Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa. METHODS: We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree–species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization. KEY RESULTS: Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches. CONCLUSIONS: Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.

研究背景：对近期发生的演化辐射类群进行系统发育关系估算颇具挑战，尤其是当近期分化所伴随的短分支导致产生多重基因树历史时。本研究结合锚富集二代测序（anchored enrichment next-generation sequencing）与物种树分析，对南非标志性演化辐射类群——帝王花属（Protea），隶属于山龙眼科（Proteaceae）的系统发育关系进行可靠估算。
方法：本研究选取帝王花属112个物种中的59个，每个物种采集多个个体，同时选取6个外类群物种，共计获取163个个体的样本；并通过锚定系统发育组学（anchored phylogenomics）技术，得到498个低拷贝直系同源核基因座的序列。本研究对比多种构建物种树的方法，并探究基因树-物种树之间的差异，以判断系统发育分辨率不佳究竟是源于信息位点不足、不完全谱系分选（incomplete lineage sorting）还是物种间杂交。
主要结果：基于物种树方法得到的系统发育估算结果彼此一致性较高，不仅恢复了帝王花属内此前已得到有力支持的演化支，还为此前分辨率较低的属内关系提供了置信度较高的系统发育假说。单个基因树之间以及基因树与物种树之间均存在显著差异。不过分析结果显示，基因树间的差异主要集中在由短分支所支持的演化支上。
结论：利用数百个核基因座的物种树分析方法，为帝王花属演化辐射中诸多此前未得到解决的系统发育关系提供了强有力的支持。对于某些类群关系支持度仍然较低的情况，其原因似乎是信息位点匮乏而非基因树间存在显著的冲突。