Data from: Population genomics reveals a possible history of backcrossing and recombination in the gynogenetic fish Poecilia formosa

Unisexual sperm-dependent vertebrates are of hybrid origins, rare, and predicted to be short-lived as a result of several challenges arising from their mode of reproduction. In particular, because of a lack of recombination, clonal species are predicted to have a low potential to respond to natural selection. However, many unisexual sperm-dependent species persist, and assessing the genetic diversity present in these species is fundamental to understanding how they avoid extinction. We used population genomic methods to assess genotypic variation within the unisexual fish Poecilia formosa. Measures of admixture and population differentiation, as well as clustering analyses, indicate that the genomes of individuals of P. formosa are admixed and intermediate between Poecilia latipinna and Poecilia mexicana, consistent with the hypothesis of their hybrid origins. Bayesian genomic cline analyses indicate that about 12% of sampled loci exhibit patterns consistent with inheritance from only one parent. The estimation of observed heterozygosity clearly suggests that P. formosa is not comprised of direct descendants of a single nonrecombining asexual F1 hybrid individual. Additionally, the estimation of observed heterozygosity provides support for the hypothesis that the history of this unisexual species has included backcrossing with the parent species before the onset of gynogenesis. We also document high levels of variation among asexual individuals, which is attributable to recombination (historical or ongoing) and the accumulation of mutations. The high genetic variation suggests that this unisexual vertebrate has more potential to respond to natural selection than if they were frozen F1 hybrids.

依赖精子的单性脊椎动物（unisexual sperm-dependent vertebrates）均为杂交起源，且极为稀有；由于其生殖模式带来的多重挑战，这类物种被认为寿命较短。具体而言，由于缺乏重组，克隆物种（clonal species）应对自然选择的潜力被认为极低。然而，诸多依赖精子的单性物种仍存续至今，解析这类物种的遗传多样性，是理解其如何规避灭绝的核心所在。本研究采用群体基因组学方法（population genomic methods），对单性鱼类亚马逊花鳉（Poecilia formosa）的基因型变异进行评估。遗传混合度与群体分化程度的测算结果，以及聚类分析均显示，亚马逊花鳉个体的基因组兼具遗传混合特征，且介于宽鳍花鳉（Poecilia latipinna）与墨西哥花鳉（Poecilia mexicana）之间，这与其杂交起源的假说相符。贝叶斯基因组梯度分析（Bayesian genomic cline analyses）结果显示，约12%的采样基因座（loci）呈现出仅从单一亲本遗传的模式。观测杂合度（observed heterozygosity）的估算结果清晰表明，亚马逊花鳉并非源自单一不发生重组的无性F1杂交个体的直接后代。此外，观测杂合度的估算结果也支持以下假说：该单性物种的演化历史中，在雌核发育（gynogenesis）启动前，曾发生过与亲本物种的回交（backcrossing）事件。本研究还揭示了无性个体间存在高水平的遗传变异，该现象可归因于（历史或持续发生的）重组以及突变的积累。这种高水平的遗传变异表明，相较于固化的F1杂交个体，这类单性脊椎动物应对自然选择的潜力更高。