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dc.contributor.authorFreedman, A. H.en_US
dc.contributor.authorSchweizer, R. M.en_US
dc.contributor.authorVecchyo, D. Ortega-Delen_US
dc.contributor.authorHan, E.en_US
dc.contributor.authorDavis, B. W.en_US
dc.contributor.authorGronau, I.en_US
dc.contributor.authorSilva, P. M.en_US
dc.contributor.authorGalaverni, M.en_US
dc.contributor.authorFan, Z.en_US
dc.contributor.authorMarx, P.en_US
dc.contributor.authorLorente-Galdos, B.en_US
dc.contributor.authorRamirez, O.en_US
dc.contributor.authorHormozdiari, F.en_US
dc.contributor.authorAlkan C.en_US
dc.contributor.authorVilà, C.en_US
dc.contributor.authorSquire K.en_US
dc.contributor.authorGeffen, E.en_US
dc.contributor.authorKusak, J.en_US
dc.contributor.authorBoyko, A. R.en_US
dc.contributor.authorParker, H. G.en_US
dc.contributor.authorLee C.en_US
dc.contributor.authorTadigotla, V.en_US
dc.contributor.authorSiepel, A.en_US
dc.contributor.authorBustamante, C. D.en_US
dc.contributor.authorHarkins, T. T.en_US
dc.contributor.authorNelson, S. F.en_US
dc.contributor.authorMarques Bonet, T.en_US
dc.contributor.authorOstrander, E. A.en_US
dc.contributor.authorWayne, R. K.en_US
dc.contributor.authorNovembre, J.en_US
dc.date.accessioned2018-04-12T10:54:15Z
dc.date.available2018-04-12T10:54:15Z
dc.date.issued2016en_US
dc.identifier.issn1553-7390
dc.identifier.urihttp://hdl.handle.net/11693/36809
dc.description.abstractControlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the domestication, we examined patterns of polymorphism in six canid genomes that were previously used to infer a demographic model of dog domestication. Using an inferred demographic model, we computed false discovery rates (FDR) and identified 349 outlier regions consistent with positive selection at a low FDR. The signals in the top 100 regions were frequently centered on candidate genes related to brain function and behavior, including LHFPL3, CADM2, GRIK3, SH3GL2, MBP, PDE7B, NTAN1, and GLRA1. These regions contained significant enrichments in behavioral ontology categories. The 3rdtop hit, CCRN4L, plays a major role in lipid metabolism, that is supported by additional metabolism related candidates revealed in our scan, including SCP2D1 and PDXC1. Comparing our method to an empirical outlier approach that does not directly account for demography, we found only modest overlaps between the two methods, with 60% of empirical outliers having no overlap with our demography-based outlier detection approach. Demography-aware approaches have lower-rates of false discovery. Our top candidates for selection, in addition to expanding the set of neurobehavioral candidate genes, include genes related to lipid metabolism, suggesting a dietary target of selection that was important during the period when proto-dogs hunted and fed alongside hunter-gatherers. © 2016, Public Library of Science. All Rights Reserved.en_US
dc.language.isoEnglishen_US
dc.source.titlePL o S Geneticsen_US
dc.relation.isversionofhttp://dx.doi.org/10.1371/journal.pgen.1005851en_US
dc.subjectSingle nucleotideen_US
dc.subjectBehavioren_US
dc.subjectBrain functionen_US
dc.subjectCADM2 geneen_US
dc.subjectCCRN4L geneen_US
dc.subjectDemographyen_US
dc.subjectDieten_US
dc.subjectDogen_US
dc.subjectDomestic animalen_US
dc.subjectDomesticationen_US
dc.subjectGeneen_US
dc.subjectGene sequenceen_US
dc.subjectGenetic polymorphismen_US
dc.subjectGenetic selectionen_US
dc.subjectGenomeen_US
dc.subjectGenomicsen_US
dc.subjectGenotypeen_US
dc.subjectGLRA1 geneen_US
dc.subjectGRIK3 geneen_US
dc.subjectLHFPL3 geneen_US
dc.subjectLipid metabolismen_US
dc.subjectMBP geneen_US
dc.subjectNonhumanen_US
dc.subjectNTAN1 geneen_US
dc.subjectPDE7B geneen_US
dc.subjectPDXC1 geneen_US
dc.subjectSCP2D1 geneen_US
dc.subjectSequence alignmenten_US
dc.subjectSH3GL2 geneen_US
dc.subjectAnimalen_US
dc.subjectGeneticsen_US
dc.subjectPopulation geneticsen_US
dc.subjectSingle nucleotide polymorphismen_US
dc.subjectDemographyen_US
dc.subjectDogsen_US
dc.subjectPopulationen_US
dc.subjectLipid Metabolismen_US
dc.subjectPolymorphismen_US
dc.subjectSelectionen_US
dc.titleDemographically-based evaluation of genomic regions under selection in domestic dogsen_US
dc.typeArticleen_US
dc.departmentDepartment of Computer Engineeringen_US
dc.citation.spage1en_US
dc.citation.epage23en_US
dc.identifier.doi10.1371/journal.pgen.1005851en_US
dc.publisherPublic Library of Scienceen_US


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