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（polyploid）。然而，尽管多倍体生物具有重要研究价值，针对其起源与遗传模式的进化推断长期以来受限于需通过杂交实验分析多个基因座（loci）的等位基因分离情况。如今，非模式物种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。本研究旨在探讨：将近似贝叶斯计算（approximate Bayesian computation, ABC）应用于贴合实际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，评估了近似贝叶斯计算对四倍体（tetraploid）物种进化推断的稳健性，该稳健性受采样个体数、采样基因座数以及是否存在外类群（outgroup）的影响。研究结果表明，基于新旧两代测序技术的数据，近似贝叶斯计算均可准确还原多倍体物种的近期进化历史。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，验证了该方法的实用性。本分析强烈支持，荠菜（C. bursa-pastoris，Capsella bursa-pastoris）的异源多倍体（allopolyploid）起源发生于约8万年前。该结论与基于同一数据集但采用其他分析方法得到的既往研究结果相悖，但与近期全基因组测序相关研究的结论一致。本研究结果表明，无需将等位基因定位至部分同源染色体对（homeologous chromosome pair），近似贝叶斯计算即可作为一种极具潜力与效力的方法，用于揭示多倍体物种的进化历程。该方法可轻松拓展至更高倍性水平的复杂进化场景中。