Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China.
Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China.
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DOI：
10.1111/cla.12570
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发表时间：
2024-01
期刊：
影响因子：
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通讯作者：
Xiang-Guang Ma;Yue-Bo Ren;Hang Sun
中科院分区：
文献类型：
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作者：
Xiang-Guang Ma;Yue-Bo Ren;Hang Sun
通过种间基因流来解决密切相关物种之间的进化关系具有挑战性。基因组规模的数据提供了机会，以澄清复杂的进化关系密切相关的物种，并观察物种的基因组中的物种关系的变化。喜马拉雅-横断亚高山栎在中国西南地区几乎完全同域分布，可能构成一个配子体。在这项研究中，我们映射的重测序数据从不同的物种在这组的Quercus aquifolioides参考基因组，以获得高质量的过滤单核苷酸多态性（SNP）数据集。我们还组装了他们的塑性体。我们重建了它们的系统发育关系，探讨了这些物种之间的基因渗入的水平和模式，并利用滑动窗口研究了这些物种基因组中的基因树变异。相同或密切相关的塑性体被发现在特定地理区域内的不同物种之间广泛共享。全基因组SNP数据的系统基因组学分析发现，大多数橡树在喜马拉雅-横断亚高山分支显示遗传一致性，但几个物种被发现是通过渐渗连接。利用滑动窗口得到的基因树表明，橡树基因组中的系统发育关系是高度异质性的，因此高度模糊。我们的研究发现，中国西南喜马拉雅-横断亚高山分支的所有橡树都形成一个配子体。模糊的系统发育关系观察经验的基因组中最好的解释种间基因流与不完整的谱系排序。
Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.