Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 # 45-03, edificio 425, Bogotá, D.C., Colombia.
School of Biological Sciences, Southern Illinois University Carbondale, 1125 Lincoln Dr., Carbondale, Illinois, 62901-6509, USA.
Am J Bot. 2022 Jul;109(7):1139-1156. doi: 10.1002/ajb2.16025. Epub 2022 Jul 15.
To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family.
We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in Brunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to infer Brunellia phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in Brunellia.
Brunellia comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses.
Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character-state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in Brunellia, the relationships among subclades remain incompletely understood.
迄今为止，单种科 Brunelliaceae 内的系统发育关系一直基于形态学证据，这不能提供足够的系统发育分辨率。在这里，我们使用靶向富集核数据来增进我们对该科系统发育关系的理解。
我们使用 Angiosperms353 工具包，从 Brunellia 中的 70 个物种中的 53 个物种和几个外群类群中靶向回收低拷贝核基因的外显子区域和超级大片段（外显子+内含子）。我们去除了表明关系有偏向推断的基因座，并应用了合并和融合方法来推断 Brunellia 的系统发育。我们确定了可能反映杂交或不完全谱系分选事件的基因树之间的冲突，并评估了它们对系统发育推断的影响。最后，我们对形态特征进行了祖先状态重建，并评估了用于定义 Brunellia 节和亚节的特征状态的同源性。
Brunellia 由两个主要的分支和几个亚分支组成。这些分支/亚分支中的大多数与以前的种下分类单元不对应。在分析中，亚分支之间存在高度的拓扑不一致性。
系统发育重建表明 Brunelliaceae 中的物种快速多样化，表现在连续物种分裂之间的分支非常短。去除可能有偏差的基因座略微提高了个别分支的系统发育支持。由于杂交和/或不完全谱系分选导致的网状进化可能都导致了基因树的不和谐。用于定义当前分类方案中分类单元的形态特征在祖先特征状态重建中是同形的。虽然靶向富集数据使我们能够拓宽对 Brunellia 多样化的理解，但亚分支之间的关系仍然不完全清楚。
