Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic.
Methods Mol Biol. 2023;2545:297-324. doi: 10.1007/978-1-0716-2561-3_16.
This chapter outlines an empirical analysis of genome-wide single-nucleotide polymorphism (SNP) variation and its underlying drivers among multiple natural populations within a diploid-autopolyploid species. The aim is to reconstruct the genetic structure among natural populations of varying ploidy and infer footprints of selection in these populations, framed around specific questions that are typically encountered when analyzing a mixed-ploidy data set,e.g., addressing the relevance of natural whole-genome duplication for speciation and adaptation. We briefly review the options for the analysis of polyploid population genomic data involving variant calling, population structure, demographic history inference, and selection scanning approaches. Further, we provide suggestions for methods and associated software, possible caveats, and examples of their application to mixed-ploidy and autopolyploid data sets.
本章概述了对二倍体-同源多倍体物种内多个自然种群的全基因组单核苷酸多态性（SNP）变异及其潜在驱动因素的实证分析。目的是重建不同倍性自然种群之间的遗传结构，并推断这些种群中的选择痕迹，围绕分析混合倍性数据集时通常遇到的具体问题，例如，解决自然全基因组复制对物种形成和适应的相关性。我们简要回顾了涉及变异调用、种群结构、人口历史推断和选择扫描方法的多倍体群体基因组数据分析的选项。此外，我们还为混合倍性和同源多倍体数据集的方法和相关软件、可能的注意事项以及应用示例提供了建议。
