Wanke Stefan, Granados Mendoza Carolina, Müller Sebastian, Paizanni Guillén Anna, Neinhuis Christoph, Lemmon Alan R, Lemmon Emily Moriarty, Samain Marie-Stéphanie
Technische Universität Dresden, Institut für Botanik, Zellescher Weg 20b, 01062 Dresden, Germany.
CONACYT División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa de San José 2055, Lomas 4a. sección, C.P. 78216 San Luis Potosí, San Luis Potosí, Mexico; Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 Coyoacán, Distrito Federal, Mexico.
Mol Phylogenet Evol. 2017 Dec;117:111-123. doi: 10.1016/j.ympev.2017.05.014. Epub 2017 May 20.
Recalcitrant relationships are characterized by very short internodes that can be found among shallow and deep phylogenetic scales all over the tree of life. Adding large amounts of presumably informative sequences, while decreasing systematic error, has been suggested as a possible approach to increase phylogenetic resolution. The development of enrichment strategies, coupled with next generation sequencing, resulted in a cost-effective way to facilitate the reconstruction of recalcitrant relationships. By applying the anchored hybrid enrichment (AHE) genome partitioning strategy to Aristolochia using an universal angiosperm probe set, we obtained 231-233 out of 517 single or low copy nuclear loci originally contained in the enrichment kit, resulting in a total alignment length of 154,756bp to 160,150bp. Since Aristolochia (Piperales; magnoliids) is distantly related to any angiosperm species whose genome has been used for the plant AHE probe design (Amborella trichopoda being the closest), it serves as a proof of universality for this probe set. Aristolochia comprises approximately 500 species grouped in several clades (OTUs), whose relationships to each other are partially unknown. Previous phylogenetic studies have shown that these lineages branched deep in time and in quick succession, seen as short-deep internodes. Short-shallow internodes are also characteristic of some Aristolochia lineages such as Aristolochia subsection Pentandrae, a clade of presumably recent diversification. This subsection is here included to test the performance of AHE at species level. Filtering and subsampling loci using the phylogenetic informativeness method resolves several recalcitrant phylogenetic relationships within Aristolochia. By assuming different ploidy levels during bioinformatics processing of raw data, first hints are obtained that polyploidization contributed to the evolution of Aristolochia. Phylogenetic results are discussed in the light of current systematics and morphology.
顽固的亲缘关系的特征是节间非常短，在生命之树的浅层和深层系统发育尺度中都能找到。有人提出，增加大量可能提供信息的序列，同时减少系统误差，是提高系统发育分辨率的一种可能方法。富集策略与下一代测序技术的结合，产生了一种经济高效的方法来促进对顽固亲缘关系的重建。通过使用通用被子植物探针组将锚定杂交富集（AHE）基因组划分策略应用于马兜铃属植物，我们从富集试剂盒最初包含的517个单拷贝或低拷贝核基因座中获得了231 - 233个，总比对长度为154,756bp至1,601,50bp。由于马兜铃属植物（胡椒目；木兰类植物）与任何其基因组已用于设计植物AHE探针的被子植物物种亲缘关系较远（最接近的是无油樟），它证明了该探针组的通用性。马兜铃属约有500个物种，分为几个分支（操作分类单元），它们彼此之间的关系部分未知。先前的系统发育研究表明，这些谱系在时间上分支很深且连续快速，表现为短而深的节间。短而浅的节间也是一些马兜铃属谱系的特征，如马兜铃亚属Pentandrae，这是一个可能近期分化的分支。本亚属在此用于测试AHE在物种水平的性能。使用系统发育信息方法对基因座进行过滤和抽样，解决了马兜铃属内几个顽固的系统发育关系。通过在原始数据的生物信息学处理过程中假设不同的倍性水平，首次获得线索表明多倍体化对马兜铃属的进化有贡献。根据当前的系统分类学和形态学对系统发育结果进行了讨论。
