Thureborn Olle, Razafimandimbison Sylvain G, Wikström Niklas, Rydin Catarina
Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.
Department of Botany, Swedish Museum of Natural History, Stockholm, Sweden.
Front Plant Sci. 2022 Sep 8;13:967456. doi: 10.3389/fpls.2022.967456. eCollection 2022.
Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.
茜草亚科是咖啡科（茜草科）主要谱系中最大的一个亚科，有超过8000个物种和29个族。尽管已经付出了相当大的努力，但该植物类群各族之间以及其他主要分支之间的系统发育关系仍仅得到部分解决。虽然先前的研究主要利用了细胞器基因组和核糖体DNA的数据，但我们在此使用通过目标捕获方法获得的大量低拷贝核基因来推断茜草亚科内的系统发育关系。我们纳入了101种茜草亚科物种，代表了目前公认的所有族（除了单属族丰奇韦族和艾奇逊族），并且除了一个非单属族外，所有族均由多个属代表。利用通用被子植物353探针组靶向的353个基因的数据，我们研究了数据类型、分析方法和潜在旁系同源基因对系统发育重建的影响。我们推断出一个稳健的茜草亚科系统发育假说，在所有分析和数据集中，绝大多数（或所有）节点都得到了高度支持，并且推断的拓扑结构之间几乎没有不一致之处。结果与先前的研究相似，但也发现了新的关系。我们发现，超级重叠群[编码序列（CDS）+非编码序列]在支持水平和基因树一致性方面明显优于CDS数据。完整数据集（353个基因）在支持水平上优于去除了潜在旁系同源基因的数据集（186个基因），但基因树不一致性略有增加。短内部分支处的基因树冲突模式通常与由于该类群快速物种形成导致的高水平不完全谱系分选（ILS）一致。虽然基于串联和合并的树主要一致，但两种方法之间观察到的系统发育不一致可能最好用它们在考虑ILS方面的差异来解释。目标捕获数据的使用极大地提高了我们对茜草亚科系统发育的信心和理解，这体现在对先前不确定关系的支持增加以及探索潜在系统发育不一致来源的可能性增加上。
