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  Quantification of GC-biased gene conversion in the human genome

Glémin, S., Arndt, P. F., Messer, P. W., Petrov, D., Galtier, N., & Duret, L. (2015). Quantification of GC-biased gene conversion in the human genome. Genome Research, 25(8), 1215-1228. doi:10.1101/gr.185488.114.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-3B22-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-3B23-3
Genre: Journal Article

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© 2015 Glémin et al.; Published by Cold Spring Harbor Laboratory Press.
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Glémin, S., Author
Arndt, P. F.1, Author              
Messer, P. W., Author
Petrov, D., Author
Galtier, N., Author
Duret, L., Author
Affiliations:
1Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479638              

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 Abstract: Much evidence indicates that GC-biased gene conversion (gBGC) has a major impact on the evolution of mammalian genomes. However, a detailed quantification of the process is still lacking. The strength of gBGC can be measured from the analysis of derived allele frequency spectra (DAF), but this approach is sensitive to a number of confounding factors. In particular, we show by simulations that the inference is pervasively affected by polymorphism polarization errors and by spatial heterogeneity in gBGC strength. We propose a new general method to quantify gBGC from DAF spectra, incorporating polarization errors, taking spatial heterogeneity into account, and jointly estimating mutation bias. Applying it to human polymorphism data from the 1000 Genomes Project, we show that the strength of gBGC does not differ between hypermutable CpG sites and non-CpG sites, suggesting that in humans gBGC is not caused by the base-excision repair machinery. Genome-wide, the intensity of gBGC is in the nearly neutral area. However, given that recombination occurs primarily within recombination hotspots, 1%-2% of the human genome is subject to strong gBGC. On average, gBGC is stronger in African than in non-African populations, reflecting differences in effective population sizes. However, due to more heterogeneous recombination landscapes, the fraction of the genome affected by strong gBGC is larger in non-African than in African populations. Given that the location of recombination hotspots evolves very rapidly, our analysis predicts that, in the long term, a large fraction of the genome is affected by short episodes of strong gBGC.

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Language(s): eng - English
 Dates: 2015-05-202015-08
 Publication Status: Published in print
 Pages: 14
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 Rev. Method: -
 Identifiers: DOI: 10.1101/gr.185488.114
ISSN: 1549-5469 (Electronic)1088-9051 (Print)
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Title: Genome Research
Source Genre: Journal
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Publ. Info: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 25 (8) Sequence Number: - Start / End Page: 1215 - 1228 Identifier: ISSN: 1088-9051
CoNE: /journals/resource/954926997202