Journal Article

Ongoing GC-Biased Evolution Is Widespread in the Human Genome and Enriched Near Recombination Hot Spots

Sol Katzman, John A. Capra, David Haussler and Katherine S. Pollard

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 3, issue , pages 614-626
Published in print January 2011 |
Published online June 2011 | e-ISSN: 1759-6653 | DOI:

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  • Bioinformatics and Computational Biology
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Fast evolving regions of many metazoan genomes show a bias toward substitutions that change weak (A,T) into strong (G,C) base pairs. Single-nucleotide polymorphisms (SNPs) do not share this pattern, suggesting that it results from biased fixation rather than biased mutation. Supporting this hypothesis, analyses of polymorphism in specific regions of the human genome have identified a positive correlation between weak to strong (W→S) SNPs and derived allele frequency (DAF), suggesting that SNPs become increasingly GC biased over time, especially in regions of high recombination. Using polymorphism data generated by the 1000 Genomes Project from 179 individuals from 4 human populations, we evaluated the extent and distribution of ongoing GC-biased evolution in the human genome. We quantified GC fixation bias by comparing the DAFs of W→S mutations and S→W mutations using a Mann–Whitney U test. Genome-wide, W→S SNPs have significantly higher DAFs than S→W SNPs. This pattern is widespread across the human genome but varies in magnitude along the chromosomes. We found extreme GC-biased evolution in neighborhoods of recombination hot spots, a significant correlation between GC bias and recombination rate, and an inverse correlation between GC bias and chromosome arm length. These findings demonstrate the presence of ongoing fixation bias favoring G and C alleles throughout the human genome and suggest that the bias is caused by a recombination-associated process, such as GC-biased gene conversion.

Keywords: fixation bias; weak to strong; biased gene conversion; polymorphism; 1000 Genomes Project

Journal Article.  8494 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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