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：推断相对近期演化辐射类群的系统发育关系颇具挑战，尤其是当与近期分化相关的短支引发多重基因树历史时。本研究结合锚定富集高通量测序（anchored enrichment next-generation sequencing）与物种树分析方法，对南非标志性演化辐射类群——山龙眼科帝王花属（Protea, Proteaceae）的系统发育关系进行可靠推断。

研究方法：本研究共采集163个个体，涵盖112个帝王花属物种中的59个物种的多个个体，以及6个外类群物种；利用锚定系统发育组学技术获取了498个低拷贝直系同源核基因座（orthologous nuclear loci）的序列。我们对比了多种构建物种树的方法，并探究基因树-物种树不一致性，以判断系统发育分辨率欠佳是源于信息位点不足、不完全谱系分选（incomplete lineage sorting）还是杂交事件。

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，不仅恢复了此前已得到有力支持的帝王花属内演化支，还为此前分辨率较差的属内系统发育关系提供了得到有力支持的系统发育假说。单个基因树之间差异显著，且与物种树亦存在分歧。不过分析表明，基因树间的差异主要集中在短支支持的演化支上。

结论：利用数百个核基因座的物种树分析方法，为帝王花属辐射演化中诸多此前未被解决的系统发育关系提供了强有力的支持。在部分分支关系支持度仍较低的案例中，这一现象似乎源于信息位点匮乏与信息不足，而非基因树间存在强烈的不一致。