Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans.
Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans.
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DOI：
10.1093/g3journal/jkac183
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发表时间：
2022-09-30
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遗传数据可以提供对种群历史的洞察，但首先，我们必须了解复杂历史在基因组中留下的模式。在这里，我们认为混合人口的卡波佛得角了解遗传变异的模式留下的社会和人口过程。卡波维迪人最早定居于15世纪末，他们是葡萄牙殖民者和被奴役的西非人民的混血后代。我们认为卡波佛得角的良好研究的历史记录，以及全基因组SNP数据从563个人从4个地区内的群岛。我们使用遗传祖先来测试模式的非随机交配和性别特异性基因流，我们研究这些过程的后果常见的人口推断方法和遗传模式。值得注意的是，假设随机交配的多种群遗传工具低估了混合的时间，但将非随机交配产生的估计更符合历史记录。我们考虑如何混合中断常见的基因组变异，如纯合性运行的摘要。虽然摘要的纯合性可能是难以解释的混合人口，区分运行的纯合性的长度类表明，运行的纯合性反映了历史差异的岛屿之间的贡献，从源人口和postmuddy人口动态。最后，我们发现X染色体上的非洲血统比常染色体上的非洲血统更高，这与基因库中欧洲男性和非洲女性的过度贡献是一致的。考虑到这些基因组见解的背景下，人口的历史卡波佛得角的历史记录，我们可以确定如何在遗传模型的假设影响人口历史的推断更广泛。
Genetic data can provide insights into population history, but first, we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde’s well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating nonrandom mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs of homozygosity. While summaries of runs of homozygosity may be difficult to interpret in admixed populations, differentiating runs of homozygosity by length class shows that runs of homozygosity reflect historical differences between the islands in their contributions from the source populations and postadmixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde’s historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.
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