Data from: Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

The molecular era has fundamentally reshaped our knowledge of the evolution and diversification of angiosperms. One outstanding question is the phylogenetic placement of Amborella trichopoda Baill., commonly thought to represent the first lineage of extant angiosperms. Here, we leverage publicly available data and provide a broad coalescent-based species tree estimation of 45 seed plants. By incorporating 310 nuclear genes, our coalescent analyses strongly support a clade containing Amborella plus water lilies (i.e., Nymphaeales) that is sister to all other angiosperms across different nucleotide rate partitions. Our results also show that commonly applied concatenation methods produce strongly supported, but incongruent placements of Amborella: slow-evolving nucleotide sites corroborate results from coalescent analyses, while fast-evolving sites place Amborella alone as the first lineage of extant angiosperms. We further explored the performance of coalescent versus concatenation methods using nucleotide sequences simulated on i) the two alternate placements of Amborella with branch lengths and substitution model parameters estimated from each of the 310 nuclear genes, and ii) three hypothetical species trees that are topologically identical except with respect to the degree of deep coalescence and branch lengths. Our results collectively suggest that the Amborella alone placement inferred using concatenation methods is likely misled by fast-evolving sites. This appears to be exacerbated by the combination of long branches in stem group angiosperms, Amborella, and Nymphaeales with the short internal branch separating Amborella and Nymphaeales. In contrast, coalescent methods appear to be more robust to elevated substitution rates.

分子时代从根本上重塑了我们对被子植物（angiosperms）演化与多样化的认知。其中一项悬而未决的核心问题是互叶梅（Amborella trichopoda Baill.）的系统发育位置，该物种通常被认为是现存被子植物的首个演化支系。本研究依托公开可用的数据，对45种种子植物开展了基于溯祖（coalescent）方法的大范围物种树估计。通过纳入310个核基因，我们的溯祖分析在不同核苷酸速率分区下均得到强有力支持：互叶梅与睡莲类（即睡莲目（Nymphaeales））构成的演化支（clade），是其余所有被子植物的姊妹群。我们的研究同时显示，常用的串联法（concatenation）会得到支持度较高但结果不一致的互叶梅系统发育位置：进化速率较慢的核苷酸位点与溯祖分析结果一致，而进化速率较快的位点则将互叶梅单独定为现存被子植物的首个演化支系。我们进一步通过两类模拟核苷酸序列评估了溯祖法与串联法的性能：其一，基于互叶梅的两种交替系统发育位置，利用310个核基因各自估算的分支长度与替换模型参数进行模拟；其二，构建3棵仅在深度溯祖程度与分支长度上存在差异、拓扑结构一致的假想物种树。综合结果表明，通过串联法推断的‘互叶梅单独为现存被子植物首个演化支系’的结论，很可能受到快速进化位点的误导。这种误导效应因被子植物茎群、互叶梅与睡莲目存在长分支，且互叶梅与睡莲目之间的内部分支较短而被加剧。与之相反，溯祖法对替换速率升高的情况具有更强的鲁棒性。