Quantifying the variation in the effective population size within a genome

Gossmann, Toni I., Woolfit, Megan and Eyre-Walker, Adam (2011) Quantifying the variation in the effective population size within a genome. Genetics, 189 4: 1389-1402. doi:10.1534/genetics.111.132654

Author Gossmann, Toni I.
Woolfit, Megan
Eyre-Walker, Adam
Title Quantifying the variation in the effective population size within a genome
Journal name Genetics   Check publisher's open access policy
ISSN 0016-6731
Publication date 2011-12
Sub-type Article (original research)
DOI 10.1534/genetics.111.132654
Volume 189
Issue 4
Start page 1389
End page 1402
Total pages 24
Place of publication Bethesda, MD, United States
Publisher Genetics Society of America
Collection year 2012
Language eng
Formatted abstract
The effective population size (Ne) is one of the most fundamental parameters in population genetics. It is thought to vary across the genome as a consequence of differences in the rate of recombination and the density of selected sites due to the processes of genetic hitchhiking and background selection. Although it is known that there is intragenomic variation in the effective population size in some species, it is not known whether this is widespread or how much variation in the effective population size there is. Here, we test whether the effective population size varies across the genome, between protein-coding genes, in 10 eukaryotic species by considering whether there is significant variation in neutral diversity, taking into account differences in the mutation rate between loci by using the divergence between species. In most species we find significant evidence of variation. We investigate whether the variation in Ne is correlated to recombination rate and the density of selected sites in four species, for which these data are available. We find that Ne is positively correlated to recombination rate in one species, Drosophila melanogaster, and negatively correlated to a measure of the density of selected sites in two others, humans and Arabidopsis thaliana. However, much of the variation remains unexplained. We use a hierarchical Bayesian analysis to quantify the amount of variation in the effective population size and show that it is quite modest in all species most genes have an Ne that is within a few fold of all other genes. Nonetheless we show that this modest variation in Ne is sufficient to cause significant differences in the efficiency of natural selection across the genome, by demonstrating that the ratio of the number of nonsynonymous to synonymous polymorphisms is significantly correlated to synonymous diversity and estimates of Ne , even taking into account the obvious nonindependence between these measures. 
Keyword Kreitman Aguade Test
Drosophila Melanogaster
Arabidopsis Thaliana
Molecular Evolution
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
School of Biological Sciences Publications
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