Adaptive protein evolution in Drosophila

Smith, Nick G.C.; Eyre‐Walker, Adam

doi:10.1038/4151022a

Cited by 650 publications

(747 citation statements)

References 17 publications

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“…To identify the proportion of differences fixed by positive selection, we calculated the average proportion of amino-acid substitutions driven by positive selection (alpha), using equation (3) in Smith and Eyre-Walker 22 .…”

Section: Methodsmentioning

confidence: 99%

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Genomic islands of divergence are not affected by geography of speciation in sunflowers

et al. 2013

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Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

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Section: Methodsmentioning

confidence: 99%

“…Confidence intervals of alpha were obtained through bootstraps (1,000 bootstraps) by randomly selecting genes with replacement as described in Smith and EyreWalker 22 . In this case, substitutions (D) were considered as SNPs in the top three percentile of the F ST distribution and polymorphisms, the bottom 97 percentile.…”

Section: Methodsmentioning

confidence: 99%

Genomic islands of divergence are not affected by geography of speciation in sunflowers

et al. 2013

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“…Previous work has suggested that a substantial fraction of nonsynonymous substitutions in Drosophila were fixed through positive selection [81][82][83][84][85] . We estimate that 33.1% of single-copy orthologues in the melanogaster group have experienced positive selection on at least a subset of codons (q-value true-positive tests 77 ) (Supplementary Information section 11.1).…”

Section: Articlesmentioning

confidence: 99%

Evolution of genes and genomes on the Drosophila phylogeny

Clark¹,

Eisen²,

Smith³

et al. 2007

Nature

1,826

1,041

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Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

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“…Several studies using the MK test show a high level of 'positive selection' on between-species aminoacid differences in comparisons between D. melanogaster and other Drosophila species (Smith and Eyre-Walker, 2002;Sawyer et al, 2007;Shapiro et al, 2007), whereas in human-chimpanzee comparisons, a much lower proportion of genes show evidence of 'positive selection' (Bustamante et al, 2005;Gojobori et al, 2007).…”

Section: The Mcdonald-kreitman Testmentioning

confidence: 99%

Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level

2007

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Recent years have seen an explosion of interest in evidence for positive Darwinian selection at the molecular level. This quest has been hampered by the use of statistical methods that fail adequately to rule out alternative hypotheses, particularly the relaxation of purifying selection and the effects of population bottlenecks, during which the effectiveness of purifying selection is reduced. A further problem has been the assumption that positive selection will generally involve repeated amino-acid changes to a single protein. This model was derived from the case of the vertebrate major histocompatibility complex (MHC), but the MHC proteins are unusual in being involved in proteinprotein recognition and in a co-evolutionary process of pathogens. There is no reason to suppose that repeated amino-acid changes to a single protein are involved in selectively advantageous phenotypes in general. Rather adaptive phenotypes are much more likely to result from other causes, including single amino-acid changes; deletion or silencing of genes or changes in the pattern of gene expression.

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Adaptive protein evolution in Drosophila

Cited by 650 publications

References 17 publications

Genomic islands of divergence are not affected by geography of speciation in sunflowers

Genomic islands of divergence are not affected by geography of speciation in sunflowers

Evolution of genes and genomes on the Drosophila phylogeny

Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level

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