@article {pmid31056485,
year = {2019},
author = {Švec, P and Hönig, V and Zubriková, D and Wittmann, M and Pfister, K and Grubhoffer, L},
title = {The use of multi-criteria evaluation for the selection of study plots for monitoring of I. ricinus ticks - Example from Central Europe.},
journal = {Ticks and tick-borne diseases},
volume = {10},
number = {4},
pages = {905-910},
doi = {10.1016/j.ttbdis.2019.04.014},
pmid = {31056485},
issn = {1877-9603},
mesh = {Altitude ; Animals ; Borrelia burgdorferi/isolation & purification ; *Ecosystem ; Encephalitis Viruses, Tick-Borne/isolation & purification ; Female ; Geographic Information Systems ; Geography ; Ixodes/*physiology ; Male ; Sampling Studies ; Tick-Borne Diseases/*epidemiology ; },
abstract = {Research projects in the field of eco-epidemiology of tick-borne diseases often require extensive sampling of arthropod vectors in the field. The aim of our study was to use geographical information systems (GIS) to select appropriate sampling sites of Ixodes ricinus ticks in central European habitat for further ecological studies of vector-borne pathogens (tick-borne encephalitis virus and Borrelia burgdorferi sensu lato). The model area was the Czech-German borderland (the region of South Bohemia and two regions in Germany: the Upper Palatinate and Lower Bavaria) where numerous human tick-borne encephalitis cases are reported annually. We prepared the sampling site design as a multi-criteria evaluation (MCE) task. In the GIS environment, we conducted MCE with a set of environmental, socio-economic and epidemiological data (altitude, vegetation cover, number of tick-borne encephalitis cases recorded in the past, tourist activity). The MCE classified the surveyed area into two classes: suitable for tick collection and unsuitable for tick collection. Subsequently, 50 tick sampling sites were randomly selected in the suitable area: 30 in South Bohemia (Czech Republic) and 20 in the Upper Palatinate and Lower Bavaria regions (Bavaria, Germany). The sampling sites were identified and surveyed in the field. The presence of ticks was confirmed by flagging at each of the selected plots. The described MCE system represents a versatile tool for semi-randomized design of tick sampling sites for research projects in the field of tick-borne pathogen ecology as well as for tick-borne pathogen surveillance programs run by local health authorities.},
}

Altitude
Animals
Borrelia burgdorferi/isolation & purification
*Ecosystem
Encephalitis Viruses, Tick-Borne/isolation & purification
Female
Geographic Information Systems
Geography
Ixodes/*physiology
Male
Sampling Studies
Tick-Borne Diseases/*epidemiology

@article {pmid29247477,
year = {2018},
author = {Haas, TC and Ferreira, SM},
title = {Finding politically feasible conservation policies: the case of wildlife trafficking.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {28},
number = {2},
pages = {473-494},
doi = {10.1002/eap.1662},
pmid = {29247477},
issn = {1051-0761},
mesh = {Animals ; Commerce ; Conservation of Natural Resources/*legislation & jurisprudence ; *Decision Support Techniques ; *Perissodactyla ; Politics ; Population Dynamics ; South Africa ; Uncertainty ; },
abstract = {Conservation management is of increasing importance in ecology as most ecosystems nowadays are essentially managed ecosystems. Conservation managers work within a political-ecological system when they develop and attempt to implement a conservation plan that is designed to meet particular conservation goals. In this article, we develop a decision support tool that can identify a conservation policy for a managed wildlife population that is both sustainable and politically feasible. Part of our tool consists of a simulation model composed of interacting influence diagrams. We build, fit, and use our tool on the case of rhino horn trafficking between South Africa and Asia. Using these diagrams, we show how a rhino poacher's belief system can be modified by such a policy and locate it in a perceived risks-benefits space before and after policy implementation. We statistically fit our model to observations on group actions and rhino abundance. We then use this fitted model to compute a politically feasible conservation policy.},
}

Animals
Commerce
Conservation of Natural Resources/*legislation & jurisprudence
*Decision Support Techniques
*Perissodactyla
Politics
Population Dynamics
South Africa
Uncertainty

@article {pmid28922513,
year = {2018},
author = {Gray, S and Voinov, A and Paolisso, M and Jordan, R and BenDor, T and Bommel, P and Glynn, P and Hedelin, B and Hubacek, K and Introne, J and Kolagani, N and Laursen, B and Prell, C and Schmitt Olabisi, L and Singer, A and Sterling, E and Zellner, M},
title = {Purpose, processes, partnerships, and products: four Ps to advance participatory socio-environmental modeling.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {28},
number = {1},
pages = {46-61},
doi = {10.1002/eap.1627},
pmid = {28922513},
issn = {1051-0761},
mesh = {Animals ; Cameroon ; *Community Participation ; *Conservation of Natural Resources ; Environment ; Geographic Information Systems ; Humans ; India ; *Models, Theoretical ; Social Environment ; Zambia ; },
abstract = {Including stakeholders in environmental model building and analysis is an increasingly popular approach to understanding ecological change. This is because stakeholders often hold valuable knowledge about socio-environmental dynamics and collaborative forms of modeling produce important boundary objects used to collectively reason about environmental problems. Although the number of participatory modeling (PM) case studies and the number of researchers adopting these approaches has grown in recent years, the lack of standardized reporting and limited reproducibility have prevented PM's establishment and advancement as a cohesive field of study. We suggest a four-dimensional framework (4P) that includes reporting on dimensions of (1) the Purpose for selecting a PM approach (the why); (2) the Process by which the public was involved in model building or evaluation (the how); (3) the Partnerships formed (the who); and (4) the Products that resulted from these efforts (the what). We highlight four case studies that use common PM software-based approaches (fuzzy cognitive mapping, agent-based modeling, system dynamics, and participatory geospatial modeling) to understand human-environment interactions and the consequences of ecological changes, including bushmeat hunting in Tanzania and Cameroon, agricultural production and deforestation in Zambia, and groundwater management in India. We demonstrate how standardizing communication about PM case studies can lead to innovation and new insights about model-based reasoning in support of ecological policy development. We suggest that our 4P framework and reporting approach provides a way for new hypotheses to be identified and tested in the growing field of PM.},
}

Animals
Cameroon
*Community Participation
*Conservation of Natural Resources
Environment
Geographic Information Systems
Humans
India
*Models, Theoretical
Social Environment
Zambia

@article {pmid30928035,
year = {2019},
author = {Louro, R and Santos-Silva, C and Nobre, T},
title = {What is in a name? Terfezia classification revisited.},
journal = {Fungal biology},
volume = {123},
number = {4},
pages = {267-273},
doi = {10.1016/j.funbio.2019.01.003},
pmid = {30928035},
issn = {1878-6146},
mesh = {Ascomycota/*classification/*genetics/growth & development ; Computational Biology ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/*genetics ; *Phylogeny ; *Terminology as Topic ; },
abstract = {Desert truffles (mycorrhizal hypogeous Ascomycota) are found in arid and semi-arid areas of the globe and have great ecological and economic importance. Terfezia is undoubtedly the most diversified of all desert truffle genera, but its taxonomy is far from resolved. Specifically, the large number of newly described species plus the high intraspecific morphological variability observed within some Terfezia lineages as rendered the use of molecular techniques mandatory for specimen's discrimination. But the subsequent increasing amount of sequence data produced also a huge number of undescribed taxa that required determination. We compiled and used the public available ITS data on Terfezia spp. on the custom-curated UNITE database to reconstruct the genus phylogeny. We found at least 17 distinct lineages within the genus and successfully resolved some of the more pressing taxonomic issues, namely the T. leptoderma/olbiensis complex and some misapplied synonymy. Based on this resolved phylogeny, and motivated by the recent new described species, we proposed an identification key to Terfezia genus highlighting the importance of morphological and ecological characterization.},
}

Ascomycota/*classification/*genetics/growth & development
Computational Biology
DNA, Fungal/*genetics
DNA, Ribosomal Spacer/*genetics
*Phylogeny
*Terminology as Topic

@article {pmid31330063,
year = {2019},
author = {Fountain-Jones, NM and Machado, G and Carver, S and Packer, C and Recamonde-Mendoza, M and Craft, ME},
title = {How to make more from exposure data? An integrated machine learning pipeline to predict pathogen exposure.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.13076},
pmid = {31330063},
issn = {1365-2656},
abstract = {1.Predicting infectious disease dynamics is a central challenge in disease ecology. Models that can assess which individuals are most at risk of being exposed to a pathogen not only provide valuable insights into disease transmission and dynamics but can also guide management interventions. Constructing such models for wild animal populations, however, is particularly challenging; often only serological data is available on a subset of individuals and non-linear relationships between variables are common. 2.Here we provide a guide to the latest advances in statistical machine learning to construct pathogen-risk models that automatically incorporate complex non-linear relationships with minimal statistical assumptions from ecological data with missing data. Our approach compares multiple machine learning algorithms in a unified environment to find the model with the best predictive performance and uses game theory to better interpret results. We apply this framework on two major pathogens that infect African lions: canine distemper virus (CDV) and feline parvovirus. 3.Our modelling approach provided enhanced predictive performance compared to more traditional approaches, as well as new insights into disease risks in a wild population. We were able to efficiently capture and visualise strong non-linear patterns, as well as model complex interactions between variables in shaping exposure risk from CDV and feline parvovirus. For example, we found that lions were more likely to be exposed to CDV at a young age but only in low rainfall years. 4.When combined with our data calibration approach, our framework helped us to answer questions about risk of pathogen exposure which are difficult to address with previous methods. Our framework not only has the potential to aid in predicting disease risk in animal populations, but also can be used to build robust predictive models suitable for other ecological applications such as modelling species distribution or diversity patterns. This article is protected by copyright. All rights reserved.},
}

@article {pmid31318965,
year = {2019},
author = {Flórián, N and Ladányi, M and Ittzés, A and Kröel-Dulay, G and Ónodi, G and Mucsi, M and Szili-Kovács, T and Gergócs, V and Dányi, L and Dombos, M},
title = {Effects of single and repeated drought on soil microarthropods in a semi-arid ecosystem depend more on timing and duration than drought severity.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0219975},
doi = {10.1371/journal.pone.0219975},
pmid = {31318965},
issn = {1932-6203},
abstract = {Soil moisture is one of the most important factors affecting soil biota. In arid and semi-arid ecosystems, soil mesofauna is adapted to temporary drought events, but, until now, we have had a limited understanding of the impacts of the different magnitudes and frequencies of drought predicted to occur according to future climate change scenarios. The present study focuses on how springtails and mites respond to simulated repeated drought events of different magnitudes in a field experiment in a Hungarian semi-arid sand steppe. Changes in soil arthropod activities were monitored with soil trapping over two years in a sandy soil. In the first year (2014), we applied an extreme drought pretreatment, and in the consecutive year, we applied less devastating treatments (severe drought, moderate drought, water addition) to these sites. In the first year, the extreme drought pretreatment tended to have a negative effect (either significantly or not significantly) on the capture of all Collembola groups, whereas all mite groups increased in activity density. However, in the consecutive year, between the extreme drought and control treatments, we only detected differences in soil microbial biomass. In the cases of severe drought, moderate drought and water addition, we did not find considerable changes across the microarthropods, except in the case of epedaphic Collembola. In the cases of the water addition and drought treatments, the duration and timing of the manipulation seemed to be more important for soil mesofauna than their severity (i.e., the level of soil moisture decrease). We suggest that in these extreme habitats, soil mesofauna are able to survive extreme conditions, and their populations recover rapidly, but they may not be able to cope with very long drought periods.},
}

@article {pmid29087435,
year = {2018},
author = {Piccolo, BD and Wankhade, UD and Chintapalli, SV and Bhattacharyya, S and Chunqiao, L and Shankar, K},
title = {Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {6},
pages = {1050-1052},
pmid = {29087435},
issn = {1367-4811},
support = {UL1 TR001449/TR/NCATS NIH HHS/United States ; },
mesh = {*Data Interpretation, Statistical ; *Ecosystem ; Microbiological Techniques ; Microbiology ; Programming Languages ; Sequence Analysis ; *Software ; },
abstract = {Summary: Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive.

DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed.

Contact: bdpiccolo@uams.edu.},
}

*Data Interpretation, Statistical
*Ecosystem
Microbiological Techniques
Microbiology
Programming Languages
Sequence Analysis
*Software

@article {pmid28833890,
year = {2017},
author = {Scales, KL and Hazen, EL and Maxwell, SM and Dewar, H and Kohin, S and Jacox, MG and Edwards, CA and Briscoe, DK and Crowder, LB and Lewison, RL and Bograd, SJ},
title = {Fit to predict? Eco-informatics for predicting the catchability of a pelagic fish in near real time.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {27},
number = {8},
pages = {2313-2329},
doi = {10.1002/eap.1610},
pmid = {28833890},
issn = {1051-0761},
mesh = {Animals ; California ; Computational Biology ; Ecology ; *Fisheries ; *Fishes ; Models, Biological ; Pacific Ocean ; Remote Sensing Technology/*methods ; },
abstract = {The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing eco-informatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 yr (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of occurrence (presence-absence) and catchability (total catch per gillnet set) of broadbill swordfish Xiphias gladius in the California Current System. Using freely available environmental data sets and open source software, we explore the physical drivers of regional swordfish distribution. Comparing models built upon remotely sensed data sets with those built upon a data-assimilative configuration of the Regional Ocean Modelling System (ROMS), we explore trade-offs in model construction, and address how physical data can affect predictive performance and operational capacity. Swordfish catchability was found to be highest in deeper waters (>1,500 m) with surface temperatures in the 14-20°C range, isothermal layer depth (ILD) of 20-40 m, positive sea surface height (SSH) anomalies, and during the new moon (<20% lunar illumination). We observed a greater influence of mesoscale variability (SSH, wind speed, isothermal layer depth, eddy kinetic energy) in driving swordfish catchability (total catch) than was evident in predicting the relative probability of presence (presence-absence), confirming the utility of generating spatiotemporally dynamic predictions. Data-assimilative ROMS circumvent the limitations of satellite remote sensing in providing physical data fields for species distribution models (e.g., cloud cover, variable resolution, subsurface data), and facilitate broad-scale prediction of dynamic species distributions in near real time.},
}

Animals
California
Computational Biology
Ecology
*Fisheries
*Fishes
Models, Biological
Pacific Ocean
Remote Sensing Technology/*methods

@article {pmid31310429,
year = {2019},
author = {di Porcia E Brugnera, M and Meunier, F and Longo, M and Krishna Moorthy, SM and De Deurwaerder, H and Schnitzer, SA and Bonal, D and Faybishenko, B and Verbeeck, H},
title = {Modelling the impact of liana infestation on the demography and carbon cycle of tropical forests.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.14769},
pmid = {31310429},
issn = {1365-2486},
abstract = {There is mounting empirical evidence that lianas affect the carbon cycle of tropical forests. However, no single vegetation model takes into account this growth form, although such efforts could greatly improve the predictions of carbon dynamics in tropical forests. In this study, we incorporated a novel mechanistic representation of lianas in a dynamic global vegetation model (the Ecosystem Demography Model). We developed a liana-specific plant functional type and mechanisms representing liana-tree interactions (such as light competition, liana-specific allometries and attachment to host trees) and parameterized them according to a comprehensive literature meta-analysis. We tested the model for an old-growth forest (Paracou, French Guiana) and a secondary forest (Gigante Peninsula, Panama). The resulting model simulations captured many features of the two forests characterized by different levels of liana infestation as revealed by a systematic comparison of the model outputs with empirical data, including local census data from forest inventories, eddy flux tower data, and terrestrial laser scanner-derived forest vertical structure. The inclusion of lianas in the simulations reduced the secondary forest net productivity by up to 0.46 tC .ha-1 .y-1 , which corresponds to a limited relative reduction of 2.6% in comparison with a reference simulation without lianas. However, this resulted in significantly reduced accumulated above-ground biomass after 70 years of regrowth by up to 20 tC .ha-1 (19% of the reference simulation). Ultimately, the simulated negative impact of lianas on the total biomass was almost completely cancelled out when the forest reached an old-growth successional stage. Our findings suggest that lianas negatively influence the forest potential carbon sink strength, especially for young, disturbed, liana-rich sites. In light of the critical role that lianas play in the profound changes currently experienced by tropical forests, this new model provides a robust numerical tool to forecast the impact of lianas on tropical forest carbon sinks. This article is protected by copyright. All rights reserved.},
}

@article {pmid29097776,
year = {2017},
author = {Iquebal, MA and Jaiswal, S and Mahato, AK and Jayaswal, PK and Angadi, UB and Kumar, N and Sharma, N and Singh, AK and Srivastav, M and Prakash, J and Singh, SK and Khan, K and Mishra, RK and Rajan, S and Bajpai, A and Sandhya, BS and Nischita, P and Ravishankar, KV and Dinesh, MR and Rai, A and Kumar, D and Sharma, TR and Singh, NK},
title = {MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {14968},
pmid = {29097776},
issn = {2045-2322},
mesh = {Databases, Genetic ; Fruit/genetics ; Genome, Plant ; Genomics ; Internet ; Mangifera/*genetics ; *Phylogeny ; Phylogeography ; *Polymorphism, Single Nucleotide ; },
abstract = {Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.},
}

Databases, Genetic
Fruit/genetics
Genome, Plant
Genomics
Internet
Mangifera/*genetics
*Phylogeny
Phylogeography
*Polymorphism, Single Nucleotide

@article {pmid31285584,
year = {2019},
author = {Edwards, RA and Vega, AA and Norman, HM and Ohaeri, M and Levi, K and Dinsdale, EA and Cinek, O and Aziz, RK and McNair, K and Barr, JJ and Bibby, K and Brouns, SJJ and Cazares, A and de Jonge, PA and Desnues, C and Díaz Muñoz, SL and Fineran, PC and Kurilshikov, A and Lavigne, R and Mazankova, K and McCarthy, DT and Nobrega, FL and Reyes Muñoz, A and Tapia, G and Trefault, N and Tyakht, AV and Vinuesa, P and Wagemans, J and Zhernakova, A and Aarestrup, FM and Ahmadov, G and Alassaf, A and Anton, J and Asangba, A and Billings, EK and Cantu, VA and Carlton, JM and Cazares, D and Cho, GS and Condeff, T and Cortés, P and Cranfield, M and Cuevas, DA and De la Iglesia, R and Decewicz, P and Doane, MP and Dominy, NJ and Dziewit, L and Elwasila, BM and Eren, AM and Franz, C and Fu, J and Garcia-Aljaro, C and Ghedin, E and Gulino, KM and Haggerty, JM and Head, SR and Hendriksen, RS and Hill, C and Hyöty, H and Ilina, EN and Irwin, MT and Jeffries, TC and Jofre, J and Junge, RE and Kelley, ST and Khan Mirzaei, M and Kowalewski, M and Kumaresan, D and Leigh, SR and Lipson, D and Lisitsyna, ES and Llagostera, M and Maritz, JM and Marr, LC and McCann, A and Molshanski-Mor, S and Monteiro, S and Moreira-Grez, B and Morris, M and Mugisha, L and Muniesa, M and Neve, H and Nguyen, NP and Nigro, OD and Nilsson, AS and O'Connell, T and Odeh, R and Oliver, A and Piuri, M and Prussin Ii, AJ and Qimron, U and Quan, ZX and Rainetova, P and Ramírez-Rojas, A and Raya, R and Reasor, K and Rice, GAO and Rossi, A and Santos, R and Shimashita, J and Stachler, EN and Stene, LC and Strain, R and Stumpf, R and Torres, PJ and Twaddle, A and Ugochi Ibekwe, M and Villagra, N and Wandro, S and White, B and Whiteley, A and Whiteson, KL and Wijmenga, C and Zambrano, MM and Zschach, H and Dutilh, BE},
title = {Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-019-0494-6},
pmid = {31285584},
issn = {2058-5276},
abstract = {Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.},
}

@article {pmid31251341,
year = {2019},
author = {Pepin, KM and Pedersen, K and Wan, XF and Cunningham, FL and Webb, CT and Wilber, MQ},
title = {Individual-level antibody dynamics reveal potential drivers of influenza A seasonality in wild pig populations.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icz118},
pmid = {31251341},
issn = {1557-7023},
abstract = {Swine are important in the ecology of influenza A viruses (IAV) globally. Understanding the ecological role of wild pigs in IAV ecology has been limited because surveillance in wild pigs is often for antibodies (serosurveillance) rather than IAVs, as in humans and domestic swine. As IAV antibodies can persist long after an infection, serosurveillance data are not necessarily indicative of current infection risk. However, antibody responses to IAV infections cause a predictable antibody response, thus time of infection can be inferred from antibody levels in serological samples, enabling identification of risk factors of infection at estimated times of infection. Recent work demonstrates that these quantitative antibody methods (QAM) can accurately recover infection dates, even when individual-level variation in antibody curves is moderately high. Also, the methodology can be implemented in a survival analysis (SA) framework to reduce bias from opportunistic sampling. Here we integrated QAM and SA and applied this novel QAM-SA framework to understand the dynamics of IAV infection risk in wild pigs seasonally and spatially, and identify risk factors. We used national-scale IAV serosurveillance data from 15 U.S. states. We found that infection risk was highest Jan.-Mar. (54% of 61 estimated peaks), with 24% of estimated peaks occurring from May-Jul., and some low-level of infection risk occurring year-round. Time-varying IAV infection risk in wild pigs was positively correlated with humidity and IAV infection trends in domestic swine and humans, and did not show wave-like spatial spread of infection among states, nor more similar levels of infection risk among states with more similar meteorological conditions. Effects of host sex on IAV infection risk in wild pigs were generally not significant. Because most of the variation in infection risk was explained by state-level factors or infection risk at long-distances, our results suggested that predicting IAV infection risk in wild pigs is complicated by local ecological factors and potentially long-distance translocation of infection. In addition to revealing factors of IAV infection risk in wild pigs, our framework is broadly applicable for quantifying risk factors of disease transmission using opportunistic serosurveillance sampling, a common methodology in wildlife disease surveillance. Future research on the factors that determine individual-level antibody kinetics will facilitate the design of serosurveillance systems that can extract more accurate estimates of time-varying disease risk from quantitative antibody data.},
}

@article {pmid29491180,
year = {2018},
author = {Reeves, DB and Magaret, AS and Greninger, AL and Johnston, C and Schiffer, JT},
title = {Model-based estimation of superinfection prevalence from limited datasets.},
journal = {Journal of the Royal Society, Interface},
volume = {15},
number = {139},
pages = {},
pmid = {29491180},
issn = {1742-5662},
mesh = {*Databases, Factual ; Female ; HIV Infections/*epidemiology ; *HIV-1 ; Herpes Genitalis/*epidemiology ; *Herpesvirus 2, Human ; Humans ; Male ; *Models, Biological ; Prevalence ; Superinfection/*epidemiology ; },
abstract = {Humans can be infected sequentially by different strains of the same virus. Estimating the prevalence of so-called 'superinfection' for a particular pathogen is vital because superinfection implies a failure of immunologic memory against a given virus despite past exposure, which may signal challenges for future vaccine development. Increasingly, viral deep sequencing and phylogenetic inference can discriminate distinct strains within a host. Yet, a population-level study may misrepresent the true prevalence of superinfection for several reasons. First, certain infections such as herpes simplex virus (HSV-2) only reactivate single strains, making multiple samples necessary to detect superinfection. Second, the number of samples collected in a study may be fewer than the actual number of independently acquired strains within a single person. Third, detecting strains that are relatively less abundant can be difficult, even for other infections such as HIV-1 where deep sequencing may identify multiple strains simultaneously. Here we develop a model of superinfection inspired by ecology. We define an infected individual's richness as the number of infecting strains and use ecological evenness to quantify the relative strain abundances. The model uses an EM methodology to infer the true prevalence of superinfection from limited clinical datasets. Simulation studies with known true prevalence are used to contrast our EM method to a standard (naive) calculation. While varying richness, evenness and sampling we quantify the accuracy and precision of our method. The EM method outperforms in all cases, particularly when sampling is low, and richness or unevenness is high. Here, sensitivity to our assumptions about clinical data is considered. The simulation studies also provide insight into optimal study designs; estimates of prevalence improve equally by enrolling more participants or gathering more samples per person. Finally, we apply our method to data from published studies of HSV-2 and HIV-1 superinfection.},
}

*Databases, Factual
Female
HIV Infections/*epidemiology
*HIV-1
Herpes Genitalis/*epidemiology
*Herpesvirus 2, Human
Humans
Male
*Models, Biological
Prevalence
Superinfection/*epidemiology

@article {pmid29934651,
year = {2018},
author = {Lane, BA and Sandoval-Solis, S and Stein, ED and Yarnell, SM and Pasternack, GB and Dahlke, HE},
title = {Beyond Metrics? The Role of Hydrologic Baseline Archetypes in Environmental Water Management.},
journal = {Environmental management},
volume = {62},
number = {4},
pages = {678-693},
pmid = {29934651},
issn = {1432-1009},
mesh = {California ; *Climate Change ; Conservation of Water Resources/*methods ; Databases, Factual ; Environmental Monitoring/*methods ; Humans ; *Hydrology ; Rivers ; Water Movements ; Water Resources/*supply & distribution ; Water Supply/standards/*statistics & numerical data ; },
abstract = {Balancing ecological and human water needs often requires characterizing key aspects of the natural flow regime and then predicting ecological response to flow alterations. Flow metrics are generally relied upon to characterize long-term average statistical properties of the natural flow regime (hydrologic baseline conditions). However, some key aspects of hydrologic baseline conditions may be better understood through more complete consideration of continuous patterns of daily, seasonal, and inter-annual variability than through summary metrics. Here we propose the additional use of high-resolution dimensionless archetypes of regional stream classes to improve understanding of baseline hydrologic conditions and inform regional environmental flows assessments. In an application to California, we describe the development and analysis of hydrologic baseline archetypes to characterize patterns of flow variability within and between stream classes. We then assess the utility of archetypes to provide context for common flow metrics and improve understanding of linkages between aquatic patterns and processes and their hydrologic controls. Results indicate that these archetypes may offer a distinct and complementary tool for researching mechanistic flow-ecology relationships, assessing regional patterns for streamflow management, or understanding impacts of changing climate.},
}

California
*Climate Change
Conservation of Water Resources/*methods
Databases, Factual
Environmental Monitoring/*methods
Humans
*Hydrology
Rivers
Water Movements
Water Resources/*supply & distribution
Water Supply/standards/*statistics & numerical data

@article {pmid30832740,
year = {2019},
author = {Song, W and Wemheuer, B and Zhang, S and Steensen, K and Thomas, T},
title = {MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {36},
doi = {10.1186/s40168-019-0649-y},
pmid = {30832740},
issn = {2049-2618},
mesh = {Bacteria/classification/*genetics ; Computational Biology/*methods ; Databases, Genetic ; Drug Resistance, Bacterial ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Humans ; Metagenomics ; Phylogeny ; Soil Microbiology ; },
abstract = {BACKGROUND: Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level.

RESULTS: Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms.

CONCLUSION: MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .},
}

Bacteria/classification/*genetics
Computational Biology/*methods
Databases, Genetic
Drug Resistance, Bacterial
Evolution, Molecular
*Gene Transfer, Horizontal
Humans
Metagenomics
Phylogeny
Soil Microbiology

@article {pmid31173423,
year = {2019},
author = {Norton, BA and Bending, GD and Clark, R and Corstanje, R and Dunnett, N and Evans, KL and Grafius, DR and Gravestock, E and Grice, SM and Harris, JA and Hilton, S and Hoyle, H and Lim, E and Mercer, TG and Pawlett, M and Pescott, OL and Richards, JP and Southon, GE and Warren, PH},
title = {Urban meadows as an alternative to short mown grassland: effects of composition and height on biodiversity.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {},
number = {},
pages = {e01946},
doi = {10.1002/eap.1946},
pmid = {31173423},
issn = {1051-0761},
abstract = {There are increasing calls to provide greenspace in urban areas, yet the ecological quality, as well as quantity, of greenspace is important. Short mown grassland designed for recreational use is the dominant form of urban greenspace in temperate regions but requires considerable maintenance and typically provides limited habitat value for most taxa. Alternatives are increasingly proposed, but the biodiversity potential of these is not well understood. In a replicated experiment across six public urban greenspaces we used nine different perennial meadow plantings to quantify the relative roles of floristic diversity and height of sown meadows on the richness and composition of three taxonomic groups - plants, invertebrates and soil microbes. We found that all meadow treatments were colonised by plant species not sown in the plots, suggesting that establishing sown meadows does not preclude further locally determined grassland development if management is appropriate. Colonising species were rarer in taller and more diverse plots, indicating competition may limit invasion rates. Urban meadow treatments contained invertebrate and microbial communities that differed from mown grassland. Invertebrate taxa responded to changes in both height and richness of meadow vegetation, but most orders were more abundant where vegetation height was longer than mown grassland. Order richness also increased in longer vegetation and Coleoptera family richness increased with plant diversity in summer. Microbial community composition seems sensitive to plant species composition at the soil surface (0-10 cm), but in deeper soils (11-20 cm) community variation was most responsive to plant height, with bacteria and fungi responding differently. In addition to improving local residents' satisfaction, native perennial meadow plantings can produce biologically diverse grasslands that support richer and more abundant invertebrate communities, and restructured plant, invertebrate and soil microbial communities compared with short mown grassland. Our results suggest that diversification of urban greenspace by planting urban meadows in place of some mown amenity grassland is likely to generate substantial biodiversity benefits, with a mosaic of meadow types likely to maximise such benefits. This article is protected by copyright. All rights reserved.},
}

@article {pmid31133727,
year = {2019},
author = {Piross, IS and Harnos, A and Rózsa, L},
title = {Rensch's rule in avian lice: contradictory allometric trends for sexual size dimorphism.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7908},
doi = {10.1038/s41598-019-44370-5},
pmid = {31133727},
issn = {2045-2322},
abstract = {Rensch's rule (RR) postulates that in comparisons across closely related species, male body size relative to female size increases with the average size of the species. This holds true in several vertebrate and also in certain free-living invertebrate taxa. Here, we document the validity of RR in avian lice using three families (Philopteridae, Menoponidae, and Ricinidae). Using published data on the body length of 989 louse species, subspecies, or distinct intraspecific lineages, we applied phylogenetic reduced major axis regression to analyse the body size of females vs. males while accounting for phylogenetic non-independence. Our results indicate that philopterid and menoponid lice follow RR, while ricinids exhibit the opposite pattern. In the case of philopterids and menoponids, we argue that larger-bodied bird species tend to host lice that are both larger in size and more abundant. Thus, sexual selection acting on males makes them relatively larger, and this is stronger than fecundity selection acting on females. Ricinids exhibit converse RR, likely because fecundity selection is stronger in their case.},
}

@article {pmid31128642,
year = {2019},
author = {Blažek, J and Zukal, J and Bandouchova, H and Berková, H and Kovacova, V and Martínková, N and Pikula, J and Řehák, Z and Škrabánek, P and Bartonička, T},
title = {Numerous cold arousals and rare arousal cascades as a hibernation strategy in European Myotis bats.},
journal = {Journal of thermal biology},
volume = {82},
number = {},
pages = {150-156},
doi = {10.1016/j.jtherbio.2019.04.002},
pmid = {31128642},
issn = {0306-4565},
abstract = {Hibernating bats optimise the duration of torpor bouts and arousals in relation to hibernaculum microclimatic conditions and fat reserves. Clustering has significant physiological and ecological benefits, promoting successful hibernation of individuals. Such aggregations may help maintain optimal temperatures, allowing better energy utilisation than in solitarily bats. However, aroused bats in a cluster could conceivably disturb those still hibernating, starting an energy-demanding arousal process. Our study was conducted over two winters in two different hibernacula (cave and mine) in the Czech Republic, where Greater mouse-eared bats (Myotis myotis) have previously been diagnosed with white-nose syndrome. In 118 arousal episodes we recorded 193 individual arousals in which a warming phase was observed, 135 (69.9%) being cold arousals, where bats ceased increasing their body temperatures at ≤ 10 °C. The remaining arousals were standard normothermic arousals, where body (fur) surface temperatures reached > 20 °C. Cold arousals occurred during the mid- and late hibernation periods, suggesting they were a response to disturbance by a neighbour in the same cluster. Arousal cascades, where bats aroused in series, were rare (12.7%) and reached a maximum in mid-January. Our data suggest that Myotis bats prolong their torpor bouts using numerous cold arousals but few arousal cascades. Upon arrival of a bat, the clustered bats show tolerance to disturbing by conspecifics.},
}

@article {pmid31086738,
year = {2019},
author = {Warwick-Dugdale, J and Solonenko, N and Moore, K and Chittick, L and Gregory, AC and Allen, MJ and Sullivan, MB and Temperton, B},
title = {Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6800},
doi = {10.7717/peerj.6800},
pmid = {31086738},
issn = {2167-8359},
abstract = {Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a lack of reference genomes and 'universal' gene markers to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution, but their assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Such features also challenge assembly across genomic islands containing niche-defining genes that drive ecological speciation. These populations and features may be successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies using short-read and long-read technology. The 'VirION' (Viral, long-read metagenomics via MinION sequencing) approach was first validated using mock communities where it was found to be as relatively quantitative as short-read methods and provided significant improvements in recovery of viral genomes. We then then applied VirION to the first metagenome from a natural viral community from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse virus populations, and (iii) captured more and longer genomic islands. Together, these findings suggest that VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.},
}

@article {pmid31073136,
year = {2019},
author = {Bátori, Z and Vojtkó, A and Maák, IE and Lőrinczi, G and Farkas, T and Kántor, N and Tanács, E and Kiss, PJ and Juhász, O and Módra, G and Tölgyesi, C and Erdős, L and Aguilon, DJ and Keppel, G},
title = {Karst dolines provide diverse microhabitats for different functional groups in multiple phyla.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {7176},
doi = {10.1038/s41598-019-43603-x},
pmid = {31073136},
issn = {2045-2322},
abstract = {Fine-scale topographic complexity creates important microclimates that can facilitate species to grow outside their main distributional range and increase biodiversity locally. Enclosed depressions in karst landscapes ('dolines') are topographically complex environments which produce microclimates that are drier and warmer (equator-facing slopes) and cooler and moister (pole-facing slopes and depression bottoms) than the surrounding climate. We show that the distribution patterns of functional groups for organisms in two different phyla, Arthropoda (ants) and Tracheophyta (vascular plants), mirror this variation of microclimate. We found that north-facing slopes and bottoms of solution dolines in northern Hungary provided key habitats for ant and plant species associated with cooler and/or moister conditions. Contrarily, south-facing slopes of dolines provided key habitats for species associated with warmer and/or drier conditions. Species occurring on the surrounding plateau were associated with intermediate conditions. We conclude that karst dolines provide a diversity of microclimatic habitats that may facilitate the persistence of taxa with diverse environmental preferences, indicating these dolines to be potential safe havens for multiple phyla under local and global climate oscillations.},
}

@article {pmid31031001,
year = {2019},
author = {Gregory, AC and Zayed, AA and Conceição-Neto, N and Temperton, B and Bolduc, B and Alberti, A and Ardyna, M and Arkhipova, K and Carmichael, M and Cruaud, C and Dimier, C and Domínguez-Huerta, G and Ferland, J and Kandels, S and Liu, Y and Marec, C and Pesant, S and Picheral, M and Pisarev, S and Poulain, J and Tremblay, JÉ and Vik, D and , and Babin, M and Bowler, C and Culley, AI and de Vargas, C and Dutilh, BE and Iudicone, D and Karp-Boss, L and Roux, S and Sunagawa, S and Wincker, P and Sullivan, MB},
title = {Marine DNA Viral Macro- and Microdiversity from Pole to Pole.},
journal = {Cell},
volume = {177},
number = {5},
pages = {1109-1123.e14},
doi = {10.1016/j.cell.2019.03.040},
pmid = {31031001},
issn = {1097-4172},
support = {T32 AI112542/AI/NIAID NIH HHS/United States ; },
abstract = {Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.},
}

@article {pmid31024009,
year = {2019},
author = {Rund, SSC and Braak, K and Cator, L and Copas, K and Emrich, SJ and Giraldo-Calderón, GI and Johansson, MA and Heydari, N and Hobern, D and Kelly, SA and Lawson, D and Lord, C and MacCallum, RM and Roche, DG and Ryan, SJ and Schigel, D and Vandegrift, K and Watts, M and Zaspel, JM and Pawar, S},
title = {MIReAD, a minimum information standard for reporting arthropod abundance data.},
journal = {Scientific data},
volume = {6},
number = {1},
pages = {40},
doi = {10.1038/s41597-019-0042-5},
pmid = {31024009},
issn = {2052-4463},
support = {BB/N013573/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/International ; HHSN272201400029C/AI/NIAID NIH HHS/United States ; R01 AI136035/AI/NIAID NIH HHS/United States ; U01 CK000510/CK/NCEZID CDC HHS/United States ; R01 AI122284/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Arthropods/physiology ; Biodiversity ; Ecosystem ; Information Dissemination ; Information Storage and Retrieval/*standards ; Population Dynamics ; },
abstract = {Arthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the "FAIR," (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests.},
}

Animals
*Arthropods/physiology
Biodiversity
Ecosystem
Information Dissemination
Information Storage and Retrieval/*standards
Population Dynamics

@article {pmid31007605,
year = {2019},
author = {Thomas, HJD and Myers-Smith, IH and Bjorkman, AD and Elmendorf, SC and Blok, D and Cornelissen, JHC and Forbes, BC and Hollister, RD and Normand, S and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Wilmking, M and Wipf, S and Cornwell, WK and Kattge, J and Goetz, SJ and Guay, KC and Alatalo, JM and Anadon-Rosell, A and Angers-Blondin, S and Berner, LT and Björk, RG and Buchwal, A and Buras, A and Carbognani, M and Christie, K and Siegwart Collier, L and Cooper, EJ and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Heijmans, MMPD and Hermanutz, L and Hudson, JMG and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Johnstone, JF and Kaarlejärvi, E and Kulonen, A and Lamarque, LJ and Lévesque, E and Little, CJ and Michelsen, A and Milbau, A and Nabe-Nielsen, J and Nielsen, SS and Ninot, JM and Oberbauer, SF and Olofsson, J and Onipchenko, VG and Petraglia, A and Rumpf, SB and Semenchuk, PR and Soudzilovskaia, NA and Spasojevic, MJ and Speed, JDM and Tape, KD and Te Beest, M and Tomaselli, M and Trant, A and Treier, UA and Venn, S and Vowles, T and Weijers, S and Zamin, T and Atkin, OK and Bahn, M and Blonder, B and Campetella, G and Cerabolini, BEL and Chapin Iii, FS and Dainese, M and de Vries, FT and Díaz, S and Green, W and Jackson, RB and Manning, P and Niinemets, Ü and Ozinga, WA and Peñuelas, J and Reich, PB and Schamp, B and Sheremetev, S and van Bodegom, PM},
title = {Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome.},
journal = {Global ecology and biogeography : a journal of macroecology},
volume = {28},
number = {2},
pages = {78-95},
doi = {10.1111/geb.12783},
pmid = {31007605},
issn = {1466-822X},
abstract = {Aim: Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits.

Location: Tundra biome.

Time period: Data collected between 1964 and 2016.

Major taxa studied: 295 tundra vascular plant species.

Methods: We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits.

Results: Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression.

Main conclusions: Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra vegetation change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insights for ecological prediction and modelling.},
}

@article {pmid30973867,
year = {2019},
author = {Stone, L and Simberloff, D and Artzy-Randrup, Y},
title = {Network motifs and their origins.},
journal = {PLoS computational biology},
volume = {15},
number = {4},
pages = {e1006749},
doi = {10.1371/journal.pcbi.1006749},
pmid = {30973867},
issn = {1553-7358},
mesh = {Computational Biology ; Ecosystem ; Gene Regulatory Networks ; Humans ; Models, Biological ; Neural Networks (Computer) ; Social Networking ; *Systems Biology ; },
abstract = {Modern network science is a new and exciting research field that has transformed the study of complex systems over the last 2 decades. Of particular interest is the identification of small "network motifs" that might be embedded in a larger network and that indicate the presence of evolutionary design principles or have an overly influential role on system-wide dynamics. Motifs are patterns of interconnections, or subgraphs, that appear in an observed network significantly more often than in compatible randomized networks. The concept of network motifs was introduced into Systems Biology by Milo, Alon and colleagues in 2002, quickly revolutionized the field, and it has had a huge impact in wider scientific domains ever since. Here, we argue that the same concept and tools for the detection of motifs were well known in the ecological literature decades into the last century, a fact that is generally not recognized. We review the early history of network motifs, their evolution in the mathematics literature, and their recent rediscoveries.},
}

Computational Biology
Ecosystem
Gene Regulatory Networks
Humans
Models, Biological
Neural Networks (Computer)
Social Networking
*Systems Biology

@article {pmid30918448,
year = {2019},
author = {Stucky, BJ and Balhoff, JP and Barve, N and Barve, V and Brenskelle, L and Brush, MH and Dahlem, GA and Gilbert, JDJ and Kawahara, AY and Keller, O and Lucky, A and Mayhew, PJ and Plotkin, D and Seltmann, KC and Talamas, E and Vaidya, G and Walls, R and Yoder, M and Zhang, G and Guralnick, R},
title = {Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.},
journal = {Biodiversity data journal},
volume = {7},
number = {},
pages = {e33303},
doi = {10.3897/BDJ.7.e33303},
pmid = {30918448},
issn = {1314-2828},
abstract = {Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.},
}

@article {pmid30918402,
year = {2019},
author = {Peters, MK and Hemp, A and Appelhans, T and Becker, JN and Behler, C and Classen, A and Detsch, F and Ensslin, A and Ferger, SW and Frederiksen, SB and Gebert, F and Gerschlauer, F and Gütlein, A and Helbig-Bonitz, M and Hemp, C and Kindeketa, WJ and Kühnel, A and Mayr, AV and Mwangomo, E and Ngereza, C and Njovu, HK and Otte, I and Pabst, H and Renner, M and Röder, J and Rutten, G and Schellenberger Costa, D and Sierra-Cornejo, N and Vollstädt, MGR and Dulle, HI and Eardley, CD and Howell, KM and Keller, A and Peters, RS and Ssymank, A and Kakengi, V and Zhang, J and Bogner, C and Böhning-Gaese, K and Brandl, R and Hertel, D and Huwe, B and Kiese, R and Kleyer, M and Kuzyakov, Y and Nauss, T and Schleuning, M and Tschapka, M and Fischer, M and Steffan-Dewenter, I},
title = {Climate-land-use interactions shape tropical mountain biodiversity and ecosystem functions.},
journal = {Nature},
volume = {568},
number = {7750},
pages = {88-92},
doi = {10.1038/s41586-019-1048-z},
pmid = {30918402},
issn = {1476-4687},
abstract = {Agriculture and the exploitation of natural resources have transformed tropical mountain ecosystems across the world, and the consequences of these transformations for biodiversity and ecosystem functioning are largely unknown1-3. Conclusions that are derived from studies in non-mountainous areas are not suitable for predicting the effects of land-use changes on tropical mountains because the climatic environment rapidly changes with elevation, which may mitigate or amplify the effects of land use4,5. It is of key importance to understand how the interplay of climate and land use constrains biodiversity and ecosystem functions to determine the consequences of global change for mountain ecosystems. Here we show that the interacting effects of climate and land use reshape elevational trends in biodiversity and ecosystem functions on Africa's largest mountain, Mount Kilimanjaro (Tanzania). We find that increasing land-use intensity causes larger losses of plant and animal species richness in the arid lowlands than in humid submontane and montane zones. Increases in land-use intensity are associated with significant changes in the composition of plant, animal and microorganism communities; stronger modifications of plant and animal communities occur in arid and humid ecosystems, respectively. Temperature, precipitation and land use jointly modulate soil properties, nutrient turnover, greenhouse gas emissions, plant biomass and productivity, as well as animal interactions. Our data suggest that the response of ecosystem functions to land-use intensity depends strongly on climate; more-severe changes in ecosystem functioning occur in the arid lowlands and the cold montane zone. Interactions between climate and land use explained-on average-54% of the variation in species richness, species composition and ecosystem functions, whereas only 30% of variation was related to single drivers. Our study reveals that climate can modulate the effects of land use on biodiversity and ecosystem functioning, and points to a lowered resistance of ecosystems in climatically challenging environments to ongoing land-use changes in tropical mountainous regions.},
}

@article {pmid30897417,
year = {2019},
author = {Szabó, B and Lang, Z and Bakonyi, G and Mariën, J and Roelofs, D and van Gestel, CAM and Seres, A},
title = {Transgenerational and multigenerational stress gene responses to the insecticide etofenprox in Folsomia candida (Collembola).},
journal = {Ecotoxicology and environmental safety},
volume = {175},
number = {},
pages = {181-191},
doi = {10.1016/j.ecoenv.2019.03.052},
pmid = {30897417},
issn = {1090-2414},
mesh = {Acclimatization ; Animals ; Arthropods/*drug effects/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; *Epigenesis, Genetic ; *Gene Expression Regulation ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Insecticides/*adverse effects ; Pyrethrins/*adverse effects ; Reproduction/drug effects ; Soil ; },
abstract = {Insecticide exposure may cause both transgenerational and multigenerational effects on populations, but the molecular mechanisms of these changes remain largely unclear. Many studies have focused on either transgenerational or multigenerational mechanisms but did neglect the comparative aspects. This study assessed whether the pyrethroid insecticide etofenprox (formulation Trebon® 30 EC) shows transgenerational and/or multigenerational effects on the survival and reproduction of Folsomia candida (Collembola). The activation of stress-related genes was studied to detect whether etofenprox modifies the expression of reproduction-associated genes in trans- and multigenerational treatments. A laboratory study was carried out for three generations with five insecticide concentrations in LUFA 2.2 soil. In the transgenerational treatment, only the parent generation (P) was exposed, but the subsequent generations were not. In the multigenerational treatment, all three generations were exposed to the insecticide in the same manner. Multigenerational exposure resulted in reduced reproduction effects over generations, suggesting that F. candida is capable of acclimating to enhanced concentration levels of etofenprox during prolonged exposure over multiple generations. In the transgenerational treatment, the heat shock protein 70 was up-regulated and cytochrome oxidase 6N4v1 expression down-regulated in a dose-dependent manner in the F2 generation. This finding raises the possibility of the epigenetic inheritance of insecticide impacts on parents. Furthermore, CYP6N4v1 expression was oppositely regulated in the trans- and multigenerational treatments. Our results draw attention to the differences in molecular level responses of F. candida to trans- and multigenerational etofenprox exposure.},
}

Acclimatization
Animals
Arthropods/*drug effects/genetics/metabolism
Electron Transport Complex IV/genetics/metabolism
*Epigenesis, Genetic
*Gene Expression Regulation
HSP70 Heat-Shock Proteins/genetics/metabolism
Insecticides/*adverse effects
Pyrethrins/*adverse effects
Reproduction/drug effects
Soil

@article {pmid30884039,
year = {2019},
author = {Piao, S and Liu, Q and Chen, A and Janssens, IA and Fu, Y and Dai, J and Liu, L and Lian, X and Shen, M and Zhu, X},
title = {Plant phenology and global climate change: Current progresses and challenges.},
journal = {Global change biology},
volume = {25},
number = {6},
pages = {1922-1940},
doi = {10.1111/gcb.14619},
pmid = {30884039},
issn = {1365-2486},
abstract = {Plant phenology, the annually recurring sequence of plant developmental stages, is important for plant functioning and ecosystem services and their biophysical and biogeochemical feedbacks to the climate system. Plant phenology depends on temperature, and the current rapid climate change has revived interest in understanding and modeling the responses of plant phenology to the warming trend and the consequences thereof for ecosystems. Here, we review recent progresses in plant phenology and its interactions with climate change. Focusing on the start (leaf unfolding) and end (leaf coloring) of plant growing seasons, we show that the recent rapid expansion in ground- and remote sensing- based phenology data acquisition has been highly beneficial and has supported major advances in plant phenology research. Studies using multiple data sources and methods generally agree on the trends of advanced leaf unfolding and delayed leaf coloring due to climate change, yet these trends appear to have decelerated or even reversed in recent years. Our understanding of the mechanisms underlying the plant phenology responses to climate warming is still limited. The interactions between multiple drivers complicate the modeling and prediction of plant phenology changes. Furthermore, changes in plant phenology have important implications for ecosystem carbon cycles and ecosystem feedbacks to climate, yet the quantification of such impacts remains challenging. We suggest that future studies should primarily focus on using new observation tools to improve the understanding of tropical plant phenology, on improving process-based phenology modeling, and on the scaling of phenology from species to landscape-level.},
}

@article {pmid30883574,
year = {2019},
author = {Giezendanner, J and Bertuzzo, E and Pasetto, D and Guisan, A and Rinaldo, A},
title = {A minimalist model of extinction and range dynamics of virtual mountain species driven by warming temperatures.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213775},
doi = {10.1371/journal.pone.0213775},
pmid = {30883574},
issn = {1932-6203},
abstract = {A longstanding question in ecology concerns the prediction of the fate of mountain species under climate change, where climatic and geomorphic factors but also endogenous species characteristics are jointly expected to control species distributions. A significant step forward would single out reliably landscape effects, given their constraining role and relative ease of theoretical manipulation. Here, we address population dynamics in ecosystems where the substrates for ecological interactions are mountain landscapes subject to climate warming. We use a minimalist model of metapopulation dynamics based on virtual species (i.e. a suitable assemblage of focus species) where dispersal processes interact with the spatial structure of the landscape. Climate warming is subsumed by an upward shift of species habitat altering the metapopulation capacity of the landscape and hence species viability. We find that the landscape structure is a powerful determinant of species survival, owing to the specific role of the predictably evolving connectivity of the various habitats. Range shifts and lags in tracking suitable habitat experienced by virtual species under warming conditions are singled out in different landscapes. The range of parameters is identified for which these virtual species (characterized by comparable viability thus restricting their possible fitnesses and niche widths) prove unable to cope with environmental change. The statistics of the proportion of species bound to survive is identified for each landscape, providing the temporal evolution of species range shifts and the related expected occupation patterns. A baseline dynamic model for predicting species fates in evolving habitats is thus provided.},
}

@article {pmid30846683,
year = {2019},
author = {George, PBL and Lallias, D and Creer, S and Seaton, FM and Kenny, JG and Eccles, RM and Griffiths, RI and Lebron, I and Emmett, BA and Robinson, DA and Jones, DL},
title = {Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {1107},
doi = {10.1038/s41467-019-09031-1},
pmid = {30846683},
issn = {2041-1723},
mesh = {Animals ; *Biodiversity ; Computational Biology ; DNA Barcoding, Taxonomic ; *Ecosystem ; Microbiota/genetics ; *Soil ; *Soil Microbiology ; Wales ; },
abstract = {Soil biota accounts for ~25% of global biodiversity and is vital to nutrient cycling and primary production. There is growing momentum to study total belowground biodiversity across large ecological scales to understand how habitat and soil properties shape belowground communities. Microbial and animal components of belowground communities follow divergent responses to soil properties and land use intensification; however, it is unclear whether this extends across heterogeneous ecosystems. Here, a national-scale metabarcoding analysis of 436 locations across 7 different temperate ecosystems shows that belowground animal and microbial (bacteria, archaea, fungi, and protists) richness follow divergent trends, whereas β-diversity does not. Animal richness is governed by intensive land use and unaffected by soil properties, while microbial richness was driven by environmental properties across land uses. Our findings demonstrate that established divergent patterns of belowground microbial and animal diversity are consistent across heterogeneous land uses and are detectable using a standardised metabarcoding approach.},
}

Animals
*Biodiversity
Computational Biology
DNA Barcoding, Taxonomic
*Ecosystem
Microbiota/genetics
*Soil
*Soil Microbiology
Wales

@article {pmid30842894,
year = {2019},
author = {Sumsion, GR and Bradshaw, MS and Hill, KT and Pinto, LDG and Piccolo, SR},
title = {Remote sensing tree classification with a multilayer perceptron.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6101},
doi = {10.7717/peerj.6101},
pmid = {30842894},
issn = {2167-8359},
abstract = {To accelerate scientific progress on remote tree classification-as well as biodiversity and ecology sampling-The National Institute of Science and Technology created a community-based competition where scientists were invited to contribute informatics methods for classifying tree species and genus using crown-level images of trees. We classified tree species and genus at the pixel level using hyperspectral and LiDAR observations. We compared three algorithms that have been implemented extensively across a broad range of research applications: support vector machines, random forests, and multilayer perceptron. At the pixel level, the multilayer perceptron algorithm classified species or genus with high accuracy (92.7% and 95.9%, respectively) on the training data and performed better than the other two algorithms (85.8-93.5%). This indicates promise for the use of the multilayer perceptron (MLP) algorithm for tree-species classification based on hyperspectral and LiDAR observations and coincides with a growing body of research in which neural network-based algorithms outperform other types of classification algorithm for machine vision. To aggregate patterns across the images, we used an ensemble approach that averages the pixel-level outputs of the MLP algorithm to classify species at the crown level. The average accuracy of these classifications on the test set was 68.8% for the nine species.},
}

@article {pmid30832282,
year = {2019},
author = {Wu, Z and Lei, S and He, BJ and Bian, Z and Wang, Y and Lu, Q and Peng, S and Duo, L},
title = {Assessment of Landscape Ecological Health: A CaseStudy of a Mining City in a Semi-Arid Steppe.},
journal = {International journal of environmental research and public health},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/ijerph16050752},
pmid = {30832282},
issn = {1660-4601},
abstract = {The ecological status of the semi-arid steppes in China is fragile. Under the long-term and high-intensity development of mining, the ecological integrity and biodiversity of steppe landscapes have been destroyed, causing soil pollution, grassland degradation, landscape function defect, and so on. Previous studies have mainly focused on ecosystem health assessment in mining areas. Landscape ecological health (LEH) pays more attention to the interactions between different ecosystems. Therefore, the ecological assessment of mining cities is more suitable on a landscape scale. Meanwhile, the existing LEH assessment index systems are not applicable in ecologically fragile areas with sparse population, underdeveloped economy, and in relatively small research areas. The purpose of this study was to construct a LEH assessment index system and evaluate the LEH of a mining city located in a semi-arid steppe. Xilinhot is a typical semi-arid steppe mining city in China. The contradictions between the human, land and ecological environment are serious. A new model Condition, Vigor, Organization, Resilience, and Ecosystem (CVORE) model was constructed that integrated five subsystems (services) from the perspectives of ecology, landscape ecology, mining science, and geography. This study used the CVORE model to systematically evaluate the LEH in Xilinhot city in terms of five LEH levels, including very healthy, healthy, sub-healthy, unhealthy and morbid landscape. Research results show that the areas of the very healthy, healthy, sub-healthy, unhealthy and morbid landscapes are 13.23, 736.35, 184.5, 66.76 and 20.63 km², respectively. The healthy landscapes area accounts for 72.08% and most grasslands are healthy. The sub-healthy landscapes are mainly located around areas with higher disturbances due to human activities. The morbid or unhealthy landscapes are concentrated in the mining areas. The proposed CVORE model can enrich the foundations for the quantitative assessment of Landscape Ecological Health of Mining Cities in Semi-arid Steppe (LEHMCSS). This study provided a new LEH assessment approach (CVORE model), which can support landscape ecological restoration, ecological environmental protection and urban planning of the semi-arid steppe mining cities.},
}

@article {pmid30782660,
year = {2019},
author = {López-Pérez, M and Jayakumar, JM and Haro-Moreno, JM and Zaragoza-Solas, A and Reddi, G and Rodriguez-Valera, F and Shapiro, OH and Alam, M and Almagro-Moreno, S},
title = {Evolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.},
journal = {mBio},
volume = {10},
number = {1},
pages = {},
doi = {10.1128/mBio.02852-18},
pmid = {30782660},
issn = {2150-7511},
mesh = {Aquaculture ; Aquatic Organisms/microbiology ; Cluster Analysis ; Computational Biology ; *Ecotype ; Evolution, Molecular ; Gene Flow ; Gene Transfer, Horizontal ; *Genetic Variation ; Genome, Bacterial ; *Genotype ; Phenotype ; Recombination, Genetic ; Vibrio vulnificus/*classification/*genetics/isolation & purification/physiology ; },
abstract = {Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel "chromids," or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic. In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.},
}

Aquaculture
Aquatic Organisms/microbiology
Cluster Analysis
Computational Biology
*Ecotype
Evolution, Molecular
Gene Flow
Gene Transfer, Horizontal
*Genetic Variation
Genome, Bacterial
*Genotype
Phenotype
Recombination, Genetic
Vibrio vulnificus/*classification/*genetics/isolation & purification/physiology

@article {pmid30721227,
year = {2019},
author = {Marsland, R and Cui, W and Goldford, J and Sanchez, A and Korolev, K and Mehta, P},
title = {Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities.},
journal = {PLoS computational biology},
volume = {15},
number = {2},
pages = {e1006793},
doi = {10.1371/journal.pcbi.1006793},
pmid = {30721227},
issn = {1553-7358},
support = {R35 GM119461/GM/NIGMS NIH HHS/United States ; },
mesh = {Computational Biology ; Databases, Factual ; *Ecosystem ; Energy Metabolism/*physiology ; Microbial Consortia/*physiology ; Models, Biological ; Stochastic Processes ; Thermodynamics ; },
abstract = {A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a "resource-limited" regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species' consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.},
}

Computational Biology
Databases, Factual
*Ecosystem
Energy Metabolism/*physiology
Microbial Consortia/*physiology
Models, Biological
Stochastic Processes
Thermodynamics

@article {pmid30713051,
year = {2019},
author = {Reiczigel, J and Marozzi, M and Fábián, I and Rózsa, L},
title = {Biostatistics for Parasitologists - A Primer to Quantitative Parasitology.},
journal = {Trends in parasitology},
volume = {35},
number = {4},
pages = {277-281},
doi = {10.1016/j.pt.2019.01.003},
pmid = {30713051},
issn = {1471-5007},
mesh = {*Biostatistics ; Parasitology/*methods ; *Software ; },
abstract = {The aggregated distributions of host-parasite systems require several different infection parameters to characterize them. We advise readers how to choose infection indices with clear and distinct biological interpretations, and recommend statistical tests to compare them across samples. A user-friendly and free software is available online to overcome technical difficulties.},
}

*Biostatistics
Parasitology/*methods
*Software

@article {pmid30695030,
year = {2019},
author = {Yenni, GM and Christensen, EM and Bledsoe, EK and Supp, SR and Diaz, RM and White, EP and Ernest, SKM},
title = {Developing a modern data workflow for regularly updated data.},
journal = {PLoS biology},
volume = {17},
number = {1},
pages = {e3000125},
doi = {10.1371/journal.pbio.3000125},
pmid = {30695030},
issn = {1545-7885},
abstract = {Over the past decade, biology has undergone a data revolution in how researchers collect data and the amount of data being collected. An emerging challenge that has received limited attention in biology is managing, working with, and providing access to data under continual active collection. Regularly updated data present unique challenges in quality assurance and control, data publication, archiving, and reproducibility. We developed a workflow for a long-term ecological study that addresses many of the challenges associated with managing this type of data. We do this by leveraging existing tools to 1) perform quality assurance and control; 2) import, restructure, version, and archive data; 3) rapidly publish new data in ways that ensure appropriate credit to all contributors; and 4) automate most steps in the data pipeline to reduce the time and effort required by researchers. The workflow leverages tools from software development, including version control and continuous integration, to create a modern data management system that automates the pipeline.},
}

@article {pmid30658302,
year = {2019},
author = {Liu, Z and Tai, P and Li, X and Kong, L and Matthews, TG and Lester, RE and Mondon, JA},
title = {Deriving site-specific water quality criteria for ammonia from national versus international toxicity data.},
journal = {Ecotoxicology and environmental safety},
volume = {171},
number = {},
pages = {665-676},
doi = {10.1016/j.ecoenv.2018.12.078},
pmid = {30658302},
issn = {1090-2414},
mesh = {Ammonia/*toxicity ; Animals ; China ; Chironomidae/drug effects ; Copepoda/drug effects ; Daphnia/drug effects ; Databases, Factual ; Endpoint Determination ; Fishes ; Fresh Water/chemistry ; Geologic Sediments/chemistry ; Models, Theoretical ; Palaemonidae/drug effects ; Rivers/chemistry ; Toxicity Tests ; Water Pollutants, Chemical/*toxicity ; Water Quality/*standards ; },
abstract = {A key question to be asked when developing regional water quality criteria with scarce toxicity data is whether such data need to be locally derived. To address this, ammonia toxicity data from local aquatic species in the Liao River were compared against data from species native and non-native to China, based on comparisons of the overall trends of species sensitivity distributions and derived water quality criteria. Liao River data were acquired by acute and chronic tests using five local freshwater invertebrate species, and then compiled alongside published data from Chinese national guidelines and international literature. Models of best fit using three species sensitivity distribution approaches (log-logistic, log-normal, and Burr III) did not vary markedly (r2 >0.9), and no specific model provided a best fit across all data sets. The comparisons of the overall trend of species sensitivity distribution curves showed no significant differences at either a national (Chinese native taxa tested in China versus non-native taxa) or regional level (Liao River taxa versus non-Liao River taxa). The comparisons also revealed that the inclusion or exclusions of different ecological groups had little influence on the overall trends of species sensitivity distributions. These findings suggested data on non-local and non-native species, and data from local species tested elsewhere, could be appropriate for guiding the derivation of ammonia water quality criteria for regions such as Liao River. However, caution is needed when using hazardous concentration 5% values in the development of site-specific water quality criteria for a river basin due to the considerable variation observed for ammonia (16.8-56.6 mg/L), although these differences were not statistically significant. Based on the toxicity test evaluation, a preliminary acute value of 10.0 mg/L and chronic value of 1.7 mg/L (at pH of 7.0 and 20 °C) are proposed as site-specific ammonia water quality criteria for the Liao River, China.},
}

Ammonia/*toxicity
Animals
China
Chironomidae/drug effects
Copepoda/drug effects
Daphnia/drug effects
Databases, Factual
Endpoint Determination
Fishes
Fresh Water/chemistry
Geologic Sediments/chemistry
Models, Theoretical
Palaemonidae/drug effects
Rivers/chemistry
Toxicity Tests
Water Pollutants, Chemical/*toxicity
Water Quality/*standards

@article {pmid30651533,
year = {2019},
author = {Perkins, DM and Perna, A and Adrian, R and Cermeño, P and Gaedke, U and Huete-Ortega, M and White, EP and Yvon-Durocher, G},
title = {Energetic equivalence underpins the size structure of tree and phytoplankton communities.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {255},
doi = {10.1038/s41467-018-08039-3},
pmid = {30651533},
issn = {2041-1723},
mesh = {Autotrophic Processes ; Biomass ; Biota/*physiology ; Energy Metabolism/*physiology ; Forests ; *Models, Biological ; Phytoplankton/*physiology ; Trees/*physiology ; },
abstract = {The size structure of autotroph communities - the relative abundance of small vs. large individuals - shapes the functioning of ecosystems. Whether common mechanisms underpin the size structure of unicellular and multicellular autotrophs is, however, unknown. Using a global data compilation, we show that individual body masses in tree and phytoplankton communities follow power-law distributions and that the average exponents of these individual size distributions (ISD) differ. Phytoplankton communities are characterized by an average ISD exponent consistent with three-quarter-power scaling of metabolism with body mass and equivalence in energy use among mass classes. Tree communities deviate from this pattern in a manner consistent with equivalence in energy use among diameter size classes. Our findings suggest that whilst universal metabolic constraints ultimately underlie the emergent size structure of autotroph communities, divergent aspects of body size (volumetric vs. linear dimensions) shape the ecological outcome of metabolic scaling in forest vs. pelagic ecosystems.},
}

Autotrophic Processes
Biomass
Biota/*physiology
Energy Metabolism/*physiology
Forests
*Models, Biological
Phytoplankton/*physiology
Trees/*physiology

@article {pmid30625219,
year = {2019},
author = {Ožana, S and Burda, M and Hykel, M and Malina, M and Prášek, M and Bárta, D and Dolný, A},
title = {Dragonfly Hunter CZ: Mobile application for biological species recognition in citizen science.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210370},
doi = {10.1371/journal.pone.0210370},
pmid = {30625219},
issn = {1932-6203},
abstract = {Citizen science and data collected from various volunteers have an interesting potential in aiding the understanding of many biological and ecological processes. We describe a mobile application that allows the public to map and report occurrences of the odonata species (dragonflies and damselflies) found in the Czech Republic. The application also helps in species classification based on observation details such as date, GPS coordinates, and the altitude, biotope, suborder, and colour. Dragonfly Hunter CZ is a free Android application built on the open-source framework NativeScript using the JavaScript programming language which is now fully available on Google Play. The server side is powered by Apache Server with PHP and MariaDB SQL database. A mobile application is a fast and accurate way to obtain data pertaining to the odonata species, which can be used after expert verification for ecological studies and conservation basis like Red Lists and policy instruments. We expect it to be effective in encouraging Citizen Science and in promoting the proactive reporting of odonates. It can also be extended to the reporting and monitoring of other plant and animal species.},
}

@article {pmid30589896,
year = {2018},
author = {Shimamoto, CY and Padial, AA and da Rosa, CM and Marques, MCM},
title = {Restoration of ecosystem services in tropical forests: A global meta-analysis.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208523},
doi = {10.1371/journal.pone.0208523},
pmid = {30589896},
issn = {1932-6203},
mesh = {Carbon/chemistry ; Databases, Factual ; Ecology ; *Ecosystem ; *Environmental Restoration and Remediation ; *Forests ; Soil/chemistry ; Tropical Climate ; },
abstract = {To reverse the effects of deforestation, tropical areas have expanded restoration efforts in recent years. As ecological restoration positively affects the structure and function of degraded ecosystems, understanding to what extent restoration recovers ecosystem services (ES) is an important step in directing large-scale restoration actions. We evaluated the effect of restoration in increasing the provision of ES in tropical forests. We performed a global meta-analysis of ecological indicators of the ES provided in restored areas, degraded areas and reference ecosystems. We tested for the effects of different restoration strategies, different types of degradation and for the effects of restoration over time. Overall, restoration actions contributed to a significant increase in levels of ecological indicators of ES (carbon pool, soil attributes and biodiversity protection) compared to disturbed areas. Among the restoration strategies, the natural regeneration was the most effective. Biodiversity protection and carbon recovered better than soil attributes. All other restoration strategies recovered ES to a substantially lesser degree, and reforestation with exotics decreased the ES of areas degraded by agriculture. In areas degraded by pasture, restoration was more effective in recovering the biodiversity protection, whereas in areas degraded by agriculture, the restoration recovered mainly the carbon pool. Our results show that by choosing the correct strategy, restoration can recover much of the ES lost by the degradation of tropical forests. These results should be considered for large-scale conservation and management efforts for this biome.},
}

Carbon/chemistry
Databases, Factual
Ecology
*Ecosystem
*Environmental Restoration and Remediation
*Forests
Soil/chemistry
Tropical Climate

@article {pmid30587126,
year = {2018},
author = {Bochkareva, OO and Moroz, EV and Davydov, II and Gelfand, MS},
title = {Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {965},
doi = {10.1186/s12864-018-5245-1},
pmid = {30587126},
issn = {1471-2164},
support = {18-14-00358//Russian Science Foundation/ ; 16-54-21004//Russian Foundation of Basic Research/ ; IZLRZ3\163872//Swiss National Science Foundation/ ; },
mesh = {Burkholderia/classification/*genetics ; *Chromosomes, Bacterial ; Databases, Genetic ; Gene Rearrangement/*genetics ; Phylogeny ; },
abstract = {BACKGROUND: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.

RESULTS: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.

CONCLUSIONS: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.},
}

Burkholderia/classification/*genetics
*Chromosomes, Bacterial
Databases, Genetic
Gene Rearrangement/*genetics
Phylogeny

@article {pmid30571696,
year = {2018},
author = {Somveille, M and Firth, JA and Aplin, LM and Farine, DR and Sheldon, BC and Thompson, RN},
title = {Movement and conformity interact to establish local behavioural traditions in animal populations.},
journal = {PLoS computational biology},
volume = {14},
number = {12},
pages = {e1006647},
doi = {10.1371/journal.pcbi.1006647},
pmid = {30571696},
issn = {1553-7358},
support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Behavior, Animal ; Computational Biology ; Ecosystem ; England ; Learning ; *Models, Biological ; Models, Psychological ; Passeriformes/physiology ; Population Dynamics ; *Social Behavior ; },
abstract = {The social transmission of information is critical to the emergence of animal culture. Two processes are predicted to play key roles in how socially-transmitted information spreads in animal populations: the movement of individuals across the landscape and conformist social learning. We develop a model that, for the first time, explicitly integrates these processes to investigate their impacts on the spread of behavioural preferences. Our results reveal a strong interplay between movement and conformity in determining whether locally-variable traditions establish across a landscape or whether a single preference dominates the whole population. The model is able to replicate a real-world cultural diffusion experiment in great tits Parus major, but also allows for a range of predictions for the emergence of animal culture under various initial conditions, habitat structure and strength of conformist bias to be made. Integrating social behaviour with ecological variation will be important for understanding the stability and diversity of culture in animals.},
}

Animals
*Behavior, Animal
Computational Biology
Ecosystem
England
Learning
*Models, Biological
Models, Psychological
Passeriformes/physiology
Population Dynamics
*Social Behavior

@article {pmid30568285,
year = {2019},
author = {Strassburg, BBN and Beyer, HL and Crouzeilles, R and Iribarrem, A and Barros, F and de Siqueira, MF and Sánchez-Tapia, A and Balmford, A and Sansevero, JBB and Brancalion, PHS and Broadbent, EN and Chazdon, RL and Filho, AO and Gardner, TA and Gordon, A and Latawiec, A and Loyola, R and Metzger, JP and Mills, M and Possingham, HP and Rodrigues, RR and Scaramuzza, CAM and Scarano, FR and Tambosi, L and Uriarte, M},
title = {Strategic approaches to restoring ecosystems can triple conservation gains and halve costs.},
journal = {Nature ecology & evolution},
volume = {3},
number = {1},
pages = {62-70},
doi = {10.1038/s41559-018-0743-8},
pmid = {30568285},
issn = {2397-334X},
mesh = {Brazil ; Carbon Sequestration ; Conservation of Natural Resources/*economics ; Cost-Benefit Analysis ; *Ecosystem ; },
abstract = {International commitments for ecosystem restoration add up to one-quarter of the world's arable land. Fulfilling them would ease global challenges such as climate change and biodiversity decline but could displace food production and impose financial costs on farmers. Here, we present a restoration prioritization approach capable of revealing these synergies and trade-offs, incorporating ecological and economic efficiencies of scale and modelling specific policy options. Using an actual large-scale restoration target of the Atlantic Forest hotspot, we show that our approach can deliver an eightfold increase in cost-effectiveness for biodiversity conservation compared with a baseline of non-systematic restoration. A compromise solution avoids 26% of the biome's current extinction debt of 2,864 plant and animal species (an increase of 257% compared with the baseline). Moreover, this solution sequesters 1 billion tonnes of CO2-equivalent (a 105% increase) while reducing costs by US$28 billion (a 57% decrease). Seizing similar opportunities elsewhere would offer substantial contributions to some of the greatest challenges for humankind.},
}

Brazil
Carbon Sequestration
Conservation of Natural Resources/*economics
Cost-Benefit Analysis
*Ecosystem

@article {pmid30565882,
year = {2019},
author = {Haller, BC and Galloway, J and Kelleher, J and Messer, PW and Ralph, PL},
title = {Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes.},
journal = {Molecular ecology resources},
volume = {19},
number = {2},
pages = {552-566},
doi = {10.1111/1755-0998.12968},
pmid = {30565882},
issn = {1755-0998},
support = {//Alfred P. Sloan Foundation/ ; 100956/Z/13/Z//Wellcome Trust/United Kingdom ; DBI-1262645//National Science Foundation/ ; SS/05/01//Predator Free 2050/ ; R21AI130635//National Institutes of Health/ ; //College of Agriculture and Life Sciences, Cornell University/ ; //Wellcome Trust/United Kingdom ; R01 GM127418/GM/NIGMS NIH HHS/United States ; R21 AI130635/AI/NIAID NIH HHS/United States ; R01GM127418//National Institutes of Health/ ; },
mesh = {*Biological Evolution ; Computational Biology ; Computer Simulation ; Genetics, Population/*methods ; Software ; },
abstract = {There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using "recapitation"; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.},
}

*Biological Evolution
Computational Biology
Computer Simulation
Genetics, Population/*methods
Software

@article {pmid30540766,
year = {2018},
author = {Taff, CC and Freeman-Gallant, CR and Streby, HM and Kramer, GR},
title = {Geolocator deployment reduces return rate, alters selection, and impacts demography in a small songbird.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0207783},
doi = {10.1371/journal.pone.0207783},
pmid = {30540766},
issn = {1932-6203},
mesh = {Animal Migration/physiology ; Animals ; Behavior, Animal/physiology ; Breeding ; Conservation of Natural Resources/methods ; Demography/*methods ; Ecology/instrumentation/methods ; Geographic Information Systems/*instrumentation/trends ; Reproduction ; Seasons ; Songbirds/physiology ; },
abstract = {In the past few years, miniature light-level geolocators have been developed for tracking wild bird species that were previously too small to track during their full annual cycle. Geolocators offer an exciting opportunity to study the full annual cycle for many species. However, the potential detrimental effects of carrying geolocators are still poorly understood, especially for small-bodied birds. Here, we deployed light-level geolocators on common yellowthroat warblers (Geothlypis trichas). Over two years, we monitored return rates and neighborhood demography for 40 warblers carrying a geolocator and 20 reference birds that did not carry a geolocator. We compared the two groups with long-term data from 108 unmanipulated birds breeding at the same location in previous and subsequent years. Overall, we found that individuals carrying a geolocator were less likely to return to the study site in the following year (21% to 33% returned, depending on inclusion criteria) than either contemporaneous controls (55%) or long-term controls (55%). Among birds marked with geolocators, we also detected viability selection for greater wing length, whereas this pattern was not present in control birds. Finally, in each year after geolocator deployment, inexperienced breeders colonized vacant territories and this demographic effect persisted for two years after deployment. Sexual selection and ornamentation are strongly age-dependent in this system, and behavioral data collected after geolocator deployment is likely to differ systematically from natural conditions. Clearly geolocators will continue to be useful tools, but we suggest that future studies should carefully consider the potential for biased returns and the ecological validity of behavioral data collected from geolocator marked populations.},
}

Animal Migration/physiology
Animals
Behavior, Animal/physiology
Breeding
Conservation of Natural Resources/methods
Demography/*methods
Ecology/instrumentation/methods
Geographic Information Systems/*instrumentation/trends
Reproduction
Seasons
Songbirds/physiology

@article {pmid30533308,
year = {2018},
author = {Jenkins, MF and White, EP and Hurlbert, AH},
title = {The proportion of core species in a community varies with spatial scale and environmental heterogeneity.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6019},
pmid = {30533308},
issn = {2167-8359},
abstract = {Ecological communities are composed of a combination of core species that maintain local viable populations and transient species that occur infrequently due to dispersal from surrounding regions. Preliminary work indicates that while core and transient species are both commonly observed in community surveys of a wide range of taxonomic groups, their relative prevalence varies substantially from one community to another depending upon the spatial scale at which the community was characterized and its environmental context. We used a geographically extensive dataset of 968 bird community time series to quantitatively describe how the proportion of core species in a community varies with spatial scale and environmental heterogeneity. We found that the proportion of core species in an assemblage increased with spatial scale in a positive decelerating fashion with a concomitant decrease in the proportion of transient species. Variation in the shape of this scaling relationship between sites was related to regional environmental heterogeneity, with lower proportions of core species at a given scale associated with high environmental heterogeneity. Understanding this influence of scale and environmental heterogeneity on the proportion of core species may help resolve discrepancies between studies of biotic interactions, resource availability, and mass effects conducted at different scales, because the importance of these and other ecological processes are expected to differ substantially between core and transient species.},
}

@article {pmid30499218,
year = {2019},
author = {Taylor, SD and Meiners, JM and Riemer, K and Orr, MC and White, EP},
title = {Comparison of large-scale citizen science data and long-term study data for phenology modeling.},
journal = {Ecology},
volume = {100},
number = {2},
pages = {e02568},
doi = {10.1002/ecy.2568},
pmid = {30499218},
issn = {0012-9658},
support = {GBMF4563//Gordon and Betty Moore Foundation/ ; //University of Florida Biodiversity Institute Graduate Research Fellowship/ ; },
abstract = {Large-scale observational data from citizen science efforts are becoming increasingly common in ecology, and researchers often choose between these and data from intensive local-scale studies for their analyses. This choice has potential trade-offs related to spatial scale, observer variance, and interannual variability. Here we explored this issue with phenology by comparing models built using data from the large-scale, citizen science USA National Phenology Network (USA-NPN) effort with models built using data from more intensive studies at Long Term Ecological Research (LTER) sites. We built statistical and process based phenology models for species common to each data set. From these models, we compared parameter estimates, estimates of phenological events, and out-of-sample errors between models derived from both USA-NPN and LTER data. We found that model parameter estimates for the same species were most similar between the two data sets when using simple models, but parameter estimates varied widely as model complexity increased. Despite this, estimates for the date of phenological events and out-of-sample errors were similar, regardless of the model chosen. Predictions for USA-NPN data had the lowest error when using models built from the USA-NPN data, while LTER predictions were best made using LTER-derived models, confirming that models perform best when applied at the same scale they were built. This difference in the cross-scale model comparison is likely due to variation in phenological requirements within species. Models using the USA-NPN data set can integrate parameters over a large spatial scale while those using an LTER data set can only estimate parameters for a single location. Accordingly, the choice of data set depends on the research question. Inferences about species-specific phenological requirements are best made with LTER data, and if USA-NPN or similar data are all that is available, then analyses should be limited to simple models. Large-scale predictive modeling is best done with the larger-scale USA-NPN data, which has high spatial representation and a large regional species pool. LTER data sets, on the other hand, have high site fidelity and thus characterize inter-annual variability extremely well. Future research aimed at forecasting phenology events for particular species over larger scales should develop models that integrate the strengths of both data sets.},
}

@article {pmid30446752,
year = {2018},
author = {Felipe-Lucia, MR and Soliveres, S and Penone, C and Manning, P and van der Plas, F and Boch, S and Prati, D and Ammer, C and Schall, P and Gossner, MM and Bauhus, J and Buscot, F and Blaser, S and Blüthgen, N and de Frutos, A and Ehbrecht, M and Frank, K and Goldmann, K and Hänsel, F and Jung, K and Kahl, T and Nauss, T and Oelmann, Y and Pena, R and Polle, A and Renner, S and Schloter, M and Schöning, I and Schrumpf, M and Schulze, ED and Solly, E and Sorkau, E and Stempfhuber, B and Tschapka, M and Weisser, WW and Wubet, T and Fischer, M and Allan, E},
title = {Multiple forest attributes underpin the supply of multiple ecosystem services.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {4839},
pmid = {30446752},
issn = {2041-1723},
mesh = {Conservation of Natural Resources/*methods ; Ecosystem ; Europe ; Forestry/*methods/trends ; *Forests ; Humans ; Trees/*physiology ; },
abstract = {Trade-offs and synergies in the supply of forest ecosystem services are common but the drivers of these relationships are poorly understood. To guide management that seeks to promote multiple services, we investigated the relationships between 12 stand-level forest attributes, including structure, composition, heterogeneity and plant diversity, plus 4 environmental factors, and proxies for 14 ecosystem services in 150 temperate forest plots. Our results show that forest attributes are the best predictors of most ecosystem services and are also good predictors of several synergies and trade-offs between services. Environmental factors also play an important role, mostly in combination with forest attributes. Our study suggests that managing forests to increase structural heterogeneity, maintain large trees, and canopy gaps would promote the supply of multiple ecosystem services. These results highlight the potential for forest management to encourage multifunctional forests and suggest that a coordinated landscape-scale strategy could help to mitigate trade-offs in human-dominated landscapes.},
}

Conservation of Natural Resources/*methods
Ecosystem
Europe
Forestry/*methods/trends
*Forests
Humans
Trees/*physiology

@article {pmid30431668,
year = {2018},
author = {Portnoy, GA and Relyea, MR and Decker, S and Shamaskin-Garroway, A and Driscoll, M and Brandt, CA and Haskell, SG},
title = {Understanding Gender Differences in Resilience Among Veterans: Trauma History and Social Ecology.},
journal = {Journal of traumatic stress},
volume = {31},
number = {6},
pages = {845-855},
doi = {10.1002/jts.22341},
pmid = {30431668},
issn = {1573-6598},
support = {VA IIR 12-118//Health Services Research and Development/ ; },
abstract = {A social-ecological framework for resilience underscores the importance of conceptualizing individuals embedded within their context when evaluating a person's vulnerability and adaptation to stress. Despite a high level of trauma exposure, most veterans exhibit psychological resilience following a traumatic event. Interpersonal trauma is associated with poorer psychological outcomes than noninterpersonal trauma and is experienced more frequently across the lifespan by women as compared to men. In the present study, we examined gender differences in trauma exposure, resilience, and protective factors among veterans. Participants included 665 veterans who completed a baseline survey assessing traumatic events; 544 veterans (81.8%) completed a 1-year follow-up survey assessing resilience, combat exposure, deployment social support, deployment preparedness, and military sexual trauma (MST). Principal component analyses revealed the Traumatic Life Events Questionnaire categorized into four meaningful components: sexual abuse, interpersonal violence, stranger violence, and accidents/unexpected trauma. Women reported greater exposure to sexual abuse, d = 0.76; interpersonal violence, d = 0.31; and MST, Cramer's V = 0.54; men reported greater exposure to stranger violence, accidents/unexpected trauma, and combat exposure, ds = 0.24-0.55. Compared to women, men also reported greater social support during deployment, d = 0.46. Hierarchical linear regression indicated that men's resilience scores were higher than women's, β = .10, p = .032, yet this association was no longer significant once we accounted for trauma type, β = .07, p = .197. Results indicate that trauma type is central to resilience and suggest one must consider the social-ecological context that can promote or inhibit resilient processes.},
}

@article {pmid30417109,
year = {2018},
author = {Mazel, F and Davis, KM and Loudon, A and Kwong, WK and Groussin, M and Parfrey, LW},
title = {Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.},
journal = {mSystems},
volume = {3},
number = {5},
pages = {},
pmid = {30417109},
issn = {2379-5077},
abstract = {Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.},
}

@article {pmid30413903,
year = {2019},
author = {Sánchez-Giraldo, C and Daza, JM},
title = {Getting better temporal and spatial ecology data for threatened species: using lightweight GPS devices for small primate monitoring in the northern Andes of Colombia.},
journal = {Primates; journal of primatology},
volume = {60},
number = {1},
pages = {93-102},
doi = {10.1007/s10329-018-0696-1},
pmid = {30413903},
issn = {1610-7365},
mesh = {Animals ; Colombia ; Ecology/*methods ; Endangered Species ; Female ; Geographic Information Systems/*instrumentation ; *Homing Behavior ; Male ; Saguinus/*physiology ; },
abstract = {The use of GPS telemetry has been a reliable research tool for the study of primate biology in recent years. Although in the past technological restrictions limited its use mainly to large primates, recent improvements in battery size make it possible to use this technology for small species. We used GPS devices for monitoring two adult white-footed tamarins (Saguinus leucopus) from a free-ranging group, and assessed its applicability for recording spatial and ecological data. GPS devices were operational for 66 and 85 days, recording 221 positions (36.6% acquisition rate; 73% of which were highly accurate) and 3195 activity values for both individuals. Depending on the estimation method, we calculated the home range size for the group to be 19.4 and 22.9 ha, which were within the range for the species in other localities. The animals were active each day for 11 h, with high activity during the early morning. The monkeys showed a constant and alternate use of four sleeping sites with a limited reuse of the same site on consecutive nights. These daily activity and sleeping site use patterns are similar to those reported for other Saguinus species. Based on the kind and quality of the data recorded, we consider GPS telemetry to be an efficient and advantageous method for tracking and obtaining ecological information from S. leucopus. In comparison to other data collection methods, GPS telemetry required fewer personnel and less time commitment to record data without compromising the accuracy of the spatial and activity information we obtained.},
}

Animals
Colombia
Ecology/*methods
Endangered Species
Female
Geographic Information Systems/*instrumentation
*Homing Behavior
Male
Saguinus/*physiology

@article {pmid30413098,
year = {2018},
author = {Trotter, RT and Lininger, MR and Camplain, R and Fofanov, VY and Camplain, C and Baldwin, JA},
title = {A Survey of Health Disparities, Social Determinants of Health, and Converging Morbidities in a County Jail: A Cultural-Ecological Assessment of Health Conditions in Jail Populations.},
journal = {International journal of environmental research and public health},
volume = {15},
number = {11},
pages = {},
pmid = {30413098},
issn = {1660-4601},
support = {U54 MD012388/MD/NIMHD NIH HHS/United States ; U54MD012388/MD/NIMHD NIH HHS/United States ; },
mesh = {Adult ; Female ; *Health Status Disparities ; Health Surveys ; Humans ; Male ; Morbidity ; *Prisoners ; Prisons ; *Social Determinants of Health ; United States ; },
abstract = {The environmental health status of jail populations in the United States constitutes a significant public health threat for prisoners and the general population. The ecology of jails creates a dynamic condition in relation to general population health due to the concentrated potential exposure to infectious diseases, difficult access to treatment for chronic health conditions, interruption in continuity of care for serious behavioral health conditions, as well as on-going issues for the prevention and treatment of substance abuse disorders. This paper reports on elements of a cross-sectional survey embedded in a parent project, "Health Disparities in Jail Populations." The overall project includes a comprehensive secondary data analysis of the health status of county jail populations, along with primary data collection that includes a cross-sectional health and health care services survey of incarcerated individuals, coupled with collection of biological samples to investigate infectious disease characteristics of a county jail population. This paper reports on the primary results of the survey data collection that indicate that this is a population with complex and interacting co-morbidities, as well as significant health disparities compared to the general population.},
}

Adult
Female
*Health Status Disparities
Health Surveys
Humans
Male
Morbidity
*Prisoners
Prisons
*Social Determinants of Health
United States

@article {pmid30410743,
year = {2018},
author = {Munos, MK and Maiga, A and Do, M and Sika, GL and Carter, ED and Mosso, R and Dosso, A and Leyton, A and Khan, SM},
title = {Linking household survey and health facility data for effective coverage measures: a comparison of ecological and individual linking methods using the Multiple Indicator Cluster Survey in Côte d'Ivoire.},
journal = {Journal of global health},
volume = {8},
number = {2},
pages = {020803},
pmid = {30410743},
issn = {2047-2986},
mesh = {Adolescent ; Adult ; Child, Preschool ; Cote d'Ivoire ; Ecology ; Feasibility Studies ; Female ; *Health Care Surveys ; Health Services Needs and Demand ; Humans ; Infant ; Infant, Newborn ; Information Storage and Retrieval/*methods ; *Medical Record Linkage ; Middle Aged ; Patient Acceptance of Health Care/*statistics & numerical data ; Pregnancy ; Quality of Health Care ; Reproducibility of Results ; Young Adult ; },
abstract = {Background: Population-based measures of intervention coverage are used in low- and middle-income countries for program planning, prioritization, and evaluation. There is increased interest in effective coverage, which integrates information about service quality or health outcomes. Approaches proposed for quality-adjusted effective coverage include linking data on need and service contact from population-based surveys with data on service quality from health facility surveys. However, there is limited evidence about the validity of different linking methods for effective coverage estimation.

Methods: We collaborated with the 2016 Côte d'Ivoire Multiple Indicator Cluster Survey (MICS) to link data from a health provider assessment to care-seeking data collected by the MICS in the Savanes region of Côte d'Ivoire. The provider assessment was conducted in a census of public and non-public health facilities and pharmacies in Savanes in May-June 2016. We also included community health workers managing sick children who served the clusters sampled for the MICS. The provider assessment collected information on structural and process quality for antenatal care, delivery and immediate newborn care, postnatal care, and sick child care. We linked the MICS and provider data using exact-match and ecological linking methods, including aggregate linking and geolinking methods. We compared the results obtained from exact-match and ecological methods.

Results: We linked 731 of 786 care-seeking episodes (93%) from the MICS to a structural quality score for the provider named by the respondent. Effective coverage estimates computed using exact-match methods were 13%-63% lower than the care-seeking estimates from the MICS. Absolute differences between exact match and ecological linking methods were ±7 percentage points for all ecological methods. Incorporating adjustments for provider category and weighting by service-specific utilization into the ecological methods generally resulted in better agreement between ecological and exact match estimates.

Conclusions: Ecological linking may be a feasible and valid approach for estimating quality-adjusted effective coverage when a census of providers is used. Adjusting for provider type and caseload may improve agreement with exact match results. There remain methodological questions to be addressed to develop guidance on using linking methods for estimating quality-adjusted effective coverage, including the effect of facility sampling and time displacement.},
}

Adolescent
Adult
Child, Preschool
Cote d'Ivoire
Ecology
Feasibility Studies
Female
*Health Care Surveys
Health Services Needs and Demand
Humans
Infant
Infant, Newborn
Information Storage and Retrieval/*methods
*Medical Record Linkage
Middle Aged
Patient Acceptance of Health Care/*statistics & numerical data
Pregnancy
Quality of Health Care
Reproducibility of Results
Young Adult

@article {pmid30409881,
year = {2018},
author = {Kubelka, V and Šálek, M and Tomkovich, P and Végvári, Z and Freckleton, RP and Székely, T},
title = {Global pattern of nest predation is disrupted by climate change in shorebirds.},
journal = {Science (New York, N.Y.)},
volume = {362},
number = {6415},
pages = {680-683},
doi = {10.1126/science.aat8695},
pmid = {30409881},
issn = {1095-9203},
mesh = {Animals ; Birds/*physiology ; *Climate Change ; Databases, Factual ; Nesting Behavior/*physiology ; Predatory Behavior/*physiology ; },
abstract = {Ongoing climate change is thought to disrupt trophic relationships, with consequences for complex interspecific interactions, yet the effects of climate change on species interactions are poorly understood, and such effects have not been documented at a global scale. Using a single database of 38,191 nests from 237 populations, we found that shorebirds have experienced a worldwide increase in nest predation over the past 70 years. Historically, there existed a latitudinal gradient in nest predation, with the highest rates in the tropics; however, this pattern has been recently reversed in the Northern Hemisphere, most notably in the Arctic. This increased nest predation is consistent with climate-induced shifts in predator-prey relationships.},
}

Animals
Birds/*physiology
*Climate Change
Databases, Factual
Nesting Behavior/*physiology
Predatory Behavior/*physiology

@article {pmid30384907,
year = {2018},
author = {Bamisile, BS and Dash, CK and Akutse, KS and Keppanan, R and Afolabi, OG and Hussain, M and Qasim, M and Wang, L},
title = {Prospects of endophytic fungal entomopathogens as biocontrol and plant growth promoting agents: An insight on how artificial inoculation methods affect endophytic colonization of host plants.},
journal = {Microbiological research},
volume = {217},
number = {},
pages = {34-50},
doi = {10.1016/j.micres.2018.08.016},
pmid = {30384907},
issn = {1618-0623},
mesh = {*Agricultural Inoculants ; Animals ; Beauveria/physiology ; Biological Control Agents/*pharmacology ; Databases, Factual ; Endophytes/growth & development/*physiology ; Host-Pathogen Interactions/physiology ; Insecta/drug effects ; Pest Control, Biological/*methods ; *Plant Development ; Plant Diseases/microbiology/*prevention & control ; Plant Roots/microbiology ; Plant Stems/microbiology ; Plants/*microbiology ; Seedlings/microbiology ; Soil ; Sorghum/microbiology ; },
abstract = {Entomopathogenic fungi (EPF) can be established as endophytes in the host plants to offer a long-term preventive measure for pests and diseases. This practice serves as a better alternative to the common practice of periodic direct application of EPF on plants or the target pests as a short-term defense strategy against pests and diseases. These fungal endophytes, aside from their role in pests and diseases prevention, also act as plant growth promoters. Several fungal endophytes have been associated with improvement in plant height, dry and wet weight and other growth parameters. However, many limiting factors have been identified as mitigating the successful colonization of the host plants by EPF. The inoculation methods used have been identified as one, but sadly, this has received little or less attention. Some previous studies carried out comparison between various artificial inoculation methods; foliar application, seedling dipping, soil drenching, seed inoculation, direct injection and others. In separate studies, some authors had suggested different application methods that are best suitable for certain fungal entomopathogens. For instance, leaf inoculation with conidial suspensions was suggested to be the best inoculation method for Beauveria bassiana in sorghum, stem injection was suggested as the most suitable for coffee, while, root dipping method proved the most successful for B. bassiana colonization of tomato plants for the management of Helicoverpa armigera. Here, we discussed entomopathogenic fungal endophytes as bio-control agents, plant growth promoters and highlighted the effect of various artificial inoculation methods on their endophytic colonization of the host plants.},
}

*Agricultural Inoculants
Animals
Beauveria/physiology
Biological Control Agents/*pharmacology
Databases, Factual
Endophytes/growth & development/*physiology
Host-Pathogen Interactions/physiology
Insecta/drug effects
Pest Control, Biological/*methods
*Plant Development
Plant Diseases/microbiology/*prevention & control
Plant Roots/microbiology
Plant Stems/microbiology
Plants/*microbiology
Seedlings/microbiology
Soil
Sorghum/microbiology

@article {pmid30366399,
year = {2018},
author = {Meng, X and Wang, F and Xie, Y and Song, G and Ma, S and Hu, S and Bai, J and Yang, Y},
title = {An Ontology-Driven Approach for Integrating Intelligence to Manage Human and Ecological Health Risks in the Geospatial Sensor Web.},
journal = {Sensors (Basel, Switzerland)},
volume = {18},
number = {11},
pages = {},
pmid = {30366399},
issn = {1424-8220},
support = {41501441//National Natural Science Foundation of China/ ; 2014HB04//Hubei Provincial Environment Protection Project/ ; GDGTKJ2017001//Guangdong Provincial Land Resource Research Project/ ; 2042017kf0212//Wuhan University Grant/ ; },
mesh = {Ecology ; Environmental Monitoring/*methods ; *Geographic Information Systems ; Humans ; Intelligence ; Software ; },
abstract = {Due to the rapid installation of a massive number of fixed and mobile sensors, monitoring machines are intentionally or unintentionally involved in the production of a large amount of geospatial data. Environmental sensors and related software applications are rapidly altering human lifestyles and even impacting ecological and human health. However, there are rarely specific geospatial sensor web (GSW) applications for certain ecological public health questions. In this paper, we propose an ontology-driven approach for integrating intelligence to manage human and ecological health risks in the GSW. We design a Human and Ecological health Risks Ontology (HERO) based on a semantic sensor network ontology template. We also illustrate a web-based prototype, the Human and Ecological Health Risk Management System (HaEHMS), which helps health experts and decision makers to estimate human and ecological health risks. We demonstrate this intelligent system through a case study of automatic prediction of air quality and related health risk.},
}

Ecology
Environmental Monitoring/*methods
*Geographic Information Systems
Humans
Intelligence
Software

@article {pmid30344120,
year = {2018},
author = {Gopalakrishnan, S and Sinding, MS and Ramos-Madrigal, J and Niemann, J and Samaniego Castruita, JA and Vieira, FG and Carøe, C and Montero, MM and Kuderna, L and Serres, A and González-Basallote, VM and Liu, YH and Wang, GD and Marques-Bonet, T and Mirarab, S and Fernandes, C and Gaubert, P and Koepfli, KP and Budd, J and Rueness, EK and Heide-Jørgensen, MP and Petersen, B and Sicheritz-Ponten, T and Bachmann, L and Wiig, Ø and Hansen, AJ and Gilbert, MTP},
title = {Interspecific Gene Flow Shaped the Evolution of the Genus Canis.},
journal = {Current biology : CB},
volume = {28},
number = {21},
pages = {3441-3449.e5},
pmid = {30344120},
issn = {1879-0445},
support = {U01 MH106874/MH/NIMH NIH HHS/United States ; },
abstract = {The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1-6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals, encompassing the global diversity of seven extant canid lineages. This includes eight new genomes, including the first resequenced Ethiopian wolf (Canis simensis), one dhole (Cuon alpinus), two East African hunting dogs (Lycaon pictus), two Eurasian golden jackals (Canis aureus), and two Middle Eastern gray wolves (Canis lupus). The relationships between the Ethiopian wolf, African golden wolf, and golden jackal were resolved. We highlight the role of interspecific hybridization in the evolution of this charismatic group. Specifically, we find gene flow between the ancestors of the dhole and African hunting dog and admixture between the gray wolf, coyote (Canis latrans), golden jackal, and African golden wolf. Additionally, we report gene flow from gray and Ethiopian wolves to the African golden wolf, suggesting that the African golden wolf originated through hybridization between these species. Finally, we hypothesize that coyotes and gray wolves carry genetic material derived from a "ghost" basal canid lineage.},
}

@article {pmid30325353,
year = {2018},
author = {Du, E},
title = {A database of annual atmospheric acid and nutrient deposition to China's forests.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180223},
pmid = {30325353},
issn = {2052-4463},
mesh = {Acid Rain ; Air Pollutants/*analysis ; China ; *Databases, Factual ; *Environmental Monitoring ; *Forests ; },
abstract = {Anthropogenic emissions have substantially altered atmospheric acid and nutrient deposition in China. Understanding the status and characteristics of acid and nutrient deposition to China's forests is crucial to assess the consequent impacts, and to better guide forest management options. Based on a comprehensive literature review, here I present an updated database for annual acid and nutrient deposition during the period 1991-2015 in China's forests (CFAND 2.0). The database includes information from 56 forested sites on the water fluxes of bulk precipitation and throughfall, the concentrations of H+ (pH), dissolved inorganic nitrogen (N) (NH4+ and NO3-), sulfur (S), dissolved phosphorus (P), potassium (K+), calcium (Ca2+) and magnesium (Mg2+) in bulk precipitation and throughfall, and the fluxes of dissolved inorganic N, S, dissolved P, K+, Ca2+ and Mg2+ in bulk deposition and throughfall. This database will help to understand the spatial patterns of acid and nutrient deposition, validate modelling results of acid and nutrient deposition and assess the ecological effects of acid and nutrient deposition in China's forests.},
}

Acid Rain
Air Pollutants/*analysis
China
*Databases, Factual
*Environmental Monitoring
*Forests

@article {pmid30269263,
year = {2018},
author = {Li, W and Liu, S and Pei, Y and He, J and Wang, Q},
title = {Zoning for eco-geological environment before mining in Yushenfu mining area, northern Shaanxi, China.},
journal = {Environmental monitoring and assessment},
volume = {190},
number = {10},
pages = {619},
pmid = {30269263},
issn = {1573-2959},
support = {2015CB251601//the National Basic Research Program of China (973 Program)/ ; 41430643//the State Key Program of the National Natural Science Foundation of China/ ; },
mesh = {China ; Ecology/*methods ; Ecosystem ; Environment ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geology ; Groundwater ; *Mining ; Remote Sensing Technology/methods ; },
abstract = {Zoning for the eco-geological environment (EGE) aims to protect and improve the regional ecological environment. It is the basis for evaluating the ecological characteristics of a mining area prior to mining activities and has the purpose of implementing water-preserved mining according to zoning type. In this study, four EGE types were proposed following field investigation in the Yushenfu mining area: oasis type with phreatic water and bottomland in desert (OTPWBD), oasis type with surface water and valley river (OTSWVR), loess gully type with surface runoff (LGTSR), and regional deep groundwater enrichment type (RDGET). Nine EGE evaluation indices were selected: rainfall, evaporation capacity, Luohe formation thickness, surface elevation, Sara Wusu aquifer water abundance, surface lithology, topography, slope, and normalized difference vegetation index (NDVI). Remote sensing technology and geographic information systems were first used to generate the evaluation index thematic maps. Then, the weight of each evaluation index was determined based on an analytic hierarchy process (AHP). Third, the index weight was used to form an improved weighted fuzzy C s clustering algorithm, and EGE zones were assigned using the MATLAB computing platform. For comparison, the AHP was also adopted for EGE zoning and a map of zoning differences was obtained. Finally, EGE field surveys of typical mines were carried out, which verified that EGE zoning using fuzzy clustering was accurate and reasonable.},
}

China
Ecology/*methods
Ecosystem
Environment
Environmental Monitoring/*methods
Geographic Information Systems
Geology
Groundwater
*Mining
Remote Sensing Technology/methods

@article {pmid30262689,
year = {2018},
author = {Song, H and Zhang, YX and Yang, MJ and Sun, JC and Zhang, T and Wang, HY},
title = {Genome survey on invasive veined rapa whelk (Rapana venosa) and development of microsatellite loci on large scale.},
journal = {Journal of genetics},
volume = {97},
number = {4},
pages = {e79-e86},
pmid = {30262689},
issn = {0973-7731},
mesh = {Animals ; China ; Computational Biology ; Gastropoda/*genetics ; Genetic Variation ; Genome/*genetics ; *Genomics ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats/*genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; },
abstract = {The veined rapa whelk (Rapana venosa) is an economically important gastropod in China, but is considered as an invasive species globally. Only a few studies have examined the R. venosa genome, a genomewide survey is necessary for improving our understanding of the genome structure and size of this organism. Microsatellite markers are powerful tools for characterizing germplasms, genetic diversity and kinship among individuals. The resultant data are applicable to breeding efforts in commercial aquaculture or for understanding invasion mechanisms. Here, we investigated the genome structure of R. venosa on an Illumina Hi-seq platform with ∼92× sequencing depth. We performed a K-mer analysis to estimate genome size, repeat sequences and heterozygosity. Clean reads were de novo assembled for the identification of simple-sequence repeat (SSR) loci that are suitable as markers. The estimated genome size of R. venosa was 2200.07 Mb, with a 1.41% heterozygosity rate and 67.04% repeats. We detected 5,477,450 simple-sequence repeats (SSRs), with 3,400,602 loci present as pure tandem repeats and 2,076,848 as compound motifs. We further selected and characterized 28 polymorphic markers in 78 individuals from Dandong, Laizhou, Weihai and Zhoushan in China. The range of alleles was 2-28 and the observed heterozygosity was 0.2857-0.8676. The data obtained from our genomic survey will aid the design of R. venosa whole-genome sequencing projects and advance the identification of SSR markers. Both these developments are valuable for further studies on ecological, evolutionary and genetic breeding in R. venosa.},
}

Animals
China
Computational Biology
Gastropoda/*genetics
Genetic Variation
Genome/*genetics
*Genomics
High-Throughput Nucleotide Sequencing
Microsatellite Repeats/*genetics
Polymorphism, Genetic
Sequence Analysis, DNA

@article {pmid30258229,
year = {2018},
author = {Bjorkman, AD and Myers-Smith, IH and Elmendorf, SC and Normand, S and Rüger, N and Beck, PSA and Blach-Overgaard, A and Blok, D and Cornelissen, JHC and Forbes, BC and Georges, D and Goetz, SJ and Guay, KC and Henry, GHR and HilleRisLambers, J and Hollister, RD and Karger, DN and Kattge, J and Manning, P and Prevéy, JS and Rixen, C and Schaepman-Strub, G and Thomas, HJD and Vellend, M and Wilmking, M and Wipf, S and Carbognani, M and Hermanutz, L and Lévesque, E and Molau, U and Petraglia, A and Soudzilovskaia, NA and Spasojevic, MJ and Tomaselli, M and Vowles, T and Alatalo, JM and Alexander, HD and Anadon-Rosell, A and Angers-Blondin, S and Beest, MT and Berner, L and Björk, RG and Buchwal, A and Buras, A and Christie, K and Cooper, EJ and Dullinger, S and Elberling, B and Eskelinen, A and Frei, ER and Grau, O and Grogan, P and Hallinger, M and Harper, KA and Heijmans, MMPD and Hudson, J and Hülber, K and Iturrate-Garcia, M and Iversen, CM and Jaroszynska, F and Johnstone, JF and Jørgensen, RH and Kaarlejärvi, E and Klady, R and Kuleza, S and Kulonen, A and Lamarque, LJ and Lantz, T and Little, CJ and Speed, JDM and Michelsen, A and Milbau, A and Nabe-Nielsen, J and Nielsen, SS and Ninot, JM and Oberbauer, SF and Olofsson, J and Onipchenko, VG and Rumpf, SB and Semenchuk, P and Shetti, R and Collier, LS and Street, LE and Suding, KN and Tape, KD and Trant, A and Treier, UA and Tremblay, JP and Tremblay, M and Venn, S and Weijers, S and Zamin, T and Boulanger-Lapointe, N and Gould, WA and Hik, DS and Hofgaard, A and Jónsdóttir, IS and Jorgenson, J and Klein, J and Magnusson, B and Tweedie, C and Wookey, PA and Bahn, M and Blonder, B and van Bodegom, PM and Bond-Lamberty, B and Campetella, G and Cerabolini, BEL and Chapin, FS and Cornwell, WK and Craine, J and Dainese, M and de Vries, FT and Díaz, S and Enquist, BJ and Green, W and Milla, R and Niinemets, Ü and Onoda, Y and Ordoñez, JC and Ozinga, WA and Penuelas, J and Poorter, H and Poschlod, P and Reich, PB and Sandel, B and Schamp, B and Sheremetev, S and Weiher, E},
title = {Plant functional trait change across a warming tundra biome.},
journal = {Nature},
volume = {562},
number = {7725},
pages = {57-62},
doi = {10.1038/s41586-018-0563-7},
pmid = {30258229},
issn = {1476-4687},
mesh = {Biometry ; Geographic Mapping ; *Global Warming ; Humidity ; Phenotype ; *Plant Physiological Phenomena ; Plants/*anatomy & histology ; Soil/chemistry ; Spatio-Temporal Analysis ; Temperature ; *Tundra ; Water/analysis ; },
abstract = {The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature-trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.},
}

Biometry
Geographic Mapping
*Global Warming
Humidity
Phenotype
*Plant Physiological Phenomena
Plants/*anatomy & histology
Soil/chemistry
Spatio-Temporal Analysis
Temperature
*Tundra
Water/analysis

@article {pmid30216600,
year = {2018},
author = {Lennox, GD and Gardner, TA and Thomson, JR and Ferreira, J and Berenguer, E and Lees, AC and Mac Nally, R and Aragão, LEOC and Ferraz, SFB and Louzada, J and Moura, NG and Oliveira, VHF and Pardini, R and Solar, RRC and Vaz-de Mello, FZ and Vieira, ICG and Barlow, J},
title = {Second rate or a second chance? Assessing biomass and biodiversity recovery in regenerating Amazonian forests.},
journal = {Global change biology},
volume = {24},
number = {12},
pages = {5680-5694},
doi = {10.1111/gcb.14443},
pmid = {30216600},
issn = {1365-2486},
mesh = {Animals ; *Biodiversity ; *Biomass ; Birds/physiology ; Carbon Cycle ; Coleoptera/physiology ; Conservation of Natural Resources ; Datasets as Topic ; Ecosystem ; *Forests ; Trees ; Tropical Climate ; },
abstract = {Secondary forests (SFs) regenerating on previously deforested land account for large, expanding areas of tropical forest cover. Given that tropical forests rank among Earth's most important reservoirs of carbon and biodiversity, SFs play an increasingly pivotal role in the carbon cycle and as potential habitat for forest biota. Nevertheless, their capacity to regain the biotic attributes of undisturbed primary forests (UPFs) remains poorly understood. Here, we provide a comprehensive assessment of SF recovery, using extensive tropical biodiversity, biomass, and environmental datasets. These data, collected in 59 naturally regenerating SFs and 30 co-located UPFs in the eastern Amazon, cover >1,600 large- and small-stemmed plant, bird, and dung beetles species and a suite of forest structure, landscape context, and topoedaphic predictors. After up to 40 years of regeneration, the SFs we surveyed showed a high degree of biodiversity resilience, recovering, on average among taxa, 88% and 85% mean UPF species richness and composition, respectively. Across the first 20 years of succession, the period for which we have accurate SF age data, biomass recovered at 1.2% per year, equivalent to a carbon uptake rate of 2.25 Mg/ha per year, while, on average, species richness and composition recovered at 2.6% and 2.3% per year, respectively. For all taxonomic groups, biomass was strongly associated with SF species distributions. However, other variables describing habitat complexity-canopy cover and understory stem density-were equally important occurrence predictors for most taxa. Species responses to biomass revealed a successional transition at approximately 75 Mg/ha, marking the influx of high-conservation-value forest species. Overall, our results show that naturally regenerating SFs can accumulate substantial amounts of carbon and support many forest species. However, given that the surveyed SFs failed to return to a typical UPF state, SFs are not substitutes for UPFs.},
}

Animals
*Biodiversity
*Biomass
Birds/physiology
Carbon Cycle
Coleoptera/physiology
Conservation of Natural Resources
Datasets as Topic
Ecosystem
*Forests
Trees
Tropical Climate

@article {pmid30208069,
year = {2018},
author = {Mariac, C and Vigouroux, Y and Duponchelle, F and García-Dávila, C and Nunez, J and Desmarais, E and Renno, JF},
title = {Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0202976},
pmid = {30208069},
issn = {1932-6203},
mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Fishes/*classification/genetics ; High-Throughput Nucleotide Sequencing ; Larva/*genetics ; },
abstract = {The ability to determine the composition and relative frequencies of fish species in large ichthyoplankton swarms could have extremely important ecological applications However, this task is currently hampered by methodological limitations. We proposed a new method for Amazonian species based on hybridization capture of the COI gene DNA from a distant species (Danio rerio), absent from our study area (the Amazon basin). The COI sequence of this species is approximately equidistant from all COI of Amazonian species available. By using this sequence as probe we successfully facilitated the simultaneous identification of fish larvae belonging to the order Siluriformes and to the Characiformes represented in our ichthyoplankton samples. Species relative frequencies, estimated by the number of reads, showed almost perfect correlations with true frequencies estimated by a Sanger approach, allowing the development of a quantitative approach. We also proposed a further improvement to a previous protocol, which enables lowering the sequencing effort by 40 times. This new Metabarcoding by Capture using a Single Probe (MCSP) methodology could have important implications for ecology, fisheries management and conservation in fish biodiversity hotspots worldwide. Our approach could easily be extended to other plant and animal taxa.},
}

Animals
Biodiversity
DNA Barcoding, Taxonomic/*methods
Databases, Genetic
Fishes/*classification/genetics
High-Throughput Nucleotide Sequencing
Larva/*genetics

@article {pmid30194403,
year = {2018},
author = {Rokas, A and Wisecaver, JH and Lind, AL},
title = {The birth, evolution and death of metabolic gene clusters in fungi.},
journal = {Nature reviews. Microbiology},
volume = {16},
number = {12},
pages = {731-744},
doi = {10.1038/s41579-018-0075-3},
pmid = {30194403},
issn = {1740-1534},
abstract = {Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.},
}

@article {pmid30181062,
year = {2019},
author = {de Jonge, PA and Nobrega, FL and Brouns, SJJ and Dutilh, BE},
title = {Molecular and Evolutionary Determinants of Bacteriophage Host Range.},
journal = {Trends in microbiology},
volume = {27},
number = {1},
pages = {51-63},
doi = {10.1016/j.tim.2018.08.006},
pmid = {30181062},
issn = {1878-4380},
abstract = {The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.},
}

@article {pmid30156039,
year = {2018},
author = {An, S and Zhu, X and Shen, M and Wang, Y and Cao, R and Chen, X and Yang, W and Chen, J and Tang, Y},
title = {Mismatch in elevational shifts between satellite observed vegetation greenness and temperature isolines during 2000-2016 on the Tibetan Plateau.},
journal = {Global change biology},
volume = {24},
number = {11},
pages = {5411-5425},
doi = {10.1111/gcb.14432},
pmid = {30156039},
issn = {1365-2486},
mesh = {Acclimatization ; Carbon Sequestration ; *Climate Change ; *Ecosystem ; Environmental Monitoring/methods ; Seasons ; Spacecraft ; *Temperature ; Tibet ; Water ; },
abstract = {Climate warming on the Tibetan Plateau tends to induce an uphill shift of temperature isolines. Observations and process-based models have both shown that climate warming has resulted in an increase in vegetation greenness on the Tibetan Plateau in recent decades. However, it is unclear whether the uphill shift of temperature isolines has caused greenness isolines to shift upward and whether the two shifts match each other. Our analysis of satellite observed vegetation greenness during the growing season (May-Sep) and gridded climate data for 2000-2016 documented a substantial mismatch between the elevational shifts of greenness and temperature isolines. This mismatch is probably associated with a lagging response of greenness to temperature change and with the elevational gradient of greenness. The lagging response of greenness may be associated with water limitation, resources availability, and acclimation. This lag may weaken carbon sequestration by Tibetan ecosystems, given that greenness is closely related to primary carbon uptake and ecosystem respiration increases exponentially with temperature. We also found that differences in terrain slope angle accounted for large spatial variations in the elevational gradient of greenness and thus the velocity of elevational shifts of greenness isolines and the sensitivity of elevational shifts of greenness isolines to temperature, highlighting the role of terrain effects on the elevational shifts of greenness isolines. The mismatches and the terrain effect found in this study suggest that there is potentially large micro-topographical difference in response and acclimation/adaptation of greenness to temperature changes in plants. More widespread in situ measurements and fine-resolution remote sensing observations and fine-gridded climate data are required to attribute the mismatch to specific environmental drivers and ecological processes such as vertical changes in community structure, plant physiology, and distribution of species.},
}

Acclimatization
Carbon Sequestration
*Climate Change
*Ecosystem
Environmental Monitoring/methods
Seasons
Spacecraft
*Temperature
Tibet
Water

@article {pmid30147447,
year = {2018},
author = {Dornelas, M and Antão, LH and Moyes, F and Bates, AE and Magurran, AE and Adam, D and Akhmetzhanova, AA and Appeltans, W and Arcos, JM and Arnold, H and Ayyappan, N and Badihi, G and Baird, AH and Barbosa, M and Barreto, TE and Bässler, C and Bellgrove, A and Belmaker, J and Benedetti-Cecchi, L and Bett, BJ and Bjorkman, AD and Błażewicz, M and Blowes, SA and Bloch, CP and Bonebrake, TC and Boyd, S and Bradford, M and Brooks, AJ and Brown, JH and Bruelheide, H and Budy, P and Carvalho, F and Castañeda-Moya, E and Chen, CA and Chamblee, JF and Chase, TJ and Siegwart Collier, L and Collinge, SK and Condit, R and Cooper, EJ and Cornelissen, JHC and Cotano, U and Kyle Crow, S and Damasceno, G and Davies, CH and Davis, RA and Day, FP and Degraer, S and Doherty, TS and Dunn, TE and Durigan, G and Duffy, JE and Edelist, D and Edgar, GJ and Elahi, R and Elmendorf, SC and Enemar, A and Ernest, SKM and Escribano, R and Estiarte, M and Evans, BS and Fan, TY and Turini Farah, F and Loureiro Fernandes, L and Farneda, FZ and Fidelis, A and Fitt, R and Fosaa, AM and Daher Correa Franco, GA and Frank, GE and Fraser, WR and García, H and Cazzolla Gatti, R and Givan, O and Gorgone-Barbosa, E and Gould, WA and Gries, C and Grossman, GD and Gutierréz, JR and Hale, S and Harmon, ME and Harte, J and Haskins, G and Henshaw, DL and Hermanutz, L and Hidalgo, P and Higuchi, P and Hoey, A and Van Hoey, G and Hofgaard, A and Holeck, K and Hollister, RD and Holmes, R and Hoogenboom, M and Hsieh, CH and Hubbell, SP and Huettmann, F and Huffard, CL and Hurlbert, AH and Macedo Ivanauskas, N and Janík, D and Jandt, U and Jażdżewska, A and Johannessen, T and Johnstone, J and Jones, J and Jones, FAM and Kang, J and Kartawijaya, T and Keeley, EC and Kelt, DA and Kinnear, R and Klanderud, K and Knutsen, H and Koenig, CC and Kortz, AR and Král, K and Kuhnz, LA and Kuo, CY and Kushner, DJ and Laguionie-Marchais, C and Lancaster, LT and Min Lee, C and Lefcheck, JS and Lévesque, E and Lightfoot, D and Lloret, F and Lloyd, JD and López-Baucells, A and Louzao, M and Madin, JS and Magnússon, B and Malamud, S and Matthews, I and McFarland, KP and McGill, B and McKnight, D and McLarney, WO and Meador, J and Meserve, PL and Metcalfe, DJ and Meyer, CFJ and Michelsen, A and Milchakova, N and Moens, T and Moland, E and Moore, J and Mathias Moreira, C and Müller, J and Murphy, G and Myers-Smith, IH and Myster, RW and Naumov, A and Neat, F and Nelson, JA and Paul Nelson, M and Newton, SF and Norden, N and Oliver, JC and Olsen, EM and Onipchenko, VG and Pabis, K and Pabst, RJ and Paquette, A and Pardede, S and Paterson, DM and Pélissier, R and Peñuelas, J and Pérez-Matus, A and Pizarro, O and Pomati, F and Post, E and Prins, HHT and Priscu, JC and Provoost, P and Prudic, KL and Pulliainen, E and Ramesh, BR and Mendivil Ramos, O and Rassweiler, A and Rebelo, JE and Reed, DC and Reich, PB and Remillard, SM and Richardson, AJ and Richardson, JP and van Rijn, I and Rocha, R and Rivera-Monroy, VH and Rixen, C and Robinson, KP and Ribeiro Rodrigues, R and de Cerqueira Rossa-Feres, D and Rudstam, L and Ruhl, H and Ruz, CS and Sampaio, EM and Rybicki, N and Rypel, A and Sal, S and Salgado, B and Santos, FAM and Savassi-Coutinho, AP and Scanga, S and Schmidt, J and Schooley, R and Setiawan, F and Shao, KT and Shaver, GR and Sherman, S and Sherry, TW and Siciński, J and Sievers, C and da Silva, AC and Rodrigues da Silva, F and Silveira, FL and Slingsby, J and Smart, T and Snell, SJ and Soudzilovskaia, NA and Souza, GBG and Maluf Souza, F and Castro Souza, V and Stallings, CD and Stanforth, R and Stanley, EH and Mauro Sterza, J and Stevens, M and Stuart-Smith, R and Rondon Suarez, Y and Supp, S and Yoshio Tamashiro, J and Tarigan, S and Thiede, GP and Thorn, S and Tolvanen, A and Teresa Zugliani Toniato, M and Totland, Ø and Twilley, RR and Vaitkus, G and Valdivia, N and Vallejo, MI and Valone, TJ and Van Colen, C and Vanaverbeke, J and Venturoli, F and Verheye, HM and Vianna, M and Vieira, RP and Vrška, T and Quang Vu, C and Van Vu, L and Waide, RB and Waldock, C and Watts, D and Webb, S and Wesołowski, T and White, EP and Widdicombe, CE and Wilgers, D and Williams, R and Williams, SB and Williamson, M and Willig, MR and Willis, TJ and Wipf, S and Woods, KD and Woehler, EJ and Zawada, K and Zettler, ML and Hickler, T},
title = {BioTIME: A database of biodiversity time series for the Anthropocene.},
journal = {Global ecology and biogeography : a journal of macroecology},
volume = {27},
number = {7},
pages = {760-786},
pmid = {30147447},
issn = {1466-822X},
support = {//Wellcome Trust/United Kingdom ; 250189//European Research Council/International ; },
abstract = {Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).

Time period and grain: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Software format: .csv and .SQL.},
}

@article {pmid30145518,
year = {2018},
author = {D'Alessandro, M and Esposito, V and Porporato, EMD and Berto, D and Renzi, M and Giacobbe, S and Scotti, G and Consoli, P and Valastro, G and Andaloro, F and Romeo, T},
title = {Relationships between plastic litter and chemical pollutants on benthic biodiversity.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {242},
number = {Pt B},
pages = {1546-1556},
doi = {10.1016/j.envpol.2018.08.002},
pmid = {30145518},
issn = {1873-6424},
mesh = {Animals ; *Biodiversity ; Ecology ; Environmental Monitoring ; Introduced Species ; Mediterranean Sea ; Mollusca/classification ; Plastics/*analysis ; Polychaeta/classification ; Water Pollutants, Chemical/*analysis ; },
abstract = {Five Descriptors (D) of Marine Strategy Framework Directive (MSFD): marine litter (D10), non-indigenous species (D2) and organic and inorganic pollutants (D8), were estimated in a coastal area of GSA 16 (Augusta harbour, Central Mediterranean Sea) in order to study their effects on the biodiversity (D1) of the benthic community D6) and to improve data for the MSFD. Investigation of plastic debris had led to the identification of 38 fragments divided into four categories, among which microplastics resulted as the most abundant. Six non-indigenous species, belonging to Polychaeta (Kirkegaardia dorsobranchialis, Notomastus aberans, Pista unibranchia, Pseudonereis anomala, Branchiomma bairdi) and Mollusca (Brachidontes pharaonis) were found. Biodiversity and benthic indices suggested a generalised, slightly disturbed ecological status. Anthracene, Zinc and Chrome were the most abundant chemical compounds in analysed sediments. Significant correlations were found between the abundance of trace elements vs biotic indices and between plastic debris vs biodiversity and benthic indices. This study represents the first report about the abundance of plastic debris and its relationship to contaminants and infauna in Augusta harbour. Our results can provide useful information for national and international laws and directives.},
}

Animals
*Biodiversity
Ecology
Environmental Monitoring
Introduced Species
Mediterranean Sea
Mollusca/classification
Plastics/*analysis
Polychaeta/classification
Water Pollutants, Chemical/*analysis

@article {pmid30108295,
year = {2018},
author = {Liebhold, AM and Yamanaka, T and Roques, A and Augustin, S and Chown, SL and Brockerhoff, EG and Pyšek, P},
title = {Plant diversity drives global patterns of insect invasions.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {12095},
pmid = {30108295},
issn = {2045-2322},
abstract = {During the last two centuries, thousands of insect species have been transported (largely inadvertently) and established outside of their native ranges worldwide, some with catastrophic ecological and economic impacts. Global variation in numbers of invading species depends on geographic variation in propagule pressure and heterogeneity of environmental resistance to invasions. Elton's diversity-invasibility hypothesis, proposed over sixty years ago, has been widely explored for plants but little is known on how biodiversity affects insect invasions. Here we use species inventories from 44 land areas, ranging from small oceanic islands to entire continents in various world regions, to show that numbers of established insect species are primarily driven by diversity of plants, with both native and non-native plant species richness being the strongest predictor of insect invasions. We find that at large spatial scales, plant diversity directly explains variation in non-native insect species richness among world regions, while geographic factors such as land area, climate and insularity largely affect insect invasions indirectly via their effects on local plant richness.},
}

@article {pmid30107371,
year = {2018},
author = {Wang, Q and Xiong, X and Wang, X and Tu, Q and Li, J and Ding, X and Li, Y and Huang, P and He, S and Yin, Y and Yang, H},
title = {Suckling Piglet Intestinal Enterocyte Nutrient Metabolism Changes.},
journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology},
volume = {48},
number = {5},
pages = {2103-2113},
doi = {10.1159/000492552},
pmid = {30107371},
issn = {1421-9778},
mesh = {Amino Acids/analysis/metabolism ; Animals ; Animals, Suckling ; Cells, Cultured ; Chromatography, High Pressure Liquid ; Citric Acid Cycle/genetics ; Databases, Factual ; Enterocytes/cytology/*metabolism ; Fatty Acids/analysis/metabolism ; Glucose/analysis/metabolism ; Jejunum/cytology ; Peptides/analysis ; Swine ; Tandem Mass Spectrometry ; },
abstract = {BACKGROUND/AIMS: Intestinal morphology and the types of enterocytes are changed in piglets during the suckling period, but it is unclear whether these changes are associated with metabolic changes in epithelium. The present study was conducted to test the hypothesis that glucose, fatty acids, and amino acid metabolism in differentiated piglet enterocytes changed during suckling.

METHODS: Twenty-four piglets (Duroc × [Landrace × Yorkshire]) from 8 litters (3 piglets/litter) were selected. A single piglet from each litter was randomly selected and euthanized at days 7, 14, and 21. Differentiated enterocytes (DE) were isolated from their mid-jejunum. Isobaric tags for relative and absolute quantification and subsequent liquid chromatography-tandem mass spectrometry were used to identify and measure protein synthesis.

RESULTS: The results showed that various activities, including: cellular processes; metabolic processes; biological regulation; pigmentation; and, localization, in DEs changed during suckling. Metabolic process analyses revealed that protein expression related to glycolysis and citrate cycle was decreased from day 7 to day 14. The number of differentiated enterocytes of 21 d piglets increased compared to 7 d piglets. Most of the proteins involved in fatty acid and amino acids metabolism had decreased DE expression between day 7 and day 14. Some, but not all, detected proteins down-regulated in DEs of 21 day piglets compared to 7 day piglets.

CONCLUSION: These results indicate that glucose, fatty acids, and amino acids metabolism changed during suckling. This may provide useful information for designing feed formulas and regulating piglet intestinal growth and development.},
}

Amino Acids/analysis/metabolism
Animals
Animals, Suckling
Cells, Cultured
Chromatography, High Pressure Liquid
Citric Acid Cycle/genetics
Databases, Factual
Enterocytes/cytology/*metabolism
Fatty Acids/analysis/metabolism
Glucose/analysis/metabolism
Jejunum/cytology
Peptides/analysis
Swine
Tandem Mass Spectrometry

@article {pmid30106390,
year = {2018},
author = {Duarte, G and Moreira, M and Branco, P and da Costa, L and Ferreira, MT and Segurado, P},
title = {One millennium of historical freshwater fish occurrence data for Portuguese rivers and streams.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180163},
pmid = {30106390},
issn = {2052-4463},
mesh = {Animals ; Databases, Factual ; Ecology/history ; Ecosystem ; *Fishes ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Medieval ; Portugal ; Rivers ; },
abstract = {The insights that historical evidence of human presence and man-made documents provide are unique. For example, using historical data may be critical to adequately understand the ecological requirements of species. However, historical information about freshwater species distribution remains largely a knowledge gap. In this Data Descriptor, we present the Portuguese Historical Fish Database (PHish-DB), a compilation of 2214 records (557 at the basin scale, 184 at the sub-basin scale and 1473 at the segment scale) resulting from a survey of 194 historical documents. The database was developed using a three-scale approach that maximises the inclusion of information by allowing different degrees of spatial acuity. PHish database contains records of 25 taxonomical groups and covers a time span of one millennium, from the 11th until the 20th century. This database has already proven useful for two scientific studies, and PHish further use will contribute to correctly assess the full range of conditions tolerated by species, by establishing adequate benchmark conditions, and/or to improve existing knowledge of the species distribution limits.},
}

Animals
Databases, Factual
Ecology/history
Ecosystem
*Fishes
History, 15th Century
History, 16th Century
History, 17th Century
History, 18th Century
History, 19th Century
History, 20th Century
History, Medieval
Portugal
Rivers

@article {pmid30096816,
year = {2018},
author = {Liu, Y and Liu, Y and Li, J and Lu, W and Wei, X and Sun, C},
title = {Evolution of Landscape Ecological Risk at the Optimal Scale: A Case Study of the Open Coastal Wetlands in Jiangsu, China.},
journal = {International journal of environmental research and public health},
volume = {15},
number = {8},
pages = {},
pmid = {30096816},
issn = {1660-4601},
mesh = {China ; Conservation of Natural Resources/*methods ; Ecology ; Environmental Monitoring/*methods ; Geographic Information Systems ; Geological Phenomena ; Human Activities ; Humans ; Remote Sensing Technology ; Risk ; *Wetlands ; },
abstract = {Detailed analysis of the evolution characteristics of landscape ecological risk is crucial for coastal sustainable management and for understanding the potential environmental impacts of a man-made landform landscapes (MMLL). As a typical open coastal wetland, large-scale human activities (e.g., tidal reclamation, fishery activities, wind farm construction, and port construction) have substantially affected the evolution of the coastal ecological environment. Previous landscape ecological risk assessment studies have documented the effectiveness of assessing the quality of ecological environment processes. However, these studies have either focused on the noncoastal zone, or they have not considered the evolution of the spatial characteristics and ecological risk evolution of the landscape at an optimal scale. Here, we present a landscape ecological risk pattern (LERP) evolution model, based on two successive steps: first, we constructed an optimal scale method with an appropriate extent and grain using multi⁻temporal Landsat TM/OLI images acquired in the years 2000, 2004, 2008, 2013 and 2017, and then we calculated landscape ecological risk indices. Based on this model, the entire process of the spatiotemporal evolution of ecological risk patterns of the open coastal wetlands in Jiangsu, China, was determined. The principal findings are as follows: (1) The main landscape types in the study area are tidal flats and farmland, and the main features of the landscape evolution are a significant increase in aquafarming and a substantial decrease in the tidal flat area, while the landscape heterogeneity increased; (2) In the past 20 years, the areas of low and relatively low ecological risk in the study region were greatly reduced, while the areas of medium, relatively high, and high ecological risk greatly increased; the areas of high-grade ecological risk areas are mainly around Dongtai and Dafeng; (3) The area of ecological risk from low-grade to high-grade occupied 71.75% of the study area during 2000⁻2017. During the previous periods (2000⁻2004 and 2004⁻2008), the areas of low-grade ecological risk were transformed to areas of middle-grade ecological risk area, while during the later periods (2008⁻2013 and 2013⁻2017) there was a substantial increase in the proportion of areas of high-grade ecological risk. Our results complement the official database of coastal landscape planning, and provide important information for assessing the potential effects of MMLL processes on coastal environments.},
}

China
Conservation of Natural Resources/*methods
Ecology
Environmental Monitoring/*methods
Geographic Information Systems
Geological Phenomena
Human Activities
Humans
Remote Sensing Technology
Risk
*Wetlands

@article {pmid30093613,
year = {2018},
author = {Albrecht, J and Classen, A and Vollstädt, MGR and Mayr, A and Mollel, NP and Schellenberger Costa, D and Dulle, HI and Fischer, M and Hemp, A and Howell, KM and Kleyer, M and Nauss, T and Peters, MK and Tschapka, M and Steffan-Dewenter, I and Böhning-Gaese, K and Schleuning, M},
title = {Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {3177},
pmid = {30093613},
issn = {2041-1723},
support = {For1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; FOR1246//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; },
mesh = {Altitude ; Animals ; Bayes Theorem ; *Biodiversity ; Birds/*physiology ; Climate ; *Ecosystem ; Feeding Behavior ; Flowers/*physiology ; Fruit ; Insecta/*physiology ; Phylogeny ; Plants ; Research Design ; Species Specificity ; *Symbiosis ; Tanzania ; },
abstract = {Species' functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird-fruit, bird-flower and insect-flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant-animal interaction networks.},
}

Altitude
Animals
Bayes Theorem
*Biodiversity
Birds/*physiology
Climate
*Ecosystem
Feeding Behavior
Flowers/*physiology
Fruit
Insecta/*physiology
Phylogeny
Plants
Research Design
Species Specificity
*Symbiosis
Tanzania

@article {pmid30061690,
year = {2018},
author = {Horsthemke, B},
title = {A critical view on transgenerational epigenetic inheritance in humans.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2973},
pmid = {30061690},
issn = {2041-1723},
mesh = {Animals ; Biological Evolution ; Culture ; *DNA Methylation ; Databases, Genetic ; Drosophila ; Ecology ; *Epigenesis, Genetic ; Gene-Environment Interaction ; Germ Cells ; Humans ; *Inheritance Patterns ; Models, Genetic ; Mutation ; Nematoda ; Phenotype ; Plants/genetics ; Proteome ; Proteomics ; },
abstract = {Transgenerational epigenetic inheritance refers to the transmission of epigenetic information through the germline. While it has been observed in plants, nematodes and fruit flies, its occurrence in mammals-and humans in particular-is the matter of controversial debate, mostly because the study of transgenerational epigenetic inheritance is confounded by genetic, ecological and cultural inheritance. In this comment, I discuss the phenomenon of transgenerational epigenetic inheritance and the difficulty of providing conclusive proof for it in experimental and observational studies.},
}

Animals
Biological Evolution
Culture
*DNA Methylation
Databases, Genetic
Drosophila
Ecology
*Epigenesis, Genetic
Gene-Environment Interaction
Germ Cells
Humans
*Inheritance Patterns
Models, Genetic
Mutation
Nematoda
Phenotype
Plants/genetics
Proteome
Proteomics

@article {pmid30061657,
year = {2018},
author = {Butler, S and O'Dwyer, JP},
title = {Stability criteria for complex microbial communities.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2970},
pmid = {30061657},
issn = {2041-1723},
mesh = {Algorithms ; Computational Biology ; *Ecology ; *Microbiota ; Models, Biological ; Software ; *Symbiosis ; },
abstract = {Competition and mutualism are inevitable processes in microbial ecology, and a central question is which and how many taxa will persist in the face of these interactions. Ecological theory has demonstrated that when direct, pairwise interactions among a group of species are too numerous, or too strong, then the coexistence of these species will be unstable to any slight perturbation. Here, we refine and to some extent overturn that understanding, by considering explicitly the resources that microbes consume and produce. In contrast to more complex organisms, microbial cells consume primarily abiotic resources, and mutualistic interactions are often mediated through the mechanism of crossfeeding. We show that if microbes consume, but do not produce resources, then any positive equilibrium will always be stable to small perturbations. We go on to show that in the presence of crossfeeding, stability is no longer guaranteed. However, positive equilibria remain stable whenever mutualistic interactions are either sufficiently weak, or when all pairs of taxa reciprocate each other's assistance.},
}

Algorithms
Computational Biology
*Ecology
*Microbiota
Models, Biological
Software
*Symbiosis

@article {pmid30055354,
year = {2018},
author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andújar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP},
title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.},
journal = {Molecular phylogenetics and evolution},
volume = {128},
number = {},
pages = {1-11},
doi = {10.1016/j.ympev.2018.07.008},
pmid = {30055354},
issn = {1095-9513},
mesh = {Algorithms ; Animals ; Base Sequence ; Coleoptera/classification/*genetics ; Databases, Genetic ; *Metagenomics ; Mitochondria/*genetics ; *Phylogeny ; },
abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.},
}

Algorithms
Animals
Base Sequence
Coleoptera/classification/*genetics
Databases, Genetic
*Metagenomics
Mitochondria/*genetics
*Phylogeny

@article {pmid30046636,
year = {2018},
author = {Bird, SM and King, R},
title = {Multiple Systems Estimation (or Capture-Recapture Estimation) to Inform Public Policy.},
journal = {Annual review of statistics and its application},
volume = {5},
number = {},
pages = {95-118},
pmid = {30046636},
issn = {2326-8298},
support = {MC_U105260794//Medical Research Council/United Kingdom ; },
abstract = {Estimating population sizes has long been of interest, from the estimation of the human or ecological population size within regions or countries to the hidden number of civilian casualties in a war. Total enumeration of the population, for example, via a census, is often infeasible or simply impractical. However, a series of partial enumerations or observations of the population is often possible. This has led to the ideas of capture-recapture methods, which have been extensively used within ecology to estimate the size of wildlife populations, with an associated measure of uncertainty, and are most effectively applied when there are multiple capture occasions. Capture-recapture ideology can be more widely applied to multiple data-sources, by the linkage of individuals across the multiple lists. This is often referred to as Multiple Systems Estimation (MSE). The MSE approach has been preferred when estimating "capture-shy" or hard-to-reach populations, including those caught up in the criminal justice system; or homeless; or trafficked; or civilian casualties of war. Motivated by a range of public policy applications of MSE, each briefly introduced, we discuss practical problems with potentially substantial methodological implications. They include: "period" definition; "case" definition; when an observed count is not a true count of the population of interest but an upper bound due to mismatched definitions; exact or probabilistic matching of "cases" across different lists; demographic or other information about the "case" which may influence capture-propensities; required permissions to access extant-lists; list-creation by research-teams or interested parties; referrals (if presence on list A results - almost surely - in presence on list B); different mathematical models leading to widely different estimated population sizes; uncertainty in estimation; computational efficiency; external validation; hypothesis-generation; and additional independent external information. Returning to our motivational applications, we focus on whether the uncertainty which qualified their estimates was sufficiently narrow to orient public policy; and, if not, what options were available and/or taken to reduce the uncertainty or to seek external validation. We also consider whether MSE was hypothesis-generating: in the sense of having spawned new lines of inquiry.},
}

@article {pmid30029348,
year = {2018},
author = {Ridding, LE and Redhead, JW and Oliver, TH and Schmucki, R and McGinlay, J and Graves, AR and Morris, J and Bradbury, RB and King, H and Bullock, JM},
title = {The importance of landscape characteristics for the delivery of cultural ecosystem services.},
journal = {Journal of environmental management},
volume = {206},
number = {},
pages = {1145-1154},
doi = {10.1016/j.jenvman.2017.11.066},
pmid = {30029348},
issn = {1095-8630},
mesh = {*Conservation of Natural Resources ; Ecology ; *Ecosystem ; England ; *Geographic Information Systems ; Humans ; },
abstract = {The importance of Cultural Ecosystem Services (CES) to human wellbeing is widely recognised. However, quantifying these non-material benefits is challenging and consequently they are often not assessed. Mapping approaches are increasingly being used to understand the spatial distribution of different CES and how this relates to landscape characteristics. This study uses an online Public Participation Geographic Information System (PPGIS) to elicit information on outdoor locations important to respondents in Wiltshire, a dynamic lowland landscape in southern England. We analysed these locations in a GIS with spatial datasets representing potential influential factors, including protected areas, land use, landform, and accessibility. We assess these characteristics at different spatial and visual scales for different types of cultural engagement. We find that areas that are accessible, near to urban centres, with larger views, and a high diversity of protected habitats, are important for the delivery of CES. Other characteristics including a larger area of woodland and the presence of sites of historic interest in the surrounding landscape were also influential. These findings have implications for land-use planning and the management of ecosystems, by demonstrating the benefits of high quality ecological sites near to towns. The importance of maintaining and restoring landscape features, such as woodlands, to enhance the delivery of CES were also highlighted.},
}

*Conservation of Natural Resources
Ecology
*Ecosystem
England
*Geographic Information Systems
Humans

@article {pmid30029345,
year = {2018},
author = {He, L and Shen, J and Zhang, Y},
title = {Ecological vulnerability assessment for ecological conservation and environmental management.},
journal = {Journal of environmental management},
volume = {206},
number = {},
pages = {1115-1125},
doi = {10.1016/j.jenvman.2017.11.059},
pmid = {30029345},
issn = {1095-8630},
mesh = {China ; *Climate Change ; *Conservation of Natural Resources ; Ecology ; Ecosystem ; *Geographic Information Systems ; Humans ; },
abstract = {Identifying ecological vulnerable regions is a significant aspect in ecological conservation and environmental management. This paper presents a first attempt to provide a prototype framework that can assess ecological vulnerability and evaluate potential impacts of natural, social, economic, environmental pollution, and human health elements on ecological vulnerability with integrating spatial analysis of Geographic Information System (GIS) method and multi-criteria decision analysis (MCDA). A general ecological vulnerability index was constructed to describe the vulnerability status in an ecological hotspot of China. The assessment results of this study confirm the poor ecological vulnerability in China that only 1.32% of the China's population lives in not vulnerable ecosystem. A very high percentage (98.68%) of Chinese with 1.34 billion people lives in vulnerable and highly vulnerable area. This situation is mainly caused by increasing population pressure, exhausted nature resources, extensive economic growth, severe environmental pollution, insufficient environmental protection investment, and accelerating population aging. The spatial comparison indicates that spatial disparity existed in China with the central and northwestern provinces showing higher ecological vulnerability than the northeastern and southern provinces. The results of ecological vulnerability assessment can support effective guidance for mid- or long-term ecologic management. The developed framework can be replicated at different spatial and temporal scales using context-specific datasets to support ecological managers and government with decision-making. With available robust climate change models, future research might incorporate climate change into the ecological vulnerability framework.},
}

China
*Climate Change
*Conservation of Natural Resources
Ecology
Ecosystem
*Geographic Information Systems
Humans

@article {pmid30029326,
year = {2018},
author = {Djikanović, V and Skorić, S and Spasić, S and Naunovic, Z and Lenhardt, M},
title = {Ecological risk assessment for different macrophytes and fish species in reservoirs using biota-sediment accumulation factors as a useful tool.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {241},
number = {},
pages = {1167-1174},
doi = {10.1016/j.envpol.2018.06.054},
pmid = {30029326},
issn = {1873-6424},
mesh = {Animals ; Aquatic Organisms/*chemistry ; Biota ; Canada ; Catfishes ; Cyprinidae ; Ecology ; Environmental Monitoring/*methods ; Gills/chemistry ; Liver/chemistry ; Metals/analysis ; Metals, Heavy/analysis ; Muscles/chemistry ; Netherlands ; Risk Assessment ; Serbia ; Trace Elements/analysis ; Water Pollutants, Chemical/*analysis ; },
abstract = {Metal content was evaluated in the sediment, macrophytes and fish in the Medjuvršje reservoir (Western Serbia). Concentrations of 16 trace elements (Ag; Al; As; B; Ba; Cd; Co; Cr; Cu; Fe; Li; Mn; Ni; Pb; Sr; Zn) were analysed in the sediment, macrophytes and fish of an aquatic ecosystem. Five macrophyte species and three fish tissues (liver, muscle, gills) from five fish species (freshwater bream, common nase, Prussian carp, chub, wels catfish) were sampled and the metal content was analysed with ICP-OES. The sediment concentrations of Cu, Cd, and Zn exceeded the Canadian sediment quality guidelines while concentrations of Cr and Ni were above the Netherlands' target values. Bioaccumulation factors (BSAF) were calculated for analysed macrophytes and fish tissue. The BSAF had higher values for macrophytes for all investigated elements except for Cu and Zn; Cu had a higher value in the liver of the freshwater bream (0.823) and Zn had a higher value in the liver of freshwater bream (0.914) and chub (0.834) as well as in gills of Prussian carp (2.58) and chub (1.26). Potamogeton pectinatus, Ceratophylum demersum and the root of Phragmites communis showed higher accumulation of elements than Trapa natans and Potamogeton fluitans and the body of P. communis. The highest BSAF values for Ba, Mn, Sr and Ni were recorded in the gills. Cd and Cu had the highest BSAF values in the liver. Results confirmed that particular macrophyte and fish species could be a good indicator of reservoir water and sediment pollution.},
}

Animals
Aquatic Organisms/*chemistry
Biota
Canada
Catfishes
Cyprinidae
Ecology
Environmental Monitoring/*methods
Gills/chemistry
Liver/chemistry
Metals/analysis
Metals, Heavy/analysis
Muscles/chemistry
Netherlands
Risk Assessment
Serbia
Trace Elements/analysis
Water Pollutants, Chemical/*analysis

@article {pmid30026187,
year = {2018},
author = {Bradburd, GS and Coop, GM and Ralph, PL},
title = {Inferring Continuous and Discrete Population Genetic Structure Across Space.},
journal = {Genetics},
volume = {210},
number = {1},
pages = {33-52},
pmid = {30026187},
issn = {1943-2631},
support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cluster Analysis ; Data Interpretation, Statistical ; Gene Flow/genetics ; Genetic Variation/genetics ; Genetics, Population/*methods/*statistics & numerical data ; Humans ; Models, Genetic ; North America ; Population Groups/genetics ; Populus/genetics ; Ursidae/genetics ; },
abstract = {A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the "clines versus clusters" problem in modeling population genetic variation, and remedies some of the overfitting to which nonspatial models are prone. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.},
}

Animals
Cluster Analysis
Data Interpretation, Statistical
Gene Flow/genetics
Genetic Variation/genetics
Genetics, Population/*methods/*statistics & numerical data
Humans
Models, Genetic
North America
Population Groups/genetics
Populus/genetics
Ursidae/genetics

@article {pmid30020436,
year = {2018},
author = {Chen, F and Zhang, J and Chen, J and Li, X and Dong, W and Hu, J and Lin, M and Liu, Y and Li, G and Wang, Z and Zhang, L},
title = {realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta).},
journal = {Database : the journal of biological databases and curation},
volume = {2018},
number = {},
pages = {},
pmid = {30020436},
issn = {1758-0463},
mesh = {Algal Proteins/chemistry/genetics/metabolism ; *Databases, Genetic ; *Genome ; Internet ; Molecular Sequence Annotation ; Rhodophyta/*genetics ; Sequence Alignment ; Transcriptome/*genetics ; },
abstract = {With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development.Database URL: http://realdb.algaegenome.org/.},
}

Algal Proteins/chemistry/genetics/metabolism
*Databases, Genetic
*Genome
Internet
Molecular Sequence Annotation
Rhodophyta/*genetics
Sequence Alignment
Transcriptome/*genetics

@article {pmid30017551,
year = {2018},
author = {Longbottom, J and Shearer, FM and Devine, M and Alcoba, G and Chappuis, F and Weiss, DJ and Ray, SE and Ray, N and Warrell, DA and Ruiz de Castañeda, R and Williams, DJ and Hay, SI and Pigott, DM},
title = {Vulnerability to snakebite envenoming: a global mapping of hotspots.},
journal = {Lancet (London, England)},
volume = {392},
number = {10148},
pages = {673-684},
pmid = {30017551},
issn = {1474-547X},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Africa, Northern/epidemiology ; Animals ; Antivenins/therapeutic use ; Geographic Mapping ; Health Resources/economics/statistics & numerical data ; Health Services Accessibility/standards ; Humans ; Indonesia/epidemiology ; Neglected Diseases/drug therapy/epidemiology/prevention & control ; Public Health/education ; Quality of Health Care/standards ; Snake Bites/*drug therapy/*epidemiology/mortality/prevention & control ; Snakes/*classification/injuries ; Vulnerable Populations/*statistics & numerical data ; },
abstract = {BACKGROUND: Snakebite envenoming is a frequently overlooked cause of mortality and morbidity. Data for snake ecology and existing snakebite interventions are scarce, limiting accurate burden estimation initiatives. Low global awareness stunts new interventions, adequate health resources, and available health care. Therefore, we aimed to synthesise currently available data to identify the most vulnerable populations at risk of snakebite, and where additional data to manage this global problem are needed.

METHODS: We assembled a list of snake species using WHO guidelines. Where relevant, we obtained expert opinion range (EOR) maps from WHO or the Clinical Toxinology Resources. We also obtained occurrence data for each snake species from a variety of websites, such as VertNet and iNaturalist, using the spocc R package (version 0.7.0). We removed duplicate occurrence data and categorised snakes into three groups: group A (no available EOR map or species occurrence records), group B (EOR map but <5 species occurrence records), and group C (EOR map and ≥5 species occurrence records). For group C species, we did a multivariate environmental similarity analysis using the 2008 WHO EOR maps and newly available evidence. Using these data and the EOR maps, we produced contemporary range maps for medically important venomous snake species at a 5 × 5 km resolution. We subsequently triangulated these data with three health system metrics (antivenom availability, accessibility to urban centres, and the Healthcare Access and Quality [HAQ] Index) to identify the populations most vulnerable to snakebite morbidity and mortality.

FINDINGS: We provide a map showing the ranges of 278 snake species globally. Although about 6·85 billion people worldwide live within range of areas inhabited by snakes, about 146·70 million live within remote areas lacking quality health-care provisioning. Comparing opposite ends of the HAQ Index, 272·91 million individuals (65·25%) of the population within the lowest decile are at risk of exposure to any snake for which no effective therapy exists compared with 519·46 million individuals (27·79%) within the highest HAQ Index decile, showing a disproportionate coverage in reported antivenom availability. Antivenoms were available for 119 (43%) of 278 snake species evaluated by WHO, while globally 750·19 million (10·95%) of those living within snake ranges live more than 1 h from population centres. In total, we identify about 92·66 million people living within these vulnerable geographies, including many sub-Saharan countries, Indonesia, and other parts of southeast Asia.

INTERPRETATION: Identifying exact populations vulnerable to the most severe outcomes of snakebite envenoming at a subnational level is important for prioritising new data collection and collation, reinforcing envenoming treatment, existing health-care systems, and deploying currently available and future interventions. These maps can guide future research efforts on snakebite envenoming from both ecological and public health perspectives and better target future estimates of the burden of this neglected tropical disease.

FUNDING: Bill & Melinda Gates Foundation.},
}

Africa, Northern/epidemiology
Animals
Antivenins/therapeutic use
Geographic Mapping
Health Resources/economics/statistics & numerical data
Health Services Accessibility/standards
Humans
Indonesia/epidemiology
Neglected Diseases/drug therapy/epidemiology/prevention & control
Public Health/education
Quality of Health Care/standards
Snake Bites/*drug therapy/*epidemiology/mortality/prevention & control
Snakes/*classification/injuries
Vulnerable Populations/*statistics & numerical data

@article {pmid30016947,
year = {2018},
author = {Song, Z and Stajich, JE and Xie, Y and Liu, X and He, Y and Chen, J and Hicks, GR and Wang, G},
title = {Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {541},
pmid = {30016947},
issn = {1471-2164},
support = {IOS-1027542//National Science Foundation/ ; CA-R-PPA-5062-H//National Institute of Food and Agriculture Hatch project/ ; 31670044//National Natural Science Foundation of China/ ; 91751115//National Natural Science Foundation of China/ ; S10 OD016290/OD/NIH HHS/United States ; # 2016YFA0601401//The National Key Research Program of China/ ; 201305022//National Marine Public Welfare Industry Special Scientific Research Project/ ; },
mesh = {Biosynthetic Pathways/genetics ; Docosahexaenoic Acids/*biosynthesis ; Ecological and Environmental Phenomena ; Fatty Acids, Unsaturated/biosynthesis ; Gene Ontology ; *Genome ; Genomics ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Stramenopiles/classification/enzymology/*genetics/metabolism ; },
abstract = {BACKGROUND: Thraustochytrids are unicellular fungal-like marine protists with ubiquitous existence in marine environments. They are well-known for their ability to produce high-valued omega-3 polyunsaturated fatty acids (ω-3-PUFAs) (e.g., docosahexaenoic acid (DHA)) and hydrolytic enzymes. Thraustochytrid biomass has been estimated to surpass that of bacterioplankton in both coastal and oceanic waters indicating they have an important role in microbial food-web. Nevertheless, the molecular pathway and regulatory network for PUFAs production and the molecular mechanisms underlying ecological functions of thraustochytrids remain largely unknown.

RESULTS: The genomes of two thraustochytrids strains (Mn4 and SW8) with ability to produce DHA were sequenced and assembled with a hybrid sequencing approach utilizing Illumina short paired-end reads and Pacific Biosciences long reads to generate a highly accurate genome assembly. Phylogenomic and comparative genomic analyses found that DHA-producing thraustochytrid strains were highly similar and possessed similar gene content. Analysis of the conventional fatty acid synthesis (FAS) and the polyketide synthase (PKS) systems for PUFAs production only detected incomplete and fragmentary pathways in the genome of these two strains. Surprisingly, secreted carbohydrate active enzymes (CAZymes) were found to be significantly depleted in the genomes of these 2 strains as compared to other sequenced relatives. Furthermore, these two strains possess an expanded gene repertoire for signal transduction and self-propelled movement, which could be important for their adaptations to dynamic marine environments.

CONCLUSIONS: Our results demonstrate the possibility of a third PUFAs synthesis pathway besides previously described FAS and PKS pathways encoded in the genome of these two thraustochytrid strains. Moreover, lack of a complete set of hydrolytic enzymatic machinery for degrading plant-derived organic materials suggests that these two DHA-producing strains play an important role as a nutritional source rather than a nutrient-producer in marine microbial-food web. Results of this study suggest the existence of two types of saprobic thraustochytrids in the world's ocean. The first group, which does not produce cellulosic enzymes and live as 'left-over' scavenger of bacterioplankton, serves as a dietary source for the plankton of higher trophic levels and the other possesses capacity to live on detrital organic matters in the marine ecosystems.},
}

Biosynthetic Pathways/genetics
Docosahexaenoic Acids/*biosynthesis
Ecological and Environmental Phenomena
Fatty Acids, Unsaturated/biosynthesis
Gene Ontology
*Genome
Genomics
Molecular Sequence Annotation
Multigene Family
Phylogeny
Stramenopiles/classification/enzymology/*genetics/metabolism

@article {pmid30011006,
year = {2018},
author = {Garamszegi, LZ and Donald, J and Francis, CD and Fuxjager, MJ and Goymann, W and Hau, M and Husak, JF and Johnson, MA and Kircher, B and Knapp, R and Martin, LB and Miller, ET and Schoenle, LA and Vitousek, MN and Williams, TD},
title = {Species-Specific Means and Within-Species Variance in Glucocorticoid Hormones and Speciation Rates in Birds.},
journal = {Integrative and comparative biology},
volume = {58},
number = {4},
pages = {763-776},
doi = {10.1093/icb/icy086},
pmid = {30011006},
issn = {1557-7023},
mesh = {Animals ; Birds/*physiology ; Databases as Topic ; Ecosystem ; *Genetic Speciation ; Glucocorticoids/*metabolism ; Species Specificity ; },
abstract = {At macroevolutionary scales, stress physiology may have consequences for species diversification and subspecies richness. Populations that exploit new resources or undergo range expansion should cope with new environmental challenges, which could favor higher mean stress responses. Within-species variation in the stress response may also play a role in mediating the speciation process: in species with broad variation, there will always be some individuals that can tolerate an unpredictable environment, whereas in species with narrow variation there will be fewer individuals that are able to thrive in a new ecological niche. We tested for the evolutionary relationship between stress response, speciation rate, and subspecies richness in birds by relying on the HormoneBase repository, from which we calculated within- and among-species variation in baseline (BL) and stress-induced (SI) corticosterone levels. To estimate speciation rates, we applied Bayesian analysis of macroevolutionary mixtures that can account for variation in diversification rate among clades and through time. Contrary to our predictions, lineages with higher diversification rates were not characterized by higher BL or SI levels of corticosterone either at the tips or at the deeper nodes of the phylogeny. We also found no association between mean hormone levels and subspecies richness. Within-species variance in corticosterone levels showed close to zero repeatability, thus it is highly unlikely that this is a species-specific trait that influences diversification rates. These results imply that stress physiology may play a minor, if any, role in determining speciation rates in birds.},
}

Animals
Birds/*physiology
Databases as Topic
Ecosystem
*Genetic Speciation
Glucocorticoids/*metabolism
Species Specificity

@article {pmid29989590,
year = {2018},
author = {Tavşanoğlu, Ç and Pausas, JG},
title = {A functional trait database for Mediterranean Basin plants.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180135},
pmid = {29989590},
issn = {2052-4463},
mesh = {*Databases, Factual ; Ecosystem ; Mediterranean Region ; *Plants ; },
abstract = {Functional trait databases are emerging as crucial tools for a wide range of ecological studies across the world. Here, we provide a database of functional traits for vascular plant species of the Mediterranean Basin. The database includes 25,764 individual records of 44 traits from 2,457 plant taxa distributed in 119 taxonomic families. This database (BROT 2.0) is an updated and enlarged version of a previous database (BROT 1.0; 8,263 records, 14 traits, 952 taxa). Trait data were obtained from a comprehensive literature review, plus some field and experimental observations. All records are fully referenced and, in many cases, include geographic coordinates. The database is structured to include different levels of accuracy of trait information for each entry. BROT 2.0 should facilitate testing hypotheses on plant functional ecology within the Mediterranean Basin, and comparing this region with other ecosystems worldwide. The BROT 2.0 database and its trait definitions can be used as a template for creating similar trait databases in other regions of the world.},
}

*Databases, Factual
Ecosystem
Mediterranean Region
*Plants

@article {pmid29985552,
year = {2018},
author = {Ma, ZS and Li, L},
title = {Measuring metagenome diversity and similarity with Hill numbers.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1339-1355},
doi = {10.1111/1755-0998.12923},
pmid = {29985552},
issn = {1755-0998},
support = {//Industry Technology Talent Grant/ ; //A China-US International Collaborative Project/ ; 71473243//National Science Foundation of China/ ; },
mesh = {Cluster Analysis ; Computational Biology/*methods ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; *Metagenome ; Metagenomics/*methods ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {The first step of any metagenome sequencing project is to get the inventory of OTU abundances (operational taxonomic units) and/or metagenomic gene abundances. The former is generated with 16S-rRNA-tagged amplicon sequencing technology, and the latter can be generated from either gene-targeted or whole-sample shotgun metagenomics technologies. With 16S-rRNA data sets, measuring community diversity with diversity indexes such as species richness and Shannon's index has been a de facto standard analysis; nevertheless, similarly comprehensive approaches to metagenomic gene abundances are still largely missing, despite that both OTU and gene abundances are DNA reads. Here, we adapt the Hill numbers, which were reintroduced to macrocommunity ecology recently and are now widely regarded as a most appropriate measure system for ecological diversity, for measuring metagenome alpha-, beta- and gamma-diversities, and similarity. Our proposal includes the following: (a) Metagenomic gene (MG) diversity measures the single-gene-level metagenome diversity; (b) Type-I metagenome functional gene cluster (MFGC) diversity measures the diversity of functional gene clusters but ignoring within-cluster gene abundance information; (c) Type-II MFGC diversity considers within-cluster gene abundances information and integrates gene-cluster-level metagenome diversity and functional gene redundancy information; and (d) Four classes of Hill-numbers-based similarity metrics, including local gene overlap, regional gene overlap, gene homogeneity measure and gene turnover complement, were introduced in terms of MG and MFGC, respectively. We demonstrate the proposal with the gut metagenomes from healthy and IBD (inflammatory bowel disease) cohorts. The Hill numbers offer a unified approach to cohesively and comprehensively measuring the ecological and metagenome diversities of microbiomes.},
}

Cluster Analysis
Computational Biology/*methods
DNA, Ribosomal/chemistry/genetics
*Genetic Variation
*Metagenome
Metagenomics/*methods
*Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid29981010,
year = {2019},
author = {Lant, C and Baggio, J and Konar, M and Mejia, A and Ruddell, B and Rushforth, R and Sabo, JL and Troy, TJ},
title = {The U.S. food-energy-water system: A blueprint to fill the mesoscale gap for science and decision-making.},
journal = {Ambio},
volume = {48},
number = {3},
pages = {251-263},
doi = {10.1007/s13280-018-1077-0},
pmid = {29981010},
issn = {1654-7209},
support = {1639529//National Science Foundation/ ; },
abstract = {Food, energy, and water (FEW) are interdependent and must be examined as a coupled natural-human system. This perspective essay defines FEW systems and outlines key findings about them as a blueprint for future models to satisfy six key objectives. The first three focus on linking the FEW production and consumption to impacts on Earth cycles in a spatially specific manner in order to diagnose problems and identify potential solutions. The second three focus on describing the evolution of FEW systems to identify risks, thus empowering the FEW actors to better achieve the goals of resilience and sustainability. Four key findings about the FEW systems that guide future model development are (1) that they engage ecological, carbon, water, and nutrient cycles most powerfully among all human systems; (2) that they operate primarily at a mesoscale best captured by counties, districts, and cities; (3) that cities are hubs within the FEW system; and (4) that the FEW system forms a complex network.},
}

@article {pmid29973596,
year = {2018},
author = {Bramon Mora, B and Gravel, D and Gilarranz, LJ and Poisot, T and Stouffer, DB},
title = {Identifying a common backbone of interactions underlying food webs from different ecosystems.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2603},
pmid = {29973596},
issn = {2041-1723},
mesh = {Animals ; Competitive Behavior/*physiology ; Datasets as Topic ; Ecosystem ; *Food Chain ; *Models, Statistical ; Predatory Behavior/*physiology ; Principal Component Analysis ; },
abstract = {Although the structure of empirical food webs can differ between ecosystems, there is growing evidence of multiple ways in which they also exhibit common topological properties. To reconcile these contrasting observations, we postulate the existence of a backbone of interactions underlying all ecological networks-a common substructure within every network comprised of species playing similar ecological roles-and a periphery of species whose idiosyncrasies help explain the differences between networks. To test this conjecture, we introduce a new approach to investigate the structural similarity of 411 food webs from multiple environments and biomes. We first find significant differences in the way species in different ecosystems interact with each other. Despite these differences, we then show that there is compelling evidence of a common backbone of interactions underpinning all food webs. We expect that identifying a backbone of interactions will shed light on the rules driving assembly of different ecological communities.},
}

Animals
Competitive Behavior/*physiology
Datasets as Topic
Ecosystem
*Food Chain
*Models, Statistical
Predatory Behavior/*physiology
Principal Component Analysis

@article {pmid29936291,
year = {2018},
author = {Venter, PC and Nitsche, F and Scherwass, A and Arndt, H},
title = {Discrepancies Between Molecular and Morphological Databases of Soil Ciliates Studied for Temperate Grasslands of Central Europe.},
journal = {Protist},
volume = {169},
number = {4},
pages = {521-538},
doi = {10.1016/j.protis.2018.04.001},
pmid = {29936291},
issn = {1618-0941},
mesh = {Ciliophora/*classification ; *Databases, Factual/standards ; Databases, Genetic ; Europe ; *Grassland ; High-Throughput Nucleotide Sequencing ; Molecular Typing ; *Soil Microbiology ; },
abstract = {By measuring the change in soil protist communities, the effect of human land use on grasslands can be monitored to promote sustainable ecosystem functioning. Protists form the active link in the rhizosphere between the plant roots and higher trophic organisms; however, only few morphological species and their ecological values have yet been described in this context. To investigate the communicability between morphological and molecular databases used in the molecular barcoding of protists and in the biomonitoring of grassland soil, the present high-throughput sequencing (HTS) study (N=150) covered the area of central Europe (mesoscale) known to be well studied for ciliated protists. HTS delivered 2,404 unique reads identifying taxa in all major ciliophoran classes but exact reference matches were few. The study identified clear discrepancies between databases for well-studied taxa, where molecular databases contained multiple gene variants for single morphospecies of dominant taxa. Gene variants presented own biogeography - the eukaryotic microdiversity along gradients (e.g., land-use intensity, soil water). It is possible that many of the so called novel phylogenetic lineages and hidden diversity pointed out in environmental surveys could be evidence for the severe lack of molecular data for already known and morphologically described species, present in morphological databases.},
}

Ciliophora/*classification
*Databases, Factual/standards
Databases, Genetic
Europe
*Grassland
High-Throughput Nucleotide Sequencing
Molecular Typing
*Soil Microbiology

@article {pmid29930200,
year = {2018},
author = {Venturelli, OS and Carr, AC and Fisher, G and Hsu, RH and Lau, R and Bowen, BP and Hromada, S and Northen, T and Arkin, AP},
title = {Deciphering microbial interactions in synthetic human gut microbiome communities.},
journal = {Molecular systems biology},
volume = {14},
number = {6},
pages = {e8157},
pmid = {29930200},
issn = {1744-4292},
support = {T32 GM008349/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacterial Physiological Phenomena ; Computational Biology/methods ; Gastrointestinal Microbiome/*physiology ; Humans ; Metabolomics ; *Microbial Interactions ; Models, Biological ; },
abstract = {The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.},
}

Bacterial Physiological Phenomena
Computational Biology/methods
Gastrointestinal Microbiome/*physiology
Humans
Metabolomics
*Microbial Interactions
Models, Biological

@article {pmid29923321,
year = {2018},
author = {Keck, F and Vasselon, V and Rimet, F and Bouchez, A and Kahlert, M},
title = {Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1299-1309},
doi = {10.1111/1755-0998.12919},
pmid = {29923321},
issn = {1755-0998},
mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Diatoms/classification/genetics ; Environmental Monitoring/*methods ; Metagenomics/*methods ; Microscopy ; Phylogeny ; Rivers/microbiology ; Sensitivity and Specificity ; },
abstract = {DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.},
}

Computational Biology/*methods
DNA Barcoding, Taxonomic/*methods
Diatoms/classification/genetics
Environmental Monitoring/*methods
Metagenomics/*methods
Microscopy
Phylogeny
Rivers/microbiology
Sensitivity and Specificity

@article {pmid29917104,
year = {2018},
author = {Celis, JS and Wibberg, D and Ramírez-Portilla, C and Rupp, O and Sczyrba, A and Winkler, A and Kalinowski, J and Wilke, T},
title = {Binning enables efficient host genome reconstruction in cnidarian holobionts.},
journal = {GigaScience},
volume = {7},
number = {7},
pages = {},
pmid = {29917104},
issn = {2047-217X},
mesh = {Algorithms ; Animals ; Anthozoa/*physiology ; Cnidaria/*genetics ; Computational Biology ; Coral Reefs ; DNA/analysis ; Ecology ; *Genome ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Symbiosis ; Transcriptome ; },
abstract = {Background: Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities-together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.

Results: Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.

Conclusions: Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.},
}

Algorithms
Animals
Anthozoa/*physiology
Cnidaria/*genetics
Computational Biology
Coral Reefs
DNA/analysis
Ecology
*Genome
Genomics/*methods
High-Throughput Nucleotide Sequencing
Metagenomics/*methods
Phylogeny
RNA, Ribosomal, 16S/analysis
Sequence Analysis, DNA
Symbiosis
Transcriptome

@article {pmid29898550,
year = {2018},
author = {Mirtl, M and T Borer, E and Djukic, I and Forsius, M and Haubold, H and Hugo, W and Jourdan, J and Lindenmayer, D and McDowell, WH and Muraoka, H and Orenstein, DE and Pauw, JC and Peterseil, J and Shibata, H and Wohner, C and Yu, X and Haase, P},
title = {Genesis, goals and achievements of Long-Term Ecological Research at the global scale: A critical review of ILTER and future directions.},
journal = {The Science of the total environment},
volume = {626},
number = {},
pages = {1439-1462},
doi = {10.1016/j.scitotenv.2017.12.001},
pmid = {29898550},
issn = {1879-1026},
abstract = {Since its founding in 1993 the International Long-term Ecological Research Network (ILTER) has gone through pronounced development phases. The current network comprises 44 active member LTER networks representing 700 LTER Sites and ~80 LTSER Platforms across all continents, active in the fields of ecosystem, critical zone and socio-ecological research. The critical challenges and most important achievements of the initial phase have now become state-of-the-art in networking for excellent science. At the same time increasing integration, accelerating technology, networking of resources and a strong pull for more socially relevant scientific information have been modifying the mission and goals of ILTER. This article provides a critical review of ILTER's mission, goals, development and impacts. Major characteristics, tools, services, partnerships and selected examples of relative strengths relevant for advancing ILTER are presented. We elaborate on the tradeoffs between the needs of the scientific community and stakeholder expectations. The embedding of ILTER in an increasingly collaborative landscape of global environmental observation and ecological research networks and infrastructures is also reflected by developments of pioneering regional and national LTER networks such as SAEON in South Africa, CERN/CEOBEX in China, TERN in Australia or eLTER RI in Europe. The primary role of ILTER is currently seen as a mechanism to investigate ecosystem structure, function, and services in response to a wide range of environmental forcings using long-term, place-based research. We suggest four main fields of activities and advancements for the next decade through development/delivery of a: (1) Global multi-disciplinary community of researchers and research institutes; (2) Strategic global framework and strong partnerships in ecosystem observation and research; (3) Global Research Infrastructure (GRI); and (4) a scientific knowledge factory for societally relevant information on sustainable use of natural resources.},
}

@article {pmid29890590,
year = {2018},
author = {Dick, J and Orenstein, DE and Holzer, JM and Wohner, C and Achard, AL and Andrews, C and Avriel-Avni, N and Beja, P and Blond, N and Cabello, J and Chen, C and Díaz-Delgado, R and Giannakis, GV and Gingrich, S and Izakovicova, Z and Krauze, K and Lamouroux, N and Leca, S and Melecis, V and Miklós, K and Mimikou, M and Niedrist, G and Piscart, C and Postolache, C and Psomas, A and Santos-Reis, M and Tappeiner, U and Vanderbilt, K and Van Ryckegem, G},
title = {What is socio-ecological research delivering? A literature survey across 25 international LTSER platforms.},
journal = {The Science of the total environment},
volume = {622-623},
number = {},
pages = {1225-1240},
doi = {10.1016/j.scitotenv.2017.11.324},
pmid = {29890590},
issn = {1879-1026},
abstract = {With an overarching goal of addressing global and regional sustainability challenges, Long Term Socio-Ecological Research Platforms (LTSER) aim to conduct place-based research, to collect and synthesize both environmental and socio-economic data, and to involve a broader stakeholder pool to set the research agenda. To date there have been few studies examining the output from LTSER platforms. In this study we enquire if the socio-ecological research from 25 self-selected LTSER platforms of the International Long-Term Ecological Research (ILTER) network has produced research products which fulfil the aims and ambitions of the paradigm shift from ecological to socio-ecological research envisaged at the turn of the century. In total we assessed 4983 publically available publications, of which 1112 were deemed relevant to the socio-ecological objectives of the platform. A series of 22 questions were scored for each publication, assessing relevance of responses in terms of the disciplinary focus of research, consideration of human health and well-being, degree of stakeholder engagement, and other relevant variables. The results reflected the diverse origins of the individual platforms and revealed a wide range in foci, temporal periods and quantity of output from participating platforms, supporting the premise that there is a growing trend in socio-ecological research at long-term monitoring platforms. Our review highlights the challenges of realizing the top-down goal to harmonize international network activities and objectives and the need for bottom-up, self-definition for research platforms. This provides support for increasing the consistency of LTSER research while preserving the diversity of regional experiences.},
}

@article {pmid29847023,
year = {2018},
author = {Dellicour, S and Flot, JF},
title = {The hitchhiker's guide to single-locus species delimitation.},
journal = {Molecular ecology resources},
volume = {18},
number = {6},
pages = {1234-1246},
doi = {10.1111/1755-0998.12908},
pmid = {29847023},
issn = {1755-0998},
mesh = {Computational Biology/*methods ; DNA Barcoding, Taxonomic/*methods ; Metagenomics/*methods ; *Phylogeny ; },
abstract = {Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus approaches are gaining fast in popularity, single-gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species-poor samples and/or tree-based approaches: as a result, travellers in the land of single-locus species delimitation lack a comprehensive "hitchhiker's guide" highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance-based (ABGD, "automatic barcode gap discovery"), allele sharing-based (haplowebs) and tree-based approaches (GMYC, "generalized mixed Yule-coalescent" and PTP, "Poisson tree processes") to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree-based approaches. The latter's error type was mostly oversplitting, whereas ABGD chiefly overlumped and haplowebs leaned either way depending on simulation parameters: such widely divergent error patterns suggest that, if all three types of methods agree, then the resulting delimitation is probably correct. Perfect congruence being quite rare, travellers in search of a one-size-fit-all approach to single-locus species delimitation should forget it; however, our hitchhiker's guide raises hope that such species delimitation's Holy Grail may be found in the relatively uncharted nearby land of multilocus species delimitation.},
}

Computational Biology/*methods
DNA Barcoding, Taxonomic/*methods
Metagenomics/*methods
*Phylogeny

@article {pmid29802772,
year = {2018},
author = {Snell Taylor, SJ and Evans, BS and White, EP and Hurlbert, AH},
title = {The prevalence and impact of transient species in ecological communities.},
journal = {Ecology},
volume = {99},
number = {8},
pages = {1825-1835},
doi = {10.1002/ecy.2398},
pmid = {29802772},
issn = {0012-9658},
abstract = {Transient species occur infrequently in a community over time and do not maintain viable local populations. Because transient species interact differently than non-transients with their biotic and abiotic environment, it is important to characterize the prevalence of these species and how they impact our understanding of ecological systems. We quantified the prevalence and impact of transient species in communities using data on over 19,000 community time series spanning an array of ecosystems, taxonomic groups, and spatial scales. We found that transient species are a general feature of communities regardless of taxa or ecosystem. The proportion of these species decreases with increasing spatial scale leading to a need to control for scale in comparative work. Removing transient species from analyses influences the form of a suite of commonly studied ecological patterns including species-abundance distributions, species-energy relationships, species-area relationships, and temporal turnover. Careful consideration should be given to whether transient species are included in analyses depending on the theoretical and practical relevance of these species for the question being studied.},
}

@article {pmid29794166,
year = {2018},
author = {Couger, MB and Arévalo, L and Campbell, P},
title = {A High Quality Genome for Mus spicilegus, a Close Relative of House Mice with Unique Social and Ecological Adaptations.},
journal = {G3 (Bethesda, Md.)},
volume = {8},
number = {7},
pages = {2145-2152},
pmid = {29794166},
issn = {2160-1836},
mesh = {Animals ; Computational Biology/methods ; Ecology ; Gene Expression Profiling ; *Genome ; *Genomics/methods ; Geography ; Hungary ; Mice ; Molecular Sequence Annotation ; Phylogeny ; Species Specificity ; Transcriptome ; },
abstract = {Genomic data for the closest relatives of house mice (Mus musculus species complex) are surprisingly limited. Here, we present the first complete genome for a behaviorally and ecologically unique member of the sister clade to house mice, the mound-building mouse, Mus spicilegus Using read cloud sequencing and de novo assembly we produced a 2.50 Gbp genome with a scaffold N50 of 2.27 Mbp. We constructed >25 000 gene models, of which the majority had high homology to other Mus species. To evaluate the utility of the M. spicilegus genome for behavioral and ecological genomics, we extracted 196 vomeronasal receptor (VR) sequences from our genome and analyzed phylogenetic relationships between M. spicilegus VRs and orthologs from M. musculus and the Algerian mouse, M. spretus While most M. spicilegus VRs clustered with orthologs in M. musculus and M. spretus, 10 VRs with evidence of rapid divergence in M. spicilegus are strong candidate modulators of species-specific chemical communication. A high quality assembly and genome for M. spicilegus will help to resolve discordant ancestry patterns in house mouse genomes, and will provide an essential foundation for genetic dissection of phenotypes that distinguish commensal from non-commensal species, and the social and ecological characteristics that make M. spicilegus unique.},
}

Animals
Computational Biology/methods
Ecology
Gene Expression Profiling
*Genome
*Genomics/methods
Geography
Hungary
Mice
Molecular Sequence Annotation
Phylogeny
Species Specificity
Transcriptome

@article {pmid29751427,
year = {2018},
author = {Meng, L and Huang, J and Dong, J},
title = {Assessment of rural ecosystem health and type classification in Jiangsu province, China.},
journal = {The Science of the total environment},
volume = {615},
number = {},
pages = {1218-1228},
doi = {10.1016/j.scitotenv.2017.09.312},
pmid = {29751427},
issn = {1879-1026},
mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Geographic Information Systems ; Urbanization ; },
abstract = {Quantitative analysis of rural ecosystem health (REH) is required to comprehend the spatial differentiation of rural landscape and promote rural sustainable development under the pressure of urbanization and industrialization, especially those with dramatic changes in rural ecology of China and other developing countries. In this study, taking Jiangsu province as the case study, appropriate indicators were selected in the perspective of compound ecosystem and the rural ecosystem health index (REHI) was developed including four rural ecological subsystems of resource, environmental, social and economic. The comprehensive indicator assessment models and geographic information system (GIS) spatial methods were used to analyze the REH status and spatial differentiation of 57 counties in Jiangsu province. The REH scores of 57 rural counties were in a higher range of 0.686-0.882 and fluctuating increased from north to south, indicating that the rural ecosystem in Jiangsu province was at a relatively healthy level and counties in southern Jiangsu were healthier than those in central and northern regions. The spatial concentration of REH in Jiangsu was poor and the spatial distribution of four subsystems health levels were significantly different by spatial Gini coefficient analysis. The REH of 57 counties in Jiangsu province were classified into 13 types according to the identification of the health levels and quantity of four subsystems. Moreover, we analyzed the influencing factors of each type and proposed paths to promote the development and management of rural ecosystem.},
}

China
Conservation of Natural Resources
*Ecosystem
*Environmental Monitoring
Geographic Information Systems
Urbanization

@article {pmid29736767,
year = {2018},
author = {Hale, BW},
title = {Mapping Potential Environmental Impacts from Tourists Using Data from Social Media: A Case Study in the Westfjords of Iceland.},
journal = {Environmental management},
volume = {62},
number = {3},
pages = {446-457},
pmid = {29736767},
issn = {1432-1009},
support = {IZK0Z2_171645//Swiss National Science Foundation/Switzerland ; },
mesh = {Ecology ; *Environment ; Estuaries ; Geographic Information Systems ; Humans ; Iceland ; *Social Media ; *Travel ; },
abstract = {With tourism increasing in remote regions, it is important to be able to estimate potential environmental impacts from the tourists in order to plan and manage natural areas. This study combines measures of ecological sensitivity with data from publicly available geotagged photographs posted on the social media site Flickr to assess the vulnerability of the locations frequented by foreign tourists in the Westfjords region of Iceland between 2014 and 2016. The results suggest that tourists cluster primarily around six hotspots that represented some of the major known tourist destinations of the region. Although tourists generally frequented areas with lower ecological sensitivity and rarely went far beyond the main roads, one of the hotspots was in an area of higher ecological sensitivity. Further, tourists also appeared to have higher intensity stays when they entered areas of higher ecological sensitivity. Overall, these findings highlight the usefulness of combining data from social media in assessing potential environmental impacts of tourism. However, natural resource managers should be aware of limitations in the use of such data.},
}

Ecology
*Environment
Estuaries
Geographic Information Systems
Humans
Iceland
*Social Media
*Travel