**3. Historical biogeography**

Molecular divergence age estimates based on DNA sequence data and the calibration of molecular changes with a dimension of time, allow inference of: i) the time of origin of monophyletic groups, and ii) the timing of dispersal to a geographic area (Renner, 2005). However, molecular divergence age estimates for clades of Begoniaceae is problematic, as the family has a poor fossil record, and suitable fossils for direct calibration are lacking

The Origin of Diversity in *Begonia*:

2009; Plana et al., 2004; Thomas, 2010.

**4. Population processes 4.1 Restricted gene flow** 

Pleistocene origin.

Genome Dynamism, Population Processes and Phylogenetic Patterns 33

taxa such sections *Loasibegonia* and *Scutobegonia* (Plana et al., 2004; Sosef, 1994), but Plana et al. (2004) emphasised that a significant proportion of *Begonia* species diversity is of pre-

Fig. 2. Molecular divergence age estimates for the Begoniaceae and *Begonia* crown groups. Crosses indicate mean estimates, and bars indicate 95% highest posterior density age ranges and 95% confidence ranges. BRC: Bayesian auto-correlated rates relaxed clock method; BRCL: Bayesian uncorrelated rates relaxed molecular clock method assuming a lognormal distribution of rates; F: fossil calibration; G: geological calibration; NPRS: Non-Parametric Rate Smoothing method; PL: Penalized Likelihood method; S: secondary calibration. Software packages used are indicated in italics in brackets. For details of calibration regimes and methods see: Clement et al., 2004; Goodall-Copestake, 2005; Goodall-Copestake et al.,

Whilst the genus *Begonia* has a very broad distribution, differentiation occurs over very local scales (Hughes, 2008). Three studies have used molecular markers to study local patterns of differentiation. Matolweni et al. (2000) investigated allozyme variation in 12 populations of *B. dregei* and 7 populations of the closely related *B. homonyma* from isolated forest patches in South Africa. This data showed little, if any, gene flow among populations of either *B. dregei* or *B. homonyma*, even between populations that are located only a few kilometers apart within the same forest. Allelic variation and heterozygosity were low, alleles were frequently unique to individual populations, and population differentiation (Fst values) for each locus were very high. This suggests strong and longterm isolation between populations

A comparable study was performed by Hughes & Hollingsworth (2008). Seven populations of the South African *B. sutherlandii* were sampled throughout the mist belt forests of

generating extensive genetic divergence and high potential for speciation.

(Stults & Axsmith, 2011). Previous studies have addressed this problem by using island emergence dates as calibration points (Plana et al., 2004) or by putting Begoniaceae in a wider phylogenetic context using suitable fossils calibrations in related taxa (Clement et al., 2004; Goodall-Copestake, 2005; Goodall-Copestake et al., 2009; Thomas, 2010).

Most mean age estimates indicate an Eocene origin (c. 40-46 Ma) for the Begoniaceae crown group diversification (Clement et al., 2004; Goodall-Copestake, 2005; Plana et al., 2004; Thomas, 2010). However, there are considerable confidence intervals depending on the methods and calibration points used (Fig. 2). The geographic origin of Begoniaceae remains enigmatic, with the geographically isolated *Hillebrandia* in Hawaii and the disjunct distribution of the two species of the putative sister family Datiscaceae, in southwestern North America and southwestern Asia. Clement et al. (2004) hypothesized a widespread most recent common ancestor of Begoniaceae in Eurasia.

The mean age estimates for the *Begonia* crown group diversification indicate an Oligocene origin (c. 23-34 Ma), although large confidence ranges have to be considered (Fig. 2) (Goodall-Copestake et al., 2009; Thomas, 2010). The earliest divergent clades in the *Begonia* phylogeny are African, suggesting an early diversification on the African continent long after the Gondwanan break-up (Goodall-Copestake et al., 2010; Plana et al., 2004; Thomas, 2010). From Africa, *Begonia* dispersed independently to both America and Asia, and the early Miocene has been inferred as the most likely timeframe for these dispersal events (Goodall-Copestake, 2005; Goodall-Copestake et al., 2010). African *Begonia* species (sections *Rostrobegonia*, *Sexalaria, Augustia* and *Peltaugustia*), which are phylogenetically closely related to Asian and American *Begonia* lineages, show adaptations to seasonally drier climate. Goodall-Copestake et al. (2010) hypothesised that these drought adaptations made the ancestors of the American and Asian lineages more resilient to intercontinental dispersal than the vast majority of African species, which require moist and shaded habitats. Intercontinental dispersal likely occurred by long-distance dispersal, or alternatively, dispersal to Asia may have occurred by an overland dispersal route via the Arabian Peninsula during a more mesic period than at present (Goodall-Copestake, 2005; Goodall-Copestake et al., 2010). The hypothesis of dispersal from Africa to western Asia is consistent with phylogenetic analyses and ancestral area reconstructions of Asian *Begonia*, which indicate an initial diversification of Asian-Socotran *Begonia* in South India-Sri Lanka, Socotra and continental Asia. This was followed by multiple dispersal events into Malesia, and a predominantly west to east colonisation of the Malesian archipelago (Thomas, 2010).

The relatively low species diversity of African *Begonia* (c. 160 species) in comparison to the species diversity in the New World (>600 species) and Asia (c. 750 species) may partly be explained by extinction of African *Begonia* species. This may be due to large-scale aridification during cooler and dry periods in Africa, especially during the pronounced climate oscillation in the Pleistocene. In addition to this, rapid diversifications in the Asian tropics and the Neotropics may explain the uneven distribution of *Begonia* diversity (de Wilde, 2011; Forrest et al., 2005; Thomas, 2010). Weakly developed mechanisms to maintain species cohesion in fragmented habitats (Hughes & Hollingsworth, 2008), in association with the formation of topographical heterogeneity caused by mountain uplift from the early Pliocene onwards, may have been major drivers of rapid *Begonia* diversification in Southeast Asia (Thomas, 2010). Moreover, the diversification of Southeast Asian *Begonia* may have been accelerated by cycles of range fragmentation and amalgamation caused by Pleistocene climate and sea-level changes (Thomas, 2010). Cyclic vicariance due to climate oscillations and Pleistocene diversification have also been hypothesised for some species-rich African

(Stults & Axsmith, 2011). Previous studies have addressed this problem by using island emergence dates as calibration points (Plana et al., 2004) or by putting Begoniaceae in a wider phylogenetic context using suitable fossils calibrations in related taxa (Clement et al.,

Most mean age estimates indicate an Eocene origin (c. 40-46 Ma) for the Begoniaceae crown group diversification (Clement et al., 2004; Goodall-Copestake, 2005; Plana et al., 2004; Thomas, 2010). However, there are considerable confidence intervals depending on the methods and calibration points used (Fig. 2). The geographic origin of Begoniaceae remains enigmatic, with the geographically isolated *Hillebrandia* in Hawaii and the disjunct distribution of the two species of the putative sister family Datiscaceae, in southwestern North America and southwestern Asia. Clement et al. (2004) hypothesized a widespread

The mean age estimates for the *Begonia* crown group diversification indicate an Oligocene origin (c. 23-34 Ma), although large confidence ranges have to be considered (Fig. 2) (Goodall-Copestake et al., 2009; Thomas, 2010). The earliest divergent clades in the *Begonia* phylogeny are African, suggesting an early diversification on the African continent long after the Gondwanan break-up (Goodall-Copestake et al., 2010; Plana et al., 2004; Thomas, 2010). From Africa, *Begonia* dispersed independently to both America and Asia, and the early Miocene has been inferred as the most likely timeframe for these dispersal events (Goodall-Copestake, 2005; Goodall-Copestake et al., 2010). African *Begonia* species (sections *Rostrobegonia*, *Sexalaria, Augustia* and *Peltaugustia*), which are phylogenetically closely related to Asian and American *Begonia* lineages, show adaptations to seasonally drier climate. Goodall-Copestake et al. (2010) hypothesised that these drought adaptations made the ancestors of the American and Asian lineages more resilient to intercontinental dispersal than the vast majority of African species, which require moist and shaded habitats. Intercontinental dispersal likely occurred by long-distance dispersal, or alternatively, dispersal to Asia may have occurred by an overland dispersal route via the Arabian Peninsula during a more mesic period than at present (Goodall-Copestake, 2005; Goodall-Copestake et al., 2010). The hypothesis of dispersal from Africa to western Asia is consistent with phylogenetic analyses and ancestral area reconstructions of Asian *Begonia*, which indicate an initial diversification of Asian-Socotran *Begonia* in South India-Sri Lanka, Socotra and continental Asia. This was followed by multiple dispersal events into Malesia, and a

predominantly west to east colonisation of the Malesian archipelago (Thomas, 2010).

The relatively low species diversity of African *Begonia* (c. 160 species) in comparison to the species diversity in the New World (>600 species) and Asia (c. 750 species) may partly be explained by extinction of African *Begonia* species. This may be due to large-scale aridification during cooler and dry periods in Africa, especially during the pronounced climate oscillation in the Pleistocene. In addition to this, rapid diversifications in the Asian tropics and the Neotropics may explain the uneven distribution of *Begonia* diversity (de Wilde, 2011; Forrest et al., 2005; Thomas, 2010). Weakly developed mechanisms to maintain species cohesion in fragmented habitats (Hughes & Hollingsworth, 2008), in association with the formation of topographical heterogeneity caused by mountain uplift from the early Pliocene onwards, may have been major drivers of rapid *Begonia* diversification in Southeast Asia (Thomas, 2010). Moreover, the diversification of Southeast Asian *Begonia* may have been accelerated by cycles of range fragmentation and amalgamation caused by Pleistocene climate and sea-level changes (Thomas, 2010). Cyclic vicariance due to climate oscillations and Pleistocene diversification have also been hypothesised for some species-rich African

2004; Goodall-Copestake, 2005; Goodall-Copestake et al., 2009; Thomas, 2010).

most recent common ancestor of Begoniaceae in Eurasia.

taxa such sections *Loasibegonia* and *Scutobegonia* (Plana et al., 2004; Sosef, 1994), but Plana et al. (2004) emphasised that a significant proportion of *Begonia* species diversity is of pre-Pleistocene origin.

Fig. 2. Molecular divergence age estimates for the Begoniaceae and *Begonia* crown groups. Crosses indicate mean estimates, and bars indicate 95% highest posterior density age ranges and 95% confidence ranges. BRC: Bayesian auto-correlated rates relaxed clock method; BRCL: Bayesian uncorrelated rates relaxed molecular clock method assuming a lognormal distribution of rates; F: fossil calibration; G: geological calibration; NPRS: Non-Parametric Rate Smoothing method; PL: Penalized Likelihood method; S: secondary calibration. Software packages used are indicated in italics in brackets. For details of calibration regimes and methods see: Clement et al., 2004; Goodall-Copestake, 2005; Goodall-Copestake et al., 2009; Plana et al., 2004; Thomas, 2010.
