Data from: Inferring the mode of origin of polyploid species from next-generation sequence data

Many eucaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for non-model species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. Application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80,000 years ago. This conclusion runs contrary to previous findings based on the same dataset but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels.许多真核生物均为多倍体。然而，尽管多倍体生物具有重要研究价值，但对其起源与遗传模式进行进化推断的研究长期受制于需通过杂交实验分析多位点等位基因分离情况的技术瓶颈。如今，非模式生物的测序数据日益丰富，使得多倍体基因组数据分析的成熟方法得以应用推广。本研究旨在探究：将近似贝叶斯计算（approximate Bayesian computation，ABC）应用于模拟的传统测序与下一代测序数据时，能否准确推断多倍体的进化与种群历史。本研究通过模拟实验，以采样个体数、位点数量以及是否存在外类群作为变量，评估近似贝叶斯计算对四倍体物种进行进化推断的稳健性。研究结果表明，无论是基于传统测序技术还是新一代测序技术，近似贝叶斯计算均能准确还原多倍体物种近期的进化历史。将近似贝叶斯计算应用于荠属（Capsella）二倍体与多倍体物种的测序数据后，其应用有效性得到了验证。本分析有力支持了荠菜（C. bursa-pastoris）的异源多倍体起源时间约为8万年前。该结论与此前基于同一数据集但采用不同分析方法得到的研究结果相悖，但与近期基于全基因组测序的相关研究结论一致。本研究结果表明，近似贝叶斯计算无需将等位基因归属至部分同源染色体对，即可有效解析多倍体物种的进化历程，是一种极具应用前景且功能强大的分析方法。该方法可轻松拓展至包含更高倍性水平的更复杂研究场景中。