Phylogenomic incongruence gives new perspectives on the taxonomic complexity of <i>Muscari</i> s.l. (Asparagaceae, Scilloideae)

Abstract Muscari s.l. (Asparagaceae, Scilloideae) is a widespread genus of bulbous geophytes native to the Mediterranean, the Middle East and into the Caucasus. Based on inflorescence and floral morphology, four distinct groups have long been recognised and treated as either genera ( Muscari s.str., Muscarimia , Leopoldia , Pseudomuscari ) or subgenera within Muscari s.l. However, a recent molecular phylogenetic investigation proposed a new subgenus, Pulchella . Despite the several morphological and molecular phylogenetic investigations of Muscari , the delineation of taxa, either at the generic or subgeneric level, remains unstable. Here we aim to evaluate the monophyly and robustness of the recognised groups using broadly sampled nuclear (low‐copy number and ribosomal cistron) and plastome sequence phylogenies of Muscari s.l. Our morphological and molecular delineation of M. subg. Muscarimia and subg. Pseudomuscari across the analyses of three data sources are broadly congruent. However, high levels of incongruence within M. subg. Leopoldia and subg. Muscari are reported and discussed here, with implications for the stability of the newly described M. subg. Pulchella . Nomenclatural rules also require a new subgenus name to replace the name Pseudomuscari , which is shown to be a synonym of subgenus Muscari and has therefore been misapplied in recent work.