The Miocene to Pleistocene colonization of the Philippine archipelago by Begonia sect. Baryandra (Begoniaceae)

• Premise of the study: One third of the species‐rich Philippine flora is endemic, and most of the islands in the archipelago have never been connected to a continental region. We currently lack any well‐sampled angiosperm phylogenies that span the archipelago, prohibiting the formation of informed hypotheses as to the evolution of this rich and highly endemic flora. • Methods: We produced time‐calibrated phylogenetic trees from both nuclear (ITS) and chloroplast ( ndhA intron, ndhF–rpl32 spacer, rpl32–trnL spacer, trnC–trnD spacer) regions of 41 species of Begonia sect. Baryandra , all except one endemic to the Philippines. Historical biogeography was reconstructed across the chloroplast phylogeny using a Bayesian binary method of character optimization. Comparison of phylogenies from the two genomes permitted insight into the prevalence of hybridization in the group. • Key results: The Philippine archipelago was colonized by Begonia sect. Baryandra in the late Miocene, via long‐distance dispersal from western Malesia and a point of entry likely to be in the northwestern region of the archipelago. Palawan, Luzon, and Panay all bear early‐branching lineages from this initial colonization. There have been Plio‐Pleistocene dispersals from these islands into Borneo and Mindanao. Hybridization was common between species as evidenced by haplotype sharing and phylogenetic incongruence. • Conclusions: The phylogenies show a high degree of geographic structure, which millions of years of exposure to typhoons have not blurred, showing long‐term species and population stability. The recent dispersals to Mindanao are congruent with the geologically recent arrival of the island at its current latitude in the southern Philippines.