Things aren't always black or white — Phylogenetic systematics of ginger‐lilies with insights into species complexes

Abstract Hedychium is distributed across seven biodiversity hotspots within the Indo‐Malayan Realm and is known for its taxonomic complexity due to high intraspecific and low interspecific variation. The first‐ever molecular phylogenetic tree of Hedychium recovered four clades based on their geographical distribution. However, it failed to provide resolution to the interspecific relationships and was represented by only less than 30% of the known diversity within the genus. To explore species relationships and the composition of its clades, we reconstructed the phylogeny of Hedychium , using two nuclear ( CaM , ITS) and five plastid markers ( ccsA , trnK/matK , rps16 , trnL , trnQ‐psbK ) across 80% of the known species from all major geographic regions. Our phylogenetic reconstructions using both Bayesian and maximum likelihood frameworks identified seven clades and an early‐branching species in Hedychium . Further, we determined the phylogenetic placements for taxa that could not be included in the molecular phylogeny. Based on the insights gained through phylogenetic reconstruction we propose that species diversity in the genus Hedychium and the presence of unresolved species complexes result from spatiotemporal overlap in flowering, insufficient reproductive isolation, and recent radiation within the Indo‐Burma ecoregion, particularly in northeastern India, southwestern China, and northern Thailand. We also classified a total of five major complexes within two classes of species complexes that we introduce here. Our study highlights the need for integrated taxonomy approaches, combining genomic, morphological, and ecological data, to clarify species boundaries to better understand evolutionary relationships of plants in the Indo‐Malayan Realm.