Patterns of Selection in Plant Genomes

Hough, Josh; Williamson, R.; Wright, Stephen I.

doi:10.1146/annurev-ecolsys-110512-135851

Cited by 56 publications

(56 citation statements)

References 141 publications

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“…This result contrasts with Drosophila and humans, where a relatively large fraction of selected sites are found in noncoding regions [6]. For example, in Drosophila , only 30%–70% of intronic and intergenic regions are nearly neutral [2], [28], [29].…”

Section: Discussionmentioning

confidence: 81%

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

Williamson

Josephs²,

Platts³

et al. 2014

PLoS Genet

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145

122

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The extent that both positive and negative selection vary across different portions of plant genomes remains poorly understood. Here, we sequence whole genomes of 13 Capsella grandiflora individuals and quantify the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we show that selection is strong in coding regions, but weak in most noncoding regions, with the exception of 5′ and 3′ untranslated regions (UTRs). However, estimates of selection on noncoding regions conserved across the Brassicaceae family show strong signals of selection. Additionally, we see reductions in neutral diversity around functional substitutions in both coding and conserved noncoding regions, indicating recent selective sweeps at these sites. Finally, using expression data from leaf tissue we show that genes that are more highly expressed experience stronger negative selection but comparable levels of positive selection to lowly expressed genes. Overall, we observe widespread positive and negative selection in coding and regulatory regions, but our results also suggest that both positive and negative selection on plant noncoding sequence are considerably rarer than in animal genomes.

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Section: Discussionmentioning

confidence: 81%

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

Williamson

Josephs²,

Platts³

et al. 2014

PLoS Genet

Self Cite

145

122

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show abstract

“…In contrast, little evidence of adaptive amino acid substitutions has been found in flowering plants (mostly with modest Ne < 100,000) (Gossmann et al 2010; Hough et al 2013). Few exceptions have been found in angiosperms with Ne >100,000 such as Capsella grandiflora (Slotte et al 2010; Williamson et al 2014); Helianthus spp .…”

Section: Discussionmentioning

confidence: 99%

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

Torre

Peer

et al. 2017

Molecular Biology and Evolution

188

150

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The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.

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“…Furthermore, given the recent origin of most selfing populations, using substitution rates to test for relaxed selection may have limited power because of the difficulty in identifying the changes that have occurred since the shift to selfing. The use of polymorphism data from selfing populations and their outcrossing progenitors can provide a more powerful means to detect evidence for the reduced efficacy of selection in the genome of selfing populations [47,48], and to assess how rapidly reductions in the efficacy of selection can occur.…”

Section: Selective Consequences Of Transitions To Selfingmentioning

confidence: 99%

The demography and population genomics of evolutionary transitions to self-fertilization in plants

Barrett

Arunkumar

Wright

2014

Phil. Trans. R. Soc. B

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100

137

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The evolution of self-fertilization from outcrossing has occurred on numerous occasions in flowering plants. This shift in mating system profoundly influences the morphology, ecology, genetics and evolution of selfing lineages. As a result, there has been sustained interest in understanding the mechanisms driving the evolution of selfing and its environmental context. Recently, patterns of molecular variation have been used to make inferences about the selective mechanisms associated with mating system transitions. However, these inferences can be complicated by the action of linked selection following the transition. Here, using multilocus simulations and comparative molecular data from related selfers and outcrossers, we demonstrate that there is little evidence for strong bottlenecks associated with initial transitions to selfing, and our simulation results cast doubt on whether it is possible to infer the role of bottlenecks associated with reproductive assurance in the evolution of selfing. They indicate that the effects of background selection on the loss of diversity and efficacy of selection occur rapidly following the shift to high selfing. Future comparative studies that integrate explicit ecological and genomic details are necessary for quantifying the independent and joint effects of selection and demography on transitions to selfing and the loss of genetic diversity.

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Patterns of Selection in Plant Genomes

Cited by 56 publications

References 141 publications

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

The demography and population genomics of evolutionary transitions to self-fertilization in plants

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