Selective constraints determine the time dependency of molecular rates for human nuclear genomes

Sankar Subramanian; D M Lambert

doi:10.1093/gbe/evs092

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Selective constraints determine the time dependency of molecular rates for human nuclear genomes

Journal article

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Selective constraints determine the time dependency of molecular rates for human nuclear genomes

Sankar Subramanian and D M Lambert

Genome Biology and Evolution, Vol.4(11), pp.1127-1132

2012

DOI: https://doi.org/10.1093/gbe/evs092

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Abstract

rates of evolution

natural selection

time dependency

deleterious polymorphisms

population genetic theory

In contrast to molecular rates forneutralmitochondrial sequences, rates for constrained sites (includingnonsynonymous sites, D-loop, and RNA) in themitochondrial genome are knownto varywith the time frame used for their estimation.Here,we examined this issue for the nuclear genomes using single-nucleotide polymorphisms (SNPs) from six complete human genomes of individuals belonging to different populations.We observed a strong time-dependent distribution of nonsynonymous SNPs (nSNPs) in highly constrained genes. Typically, the proportion of young nSNPs specific to a single populationwas found to be up to three times higher than that of the ancient nSNPs shared between diverse human populations. In contrast, this trend disappeared, and a uniform distribution of young and old nSNPs was observed in genes under relaxed selective constraints. This suggests that because mutations in constrained genes are highly deleterious, they are removed over time, resulting in a relative overabundance of young nSNPs. In contrast, mutations in genes under relaxed constraints are nearly neutral, which leads to similar proportions of young and old SNPs. These results could be useful to researchers aiming to select appropriate genes or genomic regions for estimating evolutionary rates and species or population divergence times. © The Author(s) 2012.

Details

Title: Selective constraints determine the time dependency of molecular rates for human nuclear genomes
Authors: Sankar Subramanian (Author) - Griffith University
D M Lambert (Author) - Griffith University
Publication details: Genome Biology and Evolution, Vol.4(11), pp.1127-1132
Publisher: Oxford University Press
Date published: 2012
DOI: 10.1093/gbe/evs092
ISSN: 1759-6653
Copyright note: Copyright The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99450357402621
Output Type: Journal article

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