Ren Chen, Wang Long, Nie Ze-Long, Johnson Gabriel, Yang Qin-Er, Wen Jun
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China.
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China.
Mol Phylogenet Evol. 2021 Sep;162:107202. doi: 10.1016/j.ympev.2021.107202. Epub 2021 May 14.
The tribe Senecioneae is one of the largest tribes in Asteraceae, with a nearly cosmopolitan distribution. Despite great efforts devoted to elucidate the evolution of Senecioneae, many questions still remain concerning the systematics of this group, from the tribal circumscription and position to species relationships in many genera. The hybridization-based target enrichment method of next-generation sequencing has been accepted as a promising approach to resolve phylogenetic problems. We herein develop a set of single-/low-copy genes for Senecioneae, and test their phylogenetic utilities. Our results demonstrate that these genes work highly efficiently for Senecioneae, with a high average gene recovery of 98.8% across the tribe and recovering robust phylogenetic hypotheses at different levels. In particular, the delimitation of the Senecioneae has been confirmed to include Abrotanella and exclude Doronicum, with the former sister to core Senecioneae and the latter shown to be more closely related to Calenduleae. Moreover, Doronicum and Calenduleae are inferred to be the closest relatives of Senecioneae, which is a new hypothesis well supported by statistical topology tests, morphological evidence, and the profile of pyrrolizidine alkaloids, a special kind of chemical characters generally used to define Senecioneae. Furthermore, this study suggests a complex reticulation history in the diversification of Senecioneae, accounting for the prevalence of polyploid groups in the tribe. With subtribe Tussilagininae s.str. as a case study showing a more evident pattern of gene duplication, we further explored reconstructing the phylogeny in the groups with high ploidy levels. Our results also demonstrate that tree topologies based on sorted paralogous copies are stable across different methods of phylogenetic inference, and more congruent with the morphological evidence and the results of previous phylogenetic studies.
千里光族是菊科中最大的族之一，分布几乎遍及全球。尽管人们为阐明千里光族的进化付出了巨大努力，但关于该类群的系统分类仍存在许多问题，从族的界定和位置到许多属内的物种关系。基于杂交的新一代测序目标富集方法已被公认为解决系统发育问题的一种有前途的方法。我们在此开发了一组用于千里光族的单拷贝/低拷贝基因，并测试了它们在系统发育分析中的效用。我们的结果表明，这些基因在千里光族中工作效率很高，全族平均基因回收率高达98.8%，并在不同水平上恢复了可靠的系统发育假设。特别是，已确认千里光族的界定包括拟鼠麴草属并排除多榔菊属，前者是核心千里光族的姐妹群，而后者与金盏花族的关系更为密切。此外，推断多榔菊属和金盏花族是千里光族最亲近的亲属，这是一个新的假设，得到了统计拓扑检验、形态学证据以及吡咯里西啶生物碱分布情况（一种通常用于界定千里光族的特殊化学特征）的有力支持。此外，本研究表明千里光族在多样化过程中有着复杂的网状进化历史，这解释了该族中多倍体类群的普遍存在。以狭义款冬亚族为例，其基因重复模式更为明显，我们进一步探索了在高倍性水平的类群中重建系统发育的方法。我们的结果还表明，基于排序后的旁系同源拷贝的系统发育树拓扑结构在不同的系统发育推断方法中是稳定的，并且与形态学证据以及先前系统发育研究的结果更为一致。
