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Background  The picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian  Begonia , a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast  rpL16  intron. The sampling includes 94  Begonia  species encompassing most major Asian clades with a special emphasized on Chinese species.    Results  Except for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone  Begonia  ( SVLB ), including sect.  Coelocentrum  (19 species sampled) and five species of sect.  Diploclinium ,  Leprosae , and  Petermannia , are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade  SVLB ), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade  SVLB , coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area.    Conclusions  Based on our phylogenetic study,  Begonia  sect.  Coelocentrum  is recircumscribed and expanded to include other members of the Clade  SVLB  (sect.  Diploclinium :  B. cavaleriei ,  B. pulvinifera , and  B. wangii ; sect.  Leprosae :  B. cylindrica  and  B. leprosa ; sect.  Petermannia :  B. sinofloribunda ). Because species of Clade  SVLB  have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and  Begonia  are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade  SVLB . Morphologically species of Clade  SVLB  differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone  Begonia  radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.    Electronic supplementary material  The online version of this article (doi:10.1186/1999-3110-55-1) contains supplementary material, which is available to authorized users.

Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora