期刊
GENETICS
卷 181, 期 4, 页码 1493-1505出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.108.098830
关键词
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资金
- National Institutes of Health (NIH) [5 T32 HG002536, 5 U01 HL084706-02]
- National Science Foundation [0516310, 0733033]
- National Human Genome Research Institute
- Division Of Environmental Biology
- Direct For Biological Sciences [0516310] Funding Source: National Science Foundation
- Emerging Frontiers
- Direct For Biological Sciences [0733033] Funding Source: National Science Foundation
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 I I gray Wolf Populations and one Coyote Population, we find that the extent of LD as measured by the distance at which r(2) = 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 r(2) value varies from similar to 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%.
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