Reconstructions of phylogenetic relationships in the flowering plant family Rubiaceae have up until now relied heavily on single‐ or multi‐gene data, primarily from the plastid compartment. With the availability of cost‐ and time‐efficient techniques for generating complete genome sequences, the opportunity arises to resolve some of the relationships that, up until now, have proven problematic. Here, we contribute new data from complete 58 plastid genome sequences, representing 55 of the currently 65 recognized tribes of the Rubiaceae. Also contributed are new data from the nuclear rDNA cistrons for corresponding taxa. Phylogenetic analyses are conducted on two plastid data sets, one including data from the protein coding genes only, and a second where protein coding data are combined with non‐coding regions, and on a nuclear rDNA data set. Our results clearly show that simply adopting a “more characters” approach does not resolve the relationships in the Rubiaceae. More importantly, we identify conflicting phylogenetic signals in the data. Analyses of the same plastid data, treated as nucleotides or as codon‐degenerated data, resolve and support conflicting topologies in the subfamily Cinchonoideae. As these analyses use the same data, we interpret the conflict to result from erroneous assumptions in the models used to reconstruct our phylogenies. Conflicting signals are also identified in the analyses of the plastid versus the nuclear rDNA data sets. These analyses use data from different genomic compartments, with different inheritance patterns, and we interpret the conflicts as representing “real” conflicts, reflecting biological processes of the past.

中文翻译：

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咖啡科（茜草科）基因组数据中相互矛盾的系统发育信号

迄今为止，开花植物茜草科系统发育关系的重建严重依赖单基因或多基因数据，主要来自质体区室。随着用于生成完整基因组序列的成本和时间效率高的技术的可用性，有机会解决一些迄今为止被证明存在问题的关系。在这里，我们提供了来自完整的 58 个质体基因组序列的新数据，代表了目前公认的 65 个茜草科部落中的 55 个。还提供了来自相应分类群的核 rDNA 顺反子的新数据。系统发育分析是在两个质体数据集上进行的，一个只包括来自蛋白质编码基因的数据，第二个将蛋白质编码数据与非编码区域相结合，以及核 rDNA 数据集。我们的结果清楚地表明，简单地采用“更多字符”的方法并不能解决茜草科中的关系。更重要的是，我们在数据中识别出相互矛盾的系统发育信号。对相同质体数据的分析，作为核苷酸或密码子退化数据处理，解决并支持金鸡亚科中的冲突拓扑。由于这些分析使用相同的数据，我们将冲突解释为用于重建系统发育的模型中的错误假设。在质体与核 rDNA 数据集的分析中也发现了相互矛盾的信号。这些分析使用来自具有不同遗传模式的不同基因组区室的数据，我们将冲突解释为代表“真实”冲突，反映了过去的生物过程。