Demographically-based evaluation of genomic regions under selection in domestic dogs
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- dc.contributor.author Freedman, Adam H.ca
- dc.contributor.author Lorente-Galdós, Belén, 1981-ca
- dc.contributor.author Ramírez, Oscarca
- dc.contributor.author Novembre, Johnca
- dc.date.accessioned 2016-06-16T13:35:26Z
- dc.date.available 2016-06-16T13:35:26Z
- dc.date.issued 2016
- dc.description.abstract Controlling 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 3rd top 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.ca
- dc.format.mimetype application/pdfca
- dc.identifier.citation Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I et al. Demographically-based evaluation of genomic regions under selection in domestic dogs. PLoS Genetics. 2016;12(3):e1005851. DOI: 10.1371/journal.pgen.1005851ca
- dc.identifier.doi http://dx.doi.org/10.1371/journal.pgen.1005851
- dc.identifier.issn 1553-7390
- dc.identifier.uri http://hdl.handle.net/10230/26930
- dc.language.iso engca
- dc.publisher Public Library of Science (PLoS)ca
- dc.relation.ispartof PLoS Genetics. 2016;12(3):e1005851
- dc.rights This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri https://creativecommons.org/publicdomain/zero/1.0/ca
- dc.subject.other Gossosca
- dc.subject.other Genètica animalca
- dc.title Demographically-based evaluation of genomic regions under selection in domestic dogsca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca