The molecular phylogeny of Alpinia (Zingiberaceae): A complex and polyphyletic genus of gingers

Alpinia is the largest, most widespread, and most taxonomically complex genus in the Zingiberaceae with 230 species occurring throughout tropical and subtropical Asia. Species of Alpinia often predominate in the understory of forests. while others are important ornamentals and medicinals. Investigations of the evolutionary relationships of a subset of species of Alpinia using DNA sequeace-based methods specifically test the monophyly of the genus and the validity of the previous classifications. Seventy-two species of , 27 non-Alpinia species in the subfamily Alpinioideae, eight species in the subfamily Zingiberoideae, one species in the subfamily Tamijioidae, and three species in the outgroup genus Siphonochilus (Siphonochiloideae) were sequenced for die plastid matK region and the nuclear internal transcribed spacer (ITS) loci. Parsimony analyse's of both individual and combined data sec, identified six polyphyletic clades containing species of Alpinia distributed across the tribe Alpiniea. These results, were Supported by a Bayesian analysis of the combined data set. Except in a few specific cases. these monophyletic groupings of species do not correspond with either Schumann's (1904) or Smith's (1990) classification of the genus. Here we build on previous molecular analyses of the Alpinioideae and propose the next steps necessary to recognize new generic boundaries in the Alpinieae.