ArticlePLoS genetics2016
Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it, 112 citations in OpenAlex.
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- Elephants as an animal model for self-domestication.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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- Analysis of dog breed diversity using a composite selection index.Scientific reports · 2023Article
- What made us "hunter-gatherers of words".Frontiers in neuroscience · 2023Article
- Bayesian mixed model analysis uncovered 21 risk loci for chronic kidney disease in boxer dogs.PLoS genetics · 2023Article
- A single-nucleus transcriptomic atlas of the dog hippocampus reveals the potential relationship between specific cell types and domestication.National science review · 2022Article
- Genetic Origins of the Two Canis lupus familiaris (Dog) Freight Dog Populations.The Journal of heredity · 2022Article
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- Whole-Genome Sequencing Reveals Lactase Persistence Adaptation in European Dogs.Molecular biology and evolution · 2021Article
Corrections and comments
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Authors and funding
30 authors at 18 institutions in 9 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.