Demographically-based evaluation of genomic regions under selection in domestic dogs
Author(s)
Date
2016Source Title
PL o S Genetics
Print ISSN
1553-7390
Publisher
Public Library of Science
Pages
1 - 23
Language
English
Type
ArticleItem Usage Stats
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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 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.
Keywords
Single nucleotideBehavior
Brain function
CADM2 gene
CCRN4L gene
Demography
Diet
Dog
Domestic animal
Domestication
Gene
Gene sequence
Genetic polymorphism
Genetic selection
Genome
Genomics
Genotype
GLRA1 gene
GRIK3 gene
LHFPL3 gene
Lipid metabolism
MBP gene
Nonhuman
NTAN1 gene
PDE7B gene
PDXC1 gene
SCP2D1 gene
Sequence alignment
SH3GL2 gene
Animal
Genetics
Population genetics
Single nucleotide polymorphism
Demography
Dogs
Population
Lipid Metabolism
Polymorphism
Selection