornavirus 1, VSBV-1).},
journal = {Microorganisms},
volume = {9},
number = {6},
pages = {},
pmid = {34070673},
issn = {2076-2607},
support = {01KI2005C//German Federal Ministry of Education and Research/ ; },
abstract = {Mammalian 2 orthobornavirus (VSBV-1) is an emerging zoonotic pathogen discovered in several exotic squirrel species and associated with fatal human encephalitis. The dynamics of VSBV-1 spread and evolution in its presumed natural hosts are unknown. Here, we present the phylogeny, micro-evolution, cross-species transmission and spread of VSBV-1 at a temporal and spatial resolution within the limits of animal husbandry. The results showed that VSBV-1 can be classified into six distinct groups and that the most recent common ancestor of the known German strains emerged at least 20 years ago. We here demonstrate that the genetic diversity of the VSBV-1 groups is shaped primarily by in situ evolution and most of the amino acid changes are deleterious polymorphisms removed by purifying selection. Evidence of adaptive evolution has been found in the G and L genes which might have an influence on transmission fitness. Furthermore, there was also evidence for some form of adaptive changes in the glycoprotein which suggests that many sites might be subjected to positive pressure evolving under episodic directional selection, indicating past occurrence of positive selection. Host switching events were detected as dominant evolutionary mechanisms driving the virus-host associations. Virus spread by animal trade followed by subsequent local micro-evolution in zoos and holdings is responsible for diversifying strains. Time-resolved phylogeny indicated that Prevost's squirrels might be the original squirrel species carrying and seeding the virus in Germany. This study provides the first insight into the ecology and micro-evolutionary dynamics of this novel viral pathogen in the captive exotic squirrel population under artificial ecological conditions (zoos and animal husbandry) and co-housing of different squirrel species.},
}

@article {pmid34021563,
year = {2021},
author = {Wright, ES and Gupta, R and Vetsigian, KH},
title = {Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {6},
pages = {},
doi = {10.1093/femsec/fiab073},
pmid = {34021563},
issn = {1574-6941},
mesh = {Bacteria/genetics ; *Microbiota ; *Models, Biological ; Population Dynamics ; },
abstract = {Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exists little experimental evidence supporting this possibility. Here, we gathered a large collection of absolute population abundances capturing population dynamics in one- to four-strain communities of soil bacteria with a complex life cycle in a feast-or-famine environment. This dataset led to several observations: (i) some pairwise competitions resulted in bistability with a separatrix near a 1:1 initial ratio across a range of population densities; (ii) bistability propagated to multi-stability in multispecies communities; and (iii) replicate microbial communities reached different stable states when starting close to initial conditions separating basins of attraction, indicating finite-sized regions where the dynamics are unpredictable. The generalized Lotka-Volterra equations qualitatively captured most competition outcomes but were unable to quantitatively recapitulate the observed dynamics. This was partly due to complex and diverse growth dynamics in monocultures that ranged from Allee effects to nonmonotonic behaviors. Overall, our results highlight that multi-stability might be generic in multispecies communities and, combined with ecological noise, can lead to unpredictable community assembly, even in simple environments.},
}

Bacteria/genetics
*Microbiota
*Models, Biological
Population Dynamics

@article {pmid34011982,
year = {2021},
author = {Rabosky, DL and Benson, RBJ},
title = {Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2945},
pmid = {34011982},
issn = {2041-1723},
mesh = {Animals ; *Biodiversity ; *Biological Evolution ; Data Interpretation, Statistical ; *Ecosystem ; Extinction, Biological ; Fossils ; Genetic Speciation ; Mathematical Concepts ; *Models, Biological ; Paleontology/methods/statistics & numerical data ; Phylogeny ; Phylogeography ; Time Factors ; },
abstract = {Estimates of evolutionary diversification rates - speciation and extinction - have been used extensively to explain global biodiversity patterns. Many studies have analyzed diversification rates derived from just two pieces of information: a clade's age and its extant species richness. This "age-richness rate" (ARR) estimator provides a convenient shortcut for comparative studies, but makes strong assumptions about the dynamics of species richness through time. Here we demonstrate that use of the ARR estimator in comparative studies is problematic on both theoretical and empirical grounds. We prove mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversification is zero. Using paleontological time series, we demonstrate that the ARR estimator has no predictive ability for real datasets. These pathologies arise because the ARR inference procedure yields "point estimates" that have been computed under a saturated statistical model with zero degrees of freedom. Although ARR estimates remain useful in some contexts, they should be avoided for comparative studies of diversification and species richness.},
}

Animals
*Biodiversity
*Biological Evolution
Data Interpretation, Statistical
*Ecosystem
Extinction, Biological
Fossils
Genetic Speciation
Mathematical Concepts
*Models, Biological
Paleontology/methods/statistics & numerical data
Phylogeny
Phylogeography
Time Factors

@article {pmid34006840,
year = {2021},
author = {Karatayev, VA and Vasconcelos, VV and Lafuite, AS and Levin, SA and Bauch, CT and Anand, M},
title = {A well-timed shift from local to global agreements accelerates climate change mitigation.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2908},
pmid = {34006840},
issn = {2041-1723},
abstract = {Recent attempts at cooperating on climate change mitigation highlight the limited efficacy of large-scale negotiations, when commitment to mitigation is costly and initially rare. Deepening existing voluntary mitigation pledges could require more stringent, legally-binding agreements that currently remain untenable at the global scale. Building-blocks approaches promise greater success by localizing agreements to regions or few-nation summits, but risk slowing mitigation adoption globally. Here, we show that a well-timed policy shift from local to global legally-binding agreements can dramatically accelerate mitigation compared to using only local, only global, or both agreement types simultaneously. This highlights the scale-specific roles of mitigation incentives: local agreements promote and sustain mitigation commitments in early-adopting groups, after which global agreements rapidly draw in late-adopting groups. We conclude that focusing negotiations on local legally-binding agreements and, as these become common, a renewed pursuit of stringent, legally-binding world-wide agreements could best overcome many current challenges facing climate mitigation.},
}

@article {pmid33961346,
year = {2021},
author = {Baptiste, YM},
title = {Digital Feast and Physical Famine: The Altered Ecosystem of Anatomy Education due to the Covid-19 Pandemic.},
journal = {Anatomical sciences education},
volume = {14},
number = {4},
pages = {399-407},
doi = {10.1002/ase.2098},
pmid = {33961346},
issn = {1935-9780},
mesh = {Anatomy/*education ; *COVID-19 ; *Cadaver ; Ecology ; Education, Distance ; Humans ; Visible Human Projects ; },
abstract = {This article explores the effects of the coronavirus disease 2019 (Covid-19) pandemic on the evolution of both physical and digital cadavers within the unique ecosystem of the anatomy laboratory. A physical cadaver is a traditional and established learning tool in anatomy education, whereas a digital cadaver is a relatively recent phenomenon. The Covid-19 pandemic presented a major disturbance and disruption to all levels and types of education, including anatomy education. This article constructs a conceptual metaphor between a typical anatomy laboratory and an ecosystem, and considers the affordances, constraints, and changing roles of physical and digital cadavers within anatomy education through an ecological lens. Adaptation of physical and digital cadavers during the disturbance is analyzed, and the resiliency of digital cadaver technology is recognized. The evolving role of the digital cadaver is considered in terms of increasing accessibility and inclusivity within the anatomy laboratory ecosystem of the future.},
}

Anatomy/*education
*COVID-19
*Cadaver
Ecology
Education, Distance
Humans
Visible Human Projects

@article {pmid33955689,
year = {2021},
author = {Huettmann, F and Hueffer, K},
title = {The ecological niche of reported rabies cases in Canada is similar to Alaska.},
journal = {Zoonoses and public health},
volume = {68},
number = {6},
pages = {677-683},
doi = {10.1111/zph.12835},
pmid = {33955689},
issn = {1863-2378},
mesh = {Alaska/epidemiology ; Animals ; *Animals, Wild ; Canada/epidemiology ; Demography ; Ecosystem ; Geographic Information Systems ; Humans ; *Livestock ; *Models, Biological ; *Pets ; Rabies/epidemiology/*veterinary ; Viral Zoonoses ; },
abstract = {The ecology of rabies in the circumpolar North is still not well understood. We use machine learning, a geographic information system and data explicit in time and space obtained for reported rabies cases and predictors in Canada to develop an ecological niche model for the distribution of reported rabies cases in the American north (Alaska and Canada). The ecological niche model based on reported rabies cases in Canada predicted reported rabies cases in Alaska, suggesting a rather robust inference and even similar drivers on a continental scale. As found in Alaska, proximity to human infrastructure-specifically along the coast-was a strong predictor in the detection of rabies cases in Canada. Also, this finding highlights the need for a more systematic landscape sampling for rabies infection model predictions to better understand and tackle the ecology of this important zoonotic disease on a landscape scale at some distance from human infrastructure in wilderness areas.},
}

Alaska/epidemiology
Animals
*Animals, Wild
Canada/epidemiology
Demography
Ecosystem
Geographic Information Systems
Humans
*Livestock
*Models, Biological
*Pets
Rabies/epidemiology/*veterinary
Viral Zoonoses

@article {pmid33948558,
year = {2021},
author = {Santos, FP and Levin, SA and Vasconcelos, VV},
title = {Biased perceptions explain collective action deadlocks and suggest new mechanisms to prompt cooperation.},
journal = {iScience},
volume = {24},
number = {4},
pages = {102375},
pmid = {33948558},
issn = {2589-0042},
abstract = {When individuals face collective action problems, their expectations about others' willingness to contribute affect their motivation to cooperate. Individuals, however, often misperceive the cooperation levels in a population. In the context of climate action, people underestimate the pro-climate positions of others. Designing incentives to enable cooperation and a sustainable future must thereby consider how social perception biases affect collective action. We propose a theoretical model and investigate the effect of social perception bias in non-linear public goods games. We show that different types of bias play a distinct role in cooperation dynamics. False uniqueness (underestimating own views) and false consensus (overestimating own views) both explain why communities get locked in suboptimal states. Such dynamics also impact the effectiveness of typical monetary incentives, such as fees. Our work contributes to understanding how targeting biases, e.g., by changing the information available to individuals, can comprise a fundamental mechanism to prompt collective action.},
}

@article {pmid33911920,
year = {2021},
author = {Nasser, M and Okely, M and Nasif, O and Alharbi, S and GadAllah, S and Al-Obaid, S and Enan, R and Bala, M and Al-Ashaal, S},
title = {Spatio-temporal analysis of Egyptian flower mantis Blepharopsis mendica (order: mantodea), with notes of its future status under climate change.},
journal = {Saudi journal of biological sciences},
volume = {28},
number = {4},
pages = {2049-2055},
pmid = {33911920},
issn = {1319-562X},
abstract = {Egyptian flower mantis Blepharopsis mendica (Order: Mantodea) is a widespread mantis species throughout the southwest Palearctic region. The ecological and geographical distribution of such interesting species is rarely known. So, through this work, habitat suitability models for its distribution through Egyptian territory were created using MaxEnt software from 90 occurrence records. One topographic (altitude) and eleven bioclimatic variables influencing the species distribution were selected to generate the models. The predicted distribution in Egypt was focused on the Delta, South Sinai, the north-eastern part of the country, and some areas in the west including Siwa Oasis. Temporal analysis between the two periods (1900-1961) and (1961-2017) show current reduction of this species distribution through Delta and its surrounding areas, may be due to urbanization. On the other hand, it increases in newly protected areas of South Sinai. Under the future climate change scenario, the MaxEnt model predicted the habitat gains for B. mendica in RCP 2.6 for 2070 and loss of habitat in RCP 8.5 for the same year. Our results can be used as a basis for conserving this species not only in Egypt, but also throughout the whole of its range, also, it show how the using of geo-information could help in studying animal ecology.},
}

@article {pmid33910068,
year = {2021},
author = {Szabó, B and Lang, Z and Kövér, S and Bakonyi, G},
title = {The inter-individual variance can provide additional information for the ecotoxicologists beside the mean.},
journal = {Ecotoxicology and environmental safety},
volume = {217},
number = {},
pages = {112260},
doi = {10.1016/j.ecoenv.2021.112260},
pmid = {33910068},
issn = {1090-2414},
mesh = {Animals ; Arthropods/*physiology ; Clutch Size ; Insecticides/*toxicity ; Phenotype ; Pyrethrins/*toxicity ; Reproduction/drug effects ; },
abstract = {The hypothesis that the inter-individual parameter variability is an unexploited area of ecotoxicology was proposed several decades ago. Although some illustrative examples were presented to support this hypothesis in the last decades, it has never been tested on an extensive, coherent database. In this study, variance changes of 105 dose-response curves were analysed. All data originated from the same experiment, where the effects of the insecticide Trebon EC were investigated in a dose-response manner on 15 traits of the collembolan Folsomia candida in four subsequent generations and two types of insecticide treatments. A consistent relationship between inter-individual variance and insecticide application was found in 2 (first clutch size and growth-reproduction trade-off) out of the 15 of the parameters. Contrary to the mean, the variance of the first clutch size showed consistent differences compared to the control. Furthermore, the variance of the growth-reproduction trade-off was consistently different from the control except in one case (F3 generation of the transgenerational treatment). Higher first clutch size variances were found in F1 and a lower one in the F2 and F3 generations than in that of the control. This overall pattern of the variance changes of the first clutch size and the trade-off seems to be a quick response to the insecticide application. In the short term, we have found that variance increased with insecticide treatment (P and F1 generation), because phenotypic variance generally increases due to environmental stress. Disruptive selection could be another mechanism between the more detoxification less reproduction strategy and the more reproduction less detoxification strategy. However, in the later generations (F2-F3) the variance decreases compared to the control, which could be because on short term selection stronger on the viability parameters and in long-term selection on reproduction becomes stronger. According to our results, analysis of the variance changes of some parameters may give information about the effects of the pesticide even when the mean does not predict any impact. Testing variance changes are important in ecotoxicology because variance change can signalise toxicant impact even when the mean does not change in certain cases.},
}

Animals
Arthropods/*physiology
Clutch Size
Insecticides/*toxicity
Phenotype
Pyrethrins/*toxicity
Reproduction/drug effects

@article {pmid33900611,
year = {2021},
author = {Ramakrishnan, M and Yrjälä, K and Satheesh, V and Zhou, MB},
title = {Bamboo Transposon Research: Current Status and Perspectives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2250},
number = {},
pages = {257-270},
pmid = {33900611},
issn = {1940-6029},
mesh = {DNA Transposable Elements/*genetics ; Databases, Genetic ; Gene Expression Regulation, Plant ; Genetic Variation ; Genome Size/genetics ; Genome, Plant/*genetics ; Genomics/*methods ; Internet ; Plant Breeding/economics/methods ; Ploidies ; Sasa/classification/*genetics ; Species Specificity ; },
abstract = {Bamboo, a fast-growing non-timber forest plant with many uses, is a valuable species for green development. However, bamboo flowering is very infrequent, extending, in general, for up to 120 years. Ecologically, bamboo species are generally better adapted to various environments than other grasses. Therefore, the species deserves a special status in what could be called Ecological Bioeconomy. An understanding of the genetic processes of bamboo can help us sustainably develop and manage bamboo forests. Transposable elements (TEs), jumping genes or transposons, are major genetic elements in plant genomes. The rapid development of the bamboo reference genome, at the chromosome level, reveals that TEs occupy over 63.24% of the genome. This is higher than found in rice, Brachypodium, and sorghum. The bamboo genome contains diverse families of TEs, which play a significant role in bamboo's biological processes including growth and development. TEs provide important clues for understanding the evolution of the bamboo genome. In this chapter, we briefly describe the current status of research on TEs in the bamboo genome, their regulation, and transposition mechanisms. Perspectives for future research are also provided.},
}

DNA Transposable Elements/*genetics
Databases, Genetic
Gene Expression Regulation, Plant
Genetic Variation
Genome Size/genetics
Genome, Plant/*genetics
Genomics/*methods
Internet
Plant Breeding/economics/methods
Ploidies
Sasa/classification/*genetics
Species Specificity

@article {pmid33846912,
year = {2021},
author = {Liu, H and Jiang, Y and Misa, R and Gao, J and Xia, M and Preusse, A and Sroka, A and Jiang, Y},
title = {Ecological environment changes of mining areas around Nansi lake with remote sensing monitoring.},
journal = {Environmental science and pollution research international},
volume = {28},
number = {32},
pages = {44152-44164},
pmid = {33846912},
issn = {1614-7499},
support = {CHN/1101176STP//Alexander von Humboldt-Stiftung/ ; 2016YFC0501105//National Research and Development Project/ ; 2018-TD-MS052//China Coal Technology & Engineering Group Project/ ; },
mesh = {China ; *Coal Mining ; Environmental Monitoring ; *Lakes ; Remote Sensing Technology ; },
abstract = {Underground mining activity has existed for more than 100 years in Nansi lake. Coal mining not only plays a supporting role in local social and economic development but also has a significant impact on the ecological environment in the region. Landsat series remote sensing data (1988~2019) are used to research the impact of coal mining on the ecological environment in Nansi lake. Then support vector machine (SVM) classifier is applied to extract the water area of the upstream lake from 1988 to 2019, and ecological environment and spatiotemporal variation characteristics are analyzed by Remote Sensing Ecology Index (RSEI). The results illustrate that the water area change is associated with annual precipitation. In terms of ecological quality, the area of poor ecological quality areas increased by 101.782 km2, while the area of good and excellent quality areas decreased by 218.988 km2 from 2009 to 2019. So compared with 2009, the ecological quality of the lake is worse in 2019, and then the reason for this change is due to large-scale underground mining. Therefore, the coal mines from the natural reserve may be closed or limited to the mining boundary for protecting the lake's ecological environment.},
}

China
*Coal Mining
Environmental Monitoring
*Lakes
Remote Sensing Technology

@article {pmid33808463,
year = {2021},
author = {Pushkareva, E and Sommer, V and Barrantes, I and Karsten, U},
title = {Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany.},
journal = {Microorganisms},
volume = {9},
number = {4},
pages = {},
pmid = {33808463},
issn = {2076-2607},
support = {20016/462//Deutsche Bundesstiftung Umwelt/ ; },
abstract = {Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples.},
}

@article {pmid33806786,
year = {2021},
author = {Peters, K and Balcke, G and Kleinenkuhnen, N and Treutler, H and Neumann, S},
title = {Untargeted In Silico Compound Classification-A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes.},
journal = {International journal of molecular sciences},
volume = {22},
number = {6},
pages = {},
pmid = {33806786},
issn = {1422-0067},
support = {322031L0107//Bundesministerium für Bildung, Wissenschaft und Forschung/ ; },
mesh = {Biodiversity ; Bryophyta/*chemistry/classification/genetics ; Cluster Analysis ; *Computational Biology/methods ; Metabolome ; *Metabolomics/methods ; Phylogeny ; Phytochemicals/*chemistry/*classification ; },
abstract = {In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)-LC/MS-QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou's diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher's exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by "zooming in" and in ecology by "zooming out". The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies.},
}

Biodiversity
Bryophyta/*chemistry/classification/genetics
Cluster Analysis
*Computational Biology/methods
Metabolome
*Metabolomics/methods
Phylogeny
Phytochemicals/*chemistry/*classification

@article {pmid33794796,
year = {2021},
author = {Moghaddam, VK and Dickerson, AS and Bazrafshan, E and Seyedhasani, SN and Najafi, F and Hadei, M and Momeni, J and Moradi, G and Sarmadi, M},
title = {Socioeconomic determinants of global distribution of multiple sclerosis: an ecological investigation based on Global Burden of Disease data.},
journal = {BMC neurology},
volume = {21},
number = {1},
pages = {145},
pmid = {33794796},
issn = {1471-2377},
support = {SRC-97-114//Torbat Heydariyeh University of Medical Sciences/ ; },
mesh = {Databases, Factual ; Educational Status ; Female ; *Global Burden of Disease ; Global Health ; Humans ; Incidence ; Income ; Male ; Multiple Sclerosis/*epidemiology ; Prevalence ; Quality-Adjusted Life Years ; *Socioeconomic Factors ; United Nations ; },
abstract = {BACKGROUND: Socioeconomic factors may be involved in risk of multiple sclerosis (MS), either indirectly or as confounding factors. In this study two comprehensive indicators reflecting socioeconomic differences, including the Human Development Index (HDI) and Prosperity Index (PI), were used to assess the impact of these factors on the worldwide distribution of MS.

METHODS: The data for this global ecological study were obtained from three comprehensive databases including the Global Burden of Disease (as the source of MS indices), United Nations Development Programme (source for HDI) and the Legatum Institute Database for PI. MS indices (including prevalence, incidence, mortality, and disability-adjusted life years) were all analyzed in the form of age- and sex-standardized. Correlation and regression analyses were used to investigate the relationship between HDI and PI and their subsets with MS indices.

RESULTS: All MS indices were correlated with HDI and PI. It was also found that developed countries had significantly higher prevalence and incidence rates of MS than developing countries. Education and governance from the PI, and gross national income and expected years of schooling from the HDI were more associated with MS. Education was significantly related to MS indices (p < 0.01) in both developed and developing countries.

CONCLUSION: In general, the difference in income and the socioeconomic development globally have created a landscape for MS that should be studied in more detail in future studies.},
}

Databases, Factual
Educational Status
Female
*Global Burden of Disease
Global Health
Humans
Incidence
Income
Male
Multiple Sclerosis/*epidemiology
Prevalence
Quality-Adjusted Life Years
*Socioeconomic Factors
United Nations

@article {pmid33793560,
year = {2021},
author = {Burthe, SJ and Schäfer, SM and Asaaga, FA and Balakrishnan, N and Chanda, MM and Darshan, N and Hoti, SL and Kiran, SK and Seshadri, T and Srinivas, PN and Vanak, AT and Purse, BV},
title = {Reviewing the ecological evidence base for management of emerging tropical zoonoses: Kyasanur Forest Disease in India as a case study.},
journal = {PLoS neglected tropical diseases},
volume = {15},
number = {4},
pages = {e0009243},
pmid = {33793560},
issn = {1935-2735},
support = {/WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Animals, Wild ; Disease Reservoirs/*veterinary/virology ; Ecosystem ; Encephalitis Viruses, Tick-Borne/*isolation & purification/physiology ; India/epidemiology ; Kyasanur Forest Disease/epidemiology/*veterinary/virology ; *Mammals ; Zoonoses/*epidemiology/virology ; },
abstract = {Zoonoses disproportionately affect tropical communities and are associated with human modification and use of ecosystems. Effective management is hampered by poor ecological understanding of disease transmission and often focuses on human vaccination or treatment. Better ecological understanding of multi-vector and multi-host transmission, social and environmental factors altering human exposure, might enable a broader suite of management options. Options may include "ecological interventions" that target vectors or hosts and require good knowledge of underlying transmission processes, which may be more effective, economical, and long lasting than conventional approaches. New frameworks identify the hierarchical series of barriers that a pathogen needs to overcome before human spillover occurs and demonstrate how ecological interventions may strengthen these barriers and complement human-focused disease control. We extend these frameworks for vector-borne zoonoses, focusing on Kyasanur Forest Disease Virus (KFDV), a tick-borne, neglected zoonosis affecting poor forest communities in India, involving complex communities of tick and host species. We identify the hierarchical barriers to pathogen transmission targeted by existing management. We show that existing interventions mainly focus on human barriers (via personal protection and vaccination) or at barriers relating to Kyasanur Forest Disease (KFD) vectors (tick control on cattle and at the sites of host (monkey) deaths). We review the validity of existing management guidance for KFD through literature review and interviews with disease managers. Efficacy of interventions was difficult to quantify due to poor empirical understanding of KFDV-vector-host ecology, particularly the role of cattle and monkeys in the disease transmission cycle. Cattle are hypothesised to amplify tick populations. Monkeys may act as sentinels of human infection or are hypothesised to act as amplifying hosts for KFDV, but the spatial scale of risk arising from ticks infected via monkeys versus small mammal reservoirs is unclear. We identified 19 urgent research priorities for refinement of current management strategies or development of ecological interventions targeting vectors and host barriers to prevent disease spillover in the future.},
}

Animals
Animals, Wild
Disease Reservoirs/*veterinary/virology
Ecosystem
Encephalitis Viruses, Tick-Borne/*isolation & purification/physiology
India/epidemiology
Kyasanur Forest Disease/epidemiology/*veterinary/virology
*Mammals
Zoonoses/*epidemiology/virology

@article {pmid33784860,
year = {2021},
author = {Todorov, OS and Blomberg, SP and Goswami, A and Sears, K and Drhlík, P and Peters, J and Weisbecker, V},
title = {Testing hypotheses of marsupial brain size variation using phylogenetic multiple imputations and a Bayesian comparative framework.},
journal = {Proceedings. Biological sciences},
volume = {288},
number = {1947},
pages = {20210394},
pmid = {33784860},
issn = {1471-2954},
mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Female ; *Marsupialia/genetics ; Organ Size ; Phylogeny ; Pregnancy ; },
abstract = {Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets of 16 predictor variables, to model the prevalent hypotheses explaining brain size evolution using phylogenetically corrected Bayesian generalized linear mixed-effects modelling. Despite this comprehensive analysis, litter size emerges as the only significant predictor. Marsupials differ from the more frequently studied placentals in displaying a much lower diversity of reproductive traits, which are known to interact extensively with many behavioural and ecological predictors of brain size. Our results therefore suggest that studies of relative brain size evolution in placental mammals may require targeted co-analysis or adjustment of reproductive parameters like litter size, weaning age or gestation length. This supports suggestions that significant associations between behavioural or ecological variables with relative brain size may be due to a confounding influence of the extensive reproductive diversity of placental mammals.},
}

Animals
Bayes Theorem
Biological Evolution
Female
*Marsupialia/genetics
Organ Size
Phylogeny
Pregnancy

@article {pmid33764467,
year = {2021},
author = {Modica, MV and Ahmad, R and Ainsworth, S and Anderluh, G and Antunes, A and Beis, D and Caliskan, F and Serra, MD and Dutertre, S and Moran, Y and Nalbantsoy, A and Oukkache, N and Pekar, S and Remm, M and von Reumont, BM and Sarigiannis, Y and Tarallo, A and Tytgat, J and Undheim, EAB and Utkin, Y and Verdes, A and Violette, A and Zancolli, G},
title = {The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics.},
journal = {GigaScience},
volume = {10},
number = {3},
pages = {},
pmid = {33764467},
issn = {2047-217X},
abstract = {Venom research is a highly multidisciplinary field that involves multiple subfields of biology, informatics, pharmacology, medicine, and other areas. These different research facets are often technologically challenging and pursued by different teams lacking connection with each other. This lack of coordination hampers the full development of venom investigation and applications. The COST Action CA19144-European Venom Network was recently launched to promote synergistic interactions among different stakeholders and foster venom research at the European level.},
}

@article {pmid33742448,
year = {2021},
author = {Soria, CD and Pacifici, M and Di Marco, M and Stephen, SM and Rondinini, C},
title = {COMBINE: a coalesced mammal database of intrinsic and extrinsic traits.},
journal = {Ecology},
volume = {102},
number = {6},
pages = {e03344},
doi = {10.1002/ecy.3344},
pmid = {33742448},
issn = {1939-9170},
support = {766417//H2020 Marie Skłodowska-Curie Actions/ ; },
mesh = {Animals ; Biodiversity ; *Data Management ; Ecosystem ; Female ; *Mammals ; Phenotype ; },
abstract = {The use of species' traits in macroecological analyses has gained popularity in the last decade, becoming an important tool to understand global biodiversity patterns. Currently, trait data can be found across a wide variety of data sets included in websites, articles, and books, each one with its own taxonomic classification, set of traits, and data management methodology. Mammals, in particular, are among the most studied taxa, with large sources of trait information readily available. To facilitate the use of these data, we did an extensive review of published mammal trait data sources between 1999 and May 2020 and produced COMBINE: a COalesced Mammal dataBase of INtrinsic and Extrinsic traits. Our aim was to create a taxonomically integrated database of mammal traits that maximized trait number and coverage without compromising data quality. COMBINE contains information on 54 traits for 6,234 extant and recently extinct mammal species, including information on morphology, reproduction, diet, biogeography, life habit, phenology, behavior, home range, and density. Additionally, we calculated other relevant traits such as habitat and altitudinal breadths for all species and dispersal for terrestrial non-volant species. All data are compatible with the taxonomies of the IUCN Red List v. 2020-2 and PHYLACINE v. 1.2. Missing data were adequately flagged and imputed for non-biogeographical traits with 20% or more data available. We obtained full data sets for 21 traits such as female maturity, litter size, maximum longevity, trophic level, and dispersal, providing imputation performance statistics for all. This data set will be especially useful for those interested in including species' traits in large-scale ecological and conservation analyses. There are no copyright or proprietary restrictions; we request citation of this publication and all relevant underlying data sources (found in Data S1: trait_data_sources.csv), upon using these data.},
}

Animals
Biodiversity
*Data Management
Ecosystem
Female
*Mammals
Phenotype

@article {pmid33654452,
year = {2021},
author = {Kim, HW and Yoon, S and Kim, M and Shin, M and Yoon, H and Kim, K},
title = {EcoBank: A flexible database platform for sharing ecological data.},
journal = {Biodiversity data journal},
volume = {9},
number = {},
pages = {e61866},
pmid = {33654452},
issn = {1314-2828},
abstract = {Background: Environmental crisis challenges the human race harder than ever before. Ecologists have produced a massive amount of data to cope with the crisis. Accordingly, many national scale ecological database systems have been developed worldwide to manage and analyse these datasets. However, in Korea, ecological datasets produced by different research institutes for different purposes have not been integrated or serviced due to poorly designed information infrastructure. To address this obstacle, we present EcoBank (www.nie-ecobank.kr), an open, web-based ecological database platform designed to play an important role in ecosystem analysis, not only in Korea, but also worldwide.

New information: The architecture of EcoBank comprises core technologies of WebGIS, Application Programming Interface (API), responsive web and open-source software (OSS). Comprehensive ecological datasets from three different sources, including the National Institute of Ecology (NIE) in Korea, related national and international platforms and repositories, enter the three conceptual modules in EcoBank: data management, analysis and service. Diverse potential stakeholders of EcoBank can be classified into three groups: researchers, policy-makers and public users. EcoBank aims to expand its horizons through mutual communication amongst these stakeholders. We opened and launched the EcoBank service in December 2019 and have now begun to broaden its network by linking it to other data platforms and repositories over the globe to find possible solutions to ecological issues in Korea.},
}

@article {pmid33639712,
year = {2021},
author = {Lei, J and Booth, DT and Rusli, MU and Zhang, Z},
title = {Spatial Ecology of Asian Water Monitors Adjacent to a Sea Turtle Nesting Beach.},
journal = {Zoological science},
volume = {38},
number = {1},
pages = {1-7},
doi = {10.2108/zs200071},
pmid = {33639712},
issn = {0289-0003},
mesh = {*Animal Distribution ; Animals ; *Ecosystem ; Female ; Geographic Information Systems ; Homing Behavior ; Lizards/*physiology ; Malaysia ; Male ; Nesting Behavior ; Predatory Behavior ; Turtles ; },
abstract = {Nest predation is the main cause of hatching failure for many turtle populations. For green turtles (Chelonia mydas) nesting at Chagar Hutang in Redang Island, Malaysia, Asian water monitors (Varanus salvator) are a potential nest predator. However, no studies have documented the space use of this species in coastal habitat adjacent to a sea turtle nesting beach to assess its potential impact on turtle nests. Here, we used Global Positioning System (GPS) data loggers to quantify space use of Asian water monitors in order to establish the extent to which they use sea turtle nesting areas. Asian water monitors had a diurnal activity pattern and spent most of their time in rain forest habitat behind the sea turtle nesting beach. The home range occupied by Asian water monitors varied between 0.015 and 0.198 km2 calculated by the Kernel Brownian Bridge method. The space use patterns of individual Asian water monitors varied between individuals. Two males had relatively small home ranges, whereas one male and the female had a relatively large home range. Because tracked Asian water monitors in this study rarely visited the sea turtle nesting areas, it is probable that only a few individuals are responsible for opening nests.},
}

*Animal Distribution
Animals
*Ecosystem
Female
Geographic Information Systems
Homing Behavior
Lizards/*physiology
Malaysia
Male
Nesting Behavior
Predatory Behavior
Turtles

@article {pmid33605211,
year = {2021},
author = {Weinstein, BG and Marconi, S and Bohlman, SA and Zare, A and Singh, A and Graves, SJ and White, EP},
title = {A remote sensing derived data set of 100 million individual tree crowns for the National Ecological Observatory Network.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {33605211},
issn = {2050-084X},
support = {GBMF4563//Gordon and Betty Moore Foundation/ ; 1926542//National Science Foundation/ ; McIntire Stennis projects #1007080//National Institute of Food and Agriculture/ ; },
abstract = {Forests provide biodiversity, ecosystem, and economic services. Information on individual trees is important for understanding forest ecosystems but obtaining individual-level data at broad scales is challenging due to the costs and logistics of data collection. While advances in remote sensing techniques allow surveys of individual trees at unprecedented extents, there remain technical challenges in turning sensor data into tangible information. Using deep learning methods, we produced an open-source data set of individual-level crown estimates for 100 million trees at 37 sites across the United States surveyed by the National Ecological Observatory Network's Airborne Observation Platform. Each canopy tree crown is represented by a rectangular bounding box and includes information on the height, crown area, and spatial location of the tree. These data have the potential to drive significant expansion of individual-level research on trees by facilitating both regional analyses and cross-region comparisons encompassing forest types from most of the United States.},
}

@article {pmid33592451,
year = {2021},
author = {Boori, MS and Choudhary, K and Paringer, R and Kupriyanov, A},
title = {Spatiotemporal ecological vulnerability analysis with statistical correlation based on satellite remote sensing in Samara, Russia.},
journal = {Journal of environmental management},
volume = {285},
number = {},
pages = {112138},
doi = {10.1016/j.jenvman.2021.112138},
pmid = {33592451},
issn = {1095-8630},
mesh = {China ; Cities ; *Ecosystem ; Environmental Monitoring ; Humans ; *Remote Sensing Technology ; Russia ; },
abstract = {In the present global situation, when everywhere ecology is degraded due to the extreme exhaustion of natural resources. Therefore spatiotemporal ecological vulnerability analysis is necessary for the current situation for sustainable development with protection of fragile eco-environment. Remote sensing is a unique tool to provide complete and continuous land surface information at different scales, which can use for eco-environment analysis. A methodology constructed on the principal component analysis (PCA) to identify satellite remote sensing ecological index (RSEI) for ecological vulnerability analysis and distribution based on four land surface parameters (dryness, greenness, temperature and moisture) by using Landsat TM/ETM+/OLI/TIRS data in the Samara region Russia. The results were verified by the following four methods: location-based, categorization-based, correlation-based and city center to outwards distance-based comparisons. Results indicate that ecological condition was improved from 2010 to 2015 as RSEI increased from 0.79 to 0.98 and from 2015 to 2020 the ecological condition was degraded as RSEI decreased from 0.98 to 0.82 but overall it was improved in this decade. RSEI distribution curve shows moderate to good and excellent ecological conditions and degraded ecological condition was basically characterized by high human interference and socioeconomic activities in the study area. Such a technique is a baseline for highly accurate ecological conditions mapping, monitoring and can use for decision making, management and sustainable development.},
}

China
Cities
*Ecosystem
Environmental Monitoring
Humans
*Remote Sensing Technology
Russia

@article {pmid33577568,
year = {2021},
author = {Titus, M and Hagstrom, G and Watson, JR},
title = {Unsupervised manifold learning of collective behavior.},
journal = {PLoS computational biology},
volume = {17},
number = {2},
pages = {e1007811},
pmid = {33577568},
issn = {1553-7358},
mesh = {Animals ; *Behavior ; *Behavior, Animal ; Computational Biology ; Ecosystem ; Fishes/physiology ; Humans ; Models, Biological ; Models, Psychological ; Social Behavior ; Synthetic Biology ; *Systems Analysis ; Systems Biology ; *Unsupervised Machine Learning ; },
abstract = {Collective behavior is an emergent property of numerous complex systems, from financial markets to cancer cells to predator-prey ecological systems. Characterizing modes of collective behavior is often done through human observation, training generative models, or other supervised learning techniques. Each of these cases requires knowledge of and a method for characterizing the macro-state(s) of the system. This presents a challenge for studying novel systems where there may be little prior knowledge. Here, we present a new unsupervised method of detecting emergent behavior in complex systems, and discerning between distinct collective behaviors. We require only metrics, d(1), d(2), defined on the set of agents, X, which measure agents' nearness in variables of interest. We apply the method of diffusion maps to the systems (X, d(i)) to recover efficient embeddings of their interaction networks. Comparing these geometries, we formulate a measure of similarity between two networks, called the map alignment statistic (MAS). A large MAS is evidence that the two networks are codetermined in some fashion, indicating an emergent relationship between the metrics d(1) and d(2). Additionally, the form of the macro-scale organization is encoded in the covariances among the two sets of diffusion map components. Using these covariances we discern between different modes of collective behavior in a data-driven, unsupervised manner. This method is demonstrated on a synthetic flocking model as well as empirical fish schooling data. We show that our state classification subdivides the known behaviors of the school in a meaningful manner, leading to a finer description of the system's behavior.},
}

Animals
*Behavior
*Behavior, Animal
Computational Biology
Ecosystem
Fishes/physiology
Humans
Models, Biological
Models, Psychological
Social Behavior
Synthetic Biology
*Systems Analysis
Systems Biology
*Unsupervised Machine Learning

@article {pmid33497378,
year = {2021},
author = {Vörös, D and Könnyű, B and Czárán, T},
title = {Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism.},
journal = {PLoS computational biology},
volume = {17},
number = {1},
pages = {e1008634},
pmid = {33497378},
issn = {1553-7358},
mesh = {Computational Biology ; Computer Simulation ; *Evolution, Chemical ; Models, Biological ; *Prebiotics ; RNA, Catalytic/chemistry/*metabolism ; Substrate Specificity/physiology ; },
abstract = {The Metabolically Coupled Replicator System (MCRS) model of early chemical evolution offers a plausible and efficient mechanism for the self-assembly and the maintenance of prebiotic RNA replicator communities, the likely predecessors of all life forms on Earth. The MCRS can keep different replicator species together due to their mandatory metabolic cooperation and limited mobility on mineral surfaces, catalysing reaction steps of a coherent reaction network that produces their own monomers from externally supplied compounds. The complexity of the MCRS chemical engine can be increased by assuming that each replicator species may catalyse more than a single reaction of metabolism, with different catalytic activities of the same RNA sequence being in a trade-off relation: one catalytic activity of a promiscuous ribozyme can increase only at the expense of the others on the same RNA strand. Using extensive spatially explicit computer simulations we have studied the possibility and the conditions of evolving ribozyme promiscuity in an initial community of single-activity replicators attached to a 2D surface, assuming an additional trade-off between replicability and catalytic activity. We conclude that our promiscuous replicators evolve under weak catalytic trade-off, relatively strong activity/replicability trade-off and low surface mobility of the replicators and the metabolites they produce, whereas catalytic specialists benefit from very strong catalytic trade-off, weak activity/replicability trade-off and high mobility. We argue that the combination of conditions for evolving promiscuity are more probable to occur for surface-bound RNA replicators, suggesting that catalytic promiscuity may have been a significant factor in the diversification of prebiotic metabolic reaction networks.},
}

Computational Biology
Computer Simulation
*Evolution, Chemical
Models, Biological
*Prebiotics
RNA, Catalytic/chemistry/*metabolism
Substrate Specificity/physiology

@article {pmid33493157,
year = {2021},
author = {Wieters, B and Steige, KA and He, F and Koch, EM and Ramos-Onsins, SE and Gu, H and Guo, YL and Sunyaev, S and de Meaux, J},
title = {Polygenic adaptation of rosette growth in Arabidopsis thaliana.},
journal = {PLoS genetics},
volume = {17},
number = {1},
pages = {e1008748},
pmid = {33493157},
issn = {1553-7404},
support = {R01 MH101244/MH/NIMH NIH HHS/United States ; R35 GM127131/GM/NIGMS NIH HHS/United States ; },
mesh = {Acclimatization/genetics ; Adaptation, Physiological/*genetics ; Arabidopsis/*genetics/growth & development ; China ; Europe ; Genetic Variation/genetics ; Genetics, Population ; Genotype ; Multifactorial Inheritance/*genetics ; Phenotype ; Plant Development/genetics ; *Selection, Genetic ; },
abstract = {The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution.},
}

Acclimatization/genetics
Adaptation, Physiological/*genetics
Arabidopsis/*genetics/growth & development
China
Europe
Genetic Variation/genetics
Genetics, Population
Genotype
Multifactorial Inheritance/*genetics
Phenotype
Plant Development/genetics
*Selection, Genetic

@article {pmid33485207,
year = {2021},
author = {Kang, A and Ren, L and Hua, C and Song, H and Dong, M and Fang, Z and Zhu, M},
title = {Environmental management strategy in response to COVID-19 in China: Based on text mining of government open information.},
journal = {The Science of the total environment},
volume = {769},
number = {},
pages = {145158},
doi = {10.1016/j.scitotenv.2021.145158},
pmid = {33485207},
issn = {1879-1026},
mesh = {*COVID-19 ; China/epidemiology ; Conservation of Natural Resources ; Data Mining ; Government ; Humans ; *Pandemics ; Retrospective Studies ; SARS-CoV-2 ; },
abstract = {Coronavirus disease 2019 (COVID-19) is a global pandemic and a major health emergency. In the process of fighting against COVID-19, the China Ministry of Ecology and Environment (MEE) responded quickly and set up a working group as soon as possible. This article uses text mining to retrospectively analyze the government's public information on the website of MEE during the epidemic, sort out the timeline of MEE's response to COVID-19. We find that MEE's work during the COVID-19 pandemic is focused on medical waste and wastewater treatment, environment emergency monitoring, pollution prevention, and other environmental management for supporting economic recovery. It drafted three main medical waste management plans, an emergency environmental monitoring plan, and formulated "two lists" - a Positive checklist for Environmental impact assessment (EIA) approval and a positive checklist for supervision and enforcement, to promote the resumption of work and production. 2020 is the final year of China's "three years of fighting pollution prevention and control". In the case of the sudden COVID-19 epidemic, the Chinese environment department has ensured that the quality of the ecological environment has not been affected by the epidemic prevention and control while ensuring the smooth progress of the fight against pollution. China's medical waste disposal capacity has also been greatly improved during this epidemic. The review of China's environmental management strategy in response to COVID-19 can provide a reference for countries in the world that are still in the critical period of epidemic control; it can provide action guidelines for the ecological environment system to respond to sudden pandemic events in the future.},
}

*COVID-19
China/epidemiology
Conservation of Natural Resources
Data Mining
Government
Humans
*Pandemics
Retrospective Studies
SARS-CoV-2

@article {pmid33480058,
year = {2021},
author = {Marconi, S and Graves, SJ and Weinstein, BG and Bohlman, S and White, EP},
title = {Estimating individual-level plant traits at scale.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {31},
number = {4},
pages = {e02300},
doi = {10.1002/eap.2300},
pmid = {33480058},
issn = {1051-0761},
support = {GBMF4563//Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative/ ; 1926542//National Science Foundation/ ; DEB-1442280//NSF Dimension of Biodiversity program/ ; FLA-FOR-005470//USDA/NIFA McIntire-Stennis program/ ; //University of Florida Biodiversity Institute (UFBI)/ ; //Informatics Institute (UFII) Graduate Fellowship/ ; },
mesh = {*Ecosystem ; *Forests ; Humans ; Plant Leaves ; Plants ; Trees ; },
abstract = {Functional ecology has increasingly focused on describing ecological communities based on their traits (measurable features affecting individuals' fitness and performance). Analyzing trait distributions within and among forests could significantly improve understanding of community composition and ecosystem function. Historically, data on trait distributions are generated by (1) collecting a small number of leaves from a small number of trees, which suffers from limited sampling but produces information at the fundamental ecological unit (the individual), or (2) using remote-sensing images to infer traits, producing information continuously across large regions, but as plots (containing multiple trees of different species) or pixels, not individuals. Remote-sensing methods that identify individual trees and estimate their traits would provide the benefits of both approaches, producing continuous large-scale data linked to biological individuals. We used data from the National Ecological Observatory Network (NEON) to develop a method to scale up functional traits from 160 trees to the millions of trees within the spatial extent of two NEON sites. The pipeline consists of three stages: (1) image segmentation, to identify individual trees and estimate structural traits; (2) an ensemble of models to infer leaf mass area (LMA), nitrogen, carbon, and phosphorus content using hyperspectral signatures, and DBH from allometry; and (3) predictions for segmented crowns for the full remote-sensing footprint at the NEON sites. The R2 values on held-out test data ranged from 0.41 to 0.75 on held-out test data. The ensemble approach performed better than single partial least-squares models. Carbon performed poorly compared to other traits (R2 of 0.41). The crown segmentation step contributed the most uncertainty in the pipeline, due to over-segmentation. The pipeline produced good estimates of DBH (R2 of 0.62 on held-out data). Trait predictions for crowns performed significantly better than comparable predictions on pixels, resulting in improvement of R2 on test data of between 0.07 and 0.26. We used the pipeline to produce individual-level trait data for ~5 million individual crowns, covering a total extent of ~360 km2 . This large data set allows testing ecological questions on landscape scales, revealing that foliar traits are correlated with structural traits and environmental conditions.},
}

*Ecosystem
*Forests
Humans
Plant Leaves
Plants
Trees

@article {pmid33479183,
year = {2021},
author = {Grunert, K and Holden, H and Jakobsen, ER and Stenseth, NC},
title = {Evolutionarily stable strategies in stable and periodically fluctuating populations: The Rosenzweig-MacArthur predator-prey model.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {4},
pages = {},
pmid = {33479183},
issn = {1091-6490},
mesh = {*Adaptation, Physiological ; Animals ; Biological Evolution ; Computational Biology ; Computer Simulation ; Ecosystem ; *Food Chain ; *Models, Biological ; Population Dynamics ; Predatory Behavior/*physiology ; },
abstract = {An evolutionarily stable strategy (ESS) is an evolutionary strategy that, if adapted by a population, cannot be invaded by any deviating (mutant) strategy. The concept of ESS has been extensively studied and widely applied in ecology and evolutionary biology [M. Smith, On Evolution (1972)] but typically on the assumption that the system is ecologically stable. With reference to a Rosenzweig-MacArthur predator-prey model [M. Rosenzweig, R. MacArthur, Am. Nat. 97, 209-223 (1963)], we derive the mathematical conditions for the existence of an ESS when the ecological dynamics have asymptotically stable limit points as well as limit cycles. By extending the framework of Reed and Stenseth [J. Reed, N. C. Stenseth, J. Theoret. Biol. 108, 491-508 (1984)], we find that ESSs occur at values of the evolutionary strategies that are local optima of certain functions of the model parameters. These functions are identified and shown to have a similar form for both stable and fluctuating populations. We illustrate these results with a concrete example.},
}

*Adaptation, Physiological
Animals
Biological Evolution
Computational Biology
Computer Simulation
Ecosystem
*Food Chain
*Models, Biological
Population Dynamics
Predatory Behavior/*physiology

@article {pmid33462369,
year = {2021},
author = {Khataee, H and Scheuring, I and Czirok, A and Neufeld, Z},
title = {Effects of social distancing on the spreading of COVID-19 inferred from mobile phone data.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1661},
pmid = {33462369},
issn = {2045-2322},
mesh = {COVID-19/epidemiology/pathology/*transmission/virology ; Cell Phone ; Europe/epidemiology ; Geographic Information Systems ; Humans ; Pandemics ; *Physical Distancing ; Quarantine ; SARS-CoV-2/isolation & purification ; Travel/statistics & numerical data ; },
abstract = {A better understanding of how the COVID-19 pandemic responds to social distancing efforts is required for the control of future outbreaks and to calibrate partial lock-downs. We present quantitative relationships between key parameters characterizing the COVID-19 epidemiology and social distancing efforts of nine selected European countries. Epidemiological parameters were extracted from the number of daily deaths data, while mitigation efforts are estimated from mobile phone tracking data. The decrease of the basic reproductive number ([Formula: see text]) as well as the duration of the initial exponential expansion phase of the epidemic strongly correlates with the magnitude of mobility reduction. Utilizing these relationships we decipher the relative impact of the timing and the extent of social distancing on the total death burden of the pandemic.},
}

COVID-19/epidemiology/pathology/*transmission/virology
Cell Phone
Europe/epidemiology
Geographic Information Systems
Humans
Pandemics
*Physical Distancing
Quarantine
SARS-CoV-2/isolation & purification
Travel/statistics & numerical data

@article {pmid33460060,
year = {2020},
author = {Pinkert, S and Friess, N and Zeuss, D and Gossner, MM and Brandl, R and Brunzel, S},
title = {Mobility costs and energy uptake mediate the effects of morphological traits on species' distribution and abundance.},
journal = {Ecology},
volume = {101},
number = {10},
pages = {e03121},
doi = {10.1002/ecy.3121},
pmid = {33460060},
issn = {1939-9170},
support = {//Stifterverband/ ; //Google/ ; //Federal Office for the Environment/ ; },
mesh = {Animals ; Biological Evolution ; Body Size ; *Butterflies ; *Energy Metabolism ; Population Dynamics ; },
abstract = {Individuals of large or dark-colored ectothermic species often have a higher reproduction and activity than small or light-colored ones. However, investments into body size or darker colors should negatively affect the fitness of individuals as they increase their growth and maintenance costs. Thus, it is unlikely that morphological traits directly affect species' distribution and abundance. Yet, this simplification is frequently made in trait-based ecological analyses. Here, we integrated the energy allocation strategies of species into an ecophysiological framework to explore the mechanisms that link species' morphological traits and population dynamics. We hypothesized that the effects of morphological traits on species' distribution and abundance are not direct but mediated by components of the energy budget and that species can allocate more energy towards dispersal and reproduction if they compensate their energetic costs by reducing mobility costs or increasing energy uptake. To classify species' energy allocation strategies, we used easily measured proxies for the mobility costs and energy uptake of butterflies that can be also applied to other taxa. We demonstrated that contrasting effects of morphological traits on distribution and abundance of butterfly species offset each other when species' energy allocation strategies are not taken into account. Larger and darker butterfly species had wider distributions and were more abundant if they compensated the investment into body size and color darkness (i.e., melanin) by reducing their mobility costs or increasing energy uptake. Adults of darker species were more mobile and foraged less compared to lighter colored ones, if an investment into melanin was indirectly compensated via a size-dependent reduction of mobility costs or increase of energy uptake. Our results indicate that differences in the energy allocations strategies of species account for a considerable part of the variation in species' distribution and abundance that is left unexplained by morphological traits alone and ignoring these differences can lead to false mechanistic conclusions. Therefore, our findings highlight the potential of integrating proxies for species' energy allocation strategies into trait-based models not only for understanding the physiological mechanisms underlying variation in species' distribution and abundance, but also for improving predictions of the population dynamics of species.},
}

Animals
Biological Evolution
Body Size
*Butterflies
*Energy Metabolism
Population Dynamics

@article {pmid33421422,
year = {2021},
author = {Hassine, TB and Ali, MB and Ghodhbane, I and Said, ZB and Hammami, S},
title = {Rabies in Tunisia: A spatio-temporal analysis in the region of CapBon-Nabeul.},
journal = {Acta tropica},
volume = {216},
number = {},
pages = {105822},
doi = {10.1016/j.actatropica.2021.105822},
pmid = {33421422},
issn = {1873-6254},
mesh = {Animals ; Disease Reservoirs/veterinary/virology ; Dog Diseases/*epidemiology ; Dogs/virology ; Geographic Information Systems ; Population Dynamics ; Rabies/*epidemiology/*veterinary ; *Seasons ; *Spatio-Temporal Analysis ; Tunisia/epidemiology ; },
abstract = {Human rabies is a significant public health concern in Tunisia. However, the spatiotemporal spread pattern of rabies in dogs, the major reservoir and vector, and its determinants are poorly understood. We collected geographic locations and timeline of reported animal rabies cases in the region of CapBon (study area), for the years 2015-2019 and integrated them in Geographical Information System (GIS) approach to explore the spatio-temporal pattern of dog rabies. The results show that roads and irrigated areas can act as ecological corridors to viral spread. Our study showed that there was a significant seasonal variation in the number of cases of rabies recorded, with a strong peak in spring and lower peak in winter and summer. These findings may play a role in updating and directing public health policy, as well as providing opportunities for authorities to explore control options in time and space. A better knowledge of the ecology and dog population dynamics is still necessary and important to achieve an effective rabies control.},
}

Animals
Disease Reservoirs/veterinary/virology
Dog Diseases/*epidemiology
Dogs/virology
Geographic Information Systems
Population Dynamics
Rabies/*epidemiology/*veterinary
*Seasons
*Spatio-Temporal Analysis
Tunisia/epidemiology

@article {pmid33408411,
year = {2021},
author = {Zhou, Y and Shearwin-Whyatt, L and Li, J and Song, Z and Hayakawa, T and Stevens, D and Fenelon, JC and Peel, E and Cheng, Y and Pajpach, F and Bradley, N and Suzuki, H and Nikaido, M and Damas, J and Daish, T and Perry, T and Zhu, Z and Geng, Y and Rhie, A and Sims, Y and Wood, J and Haase, B and Mountcastle, J and Fedrigo, O and Li, Q and Yang, H and Wang, J and Johnston, SD and Phillippy, AM and Howe, K and Jarvis, ED and Ryder, OA and Kaessmann, H and Donnelly, P and Korlach, J and Lewin, HA and Graves, J and Belov, K and Renfree, MB and Grutzner, F and Zhou, Q and Zhang, G},
title = {Platypus and echidna genomes reveal mammalian biology and evolution.},
journal = {Nature},
volume = {592},
number = {7856},
pages = {756-762},
pmid = {33408411},
issn = {1476-4687},
abstract = {Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.},
}

@article {pmid33392900,
year = {2021},
author = {Keshavarzi, A and Kumar, V and Ertunç, G and Brevik, EC},
title = {Ecological risk assessment and source apportionment of heavy metals contamination: an appraisal based on the Tellus soil survey.},
journal = {Environmental geochemistry and health},
volume = {43},
number = {5},
pages = {2121-2142},
pmid = {33392900},
issn = {1573-2983},
mesh = {Agriculture ; Cities ; Databases, Factual ; Ecology ; Environmental Monitoring/methods ; Environmental Pollution/analysis ; Humans ; Ireland ; Metals, Heavy/*analysis/toxicity ; Multivariate Analysis ; Risk Assessment ; Soil/chemistry ; Soil Pollutants/*analysis ; Surveys and Questionnaires ; },
abstract = {It is imperative to comprehend the level and spatial distribution of soil pollution with heavy metals to find sustainable management approaches for affected soils. Selected heavy metals (Mn, Zn, Pb, Cu, Cr, Ni, As, Co, and Cd) and physiochemical parameters were appraised for 620 samples from industrial, agricultural and urban sites in Northern Ireland using the Tellus database. The findings of this study showed that among the analyzed heavy metals, Mn content was the highest and Cd content the lowest. Pearson's correlation analysis revealed that heavy metals were highly correlated with each other, signifying similar sources for the heavy metals. Mixed factors (anthropogenic and lithogenic) were responsible for the contribution of heavy metals as revealed by multivariate statistical analysis. The results of contamination factor and enrichment factor analyses suggest that As, Cd, and Pb showed very high risk for pollution in the study area. The geoaccumulation index revealed that with the exception of Cd, all analyzed heavy metals showed severe accumulation in the soils. The potential and modified ecological risk indices inferred that Cd, As, and Pb represented ecological threats in the soils of Northern Ireland. The findings of this study will aid in forming approaches to decrease the risks associated with heavy metals in industrial, urban and agricultural soils, and help create guidelines to protect the environment from long-term accumulation of heavy metals.},
}

Agriculture
Cities
Databases, Factual
Ecology
Environmental Monitoring/methods
Environmental Pollution/analysis
Humans
Ireland
Metals, Heavy/*analysis/toxicity
Multivariate Analysis
Risk Assessment
Soil/chemistry
Soil Pollutants/*analysis
Surveys and Questionnaires

@article {pmid33372367,
year = {2021},
author = {Lemm, JU and Venohr, M and Globevnik, L and Stefanidis, K and Panagopoulos, Y and van Gils, J and Posthuma, L and Kristensen, P and Feld, CK and Mahnkopf, J and Hering, D and Birk, S},
title = {Multiple stressors determine river ecological status at the European scale: Towards an integrated understanding of river status deterioration.},
journal = {Global change biology},
volume = {27},
number = {9},
pages = {1962-1975},
doi = {10.1111/gcb.15504},
pmid = {33372367},
issn = {1365-2486},
support = {//European Commission: FP7 Environment/ ; //Dutch 'Water Quality Knowledge Impulse' project/ ; },
mesh = {Ecosystem ; *Environmental Monitoring ; Hydrology ; *Rivers ; Water Quality ; },
abstract = {The biota of European rivers are affected by a wide range of stressors impairing water quality and hydro-morphology. Only about 40% of Europe's rivers reach 'good ecological status', a target set by the European Water Framework Directive (WFD) and indicated by the biota. It is yet unknown how the different stressors in concert impact ecological status and how the relationship between stressors and status differs between river types. We linked the intensity of seven stressors to recently measured ecological status data for more than 50,000 sub-catchment units (covering almost 80% of Europe's surface area), which were distributed among 12 broad river types. Stressor data were either derived from remote sensing data (extent of urban and agricultural land use in the riparian zone) or modelled (alteration of mean annual flow and of base flow, total phosphorous load, total nitrogen load and mixture toxic pressure, a composite metric for toxic substances), while data on ecological status were taken from national statutory reporting of the second WFD River Basin Management Plans for the years 2010-2015. We used Boosted Regression Trees to link ecological status to stressor intensities. The stressors explained on average 61% of deviance in ecological status for the 12 individual river types, with all seven stressors contributing considerably to this explanation. On average, 39.4% of the deviance was explained by altered hydro-morphology (morphology: 23.2%; hydrology: 16.2%), 34.4% by nutrient enrichment and 26.2% by toxic substances. More than half of the total deviance was explained by stressor interaction, with nutrient enrichment and toxic substances interacting most frequently and strongly. Our results underline that the biota of all European river types are determined by co-occurring and interacting multiple stressors, lending support to the conclusion that fundamental management strategies at the catchment scale are required to reach the ambitious objective of good ecological status of surface waters.},
}

Ecosystem
*Environmental Monitoring
Hydrology
*Rivers
Water Quality

@article {pmid33365126,
year = {2020},
author = {Allen, DC and Datry, T and Boersma, KS and Bogan, MT and Boulton, AJ and Bruno, D and Busch, MH and Costigan, KH and Dodds, WK and Fritz, KM and Godsey, SE and Jones, JB and Kaletova, T and Kampf, SK and Mims, MC and Neeson, TM and Olden, JD and Pastor, AV and Poff, NL and Ruddell, BL and Ruhi, A and Singer, G and Vezza, P and Ward, AS and Zimmer, M},
title = {River ecosystem conceptual models and non-perennial rivers: A critical review.},
journal = {WIREs. Water},
volume = {7},
number = {5},
pages = {},
pmid = {33365126},
issn = {2049-1948},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {Conceptual models underpin river ecosystem research. However, current models focus on continuously flowing rivers and few explicitly address characteristics such as flow cessation and drying. The applicability of existing conceptual models to nonperennial rivers that cease to flow (intermittent rivers and ephemeral streams, IRES) has not been evaluated. We reviewed 18 models, finding that they collectively describe main drivers of biogeochemical and ecological patterns and processes longitudinally (upstream-downstream), laterally (channel-riparian-floodplain), vertically (surface water-groundwater), and temporally across local and landscape scales. However, perennial rivers are longitudinally continuous while IRES are longitudinally discontinuous. Whereas perennial rivers have bidirectional lateral connections between aquatic and terrestrial ecosystems, in IRES, this connection is unidirectional for much of the time, from terrestrial-to-aquatic only. Vertical connectivity between surface and subsurface water occurs bidirectionally and is temporally consistent in perennial rivers. However, in IRES, this exchange is temporally variable, and can become unidirectional during drying or rewetting phases. Finally, drying adds another dimension of flow variation to be considered across temporal and spatial scales in IRES, much as flooding is considered as a temporally and spatially dynamic process in perennial rivers. Here, we focus on ways in which existing models could be modified to accommodate drying as a fundamental process that can alter these patterns and processes across spatial and temporal dimensions in streams. This perspective is needed to support river science and management in our era of rapid global change, including increasing duration, frequency, and occurrence of drying.},
}

@article {pmid33293507,
year = {2020},
author = {Grantham, HS and Duncan, A and Evans, TD and Jones, KR and Beyer, HL and Schuster, R and Walston, J and Ray, JC and Robinson, JG and Callow, M and Clements, T and Costa, HM and DeGemmis, A and Elsen, PR and Ervin, J and Franco, P and Goldman, E and Goetz, S and Hansen, A and Hofsvang, E and Jantz, P and Jupiter, S and Kang, A and Langhammer, P and Laurance, WF and Lieberman, S and Linkie, M and Malhi, Y and Maxwell, S and Mendez, M and Mittermeier, R and Murray, NJ and Possingham, H and Radachowsky, J and Saatchi, S and Samper, C and Silverman, J and Shapiro, A and Strassburg, B and Stevens, T and Stokes, E and Taylor, R and Tear, T and Tizard, R and Venter, O and Visconti, P and Wang, S and Watson, JEM},
title = {Anthropogenic modification of forests means only 40% of remaining forests have high ecosystem integrity.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5978},
pmid = {33293507},
issn = {2041-1723},
mesh = {Africa, Central ; *Biodiversity ; Canada ; Climate Change ; Conservation of Natural Resources/legislation & jurisprudence/*statistics & numerical data ; *Environmental Policy ; *Forests ; New Guinea ; Russia ; },
abstract = {Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remain poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate a globally consistent, continuous index of forest condition as determined by the degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) has high landscape-level integrity (mostly found in Canada, Russia, the Amazon, Central Africa, and New Guinea) and only 27% of this area is found in nationally designated protected areas. Of the forest inside protected areas, only 56% has high landscape-level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally.},
}

Africa, Central
*Biodiversity
Canada
Climate Change
Conservation of Natural Resources/legislation & jurisprudence/*statistics & numerical data
*Environmental Policy
*Forests
New Guinea
Russia

@article {pmid33263214,
year = {2021},
author = {Hassell, JM and Bettridge, JM and Ward, MJ and Ogendo, A and Imboma, T and Muloi, D and Fava, F and Robinson, TP and Begon, M and Fèvre, EM},
title = {Socio-ecological drivers of vertebrate biodiversity and human-animal interfaces across an urban landscape.},
journal = {Global change biology},
volume = {27},
number = {4},
pages = {781-792},
pmid = {33263214},
issn = {1365-2486},
support = {MR/R015090/1/MRC_/Medical Research Council/United Kingdom ; G1100783/1//Natural Environment Research Council/ ; WT103953MA/WT_/Wellcome Trust/United Kingdom ; //Biotechnology and Biological Science Research Council/ ; /WT_/Wellcome Trust/United Kingdom ; NA//CGIAR Research Program on Agriculture for Nutrition and Health/ ; //Economic and Social Research Council/ ; },
mesh = {Animals ; *Biodiversity ; Cities ; Conservation of Natural Resources ; *Ecosystem ; Europe ; Humans ; Kenya ; North America ; Urbanization ; Vertebrates ; },
abstract = {Urbanization can have profound impacts on the distributional ecology of wildlife and livestock, with implications for biodiversity conservation, ecosystem services and human health. A wealth of studies have assessed biotic responses to urbanization in North America and Europe, but there is little empirical evidence that directly links human activities to urban biodiversity in the tropics. Results from a large-scale field study conducted in Nairobi, Kenya, are used to explore the impact of human activities on the biodiversity of wildlife and livestock with which humans co-exist across the city. The structure of sympatric wildlife, livestock and human populations are characterized using unsupervised machine learning, and statistical modelling is used to relate compositional variation in these communities to socio-ecological drivers occurring across the city. By characterizing landscape-scale drivers acting on these interfaces, we demonstrate that socioeconomics, elevation and subsequent changes in habitat have measurable impacts upon the diversity, density and species assemblage of wildlife, livestock and humans. Restructuring of wildlife and livestock assemblages (both in terms of species diversity and composition) has important implications for the emergence of novel diseases at urban interfaces, and we therefore use our results to generate a set of testable hypotheses that explore the influence of urban change on microbial communities. These results provide novel insight into the impact of urbanization on biodiversity in the tropics. An understanding of associations between urban processes and the structure of human and animal populations is required to link urban development to conservation efforts and risks posed by disease emergence to human health, ultimately informing sustainable urban development policy.},
}

Animals
*Biodiversity
Cities
Conservation of Natural Resources
*Ecosystem
Europe
Humans
Kenya
North America
Urbanization
Vertebrates

@article {pmid33230292,
year = {2021},
author = {Dührkop, K and Nothias, LF and Fleischauer, M and Reher, R and Ludwig, M and Hoffmann, MA and Petras, D and Gerwick, WH and Rousu, J and Dorrestein, PC and Böcker, S},
title = {Systematic classification of unknown metabolites using high-resolution fragmentation mass spectra.},
journal = {Nature biotechnology},
volume = {39},
number = {4},
pages = {462-471},
pmid = {33230292},
issn = {1546-1696},
support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Aquatic Organisms/*chemistry ; Biological Products/*analysis ; Chromatography, Liquid ; Computational Biology/*methods ; Euphorbia/*chemistry ; Gastrointestinal Microbiome ; Metabolomics/*methods ; Mice ; Neural Networks, Computer ; Tandem Mass Spectrometry ; },
abstract = {Metabolomics using nontargeted tandem mass spectrometry can detect thousands of molecules in a biological sample. However, structural molecule annotation is limited to structures present in libraries or databases, restricting analysis and interpretation of experimental data. Here we describe CANOPUS (class assignment and ontology prediction using mass spectrometry), a computational tool for systematic compound class annotation. CANOPUS uses a deep neural network to predict 2,497 compound classes from fragmentation spectra, including all biologically relevant classes. CANOPUS explicitly targets compounds for which neither spectral nor structural reference data are available and predicts classes lacking tandem mass spectrometry training data. In evaluation using reference data, CANOPUS reached very high prediction performance (average accuracy of 99.7% in cross-validation) and outperformed four baseline methods. We demonstrate the broad utility of CANOPUS by investigating the effect of microbial colonization in the mouse digestive system, through analysis of the chemodiversity of different Euphorbia plants and regarding the discovery of a marine natural product, revealing biological insights at the compound class level.},
}

Animals
Aquatic Organisms/*chemistry
Biological Products/*analysis
Chromatography, Liquid
Computational Biology/*methods
Euphorbia/*chemistry
Gastrointestinal Microbiome
Metabolomics/*methods
Mice
Neural Networks, Computer
Tandem Mass Spectrometry

@article {pmid33226631,
year = {2021},
author = {McLean, BS and Guralnick, RP},
title = {Digital biodiversity data sets reveal breeding phenology and its drivers in a widespread North American mammal.},
journal = {Ecology},
volume = {102},
number = {3},
pages = {e03258},
doi = {10.1002/ecy.3258},
pmid = {33226631},
issn = {1939-9170},
mesh = {Animals ; Biodiversity ; *Climate Change ; *Ecosystem ; Female ; Mammals ; Mice ; Reproduction ; Seasons ; United States ; },
abstract = {Shifts in reproductive timing are among the most commonly documented responses of organisms to global climate change. However, our knowledge of these responses is biased towards taxa that are easily observable and abundant in existing biodiversity data sets. Mammals are common subjects in reproductive biology, but mammalian phenology and its drivers in the wild remain poorly understood because many species are small, secretive, or too labor-intensive to monitor. We took an informatics-based approach to reconstructing breeding phenology in the widespread North American deer mouse (Peromyscus maniculatus) using individual-level reproductive observations from digitized museum specimens and field censuses spanning >100 yr and >45 degrees of latitude. We reconstructed female phenology in different regions and tested the importance of three environmental variables (photoperiod, temperature, precipitation) as breeding cues. Photoperiod and temperature were strong positive and negative breeding cues, respectively, whereas precipitation was not a significant predictor of breeding phenology. However, phenologies and the use of environmental cues varied substantially among regions, and we found evidence that these cueing repertoires are tuned to ecosystem-specific limiting conditions. Our results reiterate the importance of ecological context in optimizing reproduction and demonstrate how harmonization across biodiversity data resources allows new insight into phenology and its drivers in wild mammals.},
}

Animals
Biodiversity
*Climate Change
*Ecosystem
Female
Mammals
Mice
Reproduction
Seasons
United States

@article {pmid33208098,
year = {2020},
author = {Wu, X and Li, X and Wang, W and Shan, Y and Wang, C and Zhu, M and La, Q and Zhong, Y and Xu, Y and Nan, P and Li, X},
title = {Integrated metabolomics and transcriptomics study of traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao reveals global metabolic profile and novel phytochemical ingredients.},
journal = {BMC genomics},
volume = {21},
number = {Suppl 10},
pages = {697},
pmid = {33208098},
issn = {1471-2164},
mesh = {*Astragalus propinquus/genetics ; Computational Biology ; Humans ; *Metabolome ; Metabolomics ; Phytochemicals ; Transcriptome ; },
abstract = {BACKGROUND: Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is one of the most common herbs widely used in South and East Asia, to enhance people's health and reinforce vital energy. Despite its prevalence, however, the knowledge about phytochemical compositions and metabolite biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao is very limited.

RESULTS: An integrated metabolomics and transcriptomics analysis using state-of-the-art UPLC-Q-Orbitrap mass spectrometer and advanced bioinformatics pipeline were conducted to study global metabolic profiles and phytochemical ingredients/biosynthesis in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. A total of 5435 metabolites were detected, from which 2190 were annotated, representing an order of magnitude increase over previously known. Metabolic profiling of Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao tissues found contents and synthetic enzymes for phytochemicals were significantly higher in leaf and stem in general, whereas the contents of the main bioactive ingredients were significantly enriched in root, underlying the value of root in herbal remedies. Using integrated metabolomics and transcriptomics data, we illustrated the complete pathways of phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis, in which some were first reported in the herb. More importantly, we discovered novel flavonoid derivatives using informatics method for neutral loss scan, in addition to inferring their likely synthesis pathways in Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao.

CONCLUSIONS: The current study represents the most comprehensive metabolomics and transcriptomics analysis on traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. We demonstrated our integrated metabolomics and transcriptomics approach offers great potentials in discovering novel metabolite structure and associated synthesis pathways. This study provides novel insights into the phytochemical ingredients, metabolite biosynthesis, and complex metabolic network in herbs, highlighting the rich natural resource and nutritional value of traditional herbal plants.},
}

*Astragalus propinquus/genetics
Computational Biology
Humans
*Metabolome
Metabolomics
Phytochemicals
Transcriptome

@article {pmid33205462,
year = {2021},
author = {Culina, A and Adriaensen, F and Bailey, LD and Burgess, MD and Charmantier, A and Cole, EF and Eeva, T and Matthysen, E and Nater, CR and Sheldon, BC and Saether, BE and Vriend, SJG and Zajkova, Z and Adamík, P and Aplin, LM and Angulo, E and Artemyev, A and Barba, E and Barišić, S and Belda, E and Bilgin, CC and Bleu, J and Both, C and Bouwhuis, S and Branston, CJ and Broggi, J and Burke, T and Bushuev, A and Camacho, C and Campobello, D and Canal, D and Cantarero, A and Caro, SP and Cauchoix, M and Chaine, A and Cichoń, M and Ćiković, D and Cusimano, CA and Deimel, C and Dhondt, AA and Dingemanse, NJ and Doligez, B and Dominoni, DM and Doutrelant, C and Drobniak, SM and Dubiec, A and Eens, M and Einar Erikstad, K and Espín, S and Farine, DR and Figuerola, J and Kavak Gülbeyaz, P and Grégoire, A and Hartley, IR and Hau, M and Hegyi, G and Hille, S and Hinde, CA and Holtmann, B and Ilyina, T and Isaksson, C and Iserbyt, A and Ivankina, E and Kania, W and Kempenaers, B and Kerimov, A and Komdeur, J and Korsten, P and Král, M and Krist, M and Lambrechts, M and Lara, CE and Leivits, A and Liker, A and Lodjak, J and Mägi, M and Mainwaring, MC and Mänd, R and Massa, B and Massemin, S and Martínez-Padilla, J and Mazgajski, TD and Mennerat, A and Moreno, J and Mouchet, A and Nakagawa, S and Nilsson, JÅ and Nilsson, JF and Cláudia Norte, A and van Oers, K and Orell, M and Potti, J and Quinn, JL and Réale, D and Kristin Reiertsen, T and Rosivall, B and Russell, AF and Rytkönen, S and Sánchez-Virosta, P and Santos, ESA and Schroeder, J and Senar, JC and Seress, G and Slagsvold, T and Szulkin, M and Teplitsky, C and Tilgar, V and Tolstoguzov, A and Török, J and Valcu, M and Vatka, E and Verhulst, S and Watson, H and Yuta, T and Zamora-Marín, JM and Visser, ME},
title = {Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub.},
journal = {The Journal of animal ecology},
volume = {90},
number = {9},
pages = {2147-2160},
doi = {10.1111/1365-2656.13388},
pmid = {33205462},
issn = {1365-2656},
support = {223257//Research Council of Norway/ ; 267511//Research Council of Norway/ ; 016.Veni.181.054//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.},
}

@article {pmid33199911,
year = {2021},
author = {Tripathi, A and Vázquez-Baeza, Y and Gauglitz, JM and Wang, M and Dührkop, K and Nothias-Esposito, M and Acharya, DD and Ernst, M and van der Hooft, JJJ and Zhu, Q and McDonald, D and Brejnrod, AD and Gonzalez, A and Handelsman, J and Fleischauer, M and Ludwig, M and Böcker, S and Nothias, LF and Knight, R and Dorrestein, PC},
title = {Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.},
journal = {Nature chemical biology},
volume = {17},
number = {2},
pages = {146-151},
pmid = {33199911},
issn = {1552-4469},
support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; },
mesh = {Algorithms ; Cluster Analysis ; DNA/chemistry ; DNA Fingerprinting ; Databases, Factual ; Ecology ; Food Analysis ; Mass Spectrometry/*methods ; *Metabolomics ; Microbiota ; Multivariate Analysis ; Software ; Tandem Mass Spectrometry ; Workflow ; },
abstract = {Untargeted mass spectrometry is employed to detect small molecules in complex biospecimens, generating data that are difficult to interpret. We developed Qemistree, a data exploration strategy based on the hierarchical organization of molecular fingerprints predicted from fragmentation spectra. Qemistree allows mass spectrometry data to be represented in the context of sample metadata and chemical ontologies. By expressing molecular relationships as a tree, we can apply ecological tools that are designed to analyze and visualize the relatedness of DNA sequences to metabolomics data. Here we demonstrate the use of tree-guided data exploration tools to compare metabolomics samples across different experimental conditions such as chromatographic shifts. Additionally, we leverage a tree representation to visualize chemical diversity in a heterogeneous collection of samples. The Qemistree software pipeline is freely available to the microbiome and metabolomics communities in the form of a QIIME2 plugin, and a global natural products social molecular networking workflow.},
}

Algorithms
Cluster Analysis
DNA/chemistry
DNA Fingerprinting
Databases, Factual
Ecology
Food Analysis
Mass Spectrometry/*methods
*Metabolomics
Microbiota
Multivariate Analysis
Software
Tandem Mass Spectrometry
Workflow

@article {pmid33193120,
year = {2020},
author = {Rosen, GL and Hammrich, P},
title = {Teaching Microbiome Analysis: From Design to Computation Through Inquiry.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {528051},
pmid = {33193120},
issn = {1664-302X},
abstract = {In this article, we present our three-class course sequence to educate students about microbiome analysis and metagenomics through experiential learning by taking them from inquiry to analysis of the microbiome: Molecular Ecology Lab, Bioinformatics, and Computational Microbiome Analysis. Students developed hypotheses, designed lab experiments, sequenced the DNA from microbiomes, learned basic python/R scripting, became proficient in at least one microbiome analysis software, and were able to analyze data generated from the microbiome experiments. While over 150 students (graduate and undergraduate) were impacted by the development of the series of courses, our assessment was only on undergraduate learning, where 45 students enrolled in at least one of the three courses and 4 students took all three. Students gained skills in bioinformatics through the courses, and several positive comments were received through surveys and private correspondence. Through a summative assessment, general trends show that students became more proficient in comparative genomic techniques and had positive attitudes toward their abilities to bridge biology and bioinformatics. While most students took individual or 2 of the courses, we show that pre- and post-surveys of these individual classes still showed progress toward learning objectives. It is expected that students trained will enter the workforce with skills needed to innovate in the biotechnology, health, and environmental industries. Students are trained to maximize impact and tackle real world problems in biology and medicine with their learned knowledge of data science and machine learning. The course materials for the new microbiome analysis course are available on Github: https://github.com/EESI/Comp_Metagenomics_resources.},
}

@article {pmid33184309,
year = {2020},
author = {García-Jiménez, R and Margalida, A and Pérez-García, JM},
title = {Influence of individual biological traits on GPS fix-loss errors in wild bird tracking.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {19621},
pmid = {33184309},
issn = {2045-2322},
mesh = {*Animal Migration ; Animals ; Animals, Wild/*physiology ; Birds/*physiology ; Breeding ; Ecosystem ; Female ; France ; *Geographic Information Systems ; Humans ; Male ; Spain ; Telemetry ; Territoriality ; },
abstract = {In recent decades, global positioning system (GPS) location data and satellite telemetry systems for data transmission have become fundamental in the study of basic ecological traits in wildlife biology. Evaluating GPS location errors is essential in assessing detailed information about the behaviour of an animal species such as migration, habitat selection, species distribution or foraging strategy. While many studies of the influence of environmental and technical factors on the fix errors of solar-powered GPS transmitters have been published, few studies have focussed on the performance of GPS systems in relation to a species' biological traits. Here, we evaluate the possible effects of the biological traits of a large raptor on the frequency of lost fixes-the fix-loss rate (FLR). We analysed 95,686 records obtained from 20 Bearded Vultures Gypaetus barbatus tracked with 17 solar-powered satellite transmitters in the Pyrenees (Spain, France and Andorra), between 2006 and 2019 to evaluate the influence of biological, technical, and environmental factors on the fix-loss rate of transmitters. We show that combined effects of technical factors and the biological traits of birds explained 23% of the deviance observed. As expected, the transmitter usage time significantly increased errors in the fix-loss rate, although the flight activity of birds revealed an unexpected trade-off: the greater the proportion of fixes recorded from perched birds, the lower the FLR. This finding seems related with the fact that territorial and breeding birds spend significantly more time flying than non-territorial individuals. The fix success rate is apparently due to the interactions between a complex of factors. Non-territorial adults and subadults, males, and breeding individuals showed a significantly lower FLR than juveniles-immatures females, territorial birds or non-breeding individuals. Animal telemetry tracking studies should include error analyses before reaching any ecological conclusions or hypotheses about spatial distribution.},
}

*Animal Migration
Animals
Animals, Wild/*physiology
Birds/*physiology
Breeding
Ecosystem
Female
France
*Geographic Information Systems
Humans
Male
Spain
Telemetry
Territoriality

@article {pmid33147272,
year = {2020},
author = {Altamiranda-Saavedra, M and Osorio-Olvera, L and Yáñez-Arenas, C and Marín-Ortiz, JC and Parra-Henao, G},
title = {Geographic abundance patterns explained by niche centrality hypothesis in two Chagas disease vectors in Latin America.},
journal = {PloS one},
volume = {15},
number = {11},
pages = {e0241710},
pmid = {33147272},
issn = {1932-6203},
mesh = {Algorithms ; Animals ; Chagas Disease/epidemiology/parasitology/*pathology/transmission ; Databases, Factual ; *Ecosystem ; Humans ; Insect Vectors ; Models, Theoretical ; Population Density ; Rhodnius/*parasitology ; South America/epidemiology ; Triatoma/*parasitology ; },
abstract = {Ecoepidemiological scenarios for Chagas disease transmission are complex, so vector control measures to decrease human-vector contact and prevent infection transmission are difficult to implement in all geographic contexts. This study assessed the geographic abundance patterns of two vector species of Chagas disease: Triatoma maculata (Erichson, 1848) and Rhodnius pallescens (Barber, 1932) in Latin America. We modeled their potential distribution using the maximum entropy algorithm implemented in Maxent and calculated distances to their niche centroid by fitting a minimum-volume ellipsoid. In addition, to determine which method would accurately explain geographic abundance patterns, we compared the correlation between population abundance and the distance to the ecological niche centroid (DNC) and between population abundance and Maxent environmental suitability. The potential distribution estimated for T. maculata showed that environmental suitability covers a large area, from Panama to Northern Brazil. R. pallescens showed a more restricted potential distribution, with environmental suitability covering mostly the coastal zone of Costa Rica and some areas in Nicaragua, Honduras, Belize and the Yucatán Peninsula in Mexico, northern Colombia, Acre, and Rondônia states in Brazil, as well as a small region of the western Brazilian Amazon. We found a negative slope in the relationship between population abundance and the DNC in both species. R. pallecens has a more extensive potential latitudinal range than previously reported, and the distribution model for T. maculata corroborates previous studies. In addition, population abundance increases according to the niche centroid proximity, indicating that population abundance is limited by the set of scenopoetic variables at coarser scales (non-interactive variables) used to determine the ecological niche. These findings might be used by public health agencies in Latin America to implement actions and support programs for disease prevention and vector control, identifying areas in which to expand entomological surveillance and maintain chemical control, in order to decrease human-vector contact.},
}

Algorithms
Animals
Chagas Disease/epidemiology/parasitology/*pathology/transmission
Databases, Factual
*Ecosystem
Humans
Insect Vectors
Models, Theoretical
Population Density
Rhodnius/*parasitology
South America/epidemiology
Triatoma/*parasitology