The pantropical orchid genus Polystachya is the subject of ongoing taxonomic work. We inferred phylogenetic relationships in the genus using 5.3 kb of plastid DNA, for 83 out of ca. 240 species and 12 out of 15 sections, as well as five outgroup species. We also collected ploidy data using chromosome counts and genome size estimates. Bayesian and parsimony trees were congruent with each other and well resolved. Polystachya appears monophyletic based on current sampling, provided that the name P. neobenthamia is used instead of Neobenthamia gracilis for that species. The current sectional classification does not define monophyletic groups, but the present study can be used as the basis for a future sectional classification. Areas postulated as Pleistocene refugia for wet tropical forests in Africa also form centres of diversity for the genus. Biogeographical analyses using DIVA and Lagrange show an early radiation in eastern Africa, followed by separate radiations in eastern and western Africa. Subsequent dispersal from western to eastern Africa has occurred at a much higher rate than from east to west. Dispersal to the Neotropics occurred more than once, and one lineage has spread recently and rapidly throughout the tropics. Polyploidy has occurred several times during the diversification of the genus, most notably in association with the recent pantropical dispersal.
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