The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations
The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations
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DOI：
10.1111/eva.12872
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发表时间：
2019-09-30
影响因子：
4.1
通讯作者：
Megens, Hendrik-Jan
中科院分区：
文献类型：
--
作者：
Bortoluzzi, Chiara;Bosse, Mirte;Megens, Hendrik-Jan
预测小种群规模对遗传变异和有害变异的影响是种群遗传学的基础。由于小种群更容易受到遗传漂变的影响，预计针对有害等位基因的净化选择效率较低，因此增加了近交抑制的风险。然而，小种群遭受遗传漂变的程度取决于瓶颈发生的性质和时间框架。驯化物种是研究种群瓶颈对小种群遗传和有害变异的影响的极好模型。这是因为它们的历史被已知的与驯化、品种形成和激烈的选择性育种有关的瓶颈所主宰。在这里，我们使用来自代表39个传统优良品种的97只鸡的全基因组测序数据，直接检查了两种类型的有害变异瓶颈的后果：严重的驯化瓶颈和最近伴随品种形成的种群下降。我们发现，相对于自驯化以来一直保持在小种群规模的种群，最近瓶颈种群具有更高比例的有害变异。我们还观察到，纯合子基因型的长束（纯合子序列）在有害变异中的富集程度比基因组的其他部分高。这种富集在最近的瓶颈种群中尤其明显，这表明这些变异的纯合性可能是由于遗传漂变和最近的近亲繁殖而发生的。我们的研究结果表明，种群瓶颈的时间和性质可以在很大程度上塑造小种群的有害变异景观。
Predictions about the consequences of a small population size on genetic and deleterious variation are fundamental to population genetics. As small populations are more affected by genetic drift, purifying selection acting against deleterious alleles is predicted to be less efficient, therefore increasing the risk of inbreeding depression. However, the extent to which small populations are subjected to genetic drift depends on the nature and time frame in which the bottleneck occurs. Domesticated species are an excellent model to investigate the consequences of population bottlenecks on genetic and deleterious variation in small populations. This is because their history is dominated by known bottlenecks associated with domestication, breed formation and intense selective breeding. Here, we use whole-genome sequencing data from 97 chickens representing 39 traditional fancy breeds to directly examine the consequences of two types of bottlenecks for deleterious variation: the severe domestication bottleneck and the recent population decline accompanying breed formation. We find that recently bottlenecked populations have a higher proportion of deleterious variants relative to populations that have been kept at small population sizes since domestication. We also observe that long tracts of homozygous genotypes (runs of homozygosity) are proportionally more enriched in deleterious variants than the rest of the genome. This enrichment is particularly evident in recently bottlenecked populations, suggesting that homozygosity of these variants is likely to occur due to genetic drift and recent inbreeding. Our results indicate that the timing and nature of population bottlenecks can substantially shape the deleterious variation landscape in small populations.