Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans.

Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans. Research Abstract Details 

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Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans. Abstract Text:

Ryan D Hernandez,Scott H Williamson,Lan Zhu,Carlos D Bustamante,Ryan D Hernandez,Scott H Williamson,Lan Zhu,Carlos D Bustamante,

Understanding the proximate and ultimate causes underlying the evolution of nucleotide composition in mammalian genomes is of fundamental interest to the study of molecular evolution. Comparative genomics studies have revealed that many more substitutions occur from G and C nucleotides to A and T nucleotides than the reverse, suggesting that mammalian genomes are not at equilibrium for base composition. Analysis of human polymorphism data suggests that mutations that increase GC-content tend to be at much higher frequencies than those that decrease or preserve GC-content when the ancestral allele is inferred via parsimony using the chimpanzee genome. These observations have been interpreted as evidence for a fixation bias in favor of G and C alleles due to either positive natural selection or biased gene conversion. Here, we test the robustness of this interpretation to violations of the parsimony assumption using a data set of 21,488 noncoding single nucleotide polymorphisms (SNPs) discovered by the National Institute of Environmental Health Sciences (NIEHS) SNPs project via direct resequencing of n = 95 individuals. Applying standard nonparametric and parametric population genetic approaches, we replicate the signatures of a fixation bias in favor of G and C alleles when the ancestral base is assumed to be the base found in the chimpanzee outgroup. However, upon taking into account the probability of misidentifying the ancestral state of each SNP using a context-dependent mutation model, the corrected distribution of SNP frequencies for GC-content increasing SNPs are nearly indistinguishable from the patterns observed for other types of mutations, suggesting that the signature of fixation bias is a spurious artifact of the parsimony assumption.

Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans. Publishing Authors By Initials

RD Hernandez,SH Williamson,L Zhu,CD Bustamante,RD Hernandez,SH Williamson,L Zhu,CD Bustamante,

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Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Molecular biology and evolution

VOLUME: 24

Page Numbers: 2196-202

Journal Abbreviation: Mol. Biol. Evol.

ISSN: 0737-4038

DAY: 26

MONTH: 07

YEAR: 2007

Context-dependent mutation rates may cause spurious signatures of a fixation bias favoring higher GC-content in humans. Information

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LANGUAGE: eng

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AFFILIATION: Biological Statistics and Computational Biology, Cornell University, USA.

Country: United States

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MEDLINETA: Mol Biol Evol

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