CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
Department of Biological Sciences, Mississippi State University, MS 39762, United States.
Mol Phylogenet Evol. 2023 Nov;188:107912. doi: 10.1016/j.ympev.2023.107912. Epub 2023 Aug 28.
Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history. We used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests to distinguish hard and soft conflict. A selective pressure analysis was also performed to assess the impact of selection on phylogenetic topology reconstruction. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene tree discordance. Furthermore, we confirmed that none of the currently proposed sections of Camellia was monophyletic. Comparisons among datasets partitioned under different selective pressure regimes showed that integrating all orthologous genes provided the best phylogenetic resolution of the species tree of Camellia. The findings of this study reveal rapid diversification as a major source of gene tree discordance in Camellia and will facilitate future investigation of reticulate relationships at the species level in this important plant genus.
基因树分歧是生物进化的重要遗产。多种因素可导致基因之间的不一致，如基因渗入、不完全谱系分选（ILS）、基因复制或丢失。解析基因树分歧的背景是揭示物种多样化过程的关键途径。
山茶花是山茶科中最大的属，由于其复杂的进化历史，其分类学和系统发育存在争议。我们使用了 55 个物种的 60 个转录组，这些物种代表了山茶花的 15 个部分，以研究其系统发育和基因树分歧的可能原因。我们使用基于 1617 个直系同源低拷贝核基因的基因树分歧分析，主要使用聚合法物种树和多系测试来区分硬冲突和软冲突。我们还进行了选择压力分析，以评估选择对系统发育拓扑重建的影响。
我们的研究结果在山茶花的骨干中检测到不同程度的基因树分歧，并发现快速多样化是基因树分歧的可能原因之一。此外，我们证实目前提出的山茶花部分都不是单系的。不同选择压力下数据集的比较表明，整合所有直系同源基因可以提供山茶花物种树的最佳系统发育分辨率。
本研究的发现揭示了快速多样化是山茶花基因树分歧的主要来源，并将有助于未来在这个重要的植物属中对物种水平的网状关系进行研究。
