Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA.
Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
Mol Phylogenet Evol. 2024 Jul;196:108089. doi: 10.1016/j.ympev.2024.108089. Epub 2024 Apr 27.
Molecular analyses of rapidly radiating groups often reveal incongruence between gene trees. This mainly results from incomplete lineage sorting, introgression, and gene tree estimation error, which complicate the estimation of phylogenetic relationships. In this study, we reconstruct the phylogeny of Theaceae using 348 nuclear loci from 68 individuals and two outgroup taxa. Sequence data were obtained by target enrichment using the recently released Angiosperm 353 universal probe set applied to herbarium specimens. The robustness of the topologies to variation in data quality was established under a range of different filtering schemes, using both coalescent and concatenation approaches. Our results confirmed most of the previously hypothesized relationships among tribes and genera, while clarifying additional interspecific relationships within the rapidly radiating genus Camellia. We recovered a remarkably high degree of gene tree heterogeneity indicative of rapid radiation in the group and observed cytonuclear conflicts, especially within Camellia. This was especially pronounced around short branches, which we primarily associate with gene tree estimation error. Our analysis also indicates that incomplete lineage sorting (ILS) contributed to gene-tree conflicts and accounted for approximately 14 % of the explained variation, whereas inferred introgression levels were low. Our study advances the understanding of the evolution of this important plant family and provides guidance on the application of target capture methods and the evaluation of key processes that influence phylogenetic discordances.
对快速辐射类群的分子分析常常揭示出基因树之间的不一致。这主要是由于不完全谱系分选、基因渗入和基因树估计错误造成的，这些因素使系统发育关系的估计变得复杂。在这项研究中，我们使用 68 个个体和两个外类群的 348 个核基因座，重建了山茶科的系统发育。通过最近发布的被子植物 353 个通用探针组在标本上进行靶向富集，获得了序列数据。使用合并和串联方法，在一系列不同的过滤方案下，确定了拓扑结构对数据质量变化的稳健性。我们的结果证实了大多数先前假设的族和属之间的关系，同时澄清了快速辐射的属茶花内的额外种间关系。我们发现了一个非常高的基因树异质性程度，表明该群体的快速辐射，并观察到核质冲突，特别是在茶花中。这在短分支周围尤为明显，我们主要将其与基因树估计错误联系起来。我们的分析还表明，不完全谱系分选（ILS）导致了基因树冲突，并解释了约 14%的变异，而推断的基因渗入水平较低。我们的研究推进了对这一重要植物科进化的理解，并为目标捕获方法的应用和影响系统发育分歧的关键过程的评估提供了指导。
