title: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs.
abstract: Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analysed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.|Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Florencia
authors.initials: F
authors.lastname: Schlamp
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Julian
authors.initials: J
authors.lastname: van der Made
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Stambler
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Lewis
authors.initials: L
authors.lastname: Chesebrough
authors.affiliation: Department of Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Adam R
authors.initials: AR
authors.lastname: Boyko
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Philipp W
authors.initials: PW
authors.lastname: Messer
mesh_terms: D000818:Animals; D001947:Breeding; D004285:Dogs / Q000145:classification / Q000235:genetics*; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012641:Selection, Genetic
keywords: adaptation; contemporary evolution; population genetics - empirical; population genetics - theoretical