ArticleJournal of molecular evolution2012
Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small.
Article in Journal of molecular evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 46 citations in OpenAlex.
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- The Role of Phylogenetically Conserved Elements in Shaping Patterns of Human Genomic Diversity.Molecular biology and evolution · 2018Article
- Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data.Genetics · 2017Article
- Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow.G3 (Bethesda, Md.) · 2016Article
- Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila.Molecular biology and evolution · 2016Article
- The rate of adaptive evolution in animal mitochondria.Molecular ecology · 2016Review
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- Inference of gorilla demographic and selective history from whole-genome sequence data.Molecular biology and evolution · 2015Article
- Adaptive evolution of genes involved in the regulation of germline stem cells in Drosophila melanogaster and D. simulans.G3 (Bethesda, Md.) · 2015Article
- The coevolutionary period of Wolbachia pipientis infecting Drosophila ananassae and its impact on the evolution of the host germline stem cell regulating genes.Molecular biology and evolution · 2014Article
- Background selection as baseline for nucleotide variation across the Drosophila genome.PLoS genetics · 2014Article
- Faster-X adaptive protein evolution in house mice.Genetics · 2014Article
- Prevalence of multinucleotide replacements in evolution of primates and Drosophila.Molecular biology and evolution · 2013Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
We investigate the extent by which the estimates of the rate of adaptive molecular evolution obtained by extending the McDonald-Kreitman test are biased if the species, subjected to analysis, diverged recently. We show that estimates can be biased if the nucleotide divergence between the species is low relative to within species variation, and that the magnitude of the bias depends on the rate of adaptive evolution and the distribution of fitness effects of new mutations. Bias appears to be because of three factors: (1) misattribution of polymorphism to divergence; (2) the contribution of ancestral polymorphism to divergence; and (3) different rates of fixation of neutral and advantageous mutations. If there is little adaptive molecular evolution, then slightly deleterious mutations inflate estimates of the rate of adaptive evolution, because these contribute proportionately more to polymorphism than to nucleotide divergence than neutral mutations. However, if there is substantial adaptive evolution, polymorphism contributing to apparent divergence may downwardly bias estimates. We propose a simple method for correcting the different contributions of slightly deleterious and neutral mutations to polymorphism and divergence, and apply it to datasets from several species. We find that estimates of the rate of adaptive molecular evolution from closely related species may be underestimates by ~10% or more. However, after the contribution of polymorphism to divergence is removed, the rate of adaptive evolution may still be overestimated as a consequence of ancestral polymorphism and time for fixation effects. This bias may be substantial if branch lengths are less than 10N (e) generations.
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