Linkage Disequilibrium and Demographic History of Wild and Domestic Canids

Abstract

Assessing the extent of linkage disequilibrium (LD) in natural populations of a nonmodel 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 LD and modeled the demographic history of wild canid populations and domestic dog breeds. In 11 gray wolf populations and one coyote population, we find that the extent of LD as measured by the distance at which r2=0.2 extends <10 kb in outbred populations to >1.7 Mb 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 approximately 20 kb to >5 Mb. 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%.

Comparative oncology: what dogs and other species can teach us about humans with cancer

“…In individual pure breeds, however, the level of genetic diversity is now variably restricted [16]. The process of breed formation over just the past 2-3 centuries has been estimated to have resulted in sevenfold greater reduction in genetic diversity than did the thousands of years of early domestication [17]. This is compounded further by the use of popular sires and gene pool decline during the twentieth century.…”

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

“…We simulated 10,000 variable sites on 10, 30, and 50 individuals, over average sequencing coverages of 1, 2, 3, 5, and 103, with error rates of 0.5%, 1%, and 2%, and varied inbreeding coefficients from 0.0 to 1.0 in steps of 0.1, for a total of 495 combinations. With these parameter choices, we tried to focus on relatively extreme data sets (small sample sizes and low coverage), with realistic error rates (Glenn 2011) and covering biologically relevant scenarios of inbreeding from <0.07 in humans (Carothers et al 2006) and ;0.3 in dogs (Kirkness et al 2003;Gray et al 2009) to 0.4-0.98 in rice (Kovach et al 2007) and 0.757 in wasps (Chapman and Stewart 1996).…”

MHC variability supports dog domestication from a large number of wolves: high diversity in Asia

“…According to Vilà et al (2005) possibly a few hundred wolf founders were involved in the domestication process. A large founding population is also supported by the finding that domestication has not considerably reduced nucleotide diversity in dogs (Gray et al, 2009).…”