ArticleGenome biology2014
Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 70 citations in OpenAlex.
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- Invasions of an obligate asexual daphnid species support the nearly neutral theory.Scientific reports · 2022Article
- Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes.Molecular biology and evolution · 2022Article
- Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC ecology and evolution · 2021Article
- Noncoding regions underpin avian bill shape diversification at macroevolutionary scales.Genome research · 2020Article
- Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates.BMC evolutionary biology · 2020Article
- Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species.Molecular biology and evolution · 2020Article
- Molecular Evolution in Small Steps under Prevailing Negative Selection: A Nearly Universal Rule of Codon Substitution.Genome biology and evolution · 2019Article
- Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.Genome biology · 2019Article
- Feather Evolution from Precocial to Altricial Birds.Zoological studies · 2019Article
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Authors and funding
4 authors at 4 institutions in 4 countries.
Funding
Abstract
backgroundThe ratio of the rates of non-synonymous and synonymous substitution (dN/dS) is commonly used to estimate selection in coding sequences. It is often suggested that, all else being equal, dN/dS should be lower in populations with large effective size (Ne) due to increased efficacy of purifying selection. As Ne is difficult to measure directly, life history traits such as body mass, which is typically negatively associated with population size, have commonly been used as proxies in empirical tests of this hypothesis. However, evidence of whether the expected positive correlation between body mass and dN/dS is consistently observed is conflicting.
resultsEmploying whole genome sequence data from 48 avian species, we assess the relationship between rates of molecular evolution and life history in birds. We find a negative correlation between dN/dS and body mass, contrary to nearly neutral expectation. This raises the question whether the correlation might be a method artefact. We therefore in turn consider non-stationary base composition, divergence time and saturation as possible explanations, but find no clear patterns. However, in striking contrast to dN/dS, the ratio of radical to conservative amino acid substitutions (Kr/Kc) correlates positively with body mass.
conclusionsOur results in principle accord with the notion that non-synonymous substitutions causing radical amino acid changes are more efficiently removed by selection in large populations, consistent with nearly neutral theory. These findings have implications for the use of dN/dS and suggest that caution is warranted when drawing conclusions about lineage-specific modes of protein evolution using this metric.
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