Šlenker Marek, Kantor Adam, Marhold Karol, Schmickl Roswitha, Mandáková Terezie, Lysak Martin A, Perný Marián, Caboňová Michaela, Slovák Marek, Zozomová-Lihová Judita
Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia.
Department of Botany, Faculty of Science, Charles University, Prague, Czechia.
Front Plant Sci. 2021 Apr 28;12:659275. doi: 10.3389/fpls.2021.659275. eCollection 2021.
Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic hybridization (GISH), to resolve the origin of tetraploid endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid-nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian-Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for , which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.
巴尔干半岛的山脉是重要的生物多样性热点地区，物种丰富，狭域特有种比例很大。然而，驱动巴尔干山区丰富植物区系进化的过程仍未得到充分探索和理解。在这里，我们聚焦于一组生长在湿润、主要是山区栖息地的十字花科多年生植物。它包括几种地中海地区特有种，包括那些仅限于巴尔干半岛的物种。我们使用基因组浅层测序的靶向富集技术（Hyb-Seq）来推断它们的系统发育关系，并结合基因组原位杂交（GISH）来解析希腊品都斯山脉南部特有的四倍体的起源。我们还探讨了多倍体物种系统基因组分析的挑战，并开发了一种将等位基因分类为同源基因的新方法，该方法可以识别从不同祖先遗传而来的亚基因组。基于1168个低拷贝核基因，我们获得了一个可靠的二倍体系统发育重建，这表明了异域物种形成和生态物种形成事件。此外，质体-核不一致的情况，与某些物种中不同的核糖体DNA（nrDNA）拷贝变体一致，表明存在种间基因流的痕迹。我们的结果还支持巴尔干地区与安纳托利亚-高加索地区之间的生物地理联系，并说明了后者对巴尔干地区高生物多样性的贡献。推断出的是异源多倍体起源，这突出了巴尔干半岛的山脉作为避难所和熔炉的作用，有利于物种接触和多倍体进化，以应对更新世气候引起的范围动态变化。总体而言，我们的研究证明了在研究受二倍体和多倍体水平网状事件影响的最近分化物种复合体的进化时，采用全面的系统基因组方法的重要性。我们强调从核基因中检索等位基因和同源变异以及从基因组浅层测序数据中检索多个nrDNA拷贝变体的重要性。
