Time calibrated tree of Dioscorea (Dioscoreaceae) indicates four origins of yams in the Neotropics since the Eocene

Abstract

The yam genus Dioscorea comprises c. 650 species of tropical vines with starch-rich tubers, useful as an energy source and often containing secondary metabolites. The Neotropical region holds the highest diversity of species and morphology of yams. We generated a time calibrated tree for Dioscorea using, for the first time, a dense sampling of Neotropical species (64 species, 20% of all Neotropical species and 22 sections) to trace the biogeography of these plants in this region. Four origins of Dioscorea in the Neotropics have been estimated since the Eocene. The two most diverse lineages originated between the Eocene and Oligocene, respectively, in the Southern Andes and in a large and disconnected group of areas including Central America, northern Andes and Atlantic forest. Both lineages occupied the South American 'Dry Diagonal' after the Miocene, but New World II clade remained associated with forest habitats. Several exchanges between Dry Diagonal and adjacent forested biomes occurred, corroborating the interchange between these vegetation types. Dispersals to Central America occurred before the closure of the Isthmus of Panama. We highlight two important events of long-distance dispersal, the colonization of Central American before the closure of the Isthmus of Panama and the dispersal of the D. antaly lineage to Madagascar. In addition, our phylogenetic tree reveals the unnatural nature of the classical infrageneric classification of Dioscorea. The taxonomic implications of our results are discussed.