Linkage Disequilibrium and Demographic History of Wild and Domestic Canids
Linkage Disequilibrium and Demographic History of Wild and Domestic Canids
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DOI：
10.1534/genetics.108.098830
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发表时间：
2009-04-01
期刊：
影响因子：
3.3
通讯作者：
Wayne, Robert
中科院分区：
文献类型：
--
作者：
Gray, Melissa M.;Granka, Julie M.;Wayne, Robert
由于缺乏可用的基因组标记，在非模式物种的自然群体中评估连锁不平衡（LD）的程度一直很困难。然而，随着基因分型和基因组测序的进展，自然种群的基因组表征已经变得可行。使用序列数据和SNP基因型，我们测量LD和建模的野生犬科动物种群和家犬品种的人口历史。在I I灰狼种群和一个郊狼种群中，我们发现，LD的程度由r（2）= 0.2的距离测量，在经历了重大的创始人事件和瓶颈的种群中延伸1.7 Mb。LD程度的这种大范围与在18个狗品种中观察到的相似，其中r（2）值从近似20 kb变化到>5 Mb。此外，在一个复合似然框架下的人口历史建模中，我们发现五分之二的野生犬科动物种群表现出历史人口收缩的证据。五个家犬品种显示证据的一个小的人口收缩在驯化和更严重的收缩在品种形成。只有5%的核苷酸多样性减少，观察到驯化的结果，而与品种形成的核苷酸多样性的损失平均为35%。
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 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%.