Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

Gossmann, Toni I.; Song, Bao‐Hua; Windsor, Aaron J.; Mitchell-Olds, Thomas; Dixon, Christopher J.; Kapralov, Maxim V.; Filatov, Dmitry A.; Eyre‐Walker, Adam

doi:10.1093/molbev/msq079

Cited by 232 publications

(332 citation statements)

References 77 publications

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“…Under population structure, mutations responsible for local adaptation are not considered in species-wide measures of fixed adaptive substitutions. Strong spatial structuring is thus suggested to explain the lack of positive selection found by Gossmann et al (2010) in various plant species, in contrast to results in Capsella grandiflora, a species with low population subdivision that appears to exhibit high rates of adaptive substitutions (a ¼ 40%; Slotte et al, 2010).…”

Section: Selection In Coding Regionsmentioning

confidence: 65%

“…These loci are housekeeping genes, chosen because they are conserved among species , and thus it is unsurprising that they exhibit high levels of purifying selection in coding regions for maintaining their functions. Strong purifying selection was also found in coding regions of other plant species (Gossmann et al, 2010;Slotte et al, 2010).…”

Section: Selection In Coding Regionsmentioning

confidence: 88%

“…The DFE can be summarized as four values representing the proportions of mutations falling into given ranges of ÀN e E(s), as used by Gossmann et al (2010) and Keightley and Eyre-Walker (2010). We show that this summary of the DFE can discriminate between the different purifying selection regimes (Figures 1a and b).…”

Section: A Tellier Et Almentioning

confidence: 92%

“…Methods to measure selection, thus, attempt to estimate the past demography of species, usually based on S sites, and simultaneously or subsequently compute the effects of selection (positive or negative) on NS and NC sites (Eyre-Walker and . Such methods have so far been applied mainly to model organisms for which genome-wide polymorphism data are available (humans, Drosophila, S. cerevisiae and Arabidopsis; Wright and Andolfatto, 2008;Eyre-Walker and Keightley, 2009;Keightley and Eyre-Walker, 2010; but see Gossmann et al, 2010 andSlotte et al, 2010 for recent studies on other plant species).…”

Section: Introductionmentioning

confidence: 99%

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Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure

et al. 2011

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A key issue in evolutionary biology is an improved understanding of the genetic mechanisms by which species adapt to various environments. Using DNA sequence data, it is possible to quantify the number of adaptive and deleterious mutations, and the distribution of fitness effects of new mutations (its mean and variance) by simultaneously taking into account the demography of a given species. We investigated how selection functions at eight housekeeping genes of four closely related, outcrossing species of wild tomatoes that are native to diverse environments in western South America (Solanum arcanum, S. chilense, S. habrochaites and S. peruvianum). We found little evidence for adaptive mutations but pervasive evidence for strong purifying selection in coding regions of the four species. In contrast, the strength of purifying selection seems to vary among the four species in non-coding (NC) regions (introns). Using F ST -based measures of fixation in subdivided populations, we suggest that weak purifying selection has affected the NC regions of S. habrochaites, S. chilense and S. peruvianum. In contrast, NC regions in S. arcanum show a distribution of fitness effects with mutations being either nearly neutral or very strongly deleterious. These results suggest that closely related species with similar genetic backgrounds but experiencing contrasting environments differ in the variance of deleterious fitness effects.

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Section: Selection In Coding Regionsmentioning

confidence: 65%

Section: Selection In Coding Regionsmentioning

confidence: 88%

Section: A Tellier Et Almentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure

et al. 2011

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“…Several recent studies have investigated evidence for adaptation in plant genomes (Gossman et al 2010), including specifically on the flowering-time gene network (Flowers et al 2009, Hall et al 2011, and have found scant evidence for adaptive evolution (but see Ingvarsson 2010and Hall et al 2011for Populus, and Slotte et al 2010 for Capsella). However, the generally employed sampling schemes and analytical methods in these and similar studies are designed to detect positive selection on a species-wide scale, and less attention has been paid to scanning sequence data for signatures of local selection within a species (Tenaillon and Tiffin 2008;Siol et al 2010).…”

Section: Molecular Adaptation Of Phenology Network Genesmentioning

confidence: 99%

Local Selection Across a Latitudinal Gradient Shapes Nucleotide Diversity in Balsam Poplar, Populus balsamifera L

et al. 2011

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Molecular studies of adaptive evolution often focus on detecting selective sweeps driven by positive selection on a specieswide scale; however, much adaptation is local, particularly of ecologically important traits. Here, we look for evidence of range-wide and local adaptation at candidate genes for adaptive phenology in balsam poplar, Populus balsamifera, a widespread forest tree whose range extends across environmental gradients of photoperiod and growing season length. We examined nucleotide diversity of 27 poplar homologs of the flowering-time network-a group of genes that control plant developmental phenology through interactions with environmental cues such as photoperiod and temperature. Only one gene, ZTL2, showed evidence of reduced diversity and an excess of fixed replacement sites, consistent with a species-wide selective sweep. Two other genes, LFY and FRI, harbored high levels of nucleotide diversity and exhibited elevated differentiation between northern and southern accessions, suggesting local adaptation along a latitudinal gradient. Interestingly, FRI has also been identified as a target of local selection between northern and southern accessions of Arabidopsis thaliana, indicating that this gene may be commonly involved in ecological adaptation in distantly related species. Our findings suggest an important role for local selection shaping molecular diversity and reveal limitations of inferring molecular adaptation from analyses designed only to detect species-wide selective sweeps.

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Adaptive Divergence in Sunflowers

Strasburg

2010

Encyclopedia of Life Sciences

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Annual sunflowers have been developed into a model system for the study of adaptation, hybridisation and speciation. Various species and populations have adapted to a wide range of extreme habitats, including salt marshes, sand dunes, desert floor and agricultural environments. In many cases, the process of adaptation has been facilitated by hybridisation between distinct species. Population genetic analyses of several species have revealed evidence of natural selection at loci potentially associated with adaptation to different environments, and genomic analyses indicate that the signature of adaptive divergence is found throughout the genomes of these species. In some cases, the genetic architecture of reproductive isolation and species differences may facilitate adaptive introgression and the formation of new hybrid species through adaptive ecological divergence. Key Concepts: Hybridisation has played an important role in adaptation in sunflowers, both through adaptive introgression and through the formation of adaptively divergent hybrid species. Evidence for adaptive divergence in sunflowers comes from a number of sources, including field experiments, genetic mapping of adaptive traits and DNA sequence analyses. The early morphological and ecological divergence of hybrid species can be experimentally replicated under environmental conditions similar to those encountered by the hybrid species in nature, providing strong evidence that it is adaptive. Data from a number of sunflower species support the hypothesis that adaptive divergence is associated with large population size.

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Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

Cited by 232 publications

References 77 publications

Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure

Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure

Local Selection Across a Latitudinal Gradient Shapes Nucleotide Diversity in Balsam Poplar, Populus balsamifera L

Adaptive Divergence in Sunflowers

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