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Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition

BACKGROUND: While effective population size (N(e)) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recomb...

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Autores principales: Weber, Claudia C, Boussau, Bastien, Romiguier, Jonathan, Jarvis, Erich D, Ellegren, Hans
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290106/
https://www.ncbi.nlm.nih.gov/pubmed/25496599
http://dx.doi.org/10.1186/s13059-014-0549-1
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author Weber, Claudia C
Boussau, Bastien
Romiguier, Jonathan
Jarvis, Erich D
Ellegren, Hans
author_facet Weber, Claudia C
Boussau, Bastien
Romiguier, Jonathan
Jarvis, Erich D
Ellegren, Hans
author_sort Weber, Claudia C
collection PubMed
description BACKGROUND: While effective population size (N(e)) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. However, shifts in chromosomal architecture and recombination landscapes between species may complicate the interpretation of these results. In birds, interchromosomal rearrangements are rare and the recombination landscape is conserved, suggesting that this group is well suited to assess the impact of life history on base composition. RESULTS: Employing data from 45 newly and 3 previously sequenced avian genomes covering a broad range of taxa, we found that lineages with large populations and short generations exhibit higher GC content. The effect extends to both coding and non-coding sites, indicating that it is not due to selection on codon usage. Consistent with recombination driving base composition, GC content and heterogeneity were positively correlated with the rate of recombination. Moreover, we observed ongoing increases in GC in the majority of lineages. CONCLUSIONS: Our results provide evidence that gBGC may drive patterns of nucleotide composition in avian genomes and are consistent with more effective gBGC in large populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord with theoretical predictions, base composition evolution is substantially modulated by species life history. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0549-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-42901062015-01-28 Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition Weber, Claudia C Boussau, Bastien Romiguier, Jonathan Jarvis, Erich D Ellegren, Hans Genome Biol Research BACKGROUND: While effective population size (N(e)) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. However, shifts in chromosomal architecture and recombination landscapes between species may complicate the interpretation of these results. In birds, interchromosomal rearrangements are rare and the recombination landscape is conserved, suggesting that this group is well suited to assess the impact of life history on base composition. RESULTS: Employing data from 45 newly and 3 previously sequenced avian genomes covering a broad range of taxa, we found that lineages with large populations and short generations exhibit higher GC content. The effect extends to both coding and non-coding sites, indicating that it is not due to selection on codon usage. Consistent with recombination driving base composition, GC content and heterogeneity were positively correlated with the rate of recombination. Moreover, we observed ongoing increases in GC in the majority of lineages. CONCLUSIONS: Our results provide evidence that gBGC may drive patterns of nucleotide composition in avian genomes and are consistent with more effective gBGC in large populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord with theoretical predictions, base composition evolution is substantially modulated by species life history. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0549-1) contains supplementary material, which is available to authorized users. BioMed Central 2014-12-11 2014 /pmc/articles/PMC4290106/ /pubmed/25496599 http://dx.doi.org/10.1186/s13059-014-0549-1 Text en © Weber et al.; licensee BioMed Central. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Weber, Claudia C
Boussau, Bastien
Romiguier, Jonathan
Jarvis, Erich D
Ellegren, Hans
Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
title Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
title_full Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
title_fullStr Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
title_full_unstemmed Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
title_short Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
title_sort evidence for gc-biased gene conversion as a driver of between-lineage differences in avian base composition
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290106/
https://www.ncbi.nlm.nih.gov/pubmed/25496599
http://dx.doi.org/10.1186/s13059-014-0549-1
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