Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

Molecular Ecology, Journal Year: 2019, Volume and Issue: 28(21), P. 4737 - 4754

Published: Sept. 24, 2019

Abstract For half a century population genetics studies have put type II restriction endonucleases to work. Now, coupled with massively‐parallel, short‐read sequencing, the family of RAD protocols that wields these enzymes has generated vast genetic knowledge from natural world. Here, we describe first software natively capable using paired‐end sequencing derive short contigs de novo data. Stacks version 2 employs Bruijn graph assembler build and connect forward reverse reads for each locus, which it then uses as reference read alignments. The new architecture allows all individuals in metapopulation be considered at same time locus is processed. This enables Bayesian genotype caller provide precise SNPs, robust algorithm phase those SNPs into long haplotypes, generating loci are 400–800 bp length. To prove its recall precision, tested simulated data compared reference‐aligned analyses three empirical sets. Our study shows latest highly accurate outperforms other assembling genotyping

Language: Английский

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Climate change effects on biodiversity, ecosystems, ecosystem services, and natural resource management in the United States

The Science of The Total Environment, Journal Year: 2020, Volume and Issue: 733, P. 137782 - 137782

Published: March 11, 2020

Climate change is a pervasive and growing global threat to biodiversity ecosystems. Here, we present the most up-to-date assessment of climate impacts on biodiversity, ecosystems, ecosystem services in U.S. implications for natural resource management. We draw from 4th National Assessment summarize observed projected changes ecosystems explore linkages important services, discuss associated challenges opportunities find that species are responding through morphology behavior, phenology, geographic range shifts, these mediated by plastic evolutionary responses. Responses populations, combined with direct effects (including more extreme events), resulting widespread productivity, interactions, vulnerability biological invasions, other emergent properties. Collectively, alter benefits can provide society. Although not all negative, even positive require costly societal adjustments. Natural managers need proactive, flexible adaptation strategies consider historical future outlooks minimize costs over long term. Many organizations beginning approaches, but implementation yet prevalent or systematic across nation.

Language: Английский

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Population genomics for wildlife conservation and management

Molecular Ecology, Journal Year: 2020, Volume and Issue: 30(1), P. 62 - 82

Published: Nov. 4, 2020

Biodiversity is under threat worldwide. Over the past decade, field of population genomics has developed across nonmodel organisms, and results this research have begun to be applied in conservation management wildlife species. Genomics tools can provide precise estimates basic features populations, such as effective size, inbreeding, demographic history structure, that are critical for efforts. Moreover, studies identify particular genetic loci variants responsible inbreeding depression or adaptation changing environments, allowing efforts estimate capacity populations evolve adapt response environmental change manage adaptive variation. While connections from been slow develop, these increasingly strengthening. Here we review primary areas which approaches management, highlight examples how they used, recommendations building on progress made field.

Language: Английский

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Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(21), P. 10418 - 10423

Published: May 6, 2019

Local adaptations can determine the potential of populations to respond environmental changes, yet adaptive genetic variation is commonly ignored in models forecasting species vulnerability and biogeographical shifts under future climate change. Here we integrate genomic ecological modeling approaches identify associated with two cryptic forest bats. We then incorporate this information directly into forecasts range changes change assessment population persistence through spread climate-adaptive (evolutionary rescue potential). Considering reduced loss projections, suggesting that failure account for intraspecific variability result overestimation losses. On other hand, overlap between was projected increase, indicating interspecific competition likely play an important role limiting species' ranges. show although evolutionary possible, it depends on a population's capacity connectivity. Hence, stress importance incorporating data landscape connectivity assessments conservation management.

Language: Английский

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Climate change vulnerability assessment of species

Wiley Interdisciplinary Reviews Climate Change, Journal Year: 2018, Volume and Issue: 10(1)

Published: Oct. 11, 2018

Assessing species' vulnerability to climate change is a prerequisite for developing effective strategies conserve them. The last three decades have seen exponential growth in the number of studies evaluating how, how much, why, when, and where species will be impacted by change. We provide an overview rapidly field assessment (CCVA) describe key concepts, terms, steps considerations. stress importance identifying full range pressures, impacts their associated mechanisms that face using this as basis selecting appropriate approaches quantifying vulnerability. outline four CCVA approaches, namely trait‐based, correlative, mechanistic combined discuss use. Since any can deliver unreliable or even misleading results when incorrect data parameters are applied, we finding, selecting, applying input examples open‐access resources. Because rare, small‐range, declining‐range often particular conservation concern while also posing significant challenges CCVA, alternative ways assess CCVAs used inform IUCN Red List assessments extinction risk. Finally, suggest future directions propose areas research efforts may particularly valuable. This article categorized under: Climate, Ecology, Conservation > Extinction Risk

Language: Английский

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Evolutionary genomics can improve prediction of species’ responses to climate change

Evolution Letters, Journal Year: 2020, Volume and Issue: 4(1), P. 4 - 18

Published: Jan. 14, 2020

Abstract Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and transformation entire ecosystems. Many species are challenged by pace GCC because they might not be able to respond fast enough changing biotic abiotic conditions. Species can either shifting their range, or persisting in local habitat. If populations persist, tolerate climatic changes phenotypic plasticity, genetically adapt conditions depending on genetic variability census population size allow for de novo mutations. Otherwise, will experience demographic collapses may go extinct. Current approaches predicting responses begin combine ecological evolutionary information distribution modelling. Including an dimension substantially improve projections which have accounted key processes such as dispersal, adaptive change, demography, interactions. However, eco-evolutionary models require new data methods estimation a species' potential, so far only been available small number model species. To represent global biodiversity, we need devise large-scale collection strategies define ecology potential broad range especially keystone We also standardized replicable modelling that integrate these account when impact survival. Here, discuss different genomic used investigate predict GCC. This serve guidance researchers looking appropriate experimental setup particular system. furthermore highlight future directions moving forward field allocating resources more effectively, implement mitigation measures before extinct ecosystems lose important functions.

Language: Английский

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Genomic Prediction of (Mal)Adaptation Across Current and Future Climatic Landscapes

Annual Review of Ecology Evolution and Systematics, Journal Year: 2020, Volume and Issue: 51(1), P. 245 - 269

Published: Aug. 10, 2020

Signals of local adaptation have been found in many plants and animals, highlighting the heterogeneity distribution adaptive genetic variation throughout species ranges. In coming decades, global climate change is expected to induce shifts selective pressures that shape this variation. These changes will likely result varying degrees maladaptation spatial reshuffling underlying distributions alleles. There a growing interest using population genomic data help predict future disruptions locally gene-environment associations. One motivation behind such work better understand how effects changing on populations’ short-term fitness could vary spatially across Here we review current use disruption climates. After assessing goals motivationsunderlying approach, main steps associated statistical methods currently explore our understanding limits potential genomics (mal)adaptation.

Language: Английский

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Generation lengths of the world's birds and their implications for extinction risk

Conservation Biology, Journal Year: 2020, Volume and Issue: 34(5), P. 1252 - 1261

Published: Feb. 14, 2020

Birds have been comprehensively assessed on the International Union for Conservation of Nature (IUCN) Red List more times than any other taxonomic group. However, to date, generation lengths not systematically estimated scale population trends when undertaking assessments, as required by criteria IUCN List. We compiled information from major databases published life-history and trait data all birds imputed missing a function species traits with generalized linear mixed models. Generation were derived species, based our modeled values age at first breeding, maximum longevity, annual adult survival. The resulting varied 1.42 27.87 years (median 2.99). Most (61%) had <3.33 years, meaning that period 3 generations-over which declines are under criterion A-was <10 is value used assessments short times. For these trait-informed estimates length suggested 10 robust precautionary threat assessment. In cases, however, whole families, genera, or individual substantial impact their extinction risk, in higher risk long-lived short-lived species. Although approach effectively addressed gaps, some may underestimated due paucity data. Overall, results will strengthen future extinction-risk augment key avian data.Duraciones Generacionales de las Aves del Mundo y sus Implicaciones para el Riesgo Extinción Resumen Las aves han sido valoradas integralmente en la Lista Roja Unión Internacional Conservación Naturaleza (UICN) más veces que cualquier otro grupo taxonómico. Sin embargo, fecha, duraciones generacionales no estimadas sistemáticamente escalar tendencias poblacionales cuando se realizan valoraciones, como lo requieren los criterios UICN. Compilamos información partir principales bases datos historias vida características publicadas todas e imputamos faltantes una función especies con modelos lineales mixtos generalizados. La duración por generación estuvo derivada base nuestros valores modelados edad durante primera reproducción, longevidad máxima supervivencia anual adultos. resultante varió años (mediana: mayoría tuvo generacional años, significa periodo tres generaciones - cual valoran declinaciones bajo Criterio A es valor usado UICN valoración tiempos cortos. Para estas especies, nuestras estimaciones informados sugieren diez un preventivo sólido amenazas. otros casos, sin familias o géneros enteros individuales, impacto sustancial sobre su riesgo extinción estimado, resultando así elevado mayor aquellas menor longevidad. Aunque nuestra estrategia lidió efectivamente vacíos datos, algunas podría estar subestimada debido escasez historia vida. En general, resultados fortalecerán futuras valoraciones aumentarán importantes características.在《世界自然保护联盟 濒危物种红色名录》中, 鸟类被全面评估的次数比其它任何类群都要多。然而, 目前的评估尚未按照《IUCN红色名单》标准的要求, 系统地估计世代时间来计算种群趋势。我们从已发表的所有鸟类生活史及特征数据的几大数据库中整理了信息, 并用广义线性混合模型构建物种特征的函数对缺失的生活史数据进行了估计。我们进而基于对初次繁殖年龄、最长寿命和成体年均存活率的模拟值, 获得了所有物种的世代时间。得到的鸟类世代时间从 年到 年不等 (中位数为 2.99 年) 。大多数物种 的世代时间小于 3.33 年, 意味着三个时代的时长小于 而这是《 红色名录》评估标准 中对种群下降的评估周期, 用于评估世代时间短的物种。对于这些物种, 基于特征估计的世代时间表明, 年是评估威胁的一个稳健预警值。而在其他情况下, 世代时间对于估计整个科、属或个别物种的灭绝风险有重大影响, 结果导致寿命长的物种灭绝风险高于寿命短的物种。虽然我们的方法有效地解决了数据缺失的问题, 但由于一些物种生活史数据缺乏, 其世代时间可能会被低估。总的来说, 我们的研究结果将强化未来的灭绝风险评估, 并扩增鸟类生活史和特征数据的关键数据库。 【翻译: 胡怡思; 审校: 聂永刚】.

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Reduction of microbial diversity in grassland soil is driven by long-term climate warming

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 1054 - 1062

Published: June 13, 2022

Language: Английский

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Redundancy analysis: A Swiss Army Knife for landscape genomics

Methods in Ecology and Evolution, Journal Year: 2021, Volume and Issue: 12(12), P. 2298 - 2309

Published: Sept. 20, 2021

Abstract Landscape genomics identifies how spatial and environmental factors structure the amount distribution of genetic variation among populations. genomic analyses have been applied across diverse taxonomic groups ecological settings, are increasingly used to analyse datasets composed large numbers markers multiple predictors. It is in this context that multivariate methods show their strengths. Redundancy analysis (RDA) a constrained ordination that, landscape framework, models linear relationships environment predictors variation, effectively identifying covarying allele frequencies associated with environment. RDA can be at both individual population levels, include covariates account for confounding directly infer genotype–environment associations on landscape. The modelling response explanatory variables allows accommodate complexity found nature, producing powerful efficient tool genomics. In review, we outline uses genomics, including variable selection, variance partitioning, associations, calculation adaptive indices offset. To illustrate these applications, use published dataset lodgepole pine includes genomic, phenotypic data. We provide an introduction statistical basis RDA, tutorial its interpretation discuss limitations guidelines avoid misuse. This review comprehensive resource community improve understanding as encourage appropriate applications. truly Swiss Army Knife genomics: multipurpose, adaptable versatile approach identifying, evaluating forecasting between variation.

Language: Английский

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