NDLI: Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes

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Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes

Content Provider	Springer Nature Link
Author	Hughes, Austin L. Friedman, Robert
Copyright Year	2008
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.
Starting Page	495
Ending Page	506
Page Count	12
File Format	PDF
ISSN	00937711
Journal	Immunogenetics
Volume Number	60
Issue Number	9
e-ISSN	14321211
Language	English
Publisher	Springer-Verlag
Publisher Date	2008-06-26
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Immune system evolution Non-synonymous substitution Positive Darwinian selection Stochastic error Synonymous substitution Allergology Cell Biology Gene Function Human Genetics Immunology
Content Type	Text
Resource Type	Article
Subject	Genetics Immunology

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