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dc.contributor.authorDe Maio, Nicola
dc.contributor.authorSchlötterer, Christian
dc.contributor.authorKosiol, Carolin
dc.identifier.citationDe Maio , N , Schlötterer , C & Kosiol , C 2013 , ' Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models ' , Molecular Biology and Evolution , vol. 30 , no. 10 , pp. 2249-62 .
dc.identifier.otherPURE: 249098788
dc.identifier.otherPURE UUID: 11e983cf-c17c-489c-a7b6-8df17af9fb00
dc.identifier.otherPubMed: 23906727
dc.identifier.otherPubMedCentral: PMC3773373
dc.identifier.otherScopus: 84888597013
dc.description.abstractThe genomes of related species contain valuable information on the history of the considered taxa. Great apes in particular exhibit variation of evolutionary patterns along their genomes. However, the great ape data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms. Previous methods for genome-scale analysis are restricted to very few individuals or cannot disentangle the contribution of mutation rates and fixation biases. This represents a limitation both for the understanding of these forces as well as for the detection of regions affected by selection. Here, we present a new model designed to estimate mutation rates and fixation biases from genetic variation within and between species. We relax the assumption of instantaneous substitutions, modeling substitutions as mutational events followed by a gradual fixation. Hence, we straightforwardly account for shared ancestral polymorphisms and incomplete lineage sorting. We analyze genome-wide synonymous site alignments of human, chimpanzee, and two orangutan species. From each taxon, we include data from several individuals. We estimate mutation rates and GC-biased gene conversion intensity. We find that both mutation rates and biased gene conversion vary with GC content. We also find lineage-specific differences, with weaker fixation biases in orangutan species, suggesting a reduced historical effective population size. Finally, our results are consistent with directional selection acting on coding sequences in relation to exonic splicing enhancers.
dc.relation.ispartofMolecular Biology and Evolutionen
dc.rights© The Author 2013. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.subjectPhylogenetics-population genetics modelen
dc.subjectMutation ratesen
dc.subjectBiased gene conversionen
dc.subjectRate heterogeneityen
dc.subjectCoding sequence evolutionen
dc.subjectPrimates evolutionen
dc.subjectQH301 Biologyen
dc.subjectQH426 Geneticsen
dc.titleLinking great apes genome evolution across time scales using polymorphism-aware phylogenetic modelsen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Biologyen
dc.contributor.institutionUniversity of St Andrews. Centre for Biological Diversityen
dc.description.statusPeer revieweden

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