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

Forester, Brenna R.; Lasky, Jesse R.; Wagner, Helene H.; Urban, Dean L.

doi:10.1101/129460

Cited by 155 publications

(337 citation statements)

References 54 publications

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“…For LFMM, there was a decreasing proportion of putatively adaptive SNPs as the genomic sample size increased, while RDA was more conservative with a much shallower slope (significant relationships were not found for other EAA software; Table 1). This follows with a recent simulation study that showed ordination approaches, such as RDA, outperformed univariate approaches when searching for signatures of selection (Forester et al, 2017). Future work should focus on the behaviours of these approaches using data from different organisms, biological samples, genomic samples and parameters within a metaanalysis framework.…”

Section: Variation In Sequencing Approaches and Genome Samplingsupporting

confidence: 60%

The search for loci under selection: trends, biases and progress

et al. 2018

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Detecting genetic variants under selection using F outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP-based selection studies and help to progress landscape and evolutionary genomics.

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Section: Variation In Sequencing Approaches and Genome Samplingsupporting

confidence: 60%

The search for loci under selection: trends, biases and progress

et al. 2018

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“…1: N East = eastern population (orange); N North = northern population (green); and N West = western population (blue). and identify adaptation with low rates of false positives and high rates of true positives across a range of demographic histories, sampling designs and sample sizes (Capblancq et al 2018, Forester et al 2018, was used to identify putative adaptive loci across climatic gradients. RDA was implemented following the methodology outlined in Forester et al (2018).…”

Section: Identifying Putative Adaptive Locimentioning

confidence: 99%

“…F ST -values between sampling localities varied in a predictable manner, with localities closer in geographic proximity (and within the same population) having lower values compared to geographically distant sampling localities or those assigned to different populations (Supplementary material Appendix 1 Table A5). Hilaria jamesii's average F ST was low (0.07), which was beneficial for implementing RDA because this value is similar to the structure in the testing dataset used in Forester et al (2018) (i.e. F ST = 0.05).…”

Section: Population Structure and Historymentioning

confidence: 99%

The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States

Massatti

Knowles

2020

Ecography

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The process of adaptation can be highly dependent upon historical and contemporary factors, especially in environmentally and topographically complex regions affected by Pleistocene glaciations. Here, we investigate Hilaria jamesii (Poaceae), a dryland C 4 graminoid, to test how patterns of adaptive genetic variation are linked to its glacial and post-glacial history. We show that the species persisted in a single, southern refugium during the last glacial period and subsequently migrated throughout its current distribution concurrent with post-glacial warming. The species' putative adaptive genetic variation correlates with climatic gradients (e.g. monsoon precipitation and mean diurnal temperature range) that covary with the species' probable route of demographic expansion. The short timescale and multiple climatic dimensions of adaptation imply that natural selection acted primarily upon standing genetic variation. These findings suggest that restoration and conservation practices should prioritize the maintenance of standing genetic variation to ensure that species have the capacity to respond to future environmental changes.

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“…More specifically, we aimed at detecting outlier loci associated with types of breeding sites distributed along a water depth gradient: the beach spawning site located in the intertidal zone, the demersal spawning site in shallow water (from 2 to 5 m), and the demersal spawning site in deeper water (from to 10 to 20 meters). As recommended by Forester et al (2018), we used a combination of latent factor mixed models (LFMM; Frichot et al 2013, Frichot & François 2015 and partial redundancy analysis (pRDA; 'rda' function in 'vegan' R package; Lasky et al 2012, Forrester et al 2018 to detect candidate loci.…”

Section: Searching For Signals Of Local Adaptation Pattern Within Thementioning

confidence: 99%

Standing genetic variation and chromosomal rearrangements facilitate local adaptation in a marine fish

Cayuela¹,

Rougemont²,

Laporte³

et al. 2019

Preprint

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Population genetic theory states that adaptation most frequently occurs from standing genetic variation, which results from the interplay between different evolutionary processes including mutation, chromosomal rearrangements, drift, gene flow and selection. To date, empirical work focusing on the contribution of standing genetic variation to local adaptation in the presence of high gene flow has been limited to a restricted number of study systems. Marine organisms are excellent biological models to address this issue since many species have to cope with variable environmental conditions acting as selective agents despite high dispersal abilities. In this study, we examined how, demographic history, standing genetic variation linked to chromosomal rearrangements and shared polymorphism among glacial lineages contribute to local adaptation to environmental conditions in the marine fish, the capelin (Mallotus villosus). We used a comprehensive dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,359 individuals collected from 31 spawning sites in the northwest Atlantic (North America and Greenland waters). First, we reconstructed the history of divergence among three glacial lineages and showed that they diverged from 3.8 to 1.8 MyA. Depending on the pair of lineages considered, historical demographic modelling provided evidence for divergence with gene flow and secondary contacts, shaped by barriers to gene flow and linked selection. We next identified candidate loci associated with reproductive isolation of these lineages. Given the absence of physical or geographic barriers, we thus propose that these lineages may represent three cryptic species of capelin. Within each of these, our analyses provided evidence for large ܰ and high gene flow at both historical and contemporary time scales among spawning sites.Furthermore, we detected a polymorphic chromosomal rearrangement leading to the coexistence of three haplogroups within the Northwest Atlantic lineage, but absent in the other two clades.Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Altogether, our study shows that standing genetic variation associated with both chromosomal rearrangements and ancestral polymorphism contribute to local adaptation in the presence of high gene flow.

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

Cited by 155 publications

References 54 publications

The search for loci under selection: trends, biases and progress

The search for loci under selection: trends, biases and progress

The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States

Standing genetic variation and chromosomal rearrangements facilitate local adaptation in a marine fish

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