The genetic differentiation at quantitative trait loci under local adaptation

Corre, Valérie Le; Kremer, Antoine

doi:10.1111/j.1365-294x.2012.05479.x

Cited by 306 publications

(356 citation statements)

References 115 publications

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“…On the other hand, more recent simulations suggest that high population differentiation can result in a higher rate of false-negatives [41], yet our study still found greater evidence for selection signatures in pairwise comparisons involving small populations.…”

Section: (A) Possible Caveats and Assumptionsmentioning

confidence: 44%

Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish

Fraser

Debes²,

Bernatchez

et al. 2014

Proc. R. Soc. B.

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Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, singlenucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest.

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Section: (A) Possible Caveats and Assumptionsmentioning

confidence: 44%

Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish

Fraser

Debes²,

Bernatchez

et al. 2014

Proc. R. Soc. B.

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“…(2016), we detected a relatively large number of significant GEAs using single‐locus analyses (Bayenv2 and LFMM). F ST outlier and GEA methods are more likely to detect moderate to strongly selected alleles because among‐population differentiation for weakly selected alleles is very difficult to distinguish from neutrally evolving loci (Le Corre & Kremer, 2012; Lotterhos & Whitlock, 2015; Yeaman, 2015). Given the small proportion of the genome surveyed here, it seems unlikely that we captured a significant amount of adaptive covariance among loci, and so we abstain from drawing conclusions about the genetic architecture of local adaptation to climate in P. strobus .…”

Section: Discussionmentioning

confidence: 99%

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

Nadeau

Meirmans

Aitken

et al. 2016

Ecology and Evolution

120

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Accurately detecting signatures of local adaptation using genetic‐environment associations (GEAs) requires controlling for neutral patterns of population structure to reduce the risk of false positives. However, a high degree of collinearity between climatic gradients and neutral population structure can greatly reduce power, and the performance of GEA methods in such case is rarely evaluated in empirical studies. In this study, we attempted to disentangle the effects of local adaptation and isolation by environment (IBE) from those of isolation by distance (IBD) and isolation by colonization from glacial refugia (IBC) using range‐wide samples in two white pine species. For this, SNPs from 168 genes, including 52 candidate genes for growth and phenology, were genotyped in 133 and 61 populations of Pinus strobus and P. monticola, respectively. For P. strobus and using all 153 SNPs, climate (IBE) did not significantly explained among‐population variation when controlling for IBD and IBC in redundancy analyses (RDAs). However, 26 SNPs were significantly associated with climate in single‐locus GEA analyses (Bayenv2 and LFMM), suggesting that local adaptation took place in the presence of high gene flow. For P. monticola, we found no evidence of IBE using RDAs and weaker signatures of local adaptation using GEA and F ST outlier tests, consistent with adaptation via phenotypic plasticity. In both species, the majority of the explained among‐population variation (69 to 96%) could not be partitioned between the effects of IBE, IBD, and IBC. GEA methods can account differently for this confounded variation, and this could explain the small overlap of SNPs detected between Bayenv2 and LFMM. Our study illustrates the inherent difficulty of taking into account neutral structure in natural populations and the importance of sampling designs that maximize climatic variation, while minimizing collinearity between climatic gradients and neutral structure.

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“…This could be overly conservative at times, as power to detect Q ST 4F ST is generally limited for species with high neutral genetic divergence (Porcher et al, 2006;Le Corre and Kremer, 2012). Moreover, several improved estimation approaches are currently not applicable for selfing species with high neutral divergence (personal communication M. Karhunen;Whitlock, 2008;Karhunen et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana

Luo¹,

Widmer

Karrenberg

2014

Heredity

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Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and 2700 m above sea level in the Swiss Alps. Seed families were grown with and without vernalization, corresponding to winter-annual and summer-annual life histories, respectively. We analyzed putatively neutral genetic divergence between these populations using 24 simple sequence repeat markers. We measured seven traits related to growth, phenology and leaf morphology that are rarely reported in A. thaliana and performed analyses of altitudinal clines, as well as overall Q ST -F ST comparisons and correlation analyses among pair-wise Q ST , F ST and altitude of origin differences. Multivariate analyses suggested adaptive differentiation along altitude in the entire suite of traits, particularly when expressed in the summer-annual life history. Of the individual traits, a decrease in rosette leaf number in the vegetative state and an increase in leaf succulence with increasing altitude could be attributed to adaptive divergence. Interestingly, these patterns relate well to common within-and between-species trends of smaller plant size and thicker leaves at high altitude. Our results thus offer exciting possibilities to unravel the underlying mechanisms for these conspicuous trends using the model species A. thaliana.

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The genetic differentiation at quantitative trait loci under local adaptation

Cited by 306 publications

References 115 publications

Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish

Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana

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