@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 = {},
doi = {10.7554/eLife.62922},
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},
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.},
}

@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 {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},
doi = {10.1371/journal.pgen.1008748},
pmid = {33493157},
issn = {1553-7404},
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.},
}

@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/ ; },
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.},
}

@article {pmid31953819,
year = {2020},
author = {Ludwig, M and Fleischauer, M and Dührkop, K and Hoffmann, MA and Böcker, S},
title = {De Novo Molecular Formula Annotation and Structure Elucidation Using SIRIUS 4.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2104},
number = {},
pages = {185-207},
doi = {10.1007/978-1-0716-0239-3_11},
pmid = {31953819},
issn = {1940-6029},
mesh = {Chromatography, Liquid ; *Computational Biology/methods ; *Databases, Factual ; Humans ; *Metabolomics/methods ; Molecular Structure ; *Software ; Spectrometry, Mass, Electrospray Ionization ; Structure-Activity Relationship ; Tandem Mass Spectrometry ; User-Computer Interface ; Workflow ; },
abstract = {SIRIUS 4 is the best-in-class computational tool for metabolite identification from high-resolution tandem mass spectrometry data. It offers de novo molecular formula annotation with outstanding accuracy. When searching fragmentation spectra in a structure database, it reaches over 70% correct identifications. A predicted fingerprint, which indicates the presence or absence of thousands of molecular properties, helps to deduce information about the compound of interest even if it is not contained in any structure database. Here, we present best practices and describe how to leverage the full potential of SIRIUS 4, how to incorporate it into your own workflow, and how it adds value to the analysis of mass spectrometry data beyond spectral library search.},
}

Chromatography, Liquid
*Computational Biology/methods
*Databases, Factual
Humans
*Metabolomics/methods
Molecular Structure
*Software
Spectrometry, Mass, Electrospray Ionization
Structure-Activity Relationship
Tandem Mass Spectrometry
User-Computer Interface
Workflow

@article {pmid33060594,
year = {2020},
author = {Middleton-Welling, J and Dapporto, L and García-Barros, E and Wiemers, M and Nowicki, P and Plazio, E and Bonelli, S and Zaccagno, M and Šašić, M and Liparova, J and Schweiger, O and Harpke, A and Musche, M and Settele, J and Schmucki, R and Shreeve, T},
title = {A new comprehensive trait database of European and Maghreb butterflies, Papilionoidea.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {351},
pmid = {33060594},
issn = {2052-4463},
mesh = {Africa, Northern ; Animals ; Biological Evolution ; Butterflies/*classification ; Conservation of Natural Resources ; Databases, Factual ; Ecology ; Europe ; Phylogeny ; },
abstract = {Trait-based analyses explaining the different responses of species and communities to environmental changes are increasing in frequency. European butterflies are an indicator group that responds rapidly to environmental changes with extensive citizen science contributions to documenting changes of abundance and distribution. Species traits have been used to explain long- and short-term responses to climate, land-use and vegetation changes. Studies are often characterised by limited trait sets being used, with risks that the relative roles of different traits are not fully explored. Butterfly trait information is dispersed amongst various sources and descriptions sometimes differ between sources. We have therefore drawn together multiple information sets to provide a comprehensive trait database covering 542 taxa and 25 traits described by 217 variables and sub-states of the butterflies of Europe and Maghreb (northwest Africa) which should serve for improved trait-based ecological, conservation-related, phylogeographic and evolutionary studies of this group of insects. We provide this data in two forms; the basic data and as processed continuous and multinomial data, to enhance its potential usage.},
}

Africa, Northern
Animals
Biological Evolution
Butterflies/*classification
Conservation of Natural Resources
Databases, Factual
Ecology
Europe
Phylogeny

@article {pmid32737307,
year = {2020},
author = {Uzun, M and Alekseeva, L and Krutkina, M and Koziaeva, V and Grouzdev, D},
title = {Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {252},
pmid = {32737307},
issn = {2052-4463},
support = {18-34-01005//Russian Foundation for Basic Research (RFBR)/International ; 18-34-01005//Russian Foundation for Basic Research (RFBR)/International ; },
mesh = {Bacteria/*classification/genetics ; Datasets as Topic ; *Genome, Bacterial ; Genomics ; Iron ; Magnetosomes/*genetics ; Phylogeny ; Sulfides ; },
abstract = {Magnetotactic bacteria (MTB) are prokaryotes that possess genes for the synthesis of membrane-bounded crystals of magnetite or greigite, called magnetosomes. Despite over half a century of studying MTB, only about 60 genomes have been sequenced. Most belong to Proteobacteria, with a minority affiliated with the Nitrospirae, Omnitrophica, Planctomycetes, and Latescibacteria. Due to the scanty information available regarding MTB phylogenetic diversity, little is known about their ecology, evolution and about the magnetosome biomineralization process. This study presents a large-scale search of magnetosome biomineralization genes and reveals 38 new MTB genomes. Several of these genomes were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported. Analysis of the obtained putative magnetosome biomineralization genes revealed a monophyletic origin capable of putative greigite magnetosome synthesis. The ecological distributions of the reconstructed MTB genomes were also analyzed and several patterns were identified. These data suggest that open databases are an excellent source for obtaining new information of interest.},
}

Bacteria/*classification/genetics
Datasets as Topic
*Genome, Bacterial
Genomics
Iron
Magnetosomes/*genetics
Phylogeny
Sulfides

@article {pmid31763752,
year = {2020},
author = {Zanne, AE and Abarenkov, K and Afkhami, ME and Aguilar-Trigueros, CA and Bates, S and Bhatnagar, JM and Busby, PE and Christian, N and Cornwell, WK and Crowther, TW and Flores-Moreno, H and Floudas, D and Gazis, R and Hibbett, D and Kennedy, P and Lindner, DL and Maynard, DS and Milo, AM and Nilsson, RH and Powell, J and Schildhauer, M and Schilling, J and Treseder, KK},
title = {Fungal functional ecology: bringing a trait-based approach to plant-associated fungi.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {95},
number = {2},
pages = {409-433},
doi = {10.1111/brv.12570},
pmid = {31763752},
issn = {1469-185X},
mesh = {Animals ; Databases, Factual ; Ecosystem ; Fungi/genetics/*physiology ; Plants/*microbiology ; },
abstract = {Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.},
}

Animals
Databases, Factual
Ecosystem
Fungi/genetics/*physiology
Plants/*microbiology

@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 = {},
number = {},
pages = {},
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 {pmid32333771,
year = {2020},
author = {Machac, A},
title = {The Dynamics of Bird Diversity in the New World.},
journal = {Systematic biology},
volume = {69},
number = {6},
pages = {1180-1199},
pmid = {32333771},
issn = {1076-836X},
mesh = {Americas ; Animals ; *Biodiversity ; Birds/*classification ; Geographic Information Systems ; *Models, Biological ; },
abstract = {Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (i) time for speciation, (ii) diversification rates, and (iii) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and geographic information systems, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon. [Biogeography; community; competition; macroevolution; phylogenetics; richness gradient.].},
}

Americas
Animals
*Biodiversity
Birds/*classification
Geographic Information Systems
*Models, Biological

@article {pmid33372367,
year = {2020},
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 = {},
number = {},
pages = {},
doi = {10.1111/gcb.15504},
pmid = {33372367},
issn = {1365-2486},
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 twelve 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 to 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 twelve 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.},
}

@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},
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 {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

@article {pmid32651419,
year = {2020},
author = {Pigeon, KE and MacNearney, D and Hebblewhite, M and Musiani, M and Neufeld, L and Cranston, J and Stenhouse, G and Schmiegelow, F and Finnegan, L},
title = {The density of anthropogenic features explains seasonal and behaviour-based functional responses in selection of linear features by a social predator.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {11437},
pmid = {32651419},
issn = {2045-2322},
mesh = {Animals ; Deer/*physiology ; Ecosystem ; *Geographic Information Systems ; Humans ; Predatory Behavior/*physiology ; Seasons ; Wolves/*physiology ; },
abstract = {Anthropogenic linear features facilitate access and travel efficiency for predators, and can influence predator distribution and encounter rates with prey. We used GPS collar data from eight wolf packs and characteristics of seismic lines to investigate whether ease-of-travel or access to areas presumed to be preferred by prey best explained seasonal selection patterns of wolves near seismic lines, and whether the density of anthropogenic features led to functional responses in habitat selection. At a broad scale, wolves showed evidence of habitat-driven functional responses by exhibiting greater selection for areas near low-vegetation height seismic lines in areas with low densities of anthropogenic features. We highlight the importance of considering landscape heterogeneity and habitat characteristics, and the functional response in habitat selection when investigating seasonal behaviour-based selection patterns. Our results support behaviour in line with search for primary prey during summer and fall, and ease-of-travel during spring, while patterns of selection during winter aligned best with ease-of-travel for the less-industrialized foothills landscape, and with search for primary prey in the more-industrialized boreal landscape. These results highlight that time-sensitive restoration actions on anthropogenic features can affect the probability of overlap between predators and threatened prey within different landscapes.},
}

Animals
Deer/*physiology
Ecosystem
*Geographic Information Systems
Humans
Predatory Behavior/*physiology
Seasons
Wolves/*physiology

@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},
doi = {10.1038/s41467-020-19493-3},
pmid = {33293507},
issn = {2041-1723},
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.},
}

@article {pmid33263214,
year = {2020},
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 = {},
number = {},
pages = {},
doi = {10.1111/gcb.15412},
pmid = {33263214},
issn = {1365-2486},
support = {NA//CGIAR Research Program on Agriculture for Nutrition and Health/ ; /MRC_/Medical Research Council/United Kingdom ; //Biotechnology and Biological Science Research Council/ ; //Economic and Social Research Council/ ; G1100783/1//Natural Environment Research Council/ ; WT103953MA/WT_/Wellcome Trust/United Kingdom ; },
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.},
}

@article {pmid31758057,
year = {2019},
author = {Sergio, F and Tavecchia, G and Tanferna, A and Blas, J and Blanco, G and Hiraldo, F},
title = {When and where mortality occurs throughout the annual cycle changes with age in a migratory bird: individual vs population implications.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {17352},
doi = {10.1038/s41598-019-54026-z},
pmid = {31758057},
issn = {2045-2322},
mesh = {Africa, Western ; Age Factors ; Animal Migration/*physiology ; Animals ; Birds/*physiology ; Geographic Information Systems ; Geography ; Longevity/physiology ; Mauritania ; Morocco ; *Mortality ; Population Dynamics ; Raptors/physiology ; Reproduction/physiology ; *Seasons ; Spain ; Time Factors ; },
abstract = {The annual cycle of most animals is structured into discrete stages, such as breeding, migration and dispersal. While there is growing appreciation of the importance of different stages of an organism's annual cycle for its fitness and population dynamics, almost nothing is known about if and how such seasonal effects can change through a species lifespan. Here, we take advantage of the opportunity offered by a long-term satellite/GPS-tracking study and a reliable method of remote death-detection to show that certain stages of both the annual and life cycle of a migratory long-lived raptor, the Black kite Milvus migrans, may represent sensitive bottlenecks for survival. In particular, migratory journeys caused bursts of concentrated-mortality throughout life, but the relative importance of stage-specific survival changed with age. On the other hand, the balance between short-stages of high mortality and long-stages of low mortality made population-growth similarly dependent on all portions of the annual cycle. Our results illustrate how the population dynamics of migratory organisms can be inextricably linked to ecological pressures balanced over multiple stages of the annual cycle and thus multiple areas of the globe, suggesting the frequent need for challenging conservation strategies targeting all portions of a species year-round range.},
}

Africa, Western
Age Factors
Animal Migration/*physiology
Animals
Birds/*physiology
Geographic Information Systems
Geography
Longevity/physiology
Mauritania
Morocco
*Mortality
Population Dynamics
Raptors/physiology
Reproduction/physiology
*Seasons
Spain
Time Factors

@article {pmid33226631,
year = {2020},
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 = {},
number = {},
pages = {e03258},
doi = {10.1002/ecy.3258},
pmid = {33226631},
issn = {1939-9170},
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 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 years 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, while 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.},
}

@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},
doi = {10.1186/s12864-020-07005-y},
pmid = {33208098},
issn = {1471-2164},
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.},
}

@article {pmid33205462,
year = {2020},
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 Can Bilgin, C and Bleu, J and Both, C and Bouwhuis, S and Branston, C 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 Erikstad, KE 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, J and Norte, AC and Oers, KV and Orell, M and Potti, J and Quinn, JL and Réale, D and Reiertsen, TK and Rosivall, B and Russel, 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 = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.13388},
pmid = {33205462},
issn = {1365-2656},
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. Further, 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 2000 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 {pmid33125392,
year = {2020},
author = {Sala, C and Giampieri, E and Vitali, S and Garagnani, P and Remondini, D and Bazzani, A and Franceschi, C and Castellani, GC},
title = {Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging.},
journal = {PloS one},
volume = {15},
number = {10},
pages = {e0237207},
pmid = {33125392},
issn = {1932-6203},
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Aging/genetics/physiology ; Biodiversity ; Child ; Child, Preschool ; Databases, Nucleic Acid ; Female ; *Gastrointestinal Microbiome/genetics/physiology ; Health Status ; Healthy Aging/genetics/physiology ; Humans ; Infant ; Infant, Newborn ; Male ; Metagenome ; Middle Aged ; *Models, Biological ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-style, and substantially contributes to the pathogenesis of age-related diseases. For these reasons, the gut microbiota is a suitable candidate for assessing and quantifying healthy aging, i.e. the capability of individuals to reach an advanced age, avoiding or postponing major age-related diseases. The importance of the gut microbiota in health and aging has been proven to be related not only to its taxonomic composition, but also to its ecological properties, namely its biodiversity. Following an ecological approach, here we intended to characterize the relationship between the gut microbiota biodiversity and healthy aging through the development a parsimonious model of gut microbiota from which biodiversity can be estimated. We analysed publicly available metagenomic data relative to subjects of different ages, countries, nutritional habits and health status and we showed that a hybrid niche-neutral model well describes the observed patterns of bacterial relative abundance. Moreover, starting from such ecological modeling, we derived an estimate of the gut microbiota biodiversity that is consistent with classical indices, while having a higher statistical power. This allowed us to unveil an increase of the gut microbiota biodiversity during aging and to provide a good predictor of health status in old age, dependent on life-style and aging disorders.},
}

Adolescent
Adult
Aged
Aged, 80 and over
*Aging/genetics/physiology
Biodiversity
Child
Child, Preschool
Databases, Nucleic Acid
Female
*Gastrointestinal Microbiome/genetics/physiology
Health Status
Healthy Aging/genetics/physiology
Humans
Infant
Infant, Newborn
Male
Metagenome
Middle Aged
*Models, Biological
RNA, Ribosomal, 16S/genetics
Young Adult

@article {pmid32512194,
year = {2020},
author = {Pirani, RM and Peloso, PLV and Prado, JR and Polo, ÉM and Knowles, LL and Ron, SR and Rodrigues, MT and Sturaro, MJ and Werneck, FP},
title = {Diversification history of clown tree frogs in Neotropical rainforests (Anura, Hylidae, Dendropsophus leucophyllatus group).},
journal = {Molecular phylogenetics and evolution},
volume = {150},
number = {},
pages = {106877},
doi = {10.1016/j.ympev.2020.106877},
pmid = {32512194},
issn = {1095-9513},
mesh = {Animals ; Anura/*classification/genetics ; Biodiversity ; Databases, Genetic ; Phylogeny ; Rainforest ; South America ; Species Specificity ; },
abstract = {General consensus emphasizes that no single biological process can explain the patterns of species' distributions and diversification in the Neotropics. Instead, the interplay of several processes across space and time must be taken into account. Here we investigated the phylogenetic relationships and biogeographic history of tree frogs in the Dendropsophus leucophyllatus species group (Amphibia: Hylidae), which is distributed across Amazonia and the Atlantic rainforests. Using Next Generation Sequencing (NGS) and double digest restriction-site associated DNA (ddRADseq), we inferred phylogenetic relationships, species limits, and temporal and geographic patterns of diversification relative to the history of these biomes. Our results indicate that the D. leucophyllatus species group includes at least 14 independent lineages, which are currently arranged into ten described species. Therefore, a significant portion of species in the group are still unnamed. Different processes were associated to the group diversification history. For instance, the Andes uplift likely caused allopatric speciation for Cis-Andean species, whereas it may also be responsible for changes in the Amazonian landscape triggering parapatric speciation by local adaptation to ecological factors. Meanwhile, Atlantic Forest ancestors unable to cross the dry diagonal biomes after rainforest's retraction, evolved in isolation into different species. Diversification in the group began in the early Miocene, when connections between Atlantic Forest and the Andes (Pacific Dominion) by way of a south corridor were possible. The historical scenario in Amazonia, characterized by several speciation events and habitat heterogeneity, helped promoting diversification, resulting in the highest species diversity for the group. This marked species diversification did not happen in Atlantic Forest, where speciation is very recent (late Pliocene and Pleistocene), despite its remarkable climatic heterogeneity.},
}

Animals
Anura/*classification/genetics
Biodiversity
Databases, Genetic
Phylogeny
Rainforest
South America
Species Specificity

@article {pmid31882957,
year = {2019},
author = {Jiguet, F and Burgess, M and Thorup, K and Conway, G and Arroyo Matos, JL and Barber, L and Black, J and Burton, N and Castelló, J and Clewley, G and Copete, JL and Czajkowski, MA and Dale, S and Davis, T and Dombrovski, V and Drew, M and Elts, J and Gilson, V and Grzegorczyk, E and Henderson, I and Holdsworth, M and Husbands, R and Lorrilliere, R and Marja, R and Minkevicius, S and Moussy, C and Olsson, P and Onrubia, A and Pérez, M and Piacentini, J and Piha, M and Pons, JM and Procházka, P and Raković, M and Robins, H and Seimola, T and Selstam, G and Skierczyński, M and Sondell, J and Thibault, JC and Tøttrup, AP and Walker, J and Hewson, C},
title = {Desert crossing strategies of migrant songbirds vary between and within species.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {20248},
pmid = {31882957},
issn = {2045-2322},
mesh = {Altitude ; Animal Migration/*physiology ; Animals ; Circadian Rhythm/physiology ; *Desert Climate ; *Environment ; Flight, Animal/*physiology ; Geographic Information Systems ; Light ; Seasons ; Songbirds/classification/*physiology ; Species Specificity ; Temperature ; Time Factors ; },
abstract = {Each year, billions of songbirds cross large ecological barriers during their migration. Understanding how they perform this incredible task is crucial to predict how global change may threaten the safety of such journeys. Earlier studies based on radar suggested that most songbirds cross deserts in intermittent flights at high altitude, stopping in the desert during the day, while recent tracking with light loggers suggested diurnal prolongation of nocturnal flights and common non-stop flights for some species. We analyzed light intensity and temperature data obtained from geolocation loggers deployed on 130 individuals of ten migratory songbird species, and show that a large variety of strategies for crossing deserts exists between, but also sometimes within species. Diurnal stopover in the desert is a common strategy in autumn, while most species prolonged some nocturnal flights into the day. Non-stop flights over the desert occurred more frequently in spring than in autumn, and more frequently in foliage gleaners. Temperature recordings suggest that songbirds crossed deserts with flight bouts performed at various altitudes according to species and season, along a gradient ranging from low above ground in autumn to probably >2000 m above ground level, and possibly at higher altitude in spring. High-altitude flights are therefore not the general rule for crossing deserts in migrant songbirds. We conclude that a diversity of migration strategies exists for desert crossing among songbirds, with variations between but also within species.},
}

Altitude
Animal Migration/*physiology
Animals
Circadian Rhythm/physiology
*Desert Climate
*Environment
Flight, Animal/*physiology
Geographic Information Systems
Light
Seasons
Songbirds/classification/*physiology
Species Specificity
Temperature
Time Factors

@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},
doi = {10.3389/fmicb.2020.528051},
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 {pmid33122629,
year = {2020},
author = {Cai, W and Snyder, J and Hastings, A and D'Souza, RM},
title = {Mutualistic networks emerging from adaptive niche-based interactions.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5470},
doi = {10.1038/s41467-020-19154-5},
pmid = {33122629},
issn = {2041-1723},
mesh = {Animals ; Biological Evolution ; Computational Biology ; Ecology/*methods ; Ecosystem ; *Food Chain ; *Models, Theoretical ; *Symbiosis ; },
abstract = {Mutualistic networks are vital ecological and social systems shaped by adaptation and evolution. They involve bipartite cooperation via the exchange of goods or services between actors of different types. Empirical observations of mutualistic networks across genres and geographic conditions reveal correlated nested and modular patterns. Yet, the underlying mechanism for the network assembly remains unclear. We propose a niche-based adaptive mechanism where both nestedness and modularity emerge simultaneously as complementary facets of an optimal niche structure. Key dynamical properties are revealed at different timescales. Foremost, mutualism can either enhance or reduce the network stability, depending on competition intensity. Moreover, structural adaptations are asymmetric, exhibiting strong hysteresis in response to environmental change. Finally, at the evolutionary timescale we show that the adaptive mechanism plays a crucial role in preserving the distinctive patterns of mutualism under species invasions and extinctions.},
}

Animals
Biological Evolution
Computational Biology
Ecology/*methods
Ecosystem
*Food Chain
*Models, Theoretical
*Symbiosis

@article {pmid31937838,
year = {2020},
author = {Li, W and Ma, ZS},
title = {FBA Ecological Guild: Trio of Firmicutes-Bacteroidetes Alliance against Actinobacteria in Human Oral Microbiome.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {287},
pmid = {31937838},
issn = {2045-2322},
mesh = {Actinobacteria/genetics/growth & development/*isolation & purification ; Bacteroidetes/genetics/growth & development/*isolation & purification ; Databases, Factual ; Firmicutes/genetics/growth & development/*isolation & purification ; Humans ; *Microbiota ; Mouth/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In a pioneering study, Zaura et al. (2009) found that majority of oral microbes fall within the five phyla including, Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and Fusobacteria. Subsequent studies further identified a set of microbes that were commonly shared among unrelated individuals (i.e., core). However, these existing studies may have not been designed to investigate the interactions among various core species. Here by harnessing the power of ecological network analysis, we identified some important ecological guilds in the form of network clusters. In particular, we found that the strongest cluster is an alliance between Firmicutes and Bacteroidetes against Actinobacteria (FBA-guild). Within the guild, we further identified two sub-guilds, the Actinobacteria-dominant sub-guild (ASG) and Firmicutes-dominant allied with Bacteroidetes sub-guild (FBSG). Furthermore, we identified so-termed guard nodes in both sub-guilds, and their role may be to inhibit the peer sub-guild given they held competitive interactions only with the outside nodes only but held cooperative interactions only with the internal nodes, which we termed civilian nodes given that they only held cooperative interactions. We postulated that FBA-guild might be to do with protection of oral health against some opportunistic pathogens from Corynebacterium and Actinomyces, the two major genera of Actinobacteria (target of FB alliance).},
}

Actinobacteria/genetics/growth & development/*isolation & purification
Bacteroidetes/genetics/growth & development/*isolation & purification
Databases, Factual
Firmicutes/genetics/growth & development/*isolation & purification
Humans
*Microbiota
Mouth/*microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid31729401,
year = {2019},
author = {Mittermayer, FH and Stiasny, MH and Clemmesen, C and Bayer, T and Puvanendran, V and Chierici, M and Jentoft, S and Reusch, TBH},
title = {Transcriptome profiling reveals exposure to predicted end-of-century ocean acidification as a stealth stressor for Atlantic cod larvae.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16908},
pmid = {31729401},
issn = {2045-2322},
mesh = {Animals ; Computational Biology/methods ; Gadus morhua/*genetics ; *Gene Expression Profiling ; Gene Ontology ; High-Throughput Nucleotide Sequencing ; *Hydrogen-Ion Concentration ; Larva ; Osmoregulation ; Seawater/*analysis/*chemistry ; *Stress, Physiological ; *Transcriptome ; },
abstract = {Ocean acidification (OA), a direct consequence of increasing atmospheric CO2 concentration dissolving in ocean waters, is impacting many fish species. Little is known about the molecular mechanisms underlying the observed physiological impacts in fish. We used RNAseq to characterize the transcriptome of 3 different larval stages of Atlantic cod (Gadus morhua) exposed to simulated OA at levels (1179 µatm CO2) representing end-of-century predictions compared to controls (503 µatm CO2), which were shown to induce tissue damage and elevated mortality in G. morhua. Only few genes were differentially expressed in 6 and 13 days-post-hatching (dph) (3 and 16 genes, respectively), during a period when maximal mortality as a response to elevated pCO2 occurred. At 36 dph, 1413 genes were differentially expressed, most likely caused by developmental asynchrony between the treatment groups, with individuals under OA growing faster. A target gene analysis revealed only few genes of the universal and well-defined cellular stress response to be differentially expressed. We thus suggest that predicted ocean acidification levels constitute a "stealth stress" for early Atlantic cod larvae, with a rapid breakdown of cellular homeostasis leading to organismal death that was missed even with an 8-fold replication implemented in this study.},
}

Animals
Computational Biology/methods
Gadus morhua/*genetics
*Gene Expression Profiling
Gene Ontology
High-Throughput Nucleotide Sequencing
*Hydrogen-Ion Concentration
Larva
Osmoregulation
Seawater/*analysis/*chemistry
*Stress, Physiological
*Transcriptome

@article {pmid31624369,
year = {2019},
author = {Habel, JC and Trusch, R and Schmitt, T and Ochse, M and Ulrich, W},
title = {Long-term large-scale decline in relative abundances of butterfly and burnet moth species across south-western Germany.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {14921},
doi = {10.1038/s41598-019-51424-1},
pmid = {31624369},
issn = {2045-2322},
mesh = {Agriculture ; *Animal Distribution ; Animals ; Biodiversity ; Butterflies/*physiology ; *Conservation of Natural Resources ; Datasets as Topic ; Ecological Parameter Monitoring/statistics & numerical data ; Germany ; Grassland ; Moths/*physiology ; Population Dynamics/statistics & numerical data/trends ; },
abstract = {Current studies have shown a severe general decline in insect species diversity, their abundance, and a biomass reduction of flying insects. Most of previous studies have been performed at single sites, or were spatially restricted at the landscape level. In this study, we analyse trends of species richness and shifts in species composition of butterflies and burnet moth species across the federal state of Baden-Württemberg in south-western Germany, covering an area of 35,750 km2. The data set consists of 233,474 records and covers a period from 1750 until today. We grouped species according to their species´ specific functional traits and analyse how species with different habitat requirements and behaviour respond to land-use changes over time. Our data document a significant loss of relative abundance for most species, especially since the 1950s until today. Species demanding specific habitat requirements are more seriously suffering under this trend than generalists. This in particular affects taxa adapted to extensively used xerothermic grasslands, bogs or other habitats maintained by traditional low-productivity agricultural practices of the past. Our data indicate large-scale decline in relative abundance of many butterfly and burnet moth species, which happened in particular during the past few decades.},
}

Agriculture
*Animal Distribution
Animals
Biodiversity
Butterflies/*physiology
*Conservation of Natural Resources
Datasets as Topic
Ecological Parameter Monitoring/statistics & numerical data
Germany
Grassland
Moths/*physiology
Population Dynamics/statistics & numerical data/trends

@article {pmid33143227,
year = {2020},
author = {Petrushin, I and Belikov, S and Chernogor, L},
title = {Cooperative Interaction of Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02 in the Diseased Sponge Lubomirskiabaicalensis.},
journal = {International journal of molecular sciences},
volume = {21},
number = {21},
pages = {},
doi = {10.3390/ijms21218128},
pmid = {33143227},
issn = {1422-0067},
support = {19-14-00088//Russian Science Foundation/ ; 0345-2019-0002 (AAAA-A16-116122110066-1)//Siberian Branch, Russian Academy of Sciences/ ; },
abstract = {Endemic freshwater sponges (demosponges, Lubomirskiidae) dominate in Lake Baikal, Central Siberia, Russia. These sponges are multicellular filter-feeding animals that represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of Lubomirskia baicalensis has been a significant problem in Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria from the families Flavobacteriaceae and Oxalobacteraceae dominate the microbiomes of diseased sponges. Both species are opportunistic pathogens common in freshwater ecosystems. The aim of our study was to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. Janthinobacterium sp. SLB01 attacks other cells using a type VI secretion system and suppresses gram-positive bacteria with violacein, and regulates its own activity via quorum sensing. It produces floc and strong biofilm by exopolysaccharide biosynthesis and PEP-CTERM/XrtA protein expression. Flavobacterium sp. SLB02 utilizes the fragments of cell walls produced by polysaccharides. These two strains have a marked difference in carbohydrate acquisition. We described a possible means of joint occupation of the ecological niche in the freshwater sponge microbial community. This study expands the understanding of the symbiotic relationship of microorganisms with freshwater Baikal sponges.},
}

@article {pmid33135271,
year = {2020},
author = {Yamaguchi, K and Koyanagi, M and Kuraku, S},
title = {Visual and non-visual opsin genes of sharks and other non-osteichthyan vertebrates: genomic exploration of underwater photoreception.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jeb.13730},
pmid = {33135271},
issn = {1420-9101},
abstract = {Vision of sharks embraces various biological and ecological themes ranging from predation and adaptation to deep-sea life. However, behavioral and genetic studies have been limited by their elusive lifestyles, repeatedly reported declines of wild populations, and their unique life history traits including low fecundity and enhanced longevity. Sharks have also not been actively studied on the cellular and molecular levels, because of additional difficulties in cell culture, tissue collection, and genome sequencing. A recent study circumvented some of these obstacles by means of genome informatics thereby portrayed the variation of visual opsin gene repertoires among elasmobranchs (sharks and rays) and spectral shifts of the rhodopsin pigment. Comprehensive surveys in whole genome sequences are also revealing the repertoires of non-visual opsins with unknown functions. This review is aimed to summarize existing studies on shark opsins with an emphasis on genomic investigation of gene repertoires and to provide insights into the better understanding of underwater ecology of marine megafauna with in vitro experimentation.},
}

@article {pmid31350429,
year = {2019},
author = {Stewart, FEC and Darlington, S and Volpe, JP and McAdie, M and Fisher, JT},
title = {Corridors best facilitate functional connectivity across a protected area network.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {10852},
doi = {10.1038/s41598-019-47067-x},
pmid = {31350429},
issn = {2045-2322},
mesh = {*Animal Migration ; Animals ; Biodiversity ; Canada ; Conservation of Natural Resources/*methods ; Ecology/methods ; *Ecosystem ; Geographic Information Systems ; Locomotion ; Mustelidae/*physiology ; *Natural Resources ; },
abstract = {Biologging data allow animal ecologists to directly measure species' fine-scale spatiotemporal responses to environments, such as movement - critical for our understanding of biodiversity declines in the Anthropocene. Animal movement between resource patches is a behavioral expression of multiple ecological processes that affect individual fitness. Protected area (PA) networks are a tool used to conserve biodiversity by sustaining habitat patches across vast heterogeneous landscapes. However, our ability to design PA networks that conserve biodiversity relies on our accurate understanding of animal movement and functional connectivity; this understanding is rarely tested in real-world situations due to the large geographic expanse of most PA networks. Using a tractable PA network mesocosm, we employ cutting-edge biologging technology to analyze animal movement decisions in response to a highly heterogeneous landscape. We analyze these data to test, in a novel way, three common hypotheses about functional connectivity - structural corridors, least cost paths, and stepping stones. Consistently, animals moved along structurally self-similar corridors. In reference to the Aichi 2020 Biodiversity Targets, relying on species to "stepping stone" across habitat remnants may not achieve protected area network conservation objectives.},
}

*Animal Migration
Animals
Biodiversity
Canada
Conservation of Natural Resources/*methods
Ecology/methods
*Ecosystem
Geographic Information Systems
Locomotion
Mustelidae/*physiology
*Natural Resources

@article {pmid31535335,
year = {2020},
author = {Contador, CA and Veas-Castillo, L and Tapia, E and Antipán, M and Miranda, N and Ruiz-Tagle, B and García-Araya, J and Andrews, BA and Marin, M and Dorador, C and Asenjo, JA},
title = {Atacama Database: a platform of the microbiome of the Atacama Desert.},
journal = {Antonie van Leeuwenhoek},
volume = {113},
number = {2},
pages = {185-195},
doi = {10.1007/s10482-019-01328-x},
pmid = {31535335},
issn = {1572-9699},
support = {FB0001//Comisión Nacional de Investigación Científica y Tecnológica/ ; },
mesh = {Archaea/genetics/physiology ; Bacteria/genetics ; Biotechnology ; *Databases, Factual ; Desert Climate ; Microbiota/physiology ; Soil Microbiology ; },
abstract = {The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.},
}

Archaea/genetics/physiology
Bacteria/genetics
Biotechnology
*Databases, Factual
Desert Climate
Microbiota/physiology
Soil Microbiology

@article {pmid33095844,
year = {2020},
author = {Snell Taylor, S and Coyle, JR and White, EP and Hurlbert, AH},
title = {A simulation study of the use of temporal occupancy for identifying core and transient species.},
journal = {PloS one},
volume = {15},
number = {10},
pages = {e0241198},
doi = {10.1371/journal.pone.0241198},
pmid = {33095844},
issn = {1932-6203},
abstract = {Transient species, which do not maintain self-sustaining populations in a system where they are observed, are ubiquitous in nature and their presence often impacts the interpretation of ecological patterns and processes. Identifying transient species from temporal occupancy, the proportion of time a species is observed at a given site over a time series, is subject to classification errors as a result of imperfect detection and source-sink dynamics. We use a simulation-based approach to assess how often errors in detection or classification occur in order to validate the use of temporal occupancy as a metric for inferring whether a species is a core or transient member of a community. We found that low detection increases error in the classification of core species, while high habitat heterogeneity and high detection increase error in classification of transient species. These findings confirm that temporal occupancy is a valid metric for inferring whether a species can maintain a self-sustaining population, but imperfect detection, low abundance, and highly heterogeneous landscapes may yield high misclassification rates.},
}

@article {pmid33087857,
year = {2020},
author = {Maák, I and Tóth, E and Lenda, M and Lőrinczi, G and Kiss, A and Juhász, O and Czechowski, W and Torma, A},
title = {Behaviours indicating cannibalistic necrophagy in ants are modulated by the perception of pathogen infection level.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {17906},
doi = {10.1038/s41598-020-74870-8},
pmid = {33087857},
issn = {2045-2322},
support = {2017-01-X-NZ8-01042//Polish National Science Centre/ ; 1324/1/MOB/IV/15/2016/0//Polish Ministry of Science and Higher Education/ ; },
abstract = {Cannibalistic necrophagy is rarely observed in social hymenopterans, although a lack of food could easily favour such behaviour. One of the main supposed reasons for the rarity of necrophagy is that eating of nestmate corpses carries the risk of rapid spread of pathogens or parasites. Here we present an experimental laboratory study on behaviour indicating consumption of nestmate corpses in the ant Formica polyctena. We examined whether starvation and the fungal infection level of the corpses affects the occurrence of cannibalistic necrophagy. Our results showed that the ants distinguished between corpses of different types and with different levels of infection risk, adjusting their behaviour accordingly. The frequency of behaviours indicating cannibalistic necrophagy increased during starvation, although these behaviours seem to be fairly common in F. polyctena even in the presence of other food sources. The occurrence and significance of cannibalistic necrophagy deserve further research because, in addition to providing additional food, it may be part of the hygienic behaviour repertoire. The ability to detect infections and handle pathogens are important behavioural adaptations for social insects, crucial for the fitness of both individual workers and the entire colony.},
}

@article {pmid32853270,
year = {2020},
author = {Xu, J and Yin, P and Hu, W and Fu, L and Zhao, H},
title = {Assessing the ecological regime and spatial spillover effects of a reclaimed mining subsided lake: A case study of the Pan'an Lake wetland in Xuzhou.},
journal = {PloS one},
volume = {15},
number = {8},
pages = {e0238243},
pmid = {32853270},
issn = {1932-6203},
mesh = {China ; Coal Mining/*methods ; Conservation of Natural Resources/*methods ; Ecology/methods ; Ecosystem ; Environmental Monitoring/methods ; Lakes ; Wetlands ; },
abstract = {In the North China Plain, coal mining subsided lakes are surface water bodies that form after the conclusion of coal mining. In China, mining subsided lakes are often transformed into artificial wetland parks for ecological restoration. While many studies have focused on evaluating coal mining subsidence lake ecosystem service value and water pollution, little attention has been paid to changes in ecological regimes and ecological spillover effects before and after the reclamation of mining areas. This paper examines the Pan'an Lake artificial wetland in Jiawang District, Xuzhou, as a case study. Changes in the ecological regime of the mining subsidence area before and after land reclamation and corresponding spatial spillover effect on land prices are assessed based on remote sensing, GIS raster calculations and geostatistical methods. The results show that the ecosystem service value and ecological storage capacity changed significantly after the mining subsided lake was transformed into an artificial wetland and the wetland ecosystem has been developing well with significantly positive spillover effects on surrounding land prices. From 2008 to 2017, service functions of the artificial wetland ecosystem of Pan'an Lake increased by 81.95%, and the system's ecological storage capacity increased from RMB 6,754 yuan/hm2 in 2008 to RMB 12,289 yuan/hm2 in 2017. The average impact of the Pan'an Lake artificial wetland on the spillover effects of surrounding residential land prices was measured at RMB 195.18 yuan/m2, and the total spillover value of planned residential land in the study area was measured at RMB 805,422,100 yuan. The present study can serve as a useful guide for evaluating the economic feasibility of land reclamation planning and ecological restoration in mining subsidence areas.},
}

China
Coal Mining/*methods
Conservation of Natural Resources/*methods
Ecology/methods
Ecosystem
Environmental Monitoring/methods
Lakes
Wetlands

@article {pmid32770154,
year = {2020},
author = {Cichocki, N and Hübschmann, T and Schattenberg, F and Kerckhof, FM and Overmann, J and Müller, S},
title = {Bacterial mock communities as standards for reproducible cytometric microbiome analysis.},
journal = {Nature protocols},
volume = {15},
number = {9},
pages = {2788-2812},
doi = {10.1038/s41596-020-0362-0},
pmid = {32770154},
issn = {1750-2799},
mesh = {Bacteria/*cytology ; Computational Biology ; Cytological Techniques/*standards ; *Microbiota ; Reference Standards ; Reproducibility of Results ; },
abstract = {Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.},
}

Bacteria/*cytology
Computational Biology
Cytological Techniques/*standards
*Microbiota
Reference Standards
Reproducibility of Results

@article {pmid31677344,
year = {2020},
author = {Dumack, K and Fiore-Donno, AM and Bass, D and Bonkowski, M},
title = {Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria).},
journal = {Molecular ecology resources},
volume = {20},
number = {2},
pages = {398-403},
doi = {10.1111/1755-0998.13112},
pmid = {31677344},
issn = {1755-0998},
support = {BO 1907/13-2//Deutsche Forschungsgemeinschaft/ ; BO 1907/18-1//Deutsche Forschungsgemeinschaft/ ; Priority Program 1374//Deutsche Forschungsgemeinschaft/ ; NE/H000887/1//NERC Science of the Environment/ ; NE/H009426/1//NERC Science of the Environment/ ; },
mesh = {Cercozoa/classification/genetics ; Databases, Genetic ; Ecosystem ; Environmental DNA/genetics ; Phenotype ; Phylogeny ; Rhizaria/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {We have compiled a database of functional traits for two widespread and ecologically important groups of protists, Cercozoa and Endomyxa (Rhizaria). The functional traits of microorganisms are crucially important for interpreting results from environmental sequencing surveys. Linking morphological and ecological traits to environmental factors is common practice in studies involving micro- and macroorganisms, but is rarely applied to protists. Our database provides functional and ecologically significant traits linked to morphology, nutrition, locomotion and habitats. We discuss how the use of functional traits may help to unveil underlying ecosystem processes. This database is intended as a common reference for the molecular ecology community and will boost the understanding of ecosystem functions, especially those driven by biological interactions.},
}

Cercozoa/classification/genetics
Databases, Genetic
Ecosystem
Environmental DNA/genetics
Phenotype
Phylogeny
Rhizaria/classification/*genetics
Sequence Analysis, DNA

@article {pmid33031625,
year = {2020},
author = {Riginos, C and Crandall, ED and Liggins, L and Gaither, MR and Ewing, RB and Meyer, C and Andrews, KR and Euclide, PT and Titus, BM and Overgaard Therkildsen, N and Salces-Castellano, A and Stewart, LC and Toonen, RJ and Deck, J},
title = {Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13269},
pmid = {33031625},
issn = {1755-0998},
abstract = {Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic datasets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDC's sequence read archive (SRA) while maintaining persistent links to standards-compliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, GEOME enables data management solutions for large collaborative groups and expedites batch retrieval of genetic data from the SRA. The article that follows describes how GEOME can enable genuinely open data workflows for researchers in the field of molecular ecology.},
}

@article {pmid31972020,
year = {2020},
author = {Pippel, M and Jebb, D and Patzold, F and Winkler, S and Vogel, H and Myers, G and Hiller, M and Hundsdoerfer, AK},
title = {A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).},
journal = {GigaScience},
volume = {9},
number = {1},
pages = {},
pmid = {31972020},
issn = {2047-217X},
mesh = {Animals ; Chiroptera/parasitology ; Computational Biology/methods ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Moths/*genetics ; },
abstract = {BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation.

RESULTS: Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51× Pacific Biosciences long reads with an average read length of 8.9 kb. Pacific Biosciences reads longer than 4 kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations.

CONCLUSIONS: Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.},
}

Animals
Chiroptera/parasitology
Computational Biology/methods
*Genome
*Genomics/methods
Molecular Sequence Annotation
Moths/*genetics

@article {pmid31904811,
year = {2020},
author = {Tang, B and Zhang, D and Li, H and Jiang, S and Zhang, H and Xuan, F and Ge, B and Wang, Z and Liu, Y and Sha, Z and Cheng, Y and Jiang, W and Jiang, H and Wang, Z and Wang, K and Li, C and Sun, Y and She, S and Qiu, Q and Wang, W and Li, X and Li, Y and Liu, Q and Ren, Y},
title = {Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus).},
journal = {GigaScience},
volume = {9},
number = {1},
pages = {},
pmid = {31904811},
issn = {2047-217X},
mesh = {Animals ; Brachyura/genetics ; *Chromosomes ; Computational Biology/methods ; *Evolution, Molecular ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Transcriptome ; },
abstract = {BACKGROUND: The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking.

FINDINGS: Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology.

CONCLUSIONS: We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.},
}

Animals
Brachyura/genetics
*Chromosomes
Computational Biology/methods
*Evolution, Molecular
Gene Expression Profiling
*Genome
*Genomics/methods
Molecular Sequence Annotation
Multigene Family
Phylogeny
Repetitive Sequences, Nucleic Acid
Transcriptome

@article {pmid31024020,
year = {2019},
author = {Milleret, C and Ordiz, A and Sanz-Pérez, A and Uzal, A and Carricondo-Sanchez, D and Eriksen, A and Sand, H and Wabakken, P and Wikenros, C and Åkesson, M and Zimmermann, B},
title = {Testing the influence of habitat experienced during the natal phase on habitat selection later in life in Scandinavian wolves.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {6526},
doi = {10.1038/s41598-019-42835-1},
pmid = {31024020},
issn = {2045-2322},
mesh = {Animals ; Behavior ; *Ecosystem ; Geographic Information Systems ; Geography ; Humans ; Models, Theoretical ; Principal Component Analysis ; Scandinavian and Nordic Countries ; Wolves/*physiology ; },
abstract = {Natal habitat preference induction (NHPI) occurs when characteristics of the natal habitat influence the future habitat selection of an animal. However, the influence of NHPI after the dispersal phase has received remarkably little attention. We tested whether exposure to humans in the natal habitat helps understand why some adult wolves Canis lupus may approach human settlements more than other conspecifics, a question of both ecological and management interest. We quantified habitat selection patterns within home ranges using resource selection functions and GPS data from 21 wolf pairs in Scandinavia. We identified the natal territory of each wolf with genetic parental assignment, and we used human-related characteristics within the natal territory to estimate the degree of anthropogenic influence in the early life of each wolf. When the female of the adult wolf pair was born in an area with a high degree of anthropogenic influence, the wolf pair tended to select areas further away from humans, compared to wolf pairs from natal territories with a low degree of anthropogenic influence. Yet the pattern was statistically weak, we suggest that our methodological approach can be useful in other systems to better understand NHPI and to inform management about human-wildlife interactions.},
}

Animals
Behavior
*Ecosystem
Geographic Information Systems
Geography
Humans
Models, Theoretical
Principal Component Analysis
Scandinavian and Nordic Countries
Wolves/*physiology

@article {pmid33011421,
year = {2020},
author = {Sannigrahi, S and Pilla, F and Zhang, Q and Chakraborti, S and Wang, Y and Basu, B and Basu, AS and Joshi, PK and Keesstra, S and Roy, PS and Sutton, PC and Bhatt, S and Rahmat, S and Jha, S and Singh, LK},
title = {Examining the effects of green revolution led agricultural expansion on net ecosystem service values in India using multiple valuation approaches.},
journal = {Journal of environmental management},
volume = {277},
number = {},
pages = {111381},
doi = {10.1016/j.jenvman.2020.111381},
pmid = {33011421},
issn = {1095-8630},
abstract = {Ecosystem Services (ESs) are bundles of natural processes and functions that are essential for human well-being, subsistence, and livelihoods. The 'Green Revolution' (GR) has substantial impact on the agricultural landscape and ESs in India. However, the effects of GR on ESs have not been adequately documented and analyzed. This leads to the main hypothesis of this work - 'the incremental trend of ESs in India is mainly prompted by GR led agricultural innovations that took place during 1960 - 1970'. The analysis was carried out through five successive steps. First, the spatiotemporal Ecosystem Service Values (ESVs) in Billion US$ for 1985, 1995, and 2005 were estimated using several value transfer approaches. Second, the sensitivity and elasticity of different ESs to land conversion were carried out using coefficient of sensitivity and coefficient of elasticity. Third, the Geographically Weighted Regression model was performed using five explanatory factors, i.e., total crop area, crop production, crop yield, net irrigated area, and cropping intensity, to explore the cumulative and individual effects of these driving factors on ESVs. Fourth, Multi-Layer Perceptron based Artificial Neural Network was employed to estimate the normalized importance of these explanatory factors. Fifth, simple and multiple linear regression modeling was done to assess the linear associations between the driving factors and the ESs. During the observation periods, cropland, forestland and water bodies contributed to 80%-90% of ESVs, followed by grassland, mangrove, wetland and urban built-up. In all three evaluation years, the highest estimated ESVs among the nine ES categories was provided by water regulation, followed by soil formation and soil-water retention, biodiversity maintenance, waste treatment, climate regulation, and greenhouse gas regulation. Among the five explanatory factors, total crop area, crop production, and net irrigated area showed strong positive associations with ESVs, while cropping intensity exhibited a negative association. Therefore, the study reveals a strong association between GR led agricultural expansion and ESVs in India. This study suggests that there should be an urgent need for formulation of rigorous ecosystem management strategies and policies to preserve ecological integrity and flow of uninterrupted ESs and to sustain human well-being.},
}

@article {pmid31596250,
year = {2020},
author = {Kaufman, JH and Elkins, CA and Davis, M and Weis, AM and Huang, BC and Mammel, MK and Patel, IR and Beck, KL and Edlund, S and Chambliss, D and Douglas, J and Bianco, S and Kunitomi, M and Weimer, BC},
title = {Insular Microbiogeography: Three Pathogens as Exemplars.},
journal = {Current issues in molecular biology},
volume = {36},
number = {},
pages = {89-108},
doi = {10.21775/cimb.036.089},
pmid = {31596250},
issn = {1467-3045},
mesh = {Bacteria/classification/*genetics/pathogenicity ; Databases, Genetic ; Ecology ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial ; Metagenome ; Microbiota/*genetics ; *Phylogeny ; Phylogeography/methods ; Whole Genome Sequencing ; },
abstract = {Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.},
}

Bacteria/classification/*genetics/pathogenicity
Databases, Genetic
Ecology
Evolution, Molecular
Genetic Variation
Genome, Bacterial
Metagenome
Microbiota/*genetics
*Phylogeny
Phylogeography/methods
Whole Genome Sequencing

@article {pmid31911493,
year = {2020},
author = {Saw, JHW and Nunoura, T and Hirai, M and Takaki, Y and Parsons, R and Michelsen, M and Longnecker, K and Kujawinski, EB and Stepanauskas, R and Landry, Z and Carlson, CA and Giovannoni, SJ},
title = {Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
pmid = {31911493},
issn = {2150-7511},
mesh = {Biodiversity ; Chloroflexi/*enzymology/*genetics ; Computational Biology/methods ; *Genome, Bacterial ; Metabolic Networks and Pathways ; Metabolomics/methods ; *Metagenome ; *Metagenomics ; *Multigene Family ; Phylogeny ; Phylogeography ; },
abstract = {It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns.IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.},
}

Biodiversity
Chloroflexi/*enzymology/*genetics
Computational Biology/methods
*Genome, Bacterial
Metabolic Networks and Pathways
Metabolomics/methods
*Metagenome
*Metagenomics
*Multigene Family
Phylogeny
Phylogeography

@article {pmid32957527,
year = {2020},
author = {Juhász, O and Fürjes-Mikó, Á and Tenyér, A and Somogyi, AÁ and Aguilon, DJ and Kiss, PJ and Bátori, Z and Maák, I},
title = {Consequences of Climate Change-Induced Habitat Conversions on Red Wood Ants in a Central European Mountain: A Case Study.},
journal = {Animals : an open access journal from MDPI},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/ani10091677},
pmid = {32957527},
issn = {2076-2615},
support = {2017-01-X-NZ8-01042//Fundacja na rzecz Nauki Polskiej/ ; NKFIH K 124796//Országos Tudományos Kutatási Alapprogramok/ ; },
abstract = {The consequences of anthropogenic climate change are one of the major concerns of conservation biology. A cascade of negative effects is expected to affect various ecosystems, one of which is Central European coniferous forests and their unique biota. These coniferous forests are the primary habitat of many forest specialist species such as red wood ants. Climate change-induced rising of temperature allows trees to skip winter hibernation, making them more vulnerable to storms that cause wind felling, and in turn, promotes bark beetle infestations that results in unscheduled clear-cuttings. Red wood ants can also be exposed to such habitat changes. We investigated the effects of bark beetle-induced clear-cutting and the absence of coniferous trees on colonies of Formica polyctena, including a mixed-coniferous forest as a reference. Our aim was to investigate how these habitat features affect the nest characteristics and nesting habits of F. polyctena. Our results indicate that, in the absence of conifers, F. polyctena tend to use different alternatives for nest material, colony structure, and food sources. However, the vitality of F. polyctena colonies significantly decreased (smaller nest mound volumes). Our study highlights the ecological flexibility of this forest specialist and its potential to survive under extreme conditions.},
}

@article {pmid32933777,
year = {2020},
author = {Laubmeier, AN and Cazelles, B and Cuddington, K and Erickson, KD and Fortin, MJ and Ogle, K and Wikle, CK and Zhu, K and Zipkin, EF},
title = {Ecological Dynamics: Integrating Empirical, Statistical, and Analytical Methods.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2020.08.006},
pmid = {32933777},
issn = {1872-8383},
abstract = {Understanding ecological processes and predicting long-term dynamics are ongoing challenges in ecology. To address these challenges, we suggest an approach combining mathematical analyses and Bayesian hierarchical statistical modeling with diverse data sources. Novel mathematical analysis of ecological dynamics permits a process-based understanding of conditions under which systems approach equilibrium, experience large oscillations, or persist in transient states. This understanding is improved by combining ecological models with empirical observations from a variety of sources. Bayesian hierarchical models explicitly couple process-based models and data, yielding probabilistic quantification of model parameters, system characteristics, and associated uncertainties. We outline relevant tools from dynamical analysis and hierarchical modeling and argue for their integration, demonstrating the value of this synthetic approach through a simple predator-prey example.},
}

@article {pmid32913322,
year = {2020},
author = {Pârvulescu, L and Iorgu, EI and Zaharia, C and Ion, MC and Satmari, A and Krapal, AM and Popa, OP and Miok, K and Petrescu, I and Popa, LO},
title = {The future of endangered crayfish in light of protected areas and habitat fragmentation.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14870},
doi = {10.1038/s41598-020-71915-w},
pmid = {32913322},
issn = {2045-2322},
support = {PN-II-ID-PCE-2008-2-1458//Romanian National Authority for Scientific Research and Innovation/ ; PN-II-ID-PCE-2008-2-1458//Romanian National Authority for Scientific Research and Innovation/ ; PN-II-ID-PCE-2008-2-1458//Romanian National Authority for Scientific Research and Innovation/ ; PN-II-ID-PCE-2008-2-1458//Romanian National Authority for Scientific Research and Innovation/ ; PN-II-ID-PCE-2008-2-1458//Romanian National Authority for Scientific Research and Innovation/ ; RO1567-IBB04/2020//Institute of Biology Bucharest of Romanian Academy/ ; },
abstract = {The long-term survival of a species requires, among other things, gene flow between populations. Approaches for the evaluation of fragmentation in the frame of freshwater habitats consider only a small amount of the information that combined demography and geography are currently able to provide. This study addresses two species of Austropotamobius crayfish in the light of population genetics, spatial ecology and protected areas of the Carpathians. Advancing the classical approaches, we defined ecological distances upon the rasterised river network as a surrogate of habitat resistance to migration, quantifying the deviations from the species´ suitability range for a set of relevant geospatial variables in each cell of the network. Molecular analyses revealed the populations of the two Austropotamobius crayfish species are clearly distinct, lacking hybridisation. Comparing pairs of populations, we found, in some cases, a strong disagreement regarding genetic and ecological distances, potentially due to human-mediated translocations or the geophysical phenomena of regressive erosion, which may have led to unexpected colonisation routes. Protected areas were found to offer appropriate local habitat conditions but failed to ensure connectivity. The methodology applied in this study allowed us to quantify the contribution of each geospatial (environmental) variable to the overall effect of fragmentation, and we found that water quality was the most important variable. A multilevel approach proved to reveal a better understanding of drivers behind the distribution patterns, which can lead to more adequate conservation measures.},
}

@article {pmid32899582,
year = {2020},
author = {Guo, Y and Wang, H and Wu, Z and Wang, S and Sun, H and Senthilnath, J and Wang, J and Robin Bryant, C and Fu, Y},
title = {Modified Red Blue Vegetation Index for Chlorophyll Estimation and Yield Prediction of Maize from Visible Images Captured by UAV.},
journal = {Sensors (Basel, Switzerland)},
volume = {20},
number = {18},
pages = {},
doi = {10.3390/s20185055},
pmid = {32899582},
issn = {1424-8220},
support = {Grant No. 31770516//the General Program of National Nature Science Foundation of China/ ; 2017YFA06036001//the National Key Research and Development Program of China/ ; 2018EYT05//the 111 Project (B18006) and Fundamental Research Funds for the Central Universities/ ; },
abstract = {The vegetation index (VI) has been successfully used to monitor the growth and to predict the yield of agricultural crops. In this paper, a long-term observation was conducted for the yield prediction of maize using an unmanned aerial vehicle (UAV) and estimations of chlorophyll contents using SPAD-502. A new vegetation index termed as modified red blue VI (MRBVI) was developed to monitor the growth and to predict the yields of maize by establishing relationships between MRBVI- and SPAD-502-based chlorophyll contents. The coefficients of determination (R2s) were 0.462 and 0.570 in chlorophyll contents' estimations and yield predictions using MRBVI, and the results were relatively better than the results from the seven other commonly used VI approaches. All VIs during the different growth stages of maize were calculated and compared with the measured values of chlorophyll contents directly, and the relative error (RE) of MRBVI is the lowest at 0.355. Further, machine learning (ML) methods such as the backpropagation neural network model (BP), support vector machine (SVM), random forest (RF), and extreme learning machine (ELM) were adopted for predicting the yields of maize. All VIs calculated for each image captured during important phenological stages of maize were set as independent variables and the corresponding yields of each plot were defined as dependent variables. The ML models used the leave one out method (LOO), where the root mean square errors (RMSEs) were 2.157, 1.099, 1.146, and 1.698 (g/hundred grain weight) for BP, SVM, RF, and ELM. The mean absolute errors (MAEs) were 1.739, 0.886, 0.925, and 1.356 (g/hundred grain weight) for BP, SVM, RF, and ELM, respectively. Thus, the SVM method performed better in predicting the yields of maize than the other ML methods. Therefore, it is strongly suggested that the MRBVI calculated from images acquired at different growth stages integrated with advanced ML methods should be used for agricultural- and ecological-related chlorophyll estimation and yield predictions.},
}

@article {pmid31631517,
year = {2020},
author = {Li, X and Wang, X and Fang, L and Batbayar, N and Natsagdorj, T and Davaasuren, B and Damba, I and Xu, Z and Cao, L and Fox, AD},
title = {Annual migratory patterns of Far East Greylag Geese (Anser anser rubrirostris) revealed by GPS tracking.},
journal = {Integrative zoology},
volume = {15},
number = {3},
pages = {213-223},
doi = {10.1111/1749-4877.12414},
pmid = {31631517},
issn = {1749-4877},
mesh = {*Animal Migration ; Animals ; China ; Geese/*physiology ; Geographic Information Systems ; Mongolia ; Seasons ; Telemetry/*veterinary ; },
abstract = {Twenty Far East Greylag Geese, Anser anser rubrirostris, were captured and fitted with Global Positioning System/Global System for Mobile Communications (GPS/GSM) loggers to identify breeding and wintering areas, migration routes and stopover sites. Telemetry data for the first time showed linkages between their Yangtze River wintering areas, stopover sites in northeastern China, and breeding/molting grounds in eastern Mongolia and northeast China. 10 of the 20 tagged individuals provided sufficient data. They stopped on migration at the Yellow River Estuary, Beidagang Reservoir and Xar Moron River, confirming these areas as being important stopover sites for this population. The median spring migration duration was 33.7 days (individuals started migrating between 25 February and 16 March and completed migrating from 1 to 9 April) compared to 52.7 days in autumn (26 September-13 October until 4 November-11 December). The median stopover duration was 31.1 and 51.3 days and the median speed of travel was 62.6 and 47.9 km/day for spring and autumn migration, respectively. The significant differences between spring and autumn migration on the migration duration, the stopover duration and the migration speed confirmed that tagged adult Greylag Geese traveled faster in spring than autumn, supporting the hypothesis that they should be more time-limited during spring migration.},
}

*Animal Migration
Animals
China
Geese/*physiology
Geographic Information Systems
Mongolia
Seasons
Telemetry/*veterinary

@article {pmid32730245,
year = {2020},
author = {D'Andrea, R and Gibbs, T and O'Dwyer, JP},
title = {Emergent neutrality in consumer-resource dynamics.},
journal = {PLoS computational biology},
volume = {16},
number = {7},
pages = {e1008102},
pmid = {32730245},
issn = {1553-7358},
mesh = {*Biodiversity ; Biological Evolution ; Computational Biology ; Computer Simulation ; Ecosystem ; *Models, Biological ; Stochastic Processes ; },
abstract = {Neutral theory assumes all species and individuals in a community are ecologically equivalent. This controversial hypothesis has been tested across many taxonomic groups and environmental contexts, and successfully predicts species abundance distributions across multiple high-diversity communities. However, it has been critiqued for its failure to predict a broader range of community properties, particularly regarding community dynamics from generational to geological timescales. Moreover, it is unclear whether neutrality can ever be a true description of a community given the ubiquity of interspecific differences, which presumably lead to ecological inequivalences. Here we derive analytical predictions for when and why non-neutral communities of consumers and resources may present neutral-like outcomes, which we verify using numerical simulations. Our results, which span both static and dynamical community properties, demonstrate the limitations of summarizing distributions to detect non-neutrality, and provide a potential explanation for the successes of neutral theory as a description of macroecological pattern.},
}

*Biodiversity
Biological Evolution
Computational Biology
Computer Simulation
Ecosystem
*Models, Biological
Stochastic Processes

@article {pmid31937263,
year = {2020},
author = {Herndon, N and Shelton, J and Gerischer, L and Ioannidis, P and Ninova, M and Dönitz, J and Waterhouse, RM and Liang, C and Damm, C and Siemanowski, J and Kitzmann, P and Ulrich, J and Dippel, S and Oberhofer, G and Hu, Y and Schwirz, J and Schacht, M and Lehmann, S and Montino, A and Posnien, N and Gurska, D and Horn, T and Seibert, J and Vargas Jentzsch, IM and Panfilio, KA and Li, J and Wimmer, EA and Stappert, D and Roth, S and Schröder, R and Park, Y and Schoppmeier, M and Chung, HR and Klingler, M and Kittelmann, S and Friedrich, M and Chen, R and Altincicek, B and Vilcinskas, A and Zdobnov, E and Griffiths-Jones, S and Ronshaugen, M and Stanke, M and Brown, SJ and Bucher, G},
title = {Enhanced genome assembly and a new official gene set for Tribolium castaneum.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {47},
pmid = {31937263},
issn = {1471-2164},
support = {SFB680//Deutsche Forschungsgemeinschaft/ ; P20 GM103418/GM/NIGMS NIH HHS/United States ; PA2044/1//Deutsche Forschungsgemeinschaft/ ; KL656/7//Deutsche Forschungsgemeinschaft/ ; BU1443/6//Deutsche Forschungsgemeinschaft/ ; WI1797/5//Deutsche Forschungsgemeinschaft/ ; FOR1234//Deutsche Forschungsgemeinschaft/ ; STA1009/10//Deutsche Forschungsgemeinschaft/ ; BU1443/7//Deutsche Forschungsgemeinschaft/ ; PP00P3_170664//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (CH)/ ; Department Herbert Jäckle//Max-Planck-Gesellschaft/ ; SFB 680 / A12//Deutsche Forschungsgemeinschaft/ ; Scho1058/4//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Binding Sites ; Computational Biology/methods ; *Genes, Insect ; *Genome, Insect ; *Genomics/methods ; MicroRNAs/genetics ; Molecular Sequence Annotation ; Phylogeny ; RNA Interference ; Reproducibility of Results ; Tribolium/*genetics ; },
abstract = {BACKGROUND: The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality.

RESULTS: Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI.

CONCLUSIONS: The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.},
}

Animals
Binding Sites
Computational Biology/methods
*Genes, Insect
*Genome, Insect
*Genomics/methods
MicroRNAs/genetics
Molecular Sequence Annotation
Phylogeny
RNA Interference
Reproducibility of Results
Tribolium/*genetics

@article {pmid32409662,
year = {2020},
author = {Cooney, CR and Sheard, C and Clark, AD and Healy, SD and Liker, A and Street, SE and Troisi, CA and Thomas, GH and Székely, T and Hemmings, N and Wright, AE},
title = {Ecology and allometry predict the evolution of avian developmental durations.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2383},
pmid = {32409662},
issn = {2041-1723},
mesh = {Animals ; Birds/*physiology ; Body Size/physiology ; Datasets as Topic ; Ecology/methods ; Embryo, Nonmammalian ; Embryonic Development/*physiology ; Female ; *Life History Traits ; Male ; *Models, Biological ; Nesting Behavior/physiology ; Time Factors ; },
abstract = {The duration of the developmental period represents a fundamental axis of life-history variation, yet broad insights regarding the drivers of this diversity are currently lacking. Here, we test mechanistic and ecological explanations for the evolution of developmental duration using embryological data and information on incubation and fledging for 3096 avian species. Developmental phases associated primarily with growth are the longest and most variable, consistent with a role for allometric constraint in determining the duration of development. In addition, developmental durations retain a strong imprint of deep evolutionary history and body size differences among species explain less variation than previously thought. Finally, we reveal ecological correlates of developmental durations, including variables associated with the relative safety of the developmental environment and pressures of breeding phenology. Overall, our results provide broad-scale insight into the relative importance of mechanistic, ecological and evolutionary constraints in shaping the diversification of this key life-history trait.},
}

Animals
Birds/*physiology
Body Size/physiology
Datasets as Topic
Ecology/methods
Embryo, Nonmammalian
Embryonic Development/*physiology
Female
*Life History Traits
Male
*Models, Biological
Nesting Behavior/physiology
Time Factors

@article {pmid32856310,
year = {2020},
author = {Nam, S and Dunton, GF and Ordway, MR and Ash, GI and Jeon, S and Vlahov, D and Whittemore, R and Nelson, LE and Sinha, R and Nunez-Smith, M and Granger, DA},
title = {Feasibility and acceptability of intensive, real-time biobehavioral data collection using ecological momentary assessment, salivary biomarkers, and accelerometers among middle-aged African Americans.},
journal = {Research in nursing & health},
volume = {},
number = {},
pages = {},
doi = {10.1002/nur.22068},
pmid = {32856310},
issn = {1098-240X},
support = {//Yale University, School of Nursing/ ; },
abstract = {Perceived racial discrimination is linked to unhealthy behaviors and stress-related morbidities. A compelling body of research indicates that perceived racial discrimination may contribute to health disparities among African Americans (AAs). The purposes of this study were to describe the study protocol including data collection procedures and study measures and to evaluate the feasibility and acceptability of intensive biobehavioral data collection using ecological momentary assessment (EMA), salivary biomarkers, and accelerometers over 7 days among middle-aged AAs with a goal of understanding the relationships between perceived racial discrimination and biobehavioral responses to stress. Twelve AA men and women participated in the feasibility/acceptability study. They completed surveys, anthropometrics, and received in-person training in EMA and saliva sample collection at baseline. Participants were asked to respond to the random prompt text message-based EMA five times a day, wear an accelerometer daily for 7 days, and to self-collect saliva samples four times a day for 4 consecutive days. The EMA surveys included perceived racial discrimination, affective states, lifestyle behaviors, and social and physical contexts. The mean EMA response rate was 82.8%. All participants collected saliva samples four times a day for 4 consecutive days. About 83% of participants wore the accelerometer on the hip 6 out of 7 days. Despite the perception that the intensive nature of assessments would result in high participant burden, the acceptability of the study procedures was uniformly favorable.},
}

@article {pmid32788594,
year = {2020},
author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S},
title = {Publisher Correction: A global database of Holocene paleotemperature records.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {271},
doi = {10.1038/s41597-020-00611-1},
pmid = {32788594},
issn = {2052-4463},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid32724218,
year = {2020},
author = {Muñoz, ÁG and Chourio, X and Rivière-Cinnamond, A and Diuk-Wasser, MA and Kache, PA and Mordecai, EA and Harrington, L and Thomson, MC},
title = {AeDES: a next-generation monitoring and forecasting system for environmental suitability of Aedes-borne disease transmission.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12640},
pmid = {32724218},
issn = {2045-2322},
support = {1R35GM133439-01/NH/NIH HHS/United States ; 2018-01754//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/International ; NA18OAR4310339//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/International ; U01CK000509-01//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/International ; U01 CK000509/CK/NCEZID CDC HHS/United States ; R35 GM133439/GM/NIGMS NIH HHS/United States ; },
mesh = {Aedes/*virology ; Animals ; Betacoronavirus/isolation & purification ; Climate ; Coronavirus Infections/pathology/transmission/virology ; Databases, Factual ; Decision Making ; *Epidemiological Monitoring/veterinary ; Humans ; Mosquito Vectors/*virology ; Pandemics ; Pneumonia, Viral/pathology/transmission/virology ; Vector Borne Diseases/epidemiology/*pathology/virology ; },
abstract = {Aedes-borne diseases, such as dengue and chikungunya, are responsible for more than 50 million infections worldwide every year, with an overall increase of 30-fold in the last 50 years, mainly due to city population growth, more frequent travels and ecological changes. In the United States of America, the vast majority of Aedes-borne infections are imported from endemic regions by travelers, who can become new sources of mosquito infection upon their return home if the exposed population is susceptible to the disease, and if suitable environmental conditions for the mosquitoes and the virus are present. Since the susceptibility of the human population can be determined via periodic monitoring campaigns, the environmental suitability for the presence of mosquitoes and viruses becomes one of the most important pieces of information for decision makers in the health sector. We present a next-generation monitoring and forecasting system for [Formula: see text]-borne diseases' environmental suitability (AeDES) of transmission in the conterminous United States and transboundary regions, using calibrated ento-epidemiological models, climate models and temperature observations. After analyzing the seasonal predictive skill of AeDES, we briefly consider the recent Zika epidemic, and the compound effects of the current Central American dengue outbreak happening during the SARS-CoV-2 pandemic, to illustrate how a combination of tailored deterministic and probabilistic forecasts can inform key prevention and control strategies .},
}

Aedes/*virology
Animals
Betacoronavirus/isolation & purification
Climate
Coronavirus Infections/pathology/transmission/virology
Databases, Factual
Decision Making
*Epidemiological Monitoring/veterinary
Humans
Mosquito Vectors/*virology
Pandemics
Pneumonia, Viral/pathology/transmission/virology
Vector Borne Diseases/epidemiology/*pathology/virology

@article {pmid32778752,
year = {2020},
author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D},
title = {A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-020-1274-7},
pmid = {32778752},
issn = {2397-334X},
support = {xxxx//United Nations (UN)/ ; NNX17AG51G//National Aeronautics and Space Administration (NASA)/ ; NNL15AA03//National Aeronautics and Space Administration (NASA)/ ; },
abstract = {Tropical forests vary in composition, structure and function such that not all forests have similar ecological value. This variability is caused by natural and anthropogenic disturbance regimes, which influence the ability of forests to support biodiversity, store carbon, mediate water yield and facilitate human well-being. While international environmental agreements mandate protecting and restoring forests, only forest extent is typically considered, while forest quality is ignored. Consequently, the locations and loss rates of forests of high ecological value are unknown and coordinated strategies for conserving these forests remain undeveloped. Here, we map locations high in forest structural integrity as a measure of ecological quality on the basis of recently developed fine-resolution maps of three-dimensional forest structure, integrated with human pressure across the global moist tropics. Our analyses reveal that tall forests with closed canopies and low human pressure typical of natural conditions comprise half of the global humid or moist tropical forest estate, largely limited to the Amazon and Congo basins. Most of these forests have no formal protection and, given recent rates of loss, are at substantial risk. With the rapid disappearance of these 'best of the last' forests at stake, we provide a policy-driven framework for their conservation and restoration, and recommend locations to maintain protections, add new protections, mitigate deleterious human impacts and restore forest structure.},
}

@article {pmid32358490,
year = {2020},
author = {Hale, KRS and Valdovinos, FS and Martinez, ND},
title = {Mutualism increases diversity, stability, and function of multiplex networks that integrate pollinators into food webs.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {2182},
pmid = {32358490},
issn = {2041-1723},
mesh = {Animals ; Biodiversity ; Biomass ; Computer Simulation ; Ecological and Environmental Phenomena ; *Food Chain ; Models, Biological ; Plants ; *Pollination ; *Symbiosis ; },
abstract = {Ecosystems are composed of complex networks of many species interacting in different ways. While ecologists have long studied food webs of feeding interactions, recent studies increasingly focus on mutualistic networks including plants that exchange food for reproductive services provided by animals such as pollinators. Here, we synthesize both types of consumer-resource interactions to better understand the controversial effects of mutualism on ecosystems at the species, guild, and whole-community levels. We find that consumer-resource mechanisms underlying plant-pollinator mutualisms can increase persistence, productivity, abundance, and temporal stability of both mutualists and non-mutualists in food webs. These effects strongly increase with floral reward productivity and are qualitatively robust to variation in the prevalence of mutualism and pollinators feeding upon resources in addition to rewards. This work advances the ability of mechanistic network theory to synthesize different types of interactions and illustrates how mutualism can enhance the diversity, stability, and function of complex ecosystems.},
}

Animals
Biodiversity
Biomass
Computer Simulation
Ecological and Environmental Phenomena
*Food Chain
Models, Biological
Plants
*Pollination
*Symbiosis

@article {pmid32760547,
year = {2020},
author = {Carraro, L and Bertuzzo, E and Fronhofer, EA and Furrer, R and Gounand, I and Rinaldo, A and Altermatt, F},
title = {Generation and application of river network analogues for use in ecology and evolution.},
journal = {Ecology and evolution},
volume = {10},
number = {14},
pages = {7537-7550},
doi = {10.1002/ece3.6479},
pmid = {32760547},
issn = {2045-7758},
abstract = {Several key processes in freshwater ecology are governed by the connectivity inherent to dendritic river networks. These have extensively been analyzed from a geomorphological and hydrological viewpoint, yet structures classically used in ecological modeling have been poorly representative of the structure of real river basins, often failing to capture well-known scaling features of natural rivers. Pioneering work identified optimal channel networks (OCNs) as spanning trees reproducing all scaling features characteristic of natural stream networks worldwide. While OCNs have been used to create landscapes for studies on metapopulations, biodiversity, and epidemiology, their generation has not been generally accessible.Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we provide the R-package OCNet. Owing to the stochastic process generating OCNs, multiple network replicas spanning the same surface can be built; this allows performing computational experiments whose results are irrespective of the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the package provides functions that aggregate OCNs into an arbitrary number of nodes, calculate several descriptors of river networks, and draw relevant network features.We describe the main functionalities of the package and its integration with other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.In conclusion, OCNet provides a powerful tool to generate realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems and enhances our knowledge on spatial processes in freshwater ecology in general.},
}

@article {pmid31791702,
year = {2020},
author = {Grebogi, C},
title = {Sudden regime shifts after apparent stasis: Comment on "Long transients in ecology: Theory and applications" by Andrew Morozov et al.},
journal = {Physics of life reviews},
volume = {32},
number = {},
pages = {41-43},
doi = {10.1016/j.plrev.2019.11.009},
pmid = {31791702},
issn = {1873-1457},
mesh = {Databases, Genetic ; *Ecology ; *Ecosystem ; Humans ; },
}

Databases, Genetic
*Ecology
*Ecosystem
Humans

@article {pmid31418863,
year = {2019},
author = {Serbin, SP and Wu, J and Ely, KS and Kruger, EL and Townsend, PA and Meng, R and Wolfe, BT and Chlus, A and Wang, Z and Rogers, A},
title = {From the Arctic to the tropics: multibiome prediction of leaf mass per area using leaf reflectance.},
journal = {The New phytologist},
volume = {224},
number = {4},
pages = {1557-1568},
doi = {10.1111/nph.16123},
pmid = {31418863},
issn = {1469-8137},
support = {WIS01809//U.S. Department of Agriculture/International ; NNX08AV07H/NASA/NASA/United States ; NNX12AQ28G/NASA/NASA/United States ; 1638720//National Science Foundation/International ; DE-SC0012704//Biological and Environmental Research/International ; NNX08AV07H/NASA/NASA/United States ; NNX12AQ28G/NASA/NASA/United States ; },
mesh = {Arctic Regions ; Databases, Factual ; Ecosystem ; *Models, Biological ; Models, Statistical ; Plant Leaves/*chemistry/*physiology ; Spatio-Temporal Analysis ; Spectrum Analysis/methods ; Tropical Climate ; },
abstract = {Leaf mass per area (LMA) is a key plant trait, reflecting tradeoffs between leaf photosynthetic function, longevity, and structural investment. Capturing spatial and temporal variability in LMA has been a long-standing goal of ecological research and is an essential component for advancing Earth system models. Despite the substantial variation in LMA within and across Earth's biomes, an efficient, globally generalizable approach to predict LMA is still lacking. We explored the capacity to predict LMA from leaf spectra across much of the global LMA trait space, with values ranging from 17 to 393 g m-2 . Our dataset contained leaves from a wide range of biomes from the high Arctic to the tropics, included broad- and needleleaf species, and upper- and lower-canopy (i.e. sun and shade) growth environments. Here we demonstrate the capacity to rapidly estimate LMA using only spectral measurements across a wide range of species, leaf age and canopy position from diverse biomes. Our model captures LMA variability with high accuracy and low error (R2 = 0.89; root mean square error (RMSE) = 15.45 g m-2). Our finding highlights the fact that the leaf economics spectrum is mirrored by the leaf optical spectrum, paving the way for this technology to predict the diversity of LMA in ecosystems across global biomes.},
}

Arctic Regions
Databases, Factual
Ecosystem
*Models, Biological
Models, Statistical
Plant Leaves/*chemistry/*physiology
Spatio-Temporal Analysis
Spectrum Analysis/methods
Tropical Climate

@article {pmid31215647,
year = {2019},
author = {Mencuccini, M and Rosas, T and Rowland, L and Choat, B and Cornelissen, H and Jansen, S and Kramer, K and Lapenis, A and Manzoni, S and Niinemets, Ü and Reich, P and Schrodt, F and Soudzilovskaia, N and Wright, IJ and Martínez-Vilalta, J},
title = {Leaf economics and plant hydraulics drive leaf : wood area ratios.},
journal = {The New phytologist},
volume = {224},
number = {4},
pages = {1544-1556},
doi = {10.1111/nph.15998},
pmid = {31215647},
issn = {1469-8137},
mesh = {Databases, Factual ; Plant Leaves/*physiology ; Trees/physiology ; Water/metabolism ; Wood/*physiology ; Xylem/physiology ; },
abstract = {Biomass and area ratios between leaves, stems and roots regulate many physiological and ecological processes. The Huber value Hv (sapwood area/leaf area ratio) is central to plant water balance and drought responses. However, its coordination with key plant functional traits is poorly understood, and prevents developing trait-based prediction models. Based on theoretical arguments, we hypothesise that global patterns in Hv of terminal woody branches can be predicted from variables related to plant trait spectra, that is plant hydraulics and size and leaf economics. Using a global compilation of 1135 species-averaged Hv , we show that Hv varies over three orders of magnitude. Higher Hv are seen in short small-leaved low-specific leaf area (SLA) shrubs with low Ks in arid relative to tall large-leaved high-SLA trees with high Ks in moist environments. All traits depend on climate but climatic correlations are stronger for explanatory traits than Hv . Negative isometry is found between Hv and Ks , suggesting a compensation to maintain hydraulic supply to leaves across species. This work identifies the major global drivers of branch sapwood/leaf area ratios. Our approach based on widely available traits facilitates the development of accurate models of above-ground biomass allocation and helps predict vegetation responses to drought.},
}

Databases, Factual
Plant Leaves/*physiology
Trees/physiology
Water/metabolism
Wood/*physiology
Xylem/physiology

@article {pmid32320389,
year = {2020},
author = {Wu, SL and Sánchez C, HM and Henry, JM and Citron, DT and Zhang, Q and Compton, K and Liang, B and Verma, A and Cummings, DAT and Le Menach, A and Scott, TW and Wilson, AL and Lindsay, SW and Moyes, CL and Hancock, PA and Russell, TL and Burkot, TR and Marshall, JM and Kiware, S and Reiner, RC and Smith, DL},
title = {Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology.},
journal = {PLoS computational biology},
volume = {16},
number = {4},
pages = {e1007446},
pmid = {32320389},
issn = {1553-7358},
mesh = {Algorithms ; Animals ; *Behavior, Animal ; Computational Biology ; Computer Simulation ; Culicidae/*physiology ; Disease Vectors ; Ecology ; Ecosystem ; Feeding Behavior ; Female ; Humans ; Malaria/*transmission ; Male ; Models, Theoretical ; Monte Carlo Method ; *Mosquito Vectors ; Oviposition ; Probability ; },
abstract = {Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new approach. Unlike most previous models, this framework considers the behavioral states and state transitions of adult mosquitoes through a sequence of activity bouts. We developed a new framework for individual-based simulation models called MBITES (Mosquito Bout-based and Individual-based Transmission Ecology Simulator). In MBITES, it is possible to build models that simulate the behavior and ecology of adult mosquitoes in exquisite detail on complex resource landscapes generated by spatial point processes. We also developed an ordinary differential equation model which is the Kolmogorov forward equations for models developed in MBITES under a specific set of simplifying assumptions. While mosquito infection and pathogen development are one possible part of a mosquito's state, that is not our main focus. Using extensive simulation using some models developed in MBITES, we show that vectorial capacity can be understood as an emergent property of simple behavioral algorithms interacting with complex resource landscapes, and that relative density or sparsity of resources and the need to search can have profound consequences for mosquito populations' capacity to transmit pathogens.},
}

Algorithms
Animals
*Behavior, Animal
Computational Biology
Computer Simulation
Culicidae/*physiology
Disease Vectors
Ecology
Ecosystem
Feeding Behavior
Female
Humans
Malaria/*transmission
Male
Models, Theoretical
Monte Carlo Method
*Mosquito Vectors
Oviposition
Probability

@article {pmid32678108,
year = {2020},
author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S},
title = {Author Correction: A global database of Holocene paleotemperature records.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {246},
doi = {10.1038/s41597-020-00584-1},
pmid = {32678108},
issn = {2052-4463},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid32671561,
year = {2020},
author = {Nautiyal, S and Goswami, M and Nidamanuri, RR and Hoffmann, EM and Buerkert, A},
title = {Structure and composition of field margin vegetation in the rural-urban interface of Bengaluru, India: a case study on an unexplored dimension of agroecosystems.},
journal = {Environmental monitoring and assessment},
volume = {192},
number = {8},
pages = {520},
doi = {10.1007/s10661-020-08428-6},
pmid = {32671561},
issn = {1573-2959},
support = {BT/IN/GERMAN/DFG/14/BVCR/2016//Department of Biotechnology, Ministry of Science and Technology/ ; },
mesh = {Agriculture ; Biodiversity ; *Conservation of Natural Resources ; Ecosystem ; *Environmental Monitoring ; Europe ; Humans ; India ; },
abstract = {Field margin vegetation (FMV) refers to the plant community in the interface between agriculture and natural environments. Substantial work has been carried out on the management of field margins in European countries with the aim of conserving field-level biodiversity and enhancing agronomic benefits. India, instead, is lagging behind in the assessment of FMV and formulating subsequent management strategies for biodiversity conservation at the field boundaries. This study is a first step to better understand the structural and functional dimensions of field margin vegetation along an agricultural transformation gradient near the megacity of Bengaluru, India. Empirical field studies along with the detection of vegetation change using remote sensing and geo-informatics technique were used to record information on field margin vegetation. The phytosociological study, revealed a total of 81 species, comprising 29 species of trees, 21 shrubs and 31 herbs at the field margins of six selected villages of northern Bengaluru. Randomly selected 355 field boundaries were delineated from high-resolution Worldview 3 images for the year 2018 and from Google Earth images for the year 2004-2005. The FMV area was around to 85.40 ha in 2004-2005 but declined to 76.69 ha in 2017-2018. The survey also indicated that local farmers have in-depth ecological knowledge on the importance of FMV in ensuring a sustainable flow of resources within the agricultural landscape. The results demonstrate that rural and transition zones of the study area have higher dominance of planted tree species on the margins, whereas urban zone exhibits comparatively uniform dominance for all species. Our study also highlights the need for conservation of FMV to ensure agroecosystem health as a prerequisite for sustainable socioecological development.},
}

Agriculture
Biodiversity
*Conservation of Natural Resources
Ecosystem
*Environmental Monitoring
Europe
Humans
India

@article {pmid32441459,
year = {2020},
author = {Han, BA and O'Regan, SM and Paul Schmidt, J and Drake, JM},
title = {Integrating data mining and transmission theory in the ecology of infectious diseases.},
journal = {Ecology letters},
volume = {23},
number = {8},
pages = {1178-1188},
doi = {10.1111/ele.13520},
pmid = {32441459},
issn = {1461-0248},
support = {1717282//Division of Environmental Biology/ ; //NIMBioS/ ; },
mesh = {Animals ; Data Mining ; Disease Outbreaks ; Humans ; Models, Theoretical ; *Rodentia ; Zoonoses/*epidemiology ; },
abstract = {Our understanding of ecological processes is built on patterns inferred from data. Applying modern analytical tools such as machine learning to increasingly high dimensional data offers the potential to expand our perspectives on these processes, shedding new light on complex ecological phenomena such as pathogen transmission in wild populations. Here, we propose a novel approach that combines data mining with theoretical models of disease dynamics. Using rodents as an example, we incorporate statistical differences in the life history features of zoonotic reservoir hosts into pathogen transmission models, enabling us to bound the range of dynamical phenomena associated with hosts, based on their traits. We then test for associations between equilibrium prevalence, a key epidemiological metric and data on human outbreaks of rodent-borne zoonoses, identifying matches between empirical evidence and theoretical predictions of transmission dynamics. We show how this framework can be generalized to other systems through a rubric of disease models and parameters that can be derived from empirical data. By linking life history components directly to their effects on disease dynamics, our mining-modelling approach integrates machine learning and theoretical models to explore mechanisms in the macroecology of pathogen transmission and their consequences for spillover infection to humans.},
}

Animals
Data Mining
Disease Outbreaks
Humans
Models, Theoretical
*Rodentia
Zoonoses/*epidemiology

@article {pmid31840098,
year = {2019},
author = {Montesinos-Navarro, A and Díaz, G and Torres, P and Caravaca, F and Roldán, A},
title = {Phylogenetic rewiring in mycorrhizal-plant interaction networks increases community stability in naturally fragmented landscapes.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {452},
pmid = {31840098},
issn = {2399-3642},
mesh = {Computational Biology/methods ; Ecosystem ; Microbiota ; Mycorrhizae/*classification/*genetics ; *Phylogeny ; Plants/*classification/*genetics ; Reproducibility of Results ; *Symbiosis ; },
abstract = {Although ecological networks are usually considered a static representation of species' interactions, the interactions can change when the preferred partners are absent (rewiring). In mutualistic networks, rewiring with non-preferred partners can palliate extinction cascades, contributing to communities' stability. In spite of its significance, whether general patterns can shape the rewiring of ecological interactions remains poorly understood. Here, we show a phylogenetic constraint in the rewiring of mycorrhizal networks, so that rewired interactions (i.e., with non-preferred hosts) tend to involve close relatives of preferred hosts. Despite this constraint, rewiring increases the robustness of the fungal community to the simulated loss of their host species. We identify preferred and non-preferred hosts based on the probability that, when the two partners co-occur, they actually interact. Understanding general patterns in the rewiring of interactions can improve our predictions of community responses to interactions' loss, which influences how global changes will affect ecosystem stability.},
}

Computational Biology/methods
Ecosystem
Microbiota
Mycorrhizae/*classification/*genetics
*Phylogeny
Plants/*classification/*genetics
Reproducibility of Results
*Symbiosis

@article {pmid32614827,
year = {2020},
author = {Ferguson, AW and Muloi, D and Ngatia, DK and Kiongo, W and Kimuyu, DM and Webala, PW and Olum, MO and Muturi, M and Thumbi, SM and Woodroffe, R and Murugi, L and Fèvre, EM and Murray, S and Martins, DJ},
title = {Volunteer based approach to dog vaccination campaigns to eliminate human rabies: Lessons from Laikipia County, Kenya.},
journal = {PLoS neglected tropical diseases},
volume = {14},
number = {7},
pages = {e0008260},
doi = {10.1371/journal.pntd.0008260},
pmid = {32614827},
issn = {1935-2735},
abstract = {BACKGROUND: An estimated 59,000 people die from rabies annually, with 99% of those deaths attributable to bites from domestic dogs (Canis lupus familiaris). This preventable Neglected Tropical Disease has a large impact across continental Africa, especially for rural populations living in close contact with livestock and wildlife. Mass vaccinations of domestic dogs are effective at eliminating rabies but require large amounts of resources, planning, and political will to implement. Grassroots campaigns provide an alternative method to successful implementation of rabies control but remain understudied in their effectiveness to eliminate the disease from larger regions.

We report on the development, implementation, and effectiveness of a grassroots mass dog rabies vaccination campaign in Kenya, the Laikipia Rabies Vaccination Campaign. During 2015-2017, a total of 13,155 domestic dogs were vaccinated against rabies in 17 communities covering approximately 1500 km2. Based on an estimated population size of 34,275 domestic dogs, percent coverages increased across years, from 2% in 2015 to 24% in 2017, with only 3 of 38 community-years of vaccination exceeding the 70% target. The average cost of vaccinating an animal was $3.44 USD with in-kind contributions and $7.44 USD without in-kind contributions.

CONCLUSIONS/SIGNIFICANCE: The evolution of the Laikipia Rabies Vaccination Campaign from a localized volunteer-effort to a large-scale program attempting to eliminate rabies at the landscape scale provides a unique opportunity to examine successes, failures, and challenges facing grassroots campaigns. Success, in the form of vaccinating more dogs across the study area, was relatively straightforward to achieve. However, lack of effective post-vaccination monitoring and education programs, limited funding, and working in diverse community types appeared to hinder achievement of 70% coverage levels. These results indicate that grassroots campaigns will inevitably be faced with a philosophical question regarding the value of local impacts versus their contributions to a larger effort to eliminate rabies at the regional, country, or global scale.},
}

@article {pmid32608729,
year = {2020},
author = {Zhu, LY and Chen, YY and Liu, J and Wang, YW and Wang, CR and Wei, YS and Zhang, YX},
title = {[Spatio-temporal Evolution and Relationship of Water Environment Quality and Phytoplankton Community in Wenyu River].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {41},
number = {2},
pages = {702-712},
doi = {10.13227/j.hjkx.201906207},
pmid = {32608729},
issn = {0250-3301},
abstract = {The Wenyu River is an important ecological corridor of Beijing. In this study, the spatio-temporal dynamics of water quality and phytoplankton community in the Wenyu River in 2006, 2011, and 2018, as well as their relationship were thoroughly analyzed by historical data analysis and field surveys. Results show that the water quality in the Wenyu River improved significantly from serious pollution owing to pollution containment. The major water pollutant has shifted from ammonia nitrogen (NH4+-N) to total nitrogen (TN). Compared with 2011, the average multiple of NH4+-N and total nitrogen TN exceeding the national standard were reduced by factors of 0.29-0.33 and 2.77-2.39, respectively, in 2018. The average concentration of NH4+-N and TN decreased from 15.52-19.16 mg·L-1 and 20.21-19.58 mg·L-1 in 2011 to 1.93-2.66 mg·L-1 and 5.66-6.79 mg·L-1 in 2018. Moreover, dissolved oxygen (DO) and NH4+-N concentrations in the Wenyu River and its tributaries, the Qinghe River, almost met requirements of their water function zoning target. Corresponding with the water quality improvement, the phytoplankton and community species increased dramatically. Phytoplankton species increased from 6 to 8 phyla, as well as community species. The dominant species changed from Chlorophyta in 2006 to the Cyanophyta in 2011, then to Bacillariophyta in 2018. The Shannon-Wiener diversity index (H') and evenness Pielou index (J) had improved. However, the major dominant species such as Cyclotella and Melosira persisted, and the Wenyu River was still in the eutrophication state in 2018. Statistical analysis results indicated that Cyanophyta, Bacillariophyta, and other algae abundance were significantly correlated with DO, pH, NH4+-N, TN, and TP.},
}

@article {pmid32586012,
year = {2020},
author = {Zhou, Y and Rodriguez, J and Fisher, N and Catullo, RA},
title = {Ecological Drivers and Sex-Based Variation in Body Size and Shape in the Queensland Fruit Fly, Bactrocera tryoni (Diptera: Tephritidae).},
journal = {Insects},
volume = {11},
number = {6},
pages = {},
doi = {10.3390/insects11060390},
pmid = {32586012},
issn = {2075-4450},
abstract = {The Queensland fruit fly (Bactrocera tryoni; Q-fly) is an Australian endemic horticultural pest species, which has caused enormous economic losses. It has the potential to expand its range to currently Q-fly-free areas and poses a serious threat to the Australian horticultural industry. A large number of studies have investigated the correlation between environmental factors and Q-fly development, reproduction, and expansion. However, it is still not clear how Q-fly morphological traits vary with the environment. Our study focused on three morphological traits (body size, wing shape, and fluctuating asymmetry) in Q-fly samples collected from 1955 to 1965. We assessed how these traits vary by sex, and in response to latitude, environmental variables, and geographic distance. First, we found sexual dimorphism in body size and wing shape, but not in fluctuating asymmetry. Females had a larger body size but shorter and wider wings than males, which may be due to reproductive and/or locomotion differences between females and males. Secondly, the body size of Q-flies varied with latitude, which conforms to Bergmann's rule. Finally, we found Q-fly wing shape was more closely related to temperature rather than aridity, and low temperature and high aridity may lead to high asymmetry in Q-fly populations.},
}

@article {pmid32572035,
year = {2020},
author = {Cansler, CA and Hood, SM and Varner, JM and van Mantgem, PJ and Agne, MC and Andrus, RA and Ayres, MP and Ayres, BD and Bakker, JD and Battaglia, MA and Bentz, BJ and Breece, CR and Brown, JK and Cluck, DR and Coleman, TW and Corace, RG and Covington, WW and Cram, DS and Cronan, JB and Crouse, JE and Das, AJ and Davis, RS and Dickinson, DM and Fitzgerald, SA and Fulé, PZ and Ganio, LM and Grayson, LM and Halpern, CB and Hanula, JL and Harvey, BJ and Kevin Hiers, J and Huffman, DW and Keifer, M and Keyser, TL and Kobziar, LN and Kolb, TE and Kolden, CA and Kopper, KE and Kreitler, JR and Kreye, JK and Latimer, AM and Lerch, AP and Lombardero, MJ and McDaniel, VL and McHugh, CW and McMillin, JD and Moghaddas, JJ and O'Brien, JJ and Perrakis, DDB and Peterson, DW and Prichard, SJ and Progar, RA and Raffa, KF and Reinhardt, ED and Restaino, JC and Roccaforte, JP and Rogers, BM and Ryan, KC and Safford, HD and Santoro, AE and Shearman, TM and Shumate, AM and Sieg, CH and Smith, SL and Smith, RJ and Stephenson, NL and Stuever, M and Stevens, JT and Stoddard, MT and Thies, WG and Vaillant, NM and Weiss, SA and Westlind, DJ and Woolley, TJ and Wright, MC},
title = {The Fire and Tree Mortality Database, for empirical modeling of individual tree mortality after fire.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {194},
doi = {10.1038/s41597-020-0522-7},
pmid = {32572035},
issn = {2052-4463},
abstract = {Wildland fires have a multitude of ecological effects in forests, woodlands, and savannas across the globe. A major focus of past research has been on tree mortality from fire, as trees provide a vast range of biological services. We assembled a database of individual-tree records from prescribed fires and wildfires in the United States. The Fire and Tree Mortality (FTM) database includes records from 164,293 individual trees with records of fire injury (crown scorch, bole char, etc.), tree diameter, and either mortality or top-kill up to ten years post-fire. Data span 142 species and 62 genera, from 409 fires occurring from 1981-2016. Additional variables such as insect attack are included when available. The FTM database can be used to evaluate individual fire-caused mortality models for pre-fire planning and post-fire decision support, to develop improved models, and to explore general patterns of individual fire-induced tree death. The database can also be used to identify knowledge gaps that could be addressed in future research.},
}

@article {pmid32019442,
year = {2020},
author = {Liddell, C and Morgan, ER and Bull, K and Ioannou, CC},
title = {Response to resources and parasites depends on health status in extensively grazed sheep.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1920},
pages = {20192905},
pmid = {32019442},
issn = {1471-2954},
support = {BB/S014748/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Ecology ; Ecosystem ; Geographic Information Systems ; Health Status ; *Host-Parasite Interactions ; Parasites/*physiology ; Sheep/*parasitology ; },
abstract = {A fundamental question in animal ecology is how an individual's internal state and the external environment together shape species distributions across habitats. The increasing availability of biologgers is driving a revolution in answering this question in a wide range of species. In this study, the position of sheep (Ovis aries) from Global Positioning System collars was integrated with remote sensing data, field sampling of parasite distributions, and parasite load and health measures for each tagged individual. This allowed inter-individual variation in habitat use to be examined. Once controlling for a positive relationship between vegetation productivity and tick abundance, healthier individuals spent more of their time at sites with higher vegetation productivity, while less healthy individuals showed a stronger (negative) response to tick abundance. These trends are likely to represent a trade-off in foraging decisions that vary between individuals based on their health status. Given the rarity of studies that explore how animal distributions are affected by health and external factors, we demonstrate the value of integrating biologging technology with remote sensing data, traditional ecological sampling and individual measures of animal health. Our study, using extensively grazed sheep as a model system, opens new possibilities to study free-living grazing systems.},
}

Animals
Ecology
Ecosystem
Geographic Information Systems
Health Status
*Host-Parasite Interactions
Parasites/*physiology
Sheep/*parasitology

@article {pmid32556537,
year = {2020},
author = {Piross, IS and Siliwal, M and Kumar, RS and Palatitz, P and Solt, S and Borbáth, P and Vili, N and Magonyi, N and Vas, Z and Rózsa, L and Harnos, A and Fehérvári, P},
title = {Sex interacts with age-dependent change in the abundance of lice-infesting Amur Falcons (Falco amurensis).},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00436-020-06753-w},
pmid = {32556537},
issn = {1432-1955},
support = {GINOP 2.3.2-15- 2016-00057//European Regional Development Fund/ ; },
abstract = {Sex-biassed and age-biassed parasite infections are common in nature, including ectoparasites-vertebrate host systems. We investigated the effect of Amur Falcons' sex, age and body size on the abundance of their lice at a migratory stopover site, where the falcons' habitat use and behaviour are more homogeneous across sex and age categories than during the breeding season. We sampled Amur Falcons in Nagaland, India at major roosting sites in 2016. We applied generalized linear models (with negative binomial distribution and log-link) to model the abundance of their two most numerous lice (Colpocephalum subzerafae and Degeeriella rufa) using the host age category (juvenile or adult) and wing length, both in interaction with sex, as explanatory variables. The abundance of C. subzerafae was only affected by host age, being nearly four times higher on juveniles than on adults. Juveniles were also more infested with D. rufa than the adults. Additionally, the abundance of the latter species was lower on adult male Falcons as compared to adult females. A juvenile bias in ectoparasite infestations is common in nature, probably due to juveniles being immunologically naïve, more resource-limited and may be inexperienced in body maintenance behaviours like preening and grooming. On the other hand, female-biassed infestations are much rarer than male-biassed infestations. We briefly discuss the possible causes of female-biassed infestations on Amur Falcons reported here, and in the closely related Red-footed Falcon and Lesser Kestrel as reported in the literature.},
}

@article {pmid32554569,
year = {2020},
author = {Anderegg, WRL and Trugman, AT and Badgley, G and Anderson, CM and Bartuska, A and Ciais, P and Cullenward, D and Field, CB and Freeman, J and Goetz, SJ and Hicke, JA and Huntzinger, D and Jackson, RB and Nickerson, J and Pacala, S and Randerson, JT},
title = {Climate-driven risks to the climate mitigation potential of forests.},
journal = {Science (New York, N.Y.)},
volume = {368},
number = {6497},
pages = {},
doi = {10.1126/science.aaz7005},
pmid = {32554569},
issn = {1095-9203},
abstract = {Forests have considerable potential to help mitigate human-caused climate change and provide society with many cobenefits. However, climate-driven risks may fundamentally compromise forest carbon sinks in the 21st century. Here, we synthesize the current understanding of climate-driven risks to forest stability from fire, drought, biotic agents, and other disturbances. We review how efforts to use forests as natural climate solutions presently consider and could more fully embrace current scientific knowledge to account for these climate-driven risks. Recent advances in vegetation physiology, disturbance ecology, mechanistic vegetation modeling, large-scale ecological observation networks, and remote sensing are improving current estimates and forecasts of the risks to forest stability. A more holistic understanding and quantification of such risks will help policy-makers and other stakeholders effectively use forests as natural climate solutions.},
}

@article {pmid32549034,
year = {2020},
author = {Duarte, ME and Vigil-Hayes, M and Littletree, S and Belarde-Lewis, M},
title = {"Of Course, Data Can Never Fully Represent Reality": Assessing the Relationship between "Indigenous Data" and "Indigenous Knowledge," "Traditional Ecological Knowledge," and "Traditional Knowledge".},
journal = {Human biology},
volume = {91},
number = {3},
pages = {163-178},
doi = {10.13110/humanbiology.91.3.03},
pmid = {32549034},
issn = {1534-6617},
abstract = {Multiple terms describe Indigenous peoples' creative expressions, including "Indigenous knowledge" (IK), "traditional ecological knowledge" (TEK), "traditional knowledge" (TK), and increasingly, "Indigenous data" (ID). Variation in terms contributes to disciplinary divides, challenges in organizing and finding prior studies about Indigenous peoples' creative expressions, and intellectually divergent chains of reference. The authors applied a decolonial, digital, feminist, ethics-of-care approach to citation analysis of records about Indigenous peoples knowledge and data, including network analyses of author-generated keywords and research areas, and content analysis of peer-reviewed studies about ID. Results reveal ambiguous uses of the term "Indigenous data"; the influence of ecology and environmental studies in research areas and topics associated with IK, TEK, and TK; and the influence of public administration and governance studies in research areas and topics associated with ID studies. Researchers of ID would benefit from applying a more nuanced and robust vocabulary, one informed by studies of IK, TEK, and TK. Researchers of TEK and TK would benefit from the more people-centered approaches of IK. Researchers and systems designers who work with data sets can practice relational accountability by centering the Indigenous peoples from whom observations are sourced, combining narrative methodologies with computational methods to sustain the holism favored by Indigenous science and the relationality of Indigenous peoples.},
}

@article {pmid32541861,
year = {2020},
author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S},
title = {Publisher Correction: A global database of Holocene paleotemperature records.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {183},
doi = {10.1038/s41597-020-0515-6},
pmid = {32541861},
issn = {2052-4463},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid32541802,
year = {2020},
author = {Birk, S and Chapman, D and Carvalho, L and Spears, BM and Andersen, HE and Argillier, C and Auer, S and Baattrup-Pedersen, A and Banin, L and Beklioğlu, M and Bondar-Kunze, E and Borja, A and Branco, P and Bucak, T and Buijse, AD and Cardoso, AC and Couture, RM and Cremona, F and de Zwart, D and Feld, CK and Ferreira, MT and Feuchtmayr, H and Gessner, MO and Gieswein, A and Globevnik, L and Graeber, D and Graf, W and Gutiérrez-Cánovas, C and Hanganu, J and Işkın, U and Järvinen, M and Jeppesen, E and Kotamäki, N and Kuijper, M and Lemm, JU and Lu, S and Solheim, AL and Mischke, U and Moe, SJ and Nõges, P and Nõges, T and Ormerod, SJ and Panagopoulos, Y and Phillips, G and Posthuma, L and Pouso, S and Prudhomme, C and Rankinen, K and Rasmussen, JJ and Richardson, J and Sagouis, A and Santos, JM and Schäfer, RB and Schinegger, R and Schmutz, S and Schneider, SC and Schülting, L and Segurado, P and Stefanidis, K and Sures, B and Thackeray, SJ and Turunen, J and Uyarra, MC and Venohr, M and von der Ohe, PC and Willby, N and Hering, D},
title = {Impacts of multiple stressors on freshwater biota across spatial scales and ecosystems.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-020-1216-4},
pmid = {32541802},
issn = {2397-334X},
support = {603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; 603378//European Commission (EC)/ ; },
abstract = {Climate and land-use change drive a suite of stressors that shape ecosystems and interact to yield complex ecological responses (that is, additive, antagonistic and synergistic effects). We know little about the spatial scales relevant for the outcomes of such interactions and little about effect sizes. These knowledge gaps need to be filled to underpin future land management decisions or climate mitigation interventions for protecting and restoring freshwater ecosystems. This study combines data across scales from 33 mesocosm experiments with those from 14 river basins and 22 cross-basin studies in Europe, producing 174 combinations of paired-stressor effects on a biological response variable. Generalized linear models showed that only one of the two stressors had a significant effect in 39% of the analysed cases, 28% of the paired-stressor combinations resulted in additive effects and 33% resulted in interactive (antagonistic, synergistic, opposing or reversal) effects. For lakes, the frequencies of additive and interactive effects were similar for all spatial scales addressed, while for rivers these frequencies increased with scale. Nutrient enrichment was the overriding stressor for lakes, with effects generally exceeding those of secondary stressors. For rivers, the effects of nutrient enrichment were dependent on the specific stressor combination and biological response variable. These results vindicate the traditional focus of lake restoration and management on nutrient stress, while highlighting that river management requires more bespoke management solutions.},
}

@article {pmid31484218,
year = {2019},
author = {Goodman, KR and Prost, S and Bi, K and Brewer, MS and Gillespie, RG},
title = {Host and geography together drive early adaptive radiation of Hawaiian planthoppers.},
journal = {Molecular ecology},
volume = {28},
number = {19},
pages = {4513-4528},
pmid = {31484218},
issn = {1365-294X},
support = {S10 OD018174/OD/NIH HHS/United States ; },
mesh = {*Adaptation, Physiological ; Animals ; *Computational Biology ; Ecology ; Exons/genetics ; Genetics, Population ; Geography ; Hawaii ; Hemiptera/genetics/*physiology ; Host Specificity ; Islands ; Male ; *Metagenomics ; Phylogeny ; Plants/*parasitology ; Species Specificity ; *Transcriptome ; },
abstract = {The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects "escape and radiate" on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co-occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.},
}

*Adaptation, Physiological
Animals
*Computational Biology
Ecology
Exons/genetics
Genetics, Population
Geography
Hawaii
Hemiptera/genetics/*physiology
Host Specificity
Islands
Male
*Metagenomics
Phylogeny
Plants/*parasitology
Species Specificity
*Transcriptome

@article {pmid32151872,
year = {2020},
author = {Wan, Y and Jiang, B and Wei, D and Ma, Y},
title = {Ecological criteria for zinc in Chinese soil as affected by soil properties.},
journal = {Ecotoxicology and environmental safety},
volume = {194},
number = {},
pages = {110418},
doi = {10.1016/j.ecoenv.2020.110418},
pmid = {32151872},
issn = {1090-2414},
mesh = {Agriculture ; China ; Databases, Factual ; Ecotoxicology ; Environmental Monitoring/*methods ; Models, Theoretical ; Risk Assessment ; *Soil/chemistry/standards ; Soil Pollutants/*analysis ; Zinc/*analysis ; },
abstract = {The increasing accumulation of zinc (Zn) in agricultural soils has led to the need to assess the potential risk of this element for terrestrial organisms. However, the soil ecological criteria in agricultural soil as a function of soil properties have been sparsely reported. In the present study, we derived the ecological criteria (expressed as predicted no effect concentration (PNEC)) for Zn in soils, based on ecotoxicity data for 19 terrestrial species in Chinese soils, the effect of soil properties on Zn ecotoxicity, differences in species sensitivity, and differences between laboratory and realistic field conditions. First, all ecotoxicity data of Zn for terrestrial organisms in Chinese soils were collected and filtered with given criteria to obtain reliable database. Second, the ecotoxicity data were normalized using Zn ecotoxicity predictive models to eliminate the effect of soil properties on Zn ecotoxicity, and corrected with leaching and aging factors to minimize the differences in Zn ecotoxicity under laboratory and field conditions. Then, species sensitivity distribution (SSD) curves were generated with a Burr Ⅲ function based on corrected ecotoxicity data. The concentration of Zn in soil that provides ecological safety for (100 - x)% of species (HCx), was calculated from the SSD curve and HC5 was used for estimation of PNEC. Finally, we developed the predictive models for HCx by quantifying the relationship between the Zn HCx and soil properties. Results showed that soil pH was the most crucial factor affecting Zn HCx values, with HC5 values varying from 38.3 mg/kg in an acidic soil to 263.3 mg/kg in an alkaline calcareous soil. Both the two-factor (soil pH and OC) and the three-factor (soil pH, OC and CEC) models predicted HCx values well, with determination coefficients (R2) of 0.941-0.959 and 0.978-0.982, respectively. This study provides a scientific and reliable basis for the improvement of ecological risk assessment and the establishment of soil environmental quality standards.},
}

Agriculture
China
Databases, Factual
Ecotoxicology
Environmental Monitoring/*methods
Models, Theoretical
Risk Assessment
*Soil/chemistry/standards
Soil Pollutants/*analysis
Zinc/*analysis

@article {pmid32518318,
year = {2020},
author = {Wang, E and Zhang, D and Braun, MS and Hotz-Wagenblatt, A and Pärt, T and Arlt, D and Schmaljohann, H and Bairlein, F and Lei, F and Wink, M},
title = {Can Mitogenomes of the Northern Wheatear (Oenanthe oenanthe) Reconstruct Its Phylogeography and Reveal the Origin of Migrant Birds?.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {9290},
doi = {10.1038/s41598-020-66287-0},
pmid = {32518318},
issn = {2045-2322},
abstract = {The Northern Wheatear (Oenanthe oenanthe, including the nominate and the two subspecies O. o. leucorhoa and O. o. libanotica) and the Seebohm's Wheatear (Oenanthe seebohmi) are today regarded as two distinct species. Before, all four taxa were regarded as four subspecies of the Northern Wheatear. Their classification has exclusively been based on ecological and morphological traits, while their molecular characterization is still missing. With this study, we used next-generation sequencing to assemble 117 complete mitochondrial genomes covering O. o. oenanthe, O. o. leucorhoa and O. seebohmi. We compared the resolution power of each individual mitochondrial marker and concatenated marker sets to reconstruct the phylogeny and estimate speciation times of three taxa. Moreover, we tried to identify the origin of migratory wheatears caught on Helgoland (Germany) and on Crete (Greece). Mitogenome analysis revealed two different ancient lineages that separated around 400,000 years ago. Both lineages consisted of a mix of subspecies and species. The phylogenetic trees, as well as haplotype networks are incongruent with the present morphology-based classification. Mitogenome could not distinguish these presumed species. The genetic panmixia among present populations and taxa might be the consequence of mitochondrial introgression between ancient wheatear populations.},
}

@article {pmid31067326,
year = {2019},
author = {Fitak, RR and Antonides, JD and Baitchman, EJ and Bonaccorso, E and Braun, J and Kubiski, S and Chiu, E and Fagre, AC and Gagne, RB and Lee, JS and Malmberg, JL and Stenglein, MD and Dusek, RJ and Forgacs, D and Fountain-Jones, NM and Gilbertson, MLJ and Worsley-Tonks, KEL and Funk, WC and Trumbo, DR and Ghersi, BM and Grimaldi, W and Heisel, SE and Jardine, CM and Kamath, PL and Karmacharya, D and Kozakiewicz, CP and Kraberger, S and Loisel, DA and McDonald, C and Miller, S and O'Rourke, D and Ott-Conn, CN and Páez-Vacas, M and Peel, AJ and Turner, WC and VanAcker, MC and VandeWoude, S and Pecon-Slattery, J},
title = {The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise.},
journal = {The Journal of heredity},
volume = {110},
number = {3},
pages = {261-274},
doi = {10.1093/jhered/esz001},
pmid = {31067326},
issn = {1465-7333},
mesh = {Animal Diseases/epidemiology/*etiology/transmission ; Animals ; *Animals, Wild ; Biodiversity ; Biological Evolution ; Computational Biology/methods ; Disease Susceptibility ; Ecology ; Environment ; Genome ; *Genomics/methods ; Host-Pathogen Interactions/genetics ; Humans ; *Research ; },
abstract = {The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented "Big Data" tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural "Genomics of Disease in Wildlife" workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) "Improving communication," 2) "Methodological and analytical advancements," 3) "Translation into practice," 4) "Integrating landscape ecology and genomics," and 5) "Emerging new questions." Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.},
}

Animal Diseases/epidemiology/*etiology/transmission
Animals
*Animals, Wild
Biodiversity
Biological Evolution
Computational Biology/methods
Disease Susceptibility
Ecology
Environment
Genome
*Genomics/methods
Host-Pathogen Interactions/genetics
Humans
*Research

@article {pmid30980778,
year = {2019},
author = {Bay, RA and Taylor, EB and Schluter, D},
title = {Parallel introgression and selection on introduced alleles in a native species.},
journal = {Molecular ecology},
volume = {28},
number = {11},
pages = {2802-2813},
doi = {10.1111/mec.15097},
pmid = {30980778},
issn = {1365-294X},
mesh = {*Alleles ; Animals ; Canada ; Gene Frequency/genetics ; Gene Ontology ; Geography ; *Inbreeding ; Oncorhynchus/genetics ; Polymorphism, Single Nucleotide/genetics ; *Selection, Genetic ; Species Specificity ; United States ; },
abstract = {As humans cause the redistribution of species ranges, hybridization between previously allopatric species is on the rise. Such hybridization can have complex effects on overall fitness of native species as new allelic combinations are tested. Widespread species introductions provide a unique opportunity to study selection on introgressed alleles in independent, replicated populations. We examined selection on alleles that repeatedly introgressed from introduced rainbow trout (Oncorhynchus mykiss) into native westslope cutthroat trout (Oncorhynchus clarkii lewisi) populations in western Canada. We found that the degree of introgression of individual single nucleotide polymorphisms from the invasive species into the native is correlated between independent watersheds. A number of rainbow trout alleles have repeatedly swept to high frequency in native populations, suggesting parallel adaptive advantages. Using simulations, we estimated large selection coefficients up to 0.05 favoring several rainbow trout alleles in the native background. Although previous studies have found reduced hybrid fitness and genome-wide resistance to introgression in westslope cutthroat trout, our results suggest that some introduced genomic regions are strongly favored by selection. Our study demonstrates the utility of replicated introductions as case studies for understanding parallel adaptation and the interactions between selection and introgression across the genome. We suggest that understanding this variation, including consideration of beneficial alleles, can inform management strategies for hybridizing species.},
}

*Alleles
Animals
Canada
Gene Frequency/genetics
Gene Ontology
Geography
*Inbreeding
Oncorhynchus/genetics
Polymorphism, Single Nucleotide/genetics
*Selection, Genetic
Species Specificity
United States

@article {pmid31290101,
year = {2019},
author = {Tian, D and Yan, Z and Ma, S and Ding, Y and Luo, Y and Chen, Y and Du, E and Han, W and Kovacs, ED and Shen, H and Hu, H and Kattge, J and Schmid, B and Fang, J},
title = {Family-level leaf nitrogen and phosphorus stoichiometry of global terrestrial plants.},
journal = {Science China. Life sciences},
volume = {62},
number = {8},
pages = {1047-1057},
doi = {10.1007/s11427-019-9584-1},
pmid = {31290101},
issn = {1869-1889},
mesh = {Databases, Factual ; Ecosystem ; Models, Statistical ; Nitrogen/*metabolism ; Phosphorus/*metabolism ; Photosynthesis ; Phylogeny ; Plant Leaves/*chemistry/*metabolism ; Plants/*metabolism ; Soil ; Stereoisomerism ; Temperature ; },
abstract = {Leaf nitrogen (N) and phosphorus (P) concentrations are critical for photosynthesis, growth, reproduction and other ecological processes of plants. Previous studies on large-scale biogeographic patterns of leaf N and P stoichiometric relationships were mostly conducted using data pooled across taxa, while family/genus-level analyses are rarely reported. Here, we examined global patterns of family-specific leaf N and P stoichiometry using a global data set of 12,716 paired leaf N and P records which includes 204 families, 1,305 genera, and 3,420 species. After determining the minimum size of samples (i.e., 35 records), we analyzed leaf N and P concentrations, N:P ratios and N∼P scaling relationships of plants for 62 families with 11,440 records. The numeric values of leaf N and P stoichiometry varied significantly across families and showed diverse trends along gradients of mean annual temperature (MAT) and mean annual precipitation (MAP). The leaf N and P concentrations and N:P ratios of 62 families ranged from 6.11 to 30.30 mg g-1, 0.27 to 2.17 mg g-1, and 10.20 to 35.40, respectively. Approximately 1/3-1/2 of the families (22-35 of 62) showed a decrease in leaf N and P concentrations and N:P ratios with increasing MAT or MAP, while the remainder either did not show a significant trend or presented the opposite pattern. Family-specific leaf N∼P scaling exponents did not converge to a certain empirical value, with a range of 0.307-0.991 for 54 out of 62 families which indicated a significant N∼P scaling relationship. Our results for the first time revealed large variation in the family-level leaf N and P stoichiometry of global terrestrial plants and that the stoichiometric relationships for at least one-third of the families were not consistent with the global trends reported previously. The numeric values of the family-specific leaf N and P stoichiometry documented in the current study provide critical synthetic parameters for biogeographic modeling and for further studies on the physiological and ecological mechanisms underlying the nutrient use strategies of plants from different phylogenetic taxa.},
}

Databases, Factual
Ecosystem
Models, Statistical
Nitrogen/*metabolism
Phosphorus/*metabolism
Photosynthesis
Phylogeny
Plant Leaves/*chemistry/*metabolism
Plants/*metabolism
Soil
Stereoisomerism
Temperature

@article {pmid32396806,
year = {2020},
author = {Herren, CM},
title = {Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities.},
journal = {Proceedings. Biological sciences},
volume = {287},
number = {1927},
pages = {20192945},
doi = {10.1098/rspb.2019.2945},
pmid = {32396806},
issn = {1471-2954},
abstract = {The strength of biotic interactions within an ecological community affects the susceptibility of the community to invasion by introduced taxa. In microbial communities, cross-feeding is a widespread type of biotic interaction that has the potential to affect community assembly and stability. Yet, there is little understanding of how the presence of cross-feeding within a community affects invasion risk. Here, I develop a metabolite-explicit model where native microbial taxa interact through both cross-feeding and competition for metabolites. I use this model to study how the strength of biotic interactions, especially cross-feeding, influence whether an introduced taxon can join the community. I found that stronger cross-feeding and competition led to much lower invasion risk, as both types of biotic interactions lead to greater metabolite scarcity for the invader. I also evaluated the impact of a successful invader on community composition and structure. The effect of invaders on the native community was greatest at intermediate levels of cross-feeding; at this 'critical' level of cross-feeding, successful invaders generally cause decreased diversity, decreased productivity, greater metabolite availability, and decreased quantities of metabolites exchanged among taxa. Furthermore, these changes resulting from a successful primary invader made communities further susceptible to future invaders. The increase in invasion risk was greatest when the network of metabolite exchange between taxa was minimally redundant. Thus, this model demonstrates a case of invasional meltdown that is mediated by initial invaders disrupting the metabolite exchange networks of the native community.},
}

@article {pmid32368363,
year = {2019},
author = {Boyce, HB and Mallick, P},
title = {Geostatistical visualization of ecological interactions in tumors.},
journal = {Proceedings. IEEE International Conference on Bioinformatics and Biomedicine},
volume = {2019},
number = {},
pages = {2741-2749},
doi = {10.1109/bibm47256.2019.8983076},
pmid = {32368363},
issn = {2156-1125},
abstract = {Recent advances in our understanding of cancer progression have highlighted the roles played by molecular heterogeneity and by the tumor microenvironment in driving drug resistance and metastasis. The coupling of single-cell measurement technologies with algorithms, such as t-sne and SPADE, have enabled deep investigation of tumor heterogeneity. However, such techniques only capture molecular heterogeneity and do not enable the quantification nor visualization of intercellular interactions. They additionally do not allow the visualization of ecological niches that are critical to understanding tumor behavior. Novel computational tools to quantify and visualize spatial patterns in the tumor microenvironment are critically needed. Here, we take a tumor ecology perspective to examine how predation, mutualism, commensalism, and parasitism may impact tumor development and spatial patterning. We additionally quantify local spatial heterogeneity and the emergent global spatial behavior of the models using geostatistics. By visualizing emergent spatial patterns we demonstrate the potential utility of a geostatistical analysis in differentiating amongst cell-cell interactions in the tumor microenvironment. These studies introduce both an ecological framework for characterizing intercellular interactions in cancer and a novel way of quantifying and visualizing spatial patterns in cancer.},
}

@article {pmid32362769,
year = {2006},
author = {Carson, E and Feng, DD and Pons, MN and Soncini-Sessa, R and van Straten, G},
title = {Dealing with bio- and ecological complexity: Challenges and opportunities.},
journal = {Annual reviews in control},
volume = {30},
number = {1},
pages = {91-101},
doi = {10.1016/j.arcontrol.2006.01.003},
pmid = {32362769},
issn = {1367-5788},
abstract = {The complexities of the dynamic processes and their control associated with biological and ecological systems offer many challenges for the control engineer. Over the past decades the application of dynamic modelling and control has aided understanding of their complexities. At the same time using such complex systems as test-beds for new control methods has highlighted their limitations (e.g. in relation to system identification) and has thus acted as a catalyst for methodological advance. This paper continues the theme of exploring opportunities and achievements in applying modelling and control in the bio- and ecological domains.},
}

@article {pmid31269286,
year = {2019},
author = {Kienzler, A and Connors, KA and Bonnell, M and Barron, MG and Beasley, A and Inglis, CG and Norberg-King, TJ and Martin, T and Sanderson, H and Vallotton, N and Wilson, P and Embry, MR},
title = {Mode of Action Classifications in the EnviroTox Database: Development and Implementation of a Consensus MOA Classification.},
journal = {Environmental toxicology and chemistry},
volume = {38},
number = {10},
pages = {2294-2304},
pmid = {31269286},
issn = {1552-8618},
mesh = {Animals ; *Consensus ; Databases, Factual ; *Ecotoxicology ; Fishes/physiology ; Invertebrates/physiology ; Risk Assessment ; Toxicity Tests, Acute ; },
abstract = {Multiple mode of action (MOA) frameworks have been developed in aquatic ecotoxicology, mainly based on fish toxicity. These frameworks provide information on a key determinant of chemical toxicity, but the MOA categories and level of specificity remain unique to each of the classification schemes. The present study aimed to develop a consensus MOA assignment within EnviroTox, a curated in vivo aquatic toxicity database, based on the following MOA classification schemes: Verhaar (modified) framework, Assessment Tool for Evaluating Risk, Toxicity Estimation Software Tool, and OASIS. The MOA classifications from each scheme were first collapsed into one of 3 categories: non-specifically acting (i.e., narcosis), specifically acting, or nonclassifiable. Consensus rules were developed based on the degree of concordance among the 4 individual MOA classifications to attribute a consensus MOA to each chemical. A confidence rank was also assigned to the consensus MOA classification based on the degree of consensus. Overall, 40% of the chemicals were classified as narcotics, 17% as specifically acting, and 43% as unclassified. Sixty percent of chemicals had a medium to high consensus MOA assignment. When compared to empirical acute toxicity data, the general trend of specifically acting chemicals being more toxic is clearly observed for both fish and invertebrates but not for algae. EnviroTox is the first approach to establishing a high-level consensus across 4 computationally and structurally distinct MOA classification schemes. This consensus MOA classification provides both a transparent understanding of the variation between MOA classification schemes and an added certainty of the MOA assignment. In terms of regulatory relevance, a reliable understanding of MOA can provide information that can be useful for the prioritization (ranking) and risk assessment of chemicals. Environ Toxicol Chem 2019;38:2294-2304. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.},
}

Animals
*Consensus
Databases, Factual
*Ecotoxicology
Fishes/physiology
Invertebrates/physiology
Risk Assessment
Toxicity Tests, Acute

@article {pmid31188063,
year = {2019},
author = {Laudadio, I and Fulci, V and Stronati, L and Carissimi, C},
title = {Next-Generation Metagenomics: Methodological Challenges and Opportunities.},
journal = {Omics : a journal of integrative biology},
volume = {23},
number = {7},
pages = {327-333},
doi = {10.1089/omi.2019.0073},
pmid = {31188063},
issn = {1557-8100},
mesh = {Animals ; Big Data ; Biodiversity ; Computational Biology/methods ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiological Techniques ; Microbiology/trends ; Microbiota ; },
abstract = {Metagenomics is not only one of the newest omics system science technologies but also one that has arguably the broadest set of applications and impacts globally. Metagenomics has found vast utility not only in environmental sciences, ecology, and public health but also in clinical medicine and looking into the future, in planetary health. In line with the One Health concept, metagenomics solicits collaboration between molecular biologists, geneticists, microbiologists, clinicians, computational biologists, plant biologists, veterinarians, and other health care professionals. Almost every ecological niche of our planet hosts an extremely diverse community of organisms that are still poorly characterized. Detailed characterization of the features of such communities is instrumental to our comprehension of ecological, biological, and clinical complexity. This expert review article evaluates how metagenomics is improving our knowledge of microbiota composition from environmental to human samples. Furthermore, we offer an analysis of the common technical and methodological challenges and potential pitfalls arising from metagenomics approaches, such as metagenomics study design, data processing, and interpretation. All in all, at this critical juncture of further growth of the metagenomics field, it is time to critically reflect on the lessons learned and the future prospects of next-generation metagenomics science, technology, and conceivable applications, particularly from the standpoint of a metagenomics methodology perspective.},
}

Animals
Big Data
Biodiversity
Computational Biology/methods
Databases, Genetic
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenome
Metagenomics/*methods
Microbiological Techniques
Microbiology/trends
Microbiota

@article {pmid31907310,
year = {2020},
author = {Le Provost, G and Badenhausser, I and Le Bagousse-Pinguet, Y and Clough, Y and Henckel, L and Violle, C and Bretagnolle, V and Roncoroni, M and Manning, P and Gross, N},
title = {Land-use history impacts functional diversity across multiple trophic groups.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {3},
pages = {1573-1579},
pmid = {31907310},
issn = {1091-6490},
mesh = {Agriculture ; Animals ; *Biodiversity ; Conservation of Natural Resources ; Databases, Factual ; Ecology ; *Ecosystem ; *Grassland ; Herbivory/classification ; Invertebrates/classification ; Plants/classification ; Population Density ; },
abstract = {Land-use change is a major driver of biodiversity loss worldwide. Although biodiversity often shows a delayed response to land-use change, previous studies have typically focused on a narrow range of current landscape factors and have largely ignored the role of land-use history in shaping plant and animal communities and their functional characteristics. Here, we used a unique database of 220,000 land-use records to investigate how 20-y of land-use changes have affected functional diversity across multiple trophic groups (primary producers, mutualists, herbivores, invertebrate predators, and vertebrate predators) in 75 grassland fields with a broad range of land-use histories. The effects of land-use history on multitrophic trait diversity were as strong as other drivers known to impact biodiversity, e.g., grassland management and current landscape composition. The diversity of animal mobility and resource-acquisition traits was lower in landscapes where much of the land had been historically converted from grassland to crop. In contrast, functional biodiversity was higher in landscapes containing old permanent grasslands, most likely because they offer a stable and high-quality habitat refuge for species with low mobility and specialized feeding niches. Our study shows that grassland-to-crop conversion has long-lasting impacts on the functional biodiversity of agricultural ecosystems. Accordingly, land-use legacy effects must be considered in conservation programs aiming to protect agricultural biodiversity. In particular, the retention of permanent grassland sanctuaries within intensive landscapes may offset ecological debts.},
}

Agriculture
Animals
*Biodiversity
Conservation of Natural Resources
Databases, Factual
Ecology
*Ecosystem
*Grassland
Herbivory/classification
Invertebrates/classification
Plants/classification
Population Density

@article {pmid31685936,
year = {2020},
author = {Bjorbækmo, MFM and Evenstad, A and Røsæg, LL and Krabberød, AK and Logares, R},
title = {The planktonic protist interactome: where do we stand after a century of research?.},
journal = {The ISME journal},
volume = {14},
number = {2},
pages = {544-559},
pmid = {31685936},
issn = {1751-7370},
mesh = {Alveolata ; Animals ; Aquatic Organisms ; Bacteria/*classification ; Biological Evolution ; Databases, Factual ; Ecology ; Ecosystem ; Eukaryota/*classification ; Metagenomics ; Microalgae ; *Microbial Interactions ; *Oceans and Seas ; Parasites ; Phylogeny ; Plankton/classification/microbiology/parasitology ; Rhizaria ; Stramenopiles ; Symbiosis ; },
abstract = {Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and 'unresolved interactions' (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Using bipartite networks, we found that protist predators seem to be 'multivorous' while parasite-host and symbiont-host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. Despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.},
}

Alveolata
Animals
Aquatic Organisms
Bacteria/*classification
Biological Evolution
Databases, Factual
Ecology
Ecosystem
Eukaryota/*classification
Metagenomics
Microalgae
*Microbial Interactions
*Oceans and Seas
Parasites
Phylogeny
Plankton/classification/microbiology/parasitology
Rhizaria
Stramenopiles
Symbiosis

@article {pmid31724378,
year = {2019},
author = {Sarkar, S and Singh, P and Lingala, MAL and Verma, P and Dhiman, RC},
title = {Malaria risk map for India based on climate, ecology and geographical modelling.},
journal = {Geospatial health},
volume = {14},
number = {2},
pages = {},
doi = {10.4081/gh.2019.767},
pmid = {31724378},
issn = {1970-7096},
mesh = {Animals ; Anopheles/growth & development ; Climate ; Geographic Information Systems ; *Geographic Mapping ; India/epidemiology ; Malaria/*epidemiology ; Malaria, Falciparum/*epidemiology ; Malaria, Vivax/*epidemiology ; Mosquito Vectors/growth & development ; Plants ; Risk Assessment ; Risk Factors ; Seasons ; Soil/chemistry ; },
abstract = {Mapping the malaria risk at various geographical levels is often undertaken considering climate suitability, infection rate and/or malaria vector distribution, while the ecological factors related to topography and vegetation cover are generally neglected. The present study abides a holistic approach to risk mapping by including topographic, climatic and vegetation components into the framework of malaria risk modelling. This work attempts to delineate the areas of Plasmodium falciparum and Plasmodium vivax malaria transmission risk in India using seven geo-ecological indicators: temperature, relative humidity, rainfall, forest cover, soil, slope, altitude and the normalized difference vegetation index using multi-criteria decision analysis based on geographical information system (GIS). The weight of the risk indicators was assigned by an analytical hierarchical process with the climate suitability (temperature and humidity) data generated using fuzzy logic. Model validation was done through both primary and secondary datasets. The spatio-ecological model was based on GIS to classify the country into five zones characterized by various levels of malaria transmission risk (very high; high; moderate; low; and very low. The study found that about 13% of the country is under very high malaria risk, which includes the malaria- endemic districts of the states of Chhattisgarh, Odisha, Jharkhand, Tripura, Assam, Meghalaya and Manipur. The study also showed that the transmission risk suitability for P. vivax is higher than that for P. falciparum in the Himalayan region. The field study corroborates the identified malaria risk zones and highlights that the low to moderate risk zones are outbreak-prone. It is expected that this information will help the National Vector Borne Disease Control Programme in India to undertake improved surveillance and conduct target based interventions.},
}

Animals
Anopheles/growth & development
Climate
Geographic Information Systems
*Geographic Mapping
India/epidemiology
Malaria/*epidemiology
Malaria, Falciparum/*epidemiology
Malaria, Vivax/*epidemiology
Mosquito Vectors/growth & development
Plants
Risk Assessment
Risk Factors
Seasons
Soil/chemistry

@article {pmid29095369,
year = {2019},
author = {Vest, JR and Menachemi, N},
title = {A population ecology perspective on the functioning and future of health information organizations.},
journal = {Health care management review},
volume = {44},
number = {4},
pages = {344-355},
doi = {10.1097/HMR.0000000000000185},
pmid = {29095369},
issn = {1550-5030},
mesh = {*Commerce ; *Efficiency, Organizational ; Electronic Health Records ; *Health Information Exchange ; Humans ; Interviews as Topic ; Models, Theoretical ; Qualitative Research ; },
abstract = {BACKGROUND: Increasingly, health care providers need to exchange information to meet policy expectations and business needs. A variety of health information organizations (HIOs) provide services to facilitate health information exchange (HIE). However, the future of these organizations is unclear.

PURPOSE: The aim of this study was to explore the environmental context, potential futures, and survivability of community HIOs, enterprise HIEs, and electronic health record vendor-mediated exchange using the population ecology theory.

APPROACH: Qualitative interviews with 33 key informants representing each type of HIE organization were analyzed using template analysis.

RESULTS: Community HIOs, enterprise HIEs, and electronic health record vendors exhibited a high degree of competition for resources, especially in the area of exchange infrastructure services. Competition resulted in closures in some areas. In response to environmental pressures, each organizational type was endeavoring to differentiate its services and unique use case, as well as pursing symbiotic relationships or attempting resource partitioning.

CONCLUSION: HIOs compete for similar resources and are reacting to environmental pressures to better position themselves for continued survival and success. Our ecological research perspective helps move the discourse away from situation of a single exchange organization type toward a view of the broader dynamics and relationships of all organizations involved in facilitating HIE activities.

PRACTICE IMPLICATIONS: HIOs are attempting to partition the environment and differentiate services. HIE options should not be construed as an "either/or" decision, but one where multiple and complementary participation may be required.},
}

*Commerce
*Efficiency, Organizational
Electronic Health Records
*Health Information Exchange
Humans
Interviews as Topic
Models, Theoretical
Qualitative Research

@article {pmid30714190,
year = {2019},
author = {Connors, KA and Beasley, A and Barron, MG and Belanger, SE and Bonnell, M and Brill, JL and de Zwart, D and Kienzler, A and Krailler, J and Otter, R and Phillips, JL and Embry, MR},
title = {Creation of a Curated Aquatic Toxicology Database: EnviroTox.},
journal = {Environmental toxicology and chemistry},
volume = {38},
number = {5},
pages = {1062-1073},
pmid = {30714190},
issn = {1552-8618},
support = {//Health and Environmental Sciences Institute Animal Alternatives in Environmental Risk Assessment Technical Committee/International ; },
mesh = {Animals ; Aquatic Organisms/drug effects ; *Databases, Factual ; *Ecotoxicology ; Risk Assessment ; Toxicity Tests, Acute ; Toxicity Tests, Chronic ; Water Pollutants, Chemical/*toxicity ; },
abstract = {Flexible, rapid, and predictive approaches that do not require the use of large numbers of vertebrate test animals are needed because the chemical universe remains largely untested for potential hazards. Development of robust new approach methodologies and nontesting approaches requires the use of existing information via curated, integrated data sets. The ecological threshold of toxicological concern (ecoTTC) represents one such new approach methodology that can predict a conservative de minimis toxicity value for chemicals with little or no information available. For the creation of an ecoTTC tool, a large, diverse environmental data set was developed from multiple sources, with harmonization, characterization, and information quality assessment steps to ensure that the information could be effectively organized and mined. The resulting EnviroTox database contains 91 217 aquatic toxicity records representing 1563 species and 4016 unique Chemical Abstracts Service numbers and is a robust, curated database containing high-quality aquatic toxicity studies that are traceable to the original information source. Chemical-specific information is also linked to each record and includes physico-chemical information, chemical descriptors, and mode of action classifications. Toxicity data are associated with the physico-chemical data, mode of action classifications, and curated taxonomic information for the organisms tested. The EnviroTox platform also includes 3 analysis tools: a predicted-no-effect concentration calculator, an ecoTTC distribution tool, and a chemical toxicity distribution tool. Although the EnviroTox database and tools were originally developed to support ecoTTC analysis and development, they have broader applicability to the field of ecological risk assessment. Environ Toxicol Chem 2019;9999:1-12. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.},
}

Animals
Aquatic Organisms/drug effects
*Databases, Factual
*Ecotoxicology
Risk Assessment
Toxicity Tests, Acute
Toxicity Tests, Chronic
Water Pollutants, Chemical/*toxicity

@article {pmid31869356,
year = {2019},
author = {Buchner, D and Beermann, AJ and Laini, A and Rolauffs, P and Vitecek, S and Hering, D and Leese, F},
title = {Analysis of 13,312 benthic invertebrate samples from German streams reveals minor deviations in ecological status class between abundance and presence/absence data.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0226547},
pmid = {31869356},
issn = {1932-6203},
mesh = {Animals ; Aquatic Organisms/*classification/cytology/genetics/growth & development ; *Biodiversity ; *Biological Evolution ; Databases, Factual/trends ; Ecosystem ; Environmental Monitoring ; Extinction, Biological ; Germany ; Invertebrates/*classification/cytology/genetics/growth & development ; Population Dynamics/trends ; *Rivers ; },
abstract = {Benthic invertebrates are the most commonly used organisms used to assess ecological status as required by the EU Water Framework Directive (WFD). For WFD-compliant assessments, benthic invertebrate communities are sampled, identified and counted. Taxa × abundance matrices are used to calculate indices and the resulting scores are compared to reference values to determine the ecological status class. DNA-based tools, such as DNA metabarcoding, provide a new and precise method for species identification but cannot deliver robust abundance data. To evaluate the applicability of DNA-based tools to ecological status assessment, we evaluated whether the results derived from presence/absence data are comparable to those derived from abundance data. We analysed benthic invertebrate community data obtained from 13,312 WFD assessments of German streams. Broken down to 30 official stream types, we compared assessment results based on abundance and presence/absence data for the assessment modules "organic pollution" (i.e., the saprobic index) and "general degradation" (a multimetric index) as well as their underlying metrics. In 76.6% of cases, the ecological status class did not change after transforming abundance data to presence/absence data. In 12% of cases, the status class was reduced by one (e.g., from good to moderate), and in 11.2% of cases, the class increased by one. In only 0.2% of cases, the status shifted by two classes. Systematic stream type-specific deviations were found and differences between abundance and presence/absence data were most prominent for stream types where abundance information contributed directly to one or several metrics of the general degradation module. For a single stream type, these deviations led to a systematic shift in status from 'good' to 'moderate' (n = 201; with only n = 3 increasing). The systematic decrease in scores was observed, even when considering simulated confidence intervals for abundance data. Our analysis suggests that presence/absence data can yield similar assessment results to those for abundance-based data, despite type-specific deviations. For most metrics, it should be possible to intercalibrate the two data types without substantial efforts. Thus, benthic invertebrate taxon lists generated by standardised DNA-based methods should be further considered as a complementary approach.},
}

Animals
Aquatic Organisms/*classification/cytology/genetics/growth & development
*Biodiversity
*Biological Evolution
Databases, Factual/trends
Ecosystem
Environmental Monitoring
Extinction, Biological
Germany
Invertebrates/*classification/cytology/genetics/growth & development
Population Dynamics/trends
*Rivers

@article {pmid31694865,
year = {2019},
author = {Greenbaum, G and Rubin, A and Templeton, AR and Rosenberg, NA},
title = {Network-based hierarchical population structure analysis for large genomic data sets.},
journal = {Genome research},
volume = {29},
number = {12},
pages = {2020-2033},
pmid = {31694865},
issn = {1549-5469},
support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; },
mesh = {*Algorithms ; *Databases, Nucleic Acid ; *Genome, Human ; *Genomics ; Humans ; *Sequence Analysis, DNA ; },
abstract = {Analysis of population structure in natural populations using genetic data is a common practice in ecological and evolutionary studies. With large genomic data sets of populations now appearing more frequently across the taxonomic spectrum, it is becoming increasingly possible to reveal many hierarchical levels of structure, including fine-scale genetic clusters. To analyze these data sets, methods need to be appropriately suited to the challenges of extracting multilevel structure from whole-genome data. Here, we present a network-based approach for constructing population structure representations from genetic data. The use of community-detection algorithms from network theory generates a natural hierarchical perspective on the representation that the method produces. The method is computationally efficient, and it requires relatively few assumptions regarding the biological processes that underlie the data. We show the approach by analyzing population structure in the model plant species Arabidopsis thaliana and in human populations. These examples illustrate how network-based approaches for population structure analysis are well-suited to extracting valuable ecological and evolutionary information in the era of large genomic data sets.},
}

*Algorithms
*Databases, Nucleic Acid
*Genome, Human
*Genomics
Humans
*Sequence Analysis, DNA

@article {pmid32286335,
year = {2020},
author = {Kaufman, D and McKay, N and Routson, C and Erb, M and Davis, B and Heiri, O and Jaccard, S and Tierney, J and Dätwyler, C and Axford, Y and Brussel, T and Cartapanis, O and Chase, B and Dawson, A and de Vernal, A and Engels, S and Jonkers, L and Marsicek, J and Moffa-Sánchez, P and Morrill, C and Orsi, A and Rehfeld, K and Saunders, K and Sommer, PS and Thomas, E and Tonello, M and Tóth, M and Vachula, R and Andreev, A and Bertrand, S and Biskaborn, B and Bringué, M and Brooks, S and Caniupán, M and Chevalier, M and Cwynar, L and Emile-Geay, J and Fegyveresi, J and Feurdean, A and Finsinger, W and Fortin, MC and Foster, L and Fox, M and Gajewski, K and Grosjean, M and Hausmann, S and Heinrichs, M and Holmes, N and Ilyashuk, B and Ilyashuk, E and Juggins, S and Khider, D and Koinig, K and Langdon, P and Larocque-Tobler, I and Li, J and Lotter, A and Luoto, T and Mackay, A and Magyari, E and Malevich, S and Mark, B and Massaferro, J and Montade, V and Nazarova, L and Novenko, E and Pařil, P and Pearson, E and Peros, M and Pienitz, R and Płóciennik, M and Porinchu, D and Potito, A and Rees, A and Reinemann, S and Roberts, S and Rolland, N and Salonen, S and Self, A and Seppä, H and Shala, S and St-Jacques, JM and Stenni, B and Syrykh, L and Tarrats, P and Taylor, K and van den Bos, V and Velle, G and Wahl, E and Walker, I and Wilmshurst, J and Zhang, E and Zhilich, S},
title = {A global database of Holocene paleotemperature records.},
journal = {Scientific data},
volume = {7},
number = {1},
pages = {115},
doi = {10.1038/s41597-020-0445-3},
pmid = {32286335},
issn = {2052-4463},
support = {AGS-1602105//National Science Foundation (NSF)/ ; AGS-1903548//National Science Foundation (NSF)/ ; AGS-1602105//National Science Foundation (NSF)/ ; AGS-1903548//National Science Foundation (NSF)/ ; AGS-1602301//National Science Foundation (NSF)/ ; },
abstract = {A comprehensive database of paleoclimate records is needed to place recent warming into the longer-term context of natural climate variability. We present a global compilation of quality-controlled, published, temperature-sensitive proxy records extending back 12,000 years through the Holocene. Data were compiled from 679 sites where time series cover at least 4000 years, are resolved at sub-millennial scale (median spacing of 400 years or finer) and have at least one age control point every 3000 years, with cut-off values slackened in data-sparse regions. The data derive from lake sediment (51%), marine sediment (31%), peat (11%), glacier ice (3%), and other natural archives. The database contains 1319 records, including 157 from the Southern Hemisphere. The multi-proxy database comprises paleotemperature time series based on ecological assemblages, as well as biophysical and geochemical indicators that reflect mean annual or seasonal temperatures, as encoded in the database. This database can be used to reconstruct the spatiotemporal evolution of Holocene temperature at global to regional scales, and is publicly available in Linked Paleo Data (LiPD) format.},
}

@article {pmid31553801,
year = {2019},
author = {Hoondert, RPJ and Oldenkamp, R and de Zwart, D and van de Meent, D and Posthuma, L},
title = {QSAR-Based Estimation of Species Sensitivity Distribution Parameters: An Exploratory Investigation.},
journal = {Environmental toxicology and chemistry},
volume = {38},
number = {12},
pages = {2764-2770},
pmid = {31553801},
issn = {1552-8618},
support = {603437//FP7 Environment/International ; },
mesh = {Databases, Chemical ; Ecotoxicology ; Models, Theoretical ; *Quantitative Structure-Activity Relationship ; Risk Assessment ; },
abstract = {Ecological risk assessments are hampered by limited availability of ecotoxicity data. The present study aimed to explore the possibility of deriving species sensitivity distribution (SSD) parameters for nontested compounds, based on simple physicochemical characteristics, known SSDs for data-rich compounds, and a quantitative structure-activity relationship (QSAR)-type approach. The median toxicity of a data-poor chemical for species assemblages significantly varies with values of the physicochemical descriptors, especially when based on high-quality SSD data (from either acute median effect concentrations or chronic no-observed-effect concentrations). Beyond exploratory uses, we discuss how the precision of QSAR-based SSDs can be improved to construct models that accurately predict the SSD parameters of data-poor chemicals. The current models show that the concept of QSAR-based SSDs supports screening-level evaluations of the potential ecotoxicity of compounds for which data are lacking. Environ Toxicol Chem 2019;38:2764-2770. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.},
}

Databases, Chemical
Ecotoxicology
Models, Theoretical
*Quantitative Structure-Activity Relationship
Risk Assessment

@article {pmid31433524,
year = {2019},
author = {Eccles, KM and Pauli, BD and Chan, HM},
title = {The Use of Geographic Information Systems for Spatial Ecological Risk Assessments: An Example from the Athabasca Oil Sands Area in Canada.},
journal = {Environmental toxicology and chemistry},
volume = {38},
number = {12},
pages = {2797-2810},
doi = {10.1002/etc.4577},
pmid = {31433524},
issn = {1552-8618},
support = {//Canada Research Chairs/International ; Joint Oil Sands Monitoring Program//Environment and Climate Change Canada/International ; CREATE grant//Natural Sciences and Engineering Research Council of Canada/International ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/International ; },
mesh = {Animals ; Canada ; Charadriiformes/growth & development ; Cluster Analysis ; Ecotoxicology ; Environmental Monitoring/*methods ; Environmental Pollutants/analysis ; Geographic Information Systems ; Mercury/analysis ; Oil and Gas Fields/*chemistry ; Ovum/chemistry/metabolism ; Plants/chemistry/metabolism ; Swallows ; },
abstract = {There is an acknowledged need in ecotoxicology for methods that integrate spatial analyses in risk assessment. This has resulted in the emergence of landscape ecotoxicology, a subdiscipline of ecotoxicology. However, landscape ecotoxicology has yet to become common practice in risk assessment due to the underdevelopment of techniques and a lack of standardized methods. In the present study, we demonstrate how geographic information systems (GISs) can serve as a standardized platform to integrate data, assess spatial patterns of ecotoxicological data for multiple species, and assess relationships between chemical mixture exposures and effects on biota for landscape ecotoxicological risks assessment. We use data collected under the Joint Oil Sands Monitoring Program in the Athabasca Oil Sands Region in Alberta, Canada. This dataset is composed of concentrations of contaminants including metals and polycyclic aromatic compounds, and health endpoints measured in 1100 biological samples, including tree swallows, amphibians, gull and tern eggs, plants, and mammals. We present 3 examples using a GIS as a platform and geospatial analysis to: 1) integrate data and assess spatial patterns of contaminant exposure in the region, 2) assess spatial patterns of exposures to complex mixtures, and 3) examine patterns of exposures and responses across the landscape. We summarize the methods used in the present study into a workflow for ease of use. The GIS methods allow researchers to identify hot spots of contamination, use georeferenced monitoring data to derive quantitative exposure-response relationships, and assess complex exposures with more realism. Environ Toxicol Chem 2019;38:2797-2810. © 2019 SETAC.},
}

Animals
Canada
Charadriiformes/growth & development
Cluster Analysis
Ecotoxicology
Environmental Monitoring/*methods
Environmental Pollutants/analysis
Geographic Information Systems
Mercury/analysis
Oil and Gas Fields/*chemistry
Ovum/chemistry/metabolism
Plants/chemistry/metabolism
Swallows

@article {pmid31295663,
year = {2019},
author = {Pitacco, V and Reizopoulou, S and Sfriso, A and Sfriso, A and Mistri, M and Munari, C},
title = {The difficulty of disentangling natural from anthropogenic forcing factors makes the evaluation of ecological quality problematic: A case study from Adriatic lagoons.},
journal = {Marine environmental research},
volume = {150},
number = {},
pages = {104756},
doi = {10.1016/j.marenvres.2019.104756},
pmid = {31295663},
issn = {1879-0291},
mesh = {Animals ; Ecology ; *Ecosystem ; *Environmental Monitoring ; Invertebrates ; Wetlands ; },
abstract = {The complex and dynamic nature of transitional ecosystems pose problems for the assessment of the Ecological Quality Status required by the European Water Framework Directive (WFD; 2000/60/EC). In six Adriatic lagoons, Ecological Quality Status was studied by comparing a biotic index based on macrophytes (MaQI), and three indices based on invertebrates (M-AMBI, M-bAMBI, and ISD). Ecological Status evaluated though MaQI and ISD resulted in quite degraded ecosystems (moderate/poor/bad), with only opportunistic algae and macrobenthic communities dominated by small size classes. Those results were supported by physico-chemical parameters, indicating high nutrients inputs, and anthropogenic pressures related with agriculture and fishery activities. Ecological Status obtained with M-AMBI and M-bAMBI was higher, with some sites reaching even the "good" status. The best response to anthropogenic pressures, in terms of a pressure index, was obtained by M-AMBI and M-bAMBI. Nevertheless, the response of used metrics (such as AMBI and bAMBI) to environmental variables not related to anthropogenic impact, and the high heterogeneity of physical-chemical conditions within lagoons, represent potential problems for the correct evaluation of Ecological Status of transitional waters. When different metrics give different responses it becomes a problem for managers who cannot easily make a decision on the remedial measures. The disagreement among indices arose because of the different response of biological elements to different stressors, and because the different indices based on macroinvertebrates focused on different aspects of the community, providing complementary information. So urge the need to find alternative approaches for a correct assessment of Ecological Status, with the combination of different biological elements, and considering the development of new indices (e.g. M-bAMBI) or refinement of the existing ones.},
}

Animals
Ecology
*Ecosystem
*Environmental Monitoring
Invertebrates
Wetlands

@article {pmid32065938,
year = {2020},
author = {Douterelo, I and Dutilh, BE and Arkhipova, K and Calero, C and Husband, S},
title = {Microbial diversity, ecological networks and functional traits associated to materials used in drinking water distribution systems.},
journal = {Water research},
volume = {173},
number = {},
pages = {115586},
doi = {10.1016/j.watres.2020.115586},
pmid = {32065938},
issn = {1879-2448},
mesh = {Bacteria ; Biofilms ; *Drinking Water ; Ecology ; Water Microbiology ; Water Quality ; Water Supply ; },
abstract = {Drinking water distribution systems host complex microbial communities as biofilms that interact continuously with delivered water. Understanding the diversity, behavioural and functional characteristics will be a requisite for developing future monitoring strategies and protection against water-borne health risks. To improve understanding, this study investigates mobilisation and accumulation behaviour, microbial community structure and functional variations of biofilms developing on different pipe materials from within an operational network. Samples were collected from four pipes during a repeated flushing operation three months after an initial visit that used hydraulic forces to mobilise regenerating biofilms yet without impacting the upstream network. To minimise confounding factors, test sections were chosen with comparable daily hydraulic regimes, physical dimensions, and all connected straight of a common trunk main and within close proximity, hence similar water chemistry, pressure and age. Taxonomical results showed differences in colonising communities between pipe materials, with several genera, including the bacteria Pseudomonas and the fungi Cladosporium, present in every sample. Diverse bacterial communities dominated compared to more homogeneous fungal, or mycobiome, community distribution. The analysis of bacterial/fungal networks based on relative abundance of operational taxonomic units (OTUs) indicated microbial communities from cast iron pipes were more stable than communities from the non-ferrous pipe materials. Novel analysis of functional traits between all samples were found to be mainly associated to mobile genetic elements that play roles in determining links between cells, including phages, prophages, transposable elements, and plasmids. The use of functional traits can be considered for development in future surveillance methods, capable of delivering network condition information beyond that of limited conventional faecal indicator tests, that will help protect water quality and public health.},
}

Bacteria
Biofilms
*Drinking Water
Ecology
Water Microbiology
Water Quality
Water Supply