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
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
The Effects of Epistasis and Pleiotropy on Genome-Wide Scans for Adaptive Outlier Loci
TL;DR: This work model two populations of a sexually reproducing, diploid organism with two quantitative traits, one of which is involved in local adaptation and considers genetic architectures with and without pleiotropy and epistasis.
Journal ArticleDOI
Perspectives in plant evolutionary genetics: A field guide in 15 “easy steps” to modern tools in evolutionary genetics and genomics
TL;DR: In this paper , the authors present a "roadmap" to take advantage of the explosion of molecular methods and opportunities to analyze genomes, and discuss how to decide which strategies are adequate for a given evolutionary or taxonomic problem by describing 15 possible (and in some cases non-consecutive) steps to taking advantage of all the genomic resources drawing from the everincreasing studies.
Journal ArticleDOI
Genetic Characterization of Maximilian Sunflower for the Development of a Locally Adapted Perennial Grain Oilseed
TL;DR: There appears to be sufficient variation to make selections for agronomic traits in local germplasm of Maximilian sunflower to support its development as a perennial oilseed.
Journal ArticleDOI
Genomic evidence for adaptive differentiation among Microhyla fissipes populations: Implications for conservation
Long Jin,Wen Bo Liao,Juha Merilä +2 more
Journal ArticleDOI
Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.
Jing Ren,Liang Chen,Xiaoli Jin,Miaomiao Zhang,Frank M. You,Jirui Wang,Vladimir Frenkel,Xuegui Yin,Eviatar Nevo,Dongfa Sun,Ming-Cheng Luo,Junhua Peng +11 more
TL;DR: Results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined, and reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity.
References
More filters
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.
Book
Generalized Linear Models
Peter McCullagh,John A. Nelder +1 more
TL;DR: In this paper, a generalization of the analysis of variance is given for these models using log- likelihoods, illustrated by examples relating to four distributions; the Normal, Binomial (probit analysis, etc.), Poisson (contingency tables), and gamma (variance components).
Journal ArticleDOI
Estimating F-statistics for the analysis of population structure.
Bruce S. Weir,C. Clark Cockerham +1 more
TL;DR: The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973).
Journal ArticleDOI
APE: Analyses of Phylogenetics and Evolution in R language
TL;DR: UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics that provides both utility functions for reading and writing data and manipulating phylogenetic trees.
Book
Natural selection in the wild
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.
Related Papers (5)
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
Matthieu Foll,Oscar E. Gaggiotti +1 more