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  Substitution patterns are under different influences in primates and rodents

Clement, Y., & Arndt, P. F. (2011). Substitution patterns are under different influences in primates and rodents. Genome Biol Evol, 3, 236-45. Retrieved from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21339508 http://gbe.oxfordjournals.org/content/3/236.full.pdf.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7930-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7931-9
Genre: Journal Article

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Clement, Y.1, Author              
Arndt, P. F.1, 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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Free keywords: Animals; Base Composition; Evolution, Molecular; Female; Genome; Humans; Male; Mice; *Point Mutation; Primates/*genetics; Rodentia/*genetics
 Abstract: There are large-scale variations of the GC-content along mammalian chromosomes that have been called isochore structures. Primates and rodents have different isochore structures, which suggests that these lineages exhibit different modes of GC-content evolution. It has been shown that, in the human lineage, GC-biased gene conversion (gBGC), a neutral process associated with meiotic recombination, acts on GC-content evolution by influencing A or T to G or C substitution rates. We computed genome-wide substitution patterns in the mouse lineage from multiple alignments and compared them with substitution patterns in the human lineage. We found that in the mouse lineage, gBGC is active but weaker than in the human lineage and that male-specific recombination better predicts GC-content evolution than female-specific recombination. Furthermore, we were able to show that G or C to A or T substitution rates are predicted by a combination of different factors in both lineages. A or T to G or C substitution rates are most strongly predicted by meiotic recombination in the human lineage but by CpG odds ratio (the observed CpG frequency normalized by the expected CpG frequency) in the mouse lineage, suggesting that substitution patterns are under different influences in primates and rodents.

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 Dates: 2011
 Publication Status: Published in print
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Title: Genome Biol Evol
Source Genre: Journal
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Pages: - Volume / Issue: 3 Sequence Number: - Start / End Page: 236 - 45 Identifier: ISSN: 1759-6653 (Electronic)