Journal Article

Substitution Patterns Are Under Different Influences in Primates and Rodents

Yves Clément and Peter F. Arndt

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 3, issue , pages 236-245
Published in print January 2011 |
Published online February 2011 | e-ISSN: 1759-6653 | DOI: http://dx.doi.org/10.1093/gbe/evr011

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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.

Keywords: genome evolution; isochore; substitution patterns; meiotic recombination; biased gene conversion

Journal Article.  6305 words.  Illustrated.

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

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