Lucena-Perez Maria, Kleinman-Ruiz Daniel, Marmesat Elena, Saveljev Alexander P, Schmidt Krzysztof, Godoy José A
Departamento de Ecología Integrativa Estación Biológica de Doñana (CSIC) Sevilla Spain.
Departamento de Genética Facultad de Biología Universidad Complutense Madrid Spain.
Evol Appl. 2021 Oct 8;14(11):2664-2679. doi: 10.1111/eva.13302. eCollection 2021 Nov.
Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic diversity following a bottleneck by comparing whole-genome diversity patterns in populations with and without severe recent documented declines of Iberian (, = 31) and Eurasian lynx (, = 29). As expected, overall genomic diversity correlated negatively with bottleneck intensity and/or duration. Correlations of genetic diversity with divergence, chromosome size, gene or functional site content, GC content, or recombination were observed in nonbottlenecked populations, but were weaker in bottlenecked populations. Also, functional features under intense purifying selection and the X chromosome showed an increase in the observed density of variants, even resulting in higher diversity than in nonbottlenecked populations. Increased diversity seems to be related to both a higher mutational input in those regions creating a large collection of low-frequency variants, a few of which increase in frequency during the bottleneck to the point they become detectable with our limited sample, and the reduced efficacy of purifying selection, which affects not only protein structure and function but also the regulation of gene expression. The results of this study alert to the possible reduction of fitness and adaptive potential associated with the genomic erosion in regulatory elements. Further, the detection of a gain of diversity in ultra-conserved elements can be used as a sensitive and easy-to-apply signature of genetic erosion in wild populations.
种群瓶颈通常会通过更强烈的遗传漂变降低遗传多样性，但由于遗传漂变的随机性以及重组、突变和选择的局部效应，其净效应可能会在基因组中有所不同。在此，我们通过比较有和没有近期记录到严重数量下降的伊比利亚猞猁（n = 31）和欧亚猞猁（n = 29）种群的全基因组多样性模式，分析了瓶颈之后遗传多样性的变化。正如预期的那样，总体基因组多样性与瓶颈强度和/或持续时间呈负相关。在非瓶颈种群中观察到遗传多样性与分化、染色体大小、基因或功能位点含量、GC含量或重组之间存在相关性，但在瓶颈种群中相关性较弱。此外，在强烈的纯化选择下的功能特征以及X染色体显示出观察到的变异密度增加，甚至导致多样性高于非瓶颈种群。多样性增加似乎既与那些区域中更高的突变输入有关，这种突变输入产生了大量低频变异，其中一些在瓶颈期间频率增加到能用我们有限的样本检测到的程度，也与纯化选择效力降低有关，纯化选择不仅影响蛋白质结构和功能，还影响基因表达的调控。本研究结果警示了与调控元件中基因组侵蚀相关的适应性和适应潜力可能降低的情况。此外，在超保守元件中检测到多样性增加可作为野生种群遗传侵蚀的一个敏感且易于应用的特征。
