Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models

Hu, Xin‐Sheng; Hu, Yang; Chen, Xiaoyang

doi:10.1016/j.tpb.2016.07.002

Cited by 4 publications

(11 citation statements)

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“…This result is different from those at the genome-wide SNP sites where epistasis occurs among many intron SNPs 37 . The results provide additional support for a recent report indicating that the 856 CNV loci are selectively neutral in each population 23 . The evolutionary processes for the low level of population divergences are different from those at the nonsynonumous SNP sites with F st < 5% where negative selection is thought to be involved 31 .…”

Section: Discussionsupporting

confidence: 86%

“…Note that our analyses are based on the three-allele system for describing the evolution at a CNV locus because the maximum number of allele copies is four in a diploid genotype. These 856 CNV loci are shown to exhibit neutrality among 1184 healthy individuals 23 . A system of more than three alleles is needed when more than four allele copies occur in a genotype at any CNV locus.…”

Section: Discussionmentioning

confidence: 99%

“…The neutrality of CNV loci has also been analyzed 21 22 . We recently developed a three-allele model to test neutrality at CNV loci, and demonstrated selective neutrality at 856 CNV loci scored in 1184 healthy individuals from the HapMap genotype data set 23 . The evolution of these CNV loci can be essentially explained by a mutation-drift process 23 .…”

mentioning

confidence: 99%

“…We recently developed a three-allele model to test neutrality at CNV loci, and demonstrated selective neutrality at 856 CNV loci scored in 1184 healthy individuals from the HapMap genotype data set 23 . The evolution of these CNV loci can be essentially explained by a mutation-drift process 23 . Here, we proceed with the same dataset to investigate population genetic divergence at the genome-wide CNV loci.…”

mentioning

confidence: 99%

“…Furthermore, the sample sizes in previous studies at CNV loci are often too small, and hence are inappropriate for population genetic structure analysis 18 34 35 . The large sample sizes in HapMap Phase III populations means that the probabilities of making either false-positive or negative CNV calls are negligible 23 .…”

mentioning

confidence: 99%

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High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens

Yeh

et al. 2017

Sci Rep

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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 (Gst = 0.05 ± 0.049). The smallest divergence is among African populations (Gst = 0.0081 ± 0.0025), with increased divergence among non-African populations (Gst = 0.0217 ± 0.0109) and then among African and non-African populations (Gst = 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.

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Section: Discussionsupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%