Estimating the Parameters of Selection on Nonsynonymous Mutations in<i>Drosophila pseudoobscura</i>and<i>D. miranda</i>

Haddrill, Penelope R.; Loewe, Laurence; Charlesworth, Brian

doi:10.1534/genetics.110.117614

Cited by 64 publications

(110 citation statements)

References 72 publications

(85 reference statements)

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“…D. pseudoobscura and D. miranda are very closely related, with a mean synonymous site divergence (K S ) of about 4 % (Bartolome´& Charlesworth, 2006 ;Haddrill et al, 2010). Introgression between the two species is thought to be absent in the wild, and laboratory hybrids are completely infertile (Dobzhansky & Tan, 1936), so that we should be safe to assume that the pattern of polymorphism observed here is not due to ongoing introgression between these species.…”

Section: (I) Theoretical Backgroundmentioning

confidence: 78%

“…This is important as ongoing hybridization would leave a pattern similar to that of ancestral polymorphism. D. affinis is another North American species that is relatively distantly related to our ingroup species, with a mean K S of about 25% for the X chromosome and 28% for the autosome (A) (Haddrill et al, 2010). The relatively large distance to the outgroup species poses some problems for the parsimony models used here, which are considered in section 2 (iii) below.…”

Section: (I) Theoretical Backgroundmentioning

confidence: 99%

“…To estimate the incidence of ancestral polymorphism for D. pseudoobscura and D. miranda, the 67 loci that did not depart significantly from neutrality on the basis of a multilocus Hudson-Kreitman-Aguade( HKA) test (Hudson et al, 1987 ;Haddrill et al, 2010) were screened for the presence of type 1, type 2/3 and type 4/5 and 6 synonymous polymorphisms in each species, using D. affinis as an outgroup. Gene sequence alignments for 34 autosomal (Muller element B or chromosome 4 in D. pseudoobscura) and 33 X-linked (Muller element A) loci that are orthologous in all three species were obtained (for details concerning Muller's elements, see Ashburner et al, 2005).…”

Section: (I) Theoretical Backgroundmentioning

confidence: 99%

“…Any alignment gaps were also excluded from the analysis. Some additional autosomal and X-linked loci that were previously identified as potentially being under selection in either D. pseudoobscura or D. miranda on the basis of the HKA test (Haddrill et al, 2010), and that were excluded from the main results presented here, are considered in the Discussion section.…”

Section: (I) Theoretical Backgroundmentioning

confidence: 99%

“…We apply it to a dataset of nearly 70 protein-coding genes for which DNA sequence polymorphism data are available in both Drosophila pseudoobscura and its close relative Drosophila miranda, using their relative Drosophila affinis as an outgroup (Haddrill et al, 2010), in an attempt to estimate the true level of ancestral polymorphism for these two species. We show that a substantial proportion of the synonymous variants in these two species are ancestral, and that a small number of genes with unusually high sequence diversity seem to show evidence of an excess of ancestral polymorphisms, suggestive of balancing selection.…”

Section: Introductionmentioning

confidence: 99%

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Ancestral polymorphisms inDrosophila pseudoobscuraandDrosophila miranda

2011

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SummaryAncestral polymorphisms are defined as variants that arose by mutation prior to the speciation event that generated the species in which they segregate. Their presence may complicate the interpretation of molecular data and lead to incorrect phylogenetic inferences. They may also be used to identify regions of the genome that are under balancing selection. It is thus important to take into account the contribution of ancestral polymorphisms to variability within species and divergence between species. Here, we extend and improve a method for estimation of the proportion of ancestral polymorphisms within a species, and apply it to a dataset of 33 X-linked and 34 autosomal protein-coding genes for which sequence polymorphism data are available in both Drosophila pseudoobscura and Drosophila miranda, using Drosophila affinis as an outgroup. We show that a substantial proportion of both X-linked and autosomal synonymous variants in these two species are ancestral, and that a small number of additional genes with unusually high sequence diversity seem to have an excess of ancestral polymorphisms, suggestive of balancing selection.

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Section: (I) Theoretical Backgroundmentioning

confidence: 78%

Section: (I) Theoretical Backgroundmentioning

confidence: 99%

Section: (I) Theoretical Backgroundmentioning

confidence: 99%

Section: (I) Theoretical Backgroundmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Ancestral polymorphisms inDrosophila pseudoobscuraandDrosophila miranda

2011

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Effective population size does not predict codon usage bias in mammals

Kessler

Dean

2014

Ecology and Evolution

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Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (Ne), with selection on CUB operating less efficiently in species with small Ne. Here, we specifically ask whether variation in Ne predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of Ne (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X-linked genes, and high-recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in Ne predicts variation in CUB. Second, across six mammalian species with genetic estimates of Ne (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), Ne and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in Ne does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between Ne and CUB.

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Variation of the adaptive substitution rate between species and within genomes

2019

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The importance of adaptive mutations in molecular evolution is extensively debated. Recent developments in population genomics allow inferring rates of adaptive mutations by fitting a distribution of fitness effects to the observed patterns of polymorphism and divergence at sites under selection and sites assumed to evolve neutrally. Here, we summarize the current state-of-the-art of these methods and review the factors that affect the molecular rate of adaptation. Several studies have reported extensive cross-species variation in the proportion of adaptive amino-acid substitutions (α) and predicted that species with larger effective population sizes undergo less genetic drift and higher rates of adaptation. Disentangling the rates of positive and negative selection, however, revealed that mutations with deleterious effects are the main driver of this population size effect and that adaptive substitution rates vary comparatively little across species. Conversely, rates of adaptive substitution have been documented to vary substantially within genomes. On a genome-wide scale, gene density, recombination and mutation rate were observed to play a role in shaping molecular rates of adaptation, as predicted under models of linked selection. At the gene level, it has been reported that the gene functional category and the macromolecular structure substantially impact the rate of adaptive mutations. Here, we deliver a comprehensive review of methods used to infer the molecular adaptive rate, the potential drivers of adaptive evolution and how positive selection shapes molecular evolution within genes, across genes within species and between species.

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Estimating the Parameters of Selection on Nonsynonymous Mutations inDrosophila pseudoobscuraandD. miranda

Cited by 64 publications

References 72 publications

Ancestral polymorphisms inDrosophila pseudoobscuraandDrosophila miranda

Ancestral polymorphisms inDrosophila pseudoobscuraandDrosophila miranda

Effective population size does not predict codon usage bias in mammals

Variation of the adaptive substitution rate between species and within genomes

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