Squills vs. Hyacinths – A revised genus delimitation in Hyacinthinae (Hyacintheae, Scilloideae, Asparagaceae) based on phylogenomics

Abstract

Scilla s.l. (Asparagaceae: Scilloideae) represents a notable Mediterranean geophyte radiation, yet genus delimitation in subtribe Hyacinthinae has long suffered from inconsistent and conflicting generic concepts. A limited set of informative morphological characters and recurrent shifts in circumscription have repeatedly hindered progress. Here we present the first densely sampled phylogenomic framework for Hyacinthinae based on Angiosperms353 target‐capture data, representing all but one genus and approximately one‐third of the known species diversity. Orthology‐aware monophyletic‐outgroup (MO) filtering yielded high gene and taxon occupancy and largely congruent topologies across concatenation and coalescent analyses. The resulting trees consistently recovered Hyacinthinae as monophyletic and revealed that Scilla s.l. is polyphyletic, with several universally accepted genera such as Hyacinthus , Muscari , and Bellevalia deeply nested within the Scilla s.l. complex. This complex resolves into a series of well‐supported, morphologically coherent lineages corresponding to previously proposed segregate genera. Topological stability was high across analytical approaches, with nuclear–plastid conflict restricted to a few nodes, notably involving the positions of Barnardia and Nectaroscilla . Backbone relationships of Hyacinthinae are robustly resolved, and discordance is largely confined to the Hyacinthus alliance, suggesting rapid early divergence or ancient reticulation. The strong correspondence among molecular results, cytological evidence, and classical morphological diagnoses supports a revised, monophyly‐based recircumscription at the generic level. We therefore propose to recognize a total of 20 genera, reinstating several historically proposed segregates that have never been widely adopted. For this, four new combinations are proposed to accommodate the revised system. A key to the genera and a taxonomic treatment summarizing all accepted genera and species are provided, establishing a solid basis for future systematic and biogeographic research on Hyacinthinae.