Linkage Disequilibrium and Demographic History of Wild and Domestic Canids

Assessing the extent of linkage disequilibrium (LD) in natural populations of a non-model species has been difficult due to the lack of available genomic markers. However, with advances in genotyping and genome sequencing, genomic characterization of natural populations has become feasible. Using sequence data and SNP genotypes, we measured linkage disequilibrium (LD) and modeled the demographic history of wild canid populations and domestic dog breeds. In 11 gray wolf and one coyote population, we find that the extent of LD as measured by the distance at which r² equals 0.2, extends <10kb in outbred populations to over 1.7Mb in populations that have experienced significant founder events and bottlenecks. This large range in the extent of LD parallels that observed in 18 dog breeds where the r² value varies from ~20kb to >5Mb. Furthermore, in modeling demographic history under a composite likelihood framework, we find that two of five wild canid populations exhibit evidence of a historical population contraction. Five domestic dog breeds display evidence for a minor population contraction during domestication, and a more severe contraction during breed formation. Only a 5% reduction in nucleotide diversity was observed as a result of domestication, whereas the loss of nucleotide diversity with breed formation averaged 35%.

Key Words: Linkage disequilibrium, demographic history, domestic dog, domestication, gray wolf

Online ISSN: 1943-2361  Print ISSN: 0016-6731
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