Stubbs Rebecca L, Folk Ryan A, Xiang Chun-Lei, Chen Shichao, Soltis Douglas E, Cellinese Nico
Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland.
Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States.
Front Plant Sci. 2020 Feb 7;10:1773. doi: 10.3389/fpls.2019.01773. eCollection 2019.
The increased availability of large phylogenomic datasets is often accompanied by difficulties in disentangling and harnessing the data. These difficulties may be enhanced for species resulting from reticulate evolution and/or rapid radiations producing large-scale discordance. As a result, there is a need for methods to investigate discordance, and in turn, use this conflict to inform and aid in downstream analyses. Therefore, we drew upon multiple analytical tools to investigate the evolution of (Saxifragaceae), a clade of primarily arctic-alpine herbs impacted by reticulate and rapid radiations. To elucidate the evolution of we sought near-complete taxon sampling with multiple accessions per species and assembled extensive nuclear (518 putatively single copy loci) and plastid (95 loci) datasets. In addition to a robust phylogeny for , this research shows that genetic discordance presents a valuable opportunity to develop hypotheses about its underlying causes, such as hybridization, polyploidization, and range shifts. Specifically, we present a multi-step approach that incorporates multiple checks points for paralogy, including reciprocally blasting targeted genes against transcriptomes, running paralogy checks during the assembly step, and grouping genes into gene families to look for duplications. We demonstrate that a thorough assessment of discordance can be a source of evidence for evolutionary processes that were not adequately captured by a bifurcating tree model, and helped to clarify processes that have structured the evolution of .
大型系统发育基因组数据集越来越容易获得，但其数据的梳理和利用往往存在困难。对于由网状进化和/或快速辐射导致大规模不一致的物种来说，这些困难可能会加剧。因此，需要有方法来研究不一致性，进而利用这种冲突为下游分析提供信息并提供帮助。因此，我们利用多种分析工具来研究虎耳草科（Saxifragaceae）的进化，这是一个主要由北极高山草本植物组成的分支，受到网状进化和快速辐射的影响。为了阐明虎耳草科的进化，我们力求实现近乎完整的分类群抽样，每个物种有多个样本，并组装了大量的核基因（518个假定的单拷贝基因座）和质体基因（95个基因座）数据集。除了构建一个可靠的虎耳草科系统发育树外，这项研究还表明，遗传不一致性为提出关于其潜在原因的假设提供了宝贵机会，如杂交、多倍体化和范围转移。具体来说，我们提出了一种多步骤方法，该方法包含多个针对旁系同源性的检查点，包括将靶向基因与转录组进行相互比对、在组装步骤中进行旁系同源性检查，以及将基因分组到基因家族中以寻找重复。我们证明，对不一致性进行全面评估可以成为进化过程证据的一个来源，而这些过程在二叉树模型中没有得到充分体现，并且有助于阐明构成虎耳草科进化的过程。
