Building a robust backbone for Astragalus using a clade‐specific target enrichment bait set

With over 3100 species, Astragalus L. (Fabaceae) has long fascinated botanists as the largest genus of flowering plants. With an origin in the Middle Miocene, Astragalus has one of the highest diversification rates known in flowering plants. Comprehensive taxonomic treatments exist, and the genus is currently subdivided into 136 sections in the eastern hemisphere and 93 sections in the western hemisphere based on morphological characters. Despite considerable efforts, a comprehensive and well-resolved phylogeny of the genus is still lacking. Here, we reconstruct the backbone phylogeny of Astragalus using a custom bait set capturing 819 loci specifically designed for a target enrichment approach in the Astragalean clade. We carefully selected a set of 107 taxa representing all major clades currently recognized in Astragalus. Of those, 80 newly sequenced taxa were obtained from herbarium specimens as old as 110 years. We retrieved all the targeted loci and additional off-target plastome sequences for all samples, including the 80 herbarium specimens. Our phylogenetic analysis reinforced the currently accepted backbone phylogeny of Astragalus with high support and novel details, additionally providing insights into cytonuclear phylogenetic conflicts in the genus. Evidence for potential reticulate evolution was found, providing a possible explanation for the conflicts observed. This work represents an important milestone in obtaining a comprehensive, herbarium-based phylogeny of Astragalus, which will constitute the base to study a wealth of relevant biological questions, for example, the still unanswered question of what drove the rapid diversification of Astragalus, with important repercussions on our understanding of diversification in natural contexts.