Population size may shape the accumulation of functional mutations following domestication

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cg.authorship.typesCGIAR and developing country instituteen
cg.contributor.affiliationHuazhong Agricultural Universityen
cg.contributor.affiliationChinese Academy of Agricultural Sciencesen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationWuhan Institute of Biotechnology, Chinaen
cg.contributor.affiliationChinese Academy of Sciencesen
cg.contributor.crpLivestock
cg.contributor.donorNatural Science Foundation of Chinaen
cg.contributor.donorNational High Technology Research and Development Program, Chinaen
cg.coverage.regionAsia
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1186/s12862-018-1120-6en
cg.isijournalISI Journalen
cg.issn1471-2148en
cg.issue1en
cg.journalBMC Evolutionary Biologyen
cg.reviewStatusPeer Reviewen
cg.subject.ilriANIMAL BREEDINGen
cg.subject.ilriGENETICSen
cg.subject.ilriLIVESTOCKen
cg.volume18en
dc.contributor.authorJianhai Chenen
dc.contributor.authorPan Nien
dc.contributor.authorXinyun Lien
dc.contributor.authorHan Jianlinen
dc.contributor.authorJakovlić, Ivanen
dc.contributor.authorChengjun Zhangen
dc.contributor.authorShuhong Zhaoen
dc.date.accessioned2018-08-24T12:08:31Zen
dc.date.available2018-08-24T12:08:31Zen
dc.identifier.urihttps://hdl.handle.net/10568/96902
dc.titlePopulation size may shape the accumulation of functional mutations following domesticationen
dcterms.abstractBackground Population genetics theory predicts an important role of differences in the effective population size (N e ) among species on shaping the accumulation of functional mutations by regulating the selection efficiency. However, this correlation has never been tested in domesticated animals. Results Here, we synthesized 62 whole genome data in eight domesticated species (cat, dog, pig, goat, sheep, chicken, cattle and horse) and compared domesticates with their wild (or ancient) relatives. Genes with significantly different selection pressures (revealed by nonsynonymous/synonymous substitution rate ratios, Ka/Ks or ω) between domesticated (Dω) and wild animals (Wω) were determined by likelihood-ratio tests. Species-level effective population sizes (N e ) were evaluated by the pairwise sequentially Markovian coalescent (PSMC) model, and Dω/Wω were calculated for each species to evaluate the changes in accumulation of functional mutations after domestication relative to pre-domestication period. Correlation analysis revealed that the most recent (~ 10.000 years ago) N e (s) are positively correlated with Dω/Wω. This result is consistent with the corollary of the nearly neutral theory, that higher N e could boost the efficiency of positive selection, which might facilitate the overall accumulation of functional mutations. In addition, we also evaluated the accumulation of radical and conservative mutations during the domestication transition as: Dradical/Wradical and Dconservative/Wconservative, respectively. Surprisingly, only Dradical/Wradical ratio exhibited a positive correlation with N e (p < 0.05), suggesting that domestication process might magnify the accumulation of radical mutations in species with larger N e .en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2018-01-19
dcterms.bibliographicCitationJianhai Chen, Pan Ni, Xinyun Li, Han Jianlin, Ivan Jakovlić, Chengjun Zhang and Shuhong Zhao. 2018. Population size may shape the accumulation of functional mutations following domestication. BMC Evolutionary Biology 18:4.en
dcterms.issued2018-12
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringeren
dcterms.subjectanimal breedingen
dcterms.subjectgeneticsen
dcterms.typeJournal Article

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