The pantropical genus Begonia is the sixth-largest genus of flowering plants, including 1870 species. The sections of Begonia are used frequently as analogues to genera in other families but, despite their taxonomic utility, few of the current sections have been examined in the light of molecular phylogenetic analyses. We present herein the largest, most representative phylogeny of Begonia published to date and a subsequent provisional sectional classification of the genus. We utilised three plastid markers for 574 species and 809 accessions of Begonia and used Hillebrandia as an outgroup to produce a dated phylogeny. The relationships between some species and sections are poorly resolved, but many sections and deeper nodes receive strong support. We recognise 70 sections of Begonia including 5 new sections: Astrothrix, Ephemera, Jackia, Kollmannia, and Stellandrae; 4 sections are reinstated from synonymy: Australes, Exalabegonia, Latistigma and Pereira; and 5 sections are newly synonymised. The new sectional classification is discussed with reference to identifying characters and previous classifications.

The Begoniaceae consist of two genera, Begonia, with approximately 1400 species that are widely distributed in the tropics, and Hillebrandia, with one species that is endemic to the Hawaiian Islands and the only member of the family native to those islands. To help explain the history of Hillebrandia on the Hawaiian Archipelago, phylogenetic relationships of the Begoniaceae and the Cucurbitales were inferred using sequence data from 18S, rbcL, and ITS, and the minimal age of both Begonia and the Begoniaceae were indirectly estimated. The analyses strongly support the placement of Hillebrandia as the sister group to the rest of the Begoniaceae and indicate that the Hillebrandia lineage is at least 51-65 million years old, an age that predates the current Hawaiian Islands by about 20 million years. Evidence that Hillebrandia sandwicensis has survived on the Hawaiian Archipelago by island hopping from older, now denuded islands to younger, more mountainous islands is presented. Various scenarios for the origin of ancestor to Hillebrandia are considered. The geographic origin of source populations unfortunately remains obscure; however, we suggest a boreotropic or a Malesian-Pacific origin is most likely. Hillebrandia represents the first example in the well-studied Hawaiian flora of a relict genus.

Variability of allozymes (1170 individuals, 47 populations) and chloroplast DNA (692 individuals, 29 populations) was examined in native European and introduced North American populations of Epipactis helleborine (Orchidaceae). At the species level, the percentage of allozyme loci that were polymorphic (P(99)) was 67%, with a mean of 2.11 alleles (A) per locus, and an expected heterozygosity (H(exp)) of 0.294. At the population level, mean P(99) = 56%, mean A = 1.81, and mean H(exp) = 0.231. Although field observations suggest that self-pollination occurs frequently, populations had a genetic structure consistent with Hardy-Weinberg expectations and random mating (mean F(IS) = 0.002). There was significant deviation from panmixia associated with population differentiation (mean F(ST) = 0.206). The distribution of two chloroplast haplotypes showed that 15 of the 29 populations were polymorphic. Using both nuclear and organelle F(ST) estimates, a pollen to seed flow ratio of 1.43 : 1 was calculated. This is very low compared with published estimates for other plant groups, consistent with the high dispersability of orchid seeds. Finally, there was no evidence for a genetic bottleneck associated with the introduction of E. helleborine to North America.

The genus Epipactis contains a problematical complex of autogamous taxa among which species limits are difficult to define. Different authors have treated these plants in different ways, some recognizing the different taxa as distinct species, others considering them as minor intraspecific variants. These contrasting treatments have a direct impact on the conservation resources and status such plants command; 'endemic orchid species' are perceived as having high conservation value, 'localized minor variants' are not. We used allozyme and chloroplast restriction fragment length polymorphism (RFLP) and sequencing analyses to investigate patterns of population genetic structure underlying the taxonomic complexity in this group. Populations of E. dunensis, E. leptochila and E. muelleri were homozygous and uniform for all loci studied here. There were, however, fixed genetic differences among these taxa. Comparisons with published data from the putative progenitor species for the autogamous taxa (the widespread, allogamous E. helleborine) suggest iterative origins of autogamy, rather than the self-pollinating taxa all being merely mutational variants of a single autogamous lineage.

Aim The origin of Neotropical hyperdiversity is one of the most intriguing questions in modern biogeography and is best answered through the investigation of large, pantropically distributed genera, allowing the comparison of closely related clades in different regions. We produced a dated phylogeny and reconstructed ancestral ranges of the megadiverse, Andean‐centred genus Begonia to discern its dispersal history throughout the Neotropics and correlates of range evolution. Neotropical and Palaeotropical diversification rates were estimated. Location Neotropics: Central America, South America, West Indies and Mexico. Methods Plastid DNA sequence data from species representing the full geographical range and majority of sections of Neotropical Begonia were analysed with a secondarily calibrated relaxed molecular clock in order to estimate the age of crown groups and divergence times within Neotropical Begonia. Ancestral areas were reconstructed with a Bayesian approach to dispersal–vicariance analysis, a likelihood framework under a dispersal–extinction–cladogenesis model, and a Bayesian binary method. Diversification rates were estimated under a Bayesian framework. Results Biogeographical reconstruction indicated two independent trans‐Atlantic colonizations of the Neotropics from Africa. Early‐diverging lineages of both clades are reconstructed as having diversified in the mid‐Miocene, with multiple dispersal events between the Brazilian Atlantic rain forest and the Andes, and single radiations within the West Indies and Central America plus Mexico. Main conclusions Begonia displays numerous radiations within regions, punctuated by long‐distance dispersal. Successful colonization and diversification is predicted by the presence of upland habitat. Recognizing the role of chance dispersal events between available habitats is vital for understanding the formation of current biogeographical patterns.