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Correlates of substitution rate variation in mammalian protein-coding sequences

Welch, John J.; Bininda-Emonds, Olaf RP; Bromham, Lindell

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BACKGROUND: Rates of molecular evolution in different lineages can vary widely, and some of this variation might be predictable from aspects of species' biology. Investigating such predictable rate variation can help us to understand the causes of molecular evolution, and could also help to improve molecular dating methods. Here we present a comprehensive study of the life history correlates of substitution rate variation across the mammals, comparing results for mitochondrial and nuclear...[Show more]

dc.contributor.authorWelch, John J.
dc.contributor.authorBininda-Emonds, Olaf RP
dc.contributor.authorBromham, Lindell
dc.date.accessioned2009-05-05T06:17:03Z
dc.date.accessioned2010-12-20T06:04:56Z
dc.date.available2009-05-05T06:17:03Z
dc.date.available2010-12-20T06:04:56Z
dc.identifier.citationBMC Evolutionary Biology 8.53 (2008)
dc.identifier.issn1471-2148
dc.identifier.urihttp://hdl.handle.net/10440/207
dc.identifier.urihttp://digitalcollections.anu.edu.au/handle/10440/207
dc.description.abstractBACKGROUND: Rates of molecular evolution in different lineages can vary widely, and some of this variation might be predictable from aspects of species' biology. Investigating such predictable rate variation can help us to understand the causes of molecular evolution, and could also help to improve molecular dating methods. Here we present a comprehensive study of the life history correlates of substitution rate variation across the mammals, comparing results for mitochondrial and nuclear loci, and for synonymous and non-synonymous sites. We use phylogenetic comparative methods, refined to take into account the special nature of substitution rate data. Particular attention is paid to the widespread correlations between the components of mammalian life history, which can complicate the interpretation of results. RESULTS: We find that mitochondrial synonymous substitution rates, estimated from the 9 longest mitochondrial genes, show strong negative correlations with body mass and with maximum recorded lifespan. But lifespan is the sole variable to remain after multiple regression and model simplification. Nuclear synonymous substitution rates, estimated from 6 genes, show strong negative correlations with body mass and generation time, and a strong positive correlation with fecundity. In contrast to the mitochondrial results, the same trends are evident in rates of nonsynonymous substitution. CONCLUSION: A substantial proportion of variation in mammalian substitution rates can be explained by aspects of their life history, implying that molecular and life history evolution are closely interlinked in this group. The strength and consistency of the nuclear body mass effect suggests that molecular dating studies may have been systematically misled, but also that methods could be improved by incorporating the finding as a priori information. Mitochondrial synonymous rates also show the body mass effect, but for apparently quite different reasons, and the strength of the relationship with maximum lifespan provides support for the hypothesis that mtDNA damage is causally linked to aging.
dc.format12 pages
dc.publisherBioMed Central
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.sourceBMC Evolutionary Biology
dc.source.urihttp://www.biomedcentral.com/content/pdf/1471-2148-8-53.pdf
dc.source.urihttp://www.biomedcentral.com/1471-2148/8/53
dc.source.urihttp://dx.doi.org/10.1186/1471-2148-8-53
dc.subjectKeywords: mitochondrial DNA; aging; article; body mass; chromosome substitution; correlation analysis; DNA damage; fertility; gene sequence; genetic variability; lifespan; mammal; mitochondrial gene; mitochondrion; molecular evolution; multiple regression; nonhuman
dc.titleCorrelates of substitution rate variation in mammalian protein-coding sequences
dc.typeJournal article
local.description.notesANU affiliation in article: Bromham, Lindell, Centre for Macroevolution and Macroecology; School of Botany and Zoology
local.identifier.citationvolume8
dcterms.dateAccepted2008-02-19
dc.date.issued2008-02-19
local.identifier.absfor060409
local.identifier.ariespublicationu9511635xPUB309
local.type.statusPublished Version
local.contributor.affiliationWelch, John J, University of Sussex
local.contributor.affiliationBininda-Emonds, Olaf RP, Institut für Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum
local.contributor.affiliationBromham, Lindell, Faculty of Science, School of Botany and Zoology
local.bibliographicCitation.issue53
local.bibliographicCitation.startpage1
local.bibliographicCitation.lastpage12
local.identifier.doi10.1186/1471-2148-8-53
dc.date.updated2015-12-09T09:53:32Z
local.identifier.scopusID2-s2.0-41949132520
local.identifier.thomsonID000255711700001
CollectionsANU Research Publications

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