ArticleImmunogenetics2008
Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes.
Article in Immunogenetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Allelic Variation and Selection in Effector Genes ofPathogens (Basel, Switzerland) · 2020Article
- Evolutionary dynamics and molecular epidemiology ofVirus evolution · 2019Article
- Article
- Significance of positive selection and gene duplication in adaptive evolution: in memory of Austin L. Hughes.Immunogenetics · 2016Review
- The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC.Molecular biology and evolution · 2013Article
- Article
- Characterisation of four major histocompatibility complex class II genes of the koala (Phascolarctos cinereus).Immunogenetics · 2013Article
- Molecular evolution of teleost neural isozymes.Journal of molecular evolution · 2012Article
- Evolution of the βGRP/GNBP/β-1,3-glucanase family of insects.Immunogenetics · 2012Article
- Statistics and truth in phylogenomics.Molecular biology and evolution · 2012Review
- Characterization and locus-specific typing of MHC class I genes in the red-billed gull (Larus scopulinus) provides evidence for major, minor, and nonclassical loci.Immunogenetics · 2011Article
- Origin and diversification of the L-amino oxidase family in innate immune defenses of animals.Immunogenetics · 2010Article
- Evolution of a cluster of innate immune genes (beta-defensins) along the ancestral lines of chicken and zebra finch.Immunome research · 2010Article
- Evolution of Conus peptide genes: duplication and positive selection in the A-superfamily.Journal of molecular evolution · 2010Article
- The evolutionary biology of poxviruses.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2010Review
- Evolutionary analysis and expression profiling of zebra finch immune genes.Genome biology and evolution · 2010Article
- Article
- Reliabilities of identifying positive selection by the branch-site and the site-prediction methods.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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2 authors.
Funding
Abstract
Using basic probability theory, we show that there is a substantial likelihood that even in the presence of strong purifying selection, there will be a number of codons in which the number of synonymous nucleotide substitutions per site (d (S)) exceeds the number of non-synonymous nucleotide substitutions per site (d (N)). In an empirical study, we examined the numbers of synonymous (b (S)) and non-synonymous substitutions (b (N)) along branches of the phylogenies of 69 single-copy orthologous genes from seven species of mammals. A pattern of b (N) > b (S) was most commonly seen in the shortest branches of the tree and was associated with a high coefficient of variation in both b (N) and b (S), suggesting that high stochastic error in b (N) and b (S) on short branches, rather than positive Darwinian selection, is the explanation of most cases where b (N) is greater than b (S) on a given branch. The branch-site method of Zhang et al. (Zhang, Nielsen, Yang, Mol Biol Evol, 22:2472-2479, 2005) identified 117 codons on 35 branches as "positively selected," but a majority of these codons lacked synonymous substitutions, while in the others, synonymous and non-synonymous differences per site occurred in approximately equal frequencies. Thus, it was impossible to rule out the hypothesis that chance variation in the pattern of mutation across sites, rather than positive selection, accounted for the observed pattern. Our results showed that b (N)/b (S) was consistently elevated in immune system genes, but neither the search for branches with b (N) > b (S) nor the branch-site method revealed this trend.
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