Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions

The American Naturalist, Journal Year: 2016, Volume and Issue: 188(4), P. 379 - 397

Published: Aug. 15, 2016

Uncovering the genetic and evolutionary basis of local adaptation is a major focus biology. The recent development cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some loci responsible adaptive differences among populations. Two basic approaches identifying putatively locally have been developed are broadly used: one that identifies with unusually high differentiation populations (differentiation outlier methods) searches correlations between population allele frequencies environments (genetic-environment association methods). Here, we review promises challenges these genome scan methods, including correcting confounding influence species' demographic history, biases caused by missing aspects genome, matching scales environmental structure, other statistical considerations. In each case, make suggestions best practices maximizing accuracy efficiency scans detect underlying adaptation. With attention their current limitations, can be an important tool in finding change.

Language: Английский

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A practical guide to environmental association analysis in landscape genomics

Molecular Ecology, Journal Year: 2015, Volume and Issue: 24(17), P. 4348 - 4370

Published: July 16, 2015

Landscape genomics is an emerging research field that aims to identify the environmental factors shape adaptive genetic variation and gene variants drive local adaptation. Its development has been facilitated by next-generation sequencing, which allows for screening thousands millions of single nucleotide polymorphisms in many individuals populations at reasonable costs. In parallel, data sets describing have greatly improved increasingly become publicly accessible. Accordingly, numerous analytical methods association studies developed. Environmental analysis identifies associated with particular potential uncover patterns are not discovered traditional tests detection outlier loci based on population differentiation. We review conducting including categorical tests, logistic regressions, matrix correlations, general linear models mixed effects models. discuss advantages disadvantages different approaches, provide a list dedicated software packages their specific properties, stress importance incorporating neutral structure analysis. also touch additional important aspects such as sampling design, preparation, pooled reduced-representation candidate-gene linearity allele-environment associations combination analyses tests. conclude summarizing expected future directions field, extension statistical ecological annotation, need replication post hoc validation studies.

Language: Английский

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Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

Nature, Journal Year: 2015, Volume and Issue: 528(7582), P. 405 - 408

Published: Nov. 4, 2015

Language: Английский

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Ecological genomics meets community‐level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation

Ecology Letters, Journal Year: 2014, Volume and Issue: 18(1), P. 1 - 16

Published: Sept. 30, 2014

Local adaptation is a central feature of most species occupying spatially heterogeneous environments, and may factor critically in responses to environmental change. However, efforts model the response climate change ignore intraspecific variation due local adaptation. Here, we present new perspective on spatial modelling organism-environment relationships that combines genomic data community-level develop scenarios regarding geographic distribution Rather than within communities, use these techniques large numbers loci across genomes. Using balsam poplar (Populus balsamifera) as case study, demonstrate how our framework can accommodate nonlinear gradients. We identify threshold temperature circadian clock gene GIGANTEA-5 (GI5), suggesting this has experienced strong temperature. also methods map ecological from data, including identification predicted differences genetic composition populations under current future climates. Community-level represents an important advance landscape genomics biodiversity moves beyond species-level assessments vulnerability.

Language: Английский

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The industrial melanism mutation in British peppered moths is a transposable element

Nature, Journal Year: 2016, Volume and Issue: 534(7605), P. 102 - 105

Published: June 1, 2016

Language: Английский

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Time to get moving: assisted gene flow of forest trees

Evolutionary Applications, Journal Year: 2015, Volume and Issue: 9(1), P. 271 - 290

Published: July 6, 2015

Abstract Geographic variation in trees has been investigated since the mid‐18th century. Similar patterns of clinal have observed along latitudinal and elevational gradients common garden experiments for many temperate boreal species. These studies convinced forest managers that a ‘local is best’ seed source policy was usually safest reforestation. In recent decades, experimental design, phenotyping methods, climatic data statistical analyses improved greatly refined but not radically changed knowledge clines. The maintenance local adaptation despite high gene flow suggests selection to climate strong. Concerns over maladaptation resulting from change motivated new genecological population genomics studies; however, few jurisdictions implemented assisted (AGF), translocation pre‐adapted individuals facilitate planted forests change. Here, we provide evidence tree species show clines sufficiently similar average or models guide AGF absence species‐specific knowledge. Composite provenancing multiple sources can be used increase diversity buffer against future uncertainty. New will continue refine improve as climates warm further.

Language: Английский

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Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(9), P. 2215 - 2233

Published: April 10, 2018

Identifying adaptive loci can provide insight into the mechanisms underlying local adaptation. Genotype-environment association (GEA) methods, which identify these based on correlations between genetic and environmental data, are particularly promising. Univariate methods have dominated GEA, despite high dimensional nature of genotype environment. Multivariate analyse many simultaneously, may be better suited to data as they consider how sets markers covary in response These also more effective at detecting processes that result weak, multilocus signatures. Here, we evaluate four multivariate five univariate differentiation-based approaches, using published simulations selection. We found Random Forest performed poorly for GEA. GEAs better, but had low detection rates under weak Constrained ordinations, redundancy analysis (RDA), showed a superior combination false-positive true-positive across all levels results were robust demographic histories, sampling designs, sample sizes population structure tested here. The value combining detections from different was variable depended study goals knowledge drivers Re-analysis genomic grey wolves highlighted unique, covarying could identified RDA. Although additional testing is needed, this indicates RDA an means adaptation, including signatures selection, providing powerful tool investigating basis

Language: Английский

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Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution ofF_ST

The American Naturalist, Journal Year: 2015, Volume and Issue: 186(S1), P. S24 - S36

Published: Sept. 15, 2015

Loci responsible for local adaptation are likely to have more genetic differentiation among populations than neutral loci. However, loci can vary widely in their amount of differentiation, even over the same geographic range. Unfortunately, distribution differentiation—as measured by an index such as FST—depends on details demographic history question, without spatially heterogeneous selection. Many methods designed detect FST outliers assume a specific model history, which result extremely high false positive rates detecting under We develop new method that infers unlikely be strongly affected diversifying selection, using data large set with unknown selective properties. Compared previous methods, this approach, called OutFLANK, has much lower and comparable power, shown simulation.

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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Genetic Management of Fragmented Animal and Plant Populations

Oxford University Press eBooks, Journal Year: 2017, Volume and Issue: unknown

Published: July 13, 2017

Abstract The biological diversity of the planet is being rapidly depleted due to direct and indirect consequences human activity. As size animal plant populations decrease fragmentation increases, loss genetic reduces their ability adapt changes in environment, with inbreeding reduced fitness inevitable for many species. Many small isolated are going extinct unnecessarily. In cases, such can be genetically rescued by gene flow into them from another population within species, but this very rarely done. This novel authoritative book addresses issues involved management fragmented populations, including depression, elevated extinction risk augmentation flow, rescue, causes outbreeding depression predicting its occurrence, desirability implementation translocations cope climate change, defining diagnosing species conservation purposes.

Language: Английский

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