Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA.
Genetics. 2023 Aug 9;224(4). doi: 10.1093/genetics/iyad107.
Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes. Understanding the history of polyploid species thus demands quantitative inferences of demographic history and rates of exchange between subgenomes. To meet this need, we developed diffusion models for genetic variation in polyploids with subgenomes that cannot be bioinformatically separated and with potentially variable inheritance patterns, implementing them in the dadi software. We validated our models using forward SLiM simulations and found that our inference approach is able to accurately infer evolutionary parameters (timing, bottleneck size) involved with the formation of auto- and allotetraploids, as well as exchange rates in segmental allotetraploids. We then applied our models to empirical data for allotetraploid shepherd's purse (Capsella bursa-pastoris), finding evidence for allelic exchange between the subgenomes. Taken together, our model provides a foundation for demographic modeling in polyploids using diffusion equations, which will help increase our understanding of the impact of demography and selection in polyploid lineages.
多倍体是生命之树中包括许多作物在内的多个群体进化新颖性的重要来源。然而，全基因组加倍的影响取决于形成方式：在单个谱系内加倍（自多倍体）与在两个不同谱系杂交后加倍（异源多倍体）。研究人员基于染色体配对模式，将这两种情况视为完全独立的情况，但这些情况代表了在重复基因组之间的染色体相互作用连续体上的理想情况。因此，了解多倍体物种的历史需要对种群历史和亚基因组之间交换率进行定量推断。为了满足这一需求，我们开发了用于具有无法在生物信息学上分离的亚基因组的多倍体的遗传变异的扩散模型，并在 dadi 软件中实现了这些模型。我们使用正向 SLIM 模拟验证了我们的模型，发现我们的推断方法能够准确推断自多倍体和异源四倍体形成以及片段异源四倍体中交换率所涉及的进化参数（时间、瓶颈大小）。然后，我们将模型应用于异源四倍体荠菜（Capsella bursa-pastoris）的实证数据，发现了亚基因组之间等位基因交换的证据。总之，我们的模型为使用扩散方程进行多倍体种群建模提供了基础，这将有助于提高我们对多倍体谱系中种群动态和选择影响的理解。
