Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangdong 510642, China.
College of Forestry and Landscape Architecture, South China Agricultural University, Guangdong 510642, China.
Sci Rep. 2017 Feb 22;7:43178. doi: 10.1038/srep43178.
Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (G = 0.05 ± 0.049). The smallest divergence is among African populations (G = 0.0081 ± 0.0025), with increased divergence among non-African populations (G = 0.0217 ± 0.0109) and then among African and non-African populations (G = 0.0324 ± 0.0064). Genetic diversity is high in African populations (0.13), low in Asian populations (0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.
拷贝数变异 (CNV) 位点在大小、突变率和在自然种群中维持的机制上与单核苷酸多态性 (SNP) 位点不同。因此，人们假设 CNV 位点的群体遗传分化将不同于 SNP 位点的遗传分化。在这里，我们通过分析来自 11 个 HapMap 群体的 1184 名健康个体的 856 个 CNV 位点来检验这一假设，这些个体的祖先背景范围很广。结果表明，CNV 位点的群体遗传分化通常比全基因组 SNP 位点低三倍以上。各群体的遗传分化通常非常小（G=0.05±0.049）。最小的遗传分化发生在非洲群体中（G=0.0081±0.0025），而非非洲群体的遗传分化增加（G=0.0217±0.0109），然后是非洲和非非洲群体之间的遗传分化（G=0.0324±0.0064）。非洲群体的遗传多样性较高（约 0.13），亚洲群体的遗传多样性较低（约 0.11），其余 11 个群体的遗传多样性处于中间水平。全基因组 CNV 位点之间很少出现显著的连锁不平衡（LDs）。配子和合子 LD 的模式表明 CNV 位点之间不存在上位性。突变率约是非非洲群体中迁移率的两倍，这表明高突变率在产生 CNV 位点的低群体遗传分化中起着主导作用。
