Building a robust backbone for Astragalus (Fabaceae) using a clade-specific target enrichment bait set

With over 3100 species, Astragalus (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.