Targeted capture of hundreds of nuclear genes unravels phylogenetic relationships of the diverse Neotropical palm tribe Geonomateae

The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically importantunderstory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced about 4,000 genes for 85% of the species of the tribe, including 84% of the species of the largest genus, Geonoma. Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.省棕族（Geonomateae）是一类分布广泛的新热带界棕榈类群，共计103个物种，涵盖6个生态意义关键的林下或亚冠层属。尽管该类群已成为诸多研究的焦点，但由于分子数据匮乏，我们对其演化历史，尤其是分类学结构复杂的省棕属（Geonoma）的认知仍远未完善。具体而言，既往基于桑格测序（Sanger sequencing）的研究仅采用少量信息性特征，且采样并不完整。为克服上述局限，本研究采用新近开发的棕榈科（Arecaceae）专属靶向捕获探针组，对省棕族开展系统发育基因组学分析。本研究为该族85%的物种（涵盖最大属省棕属84%的物种）测序了约4000个基因。研究同时采用串联法与溯祖法推断系统发育关系。整体而言，本研究构建的系统发育树支持度极高，且与分类学界定结果一致，但有若干形态学类群被证实为非单系群。这是棕榈科内首次针对整个族级类群提供如此大规模的基因组数据集。本研究不仅为该类群内细致的宏观与微观演化研究奠定了基础，同时也为解析生命之树中其他物种复合群提供了可行的研究范式。