Journal ArticleDOI
Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations
Stéphane De Mita,Anne-Céline Thuillet,Nourollah Ahmadi,Stéphanie Manel,Joëlle Ronfort,Yves Vigouroux +5 more
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TLDR
In this paper, the authors provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection, and investigate the power and robustness of eight methods to identify loci potentially under selection.Abstract:
Thanks to genome-scale diversity data, present-day studies can provide a detailed view of how natural and cultivated species adapt to their environment and particularly to environmental gradients. However, due to their sensitivity, up-to-date studies might be more sensitive to undocumented demographic effects such as the pattern of migration and the reproduction regime. In this study, we provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection. We simulated 100 populations along a selective gradient and explored different migration models, sampling schemes and rates of self-fertilization. We investigated the power and robustness of eight methods to detect loci potentially under selection: three designed to detect genotype–environment correlations and five designed to detect adaptive differentiation (based on FST or similar measures). We show that genotype– environment correlation methods have substantially more power to detect selection than differentiation-based methods but that they generally suffer from high rates of false positives. This effect is exacerbated whenever allele frequencies are correlated, either between populations or within populations. Our results suggest that, when the underlying genetic structure of the data is unknown, a number of robust methods are preferable. Moreover, in the simulated scenario we used, sampling many populations led to better results than sampling many individuals per population. Finally, care should be taken when using methods to identify genotype–environment correlations without correcting for allele frequency autocorrelation because of the risk of spurious signals due to allele frequency correlations between populations.read more
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The genomics of local adaptation in trees: Are we out of the woods yet?
TL;DR: The success of future endeavors should not be predicated on the shortcomings of past studies and will instead be dependent upon the application of theory to empiricism, standardized reporting, centralized open-access databases, and continual input and review of the community’s research.
Journal ArticleDOI
Prediction and Prevention of Parasitic Diseases Using a Landscape Genomics Framework.
Philipp Schwabl,Martin S. Llewellyn,Erin L. Landguth,Björn Andersson,Uriel Kitron,Jaime A. Costales,Sofia Ocaña,Mario J. Grijalva +7 more
TL;DR: The specific challenges and practical prospects for the use of landscape genetics and genomics to understand the biology and control of parasitic disease are discussed and a practical framework for doing so is presented.
Journal ArticleDOI
A field ornithologist's guide to genomics: Practical considerations for ecology and conservation
TL;DR: This review provides a guide for field ornithologists interested in incorporating genomic approaches into their research program, with an emphasis on techniques related to ecology and conservation.
Journal ArticleDOI
Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon.
Dorothy A. Steane,Dorothy A. Steane,Brad M. Potts,Elizabeth H. McLean,Lesley J. Collins,Barbara R. Holland,Suzanne M. Prober,William D. Stock,René E. Vaillancourt,Margaret Byrne +9 more
TL;DR: Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, the probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes.
Journal ArticleDOI
Genetic variation and signatures of natural selection in populations of European beech (Fagus sylvatica L.) along precipitation gradients
Laura Cuervo-Alarcon,Matthias Arend,Matthias Arend,Markus Müller,Christoph Sperisen,Reiner Finkeldey,Konstantin V. Krutovsky +6 more
TL;DR: The obtained data will help to better understand the genetic variation underlying adaptation to environmentally changing conditions in European beech, which is of great importance for the development of scientific guidelines for the sustainable management and conservation of this important species.
References
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Journal ArticleDOI
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
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TL;DR: It is argued that the common assumption that selection is usually weak in natural populations is no longer tenable, but that natural selection is only one component of the process of evolution; natural selection can explain the change of frequencies of variants, but not their origins.
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