Acknowledgements 1 The Biogeography of Neotropical Begonia L.
Correlation between Mountain Evolution and Range Evolution in an Andean-centred Group.
Peter Moonlight
August 2013
Thesis submitted in partial fulfilment of the MSc in the Biodiversity and Taxonomy of Plants. Acknowledgements 2
Acknowledgements Although mine is the only name on the spine of this thesis, the work inside would not have been possible without the support of numerous people whose names have equal right to be there. Particular gratitude must go to my supervisors, Mark Hughes and James Richardson. It was their vision that expanded what was initially a relatively small investigation into a mammoth project and their confidence in me that made me believe it was possible, just. I wish to thank them for their advice on everything from Bayesian inference to Taiwanese restaurant etiquette. Especially appreciated was Mark's patient laboratory tuition and enthusiasm in persuading me to visit Taipei, while James' suggestion that I write my thesis in part as a paper was invaluable. Both must be commended for their expert critiques of my manuscript and tolerance of my infuriating tendency to miss words out of sentences.
Special thanks must go to Dr Ching-I Peng of the HAST Institute, Taipei, who not only allowed me privileged access to his lab, outstanding Begonia collection, and photography studio, but also shared his research grant with me and acted as the perfect host in a new city. I also thank Dr Peng's family and many assistants, in particular Annie Yang, for helping me be as productive as possible yet enjoy my time in Taipei to the full.
No matter how much data I was able to amass myself, my project would not have been half as extensive if not for the sequences produced by Ruth McGregor, Daniel Thomas, and Mark Hughes. I sincerely thank Ruth, Michelle Hollingsworth, Laura Forrest, and Annie for their help the labs in Edinburgh and Taipei and for teaching me the mysterious ways of their numerous machines.
To my fellow MSc students, thank you for your support and tolerance of rants about dead botanists and primer design over much-needed cups of tea and coffee. Special thanks go to James Clugston for helping me see the hills from the shadows and Daniel Borg for helping me tame BEAUti and the BEAST .
Last but certainly not least, I would like to thank my family for tolerating yet another year of University Education and Sarah for indulging ten too many conversations about Begonia . I promise to do the dishes more often from now on.
Abstract 3
Abstract The origin of the Neotropical hyperdiversity is one of the most intriguing questions in biogeography, requiring the investigation of biogeographic histories of a variety of lineages. We produced a dated phylogeny of the species-rich, Andean-centred genus Begonia L. to determine the genus' dispersal history throughout the Neotropics and correlates of range evolution. Plastid DNA sequence data (three regions, ca. 3000 bp) from species representing selected Paleotropical Begonia (131 species) and the full geographic and sectional range of Neotropical Begonia (137 species) were analysed using a secondarily-calibrated uncorrelated-rates relaxed molecular clock. Ancestral areas were reconstructed using three widely-implemented methods of range reconstruction. Results indicate two independent long-distance dispersals from Africa to South America with multiple dispersal events between South American regions, a single radiation within Central America, and a single radiation within the Antilles. The phylogeny of Neotropical Begonia is one of numerous radiations within regions punctuated by long-distance dispersal. Successful colonisation and diversification is predicted by the presence of upland habitat and appears to be mediated by niche pre-emption. Successful colonisation of the northern Andes and southern Central America by multiple lineages may be due to the lack of niche pre-emption in newly-created habitat.
Abstract 4
Table of Contents Acknowledgements ...... 2 Abstract ...... 3 List of Figures ...... 6 List of Tables ...... 6 Introduction to Molecular Biogeography ...... 7 1.1 The History of Historical Biogeography ...... 7 1.2 Phylogenetics for Molecular Biogeography ...... 8 1.2.1 Types of Data ...... 8 1.2.2 Phylogenetic Inference ...... 9 1.2.3 Dating Phylogenies ...... 9 1.2.4 Ancestral Area Reconstruction ...... 10 2 Introduction to Neotropical Biogeography ...... 13 2.1 Geology, Geography, and Ecology of the Neotropics ...... 13 2.1.1 Neotropical Floristic Regions ...... 13 2.1.2 'Splendid Isolation' - South American Geography ...... 15 2.1.3 North America Geography ...... 16 2.1.4 Formation of the Antilles ...... 16 2.1.5 Formation of Central America ...... 16 2.1.6 Closure of the Isthmus of Panama ...... 17 2.1.7 The Andean Orogeny ...... 18 2.2 Biogeography of the Neotropics ...... 19 2.2.1 Origins of Neotropical Clades ...... 19 2.2.2 Effects of the Andean Orogeny ...... 20 2.2.3 Crossing the Isthmus of Panama ...... 22 2.2.4 Colonisation of the Caribbean ...... 23 2.2.5 Biogeography of the Mata Atlantica ...... 23 2.2.6 Dispersal throughout the Americas: Niche Conservation or Niche Evolution? ...... 23 3 Introduction to Begonia ...... 25 3.1 Begonia Classification and Phylogeny ...... 25 3.2 Begonia Biogeography ...... 28 3.2.1 Habitats, Ecology, and Sections of Neotropical Begonia ...... 30 4 Abstract ...... 32 4.1 Aim ...... 32 Abstract 5
4.2 Location ...... 32 4.3 Methods ...... 32 4.4 Results ...... 32 4.5 Main Conclusions ...... 32 4.6 Keywords ...... 32 5 Introduction ...... 33 6 Materials and Methods ...... 37 6.1 Taxon Sampling ...... 37 6.2 Laboratory Methods ...... 37 6.3 Alignment ...... 38 6.4 Phylogenetic Analyses ...... 39 6.5 Bayesian Divergence Age Estimation ...... 39 6.5.1 Secondary Calibration ...... 39 6.5.2 Bayesian Divergence Time Estimation ...... 40 6.6 Ancestral Area Reconstruction ...... 40 6.6.1 Area Delimitation ...... 40 6.6.2 Area Coding ...... 41 6.6.3 Ancestral Area Reconstructions ...... 42 6.7 Diversification Rate Estimates ...... 42 7 Results ...... 44 7.1 Phylogenetics of Neotropical Begonia ...... 44 7.2 Molecular Age Estimates ...... 45 7.3 Ancestral Area Reconstructions ...... 45 7.4 Diversification Rates ...... 58 8 Discussion ...... 62 8.1 Neotropical Begonia Taxonomy ...... 62 8.2 Ancient hybridisation in Neotropical Begonia ? ...... 62 8.3 Colonisation of the Neotropics ...... 63 8.4 West Indian Begonia ...... 64 8.5 Dispersal to the Andes ...... 64 8.6 Colonisation of Central America ...... 66 8.7 Diversification rates in Begonia ...... 67 8.8 Niche pre-emption ...... 68 9 Conclusions ...... 68 List of Figures 6
10 References ...... 70 11 Appendices ...... 85 11.1 Appendix 1 - Accession Details ...... 85
List of Figures Figure 1 Biodiversity hotspots in the Neotropics...... 14 Figure 2 Worldwide distribution of the Begoniaceae ...... 28 Figure 3 Neotropical Begonia occurrence records from the Global Biodiversity Information Facility (GBIF) ...... 33 Figure 4 Bayesian majority rule consensus tree ...... 60 Figure 5 Maximum clade credibility cladogram of BEAST analysis ...... 61
List of Tables Table 1 Published Phylogenies of Begonia ...... 26 Table 2 Primers used in this study...... 38 Table 3 Literature and online resources describing distributions of Neotropical Begonia ...... 41 Table 4 Comparison of Bayesian Posterior Probability node support and BEAST date estimates between analyses containing all data and analyses with missing data removed...... 45 Table 5 Bayesian Posterior Probabilities, divergence time estimates, and ancestral range reconstructions for nodes as defined in Figure 5 ...... 47 Table 6 Estimated diversification rates for selected groups of Begonia ...... 59 Table 7 List of accessions used in analyses ...... 85
Introduction to Molecular Biogeography 7
Introduction to Molecular Biogeography
1.1 The History of Historical Biogeography Historical biogeography is "the science that attempts to document and understand spatial patterns in biodiversity," (Lomolino et al., 2011) and its primary goal is to reconstruct the ancestral ranges of taxa, allowing inference about the development of species assemblages on a variety of scales. This goal has led to the development of a number of methods of range reconstruction, the earliest of which relied upon simple rules. These included the assumption that the areas with the largest species diversity or most primitive forms are likely to include the ancestral range (reviewed in Lomolino et al., 2011). These rules were logical but liable to bias where large radiations (e.g. Andean Lupinus [Hughes and Eastwood, 2006]) or rapid morphological evolution have occurred (e.g. Macaronesian Echium [Bohle et al., 1996]) while the methodology fails to account for the evolutionary relationships of terminal taxa. Furthermore, using only a single group of related species in analyses provides only an estimate of that group's history, not the history of whole regions or biomes (Lomolino et al., 2011).
The shortcomings of centres of origin approaches led to the development of the assumption that similar disjunctions and distributions in different taxa require general explanations (Donoghue and Moore, 2003), sometimes termed distributional homology (Morrone, 2001). An early attempt to combine data from many taxa is now termed panbiogeography (Lomolino et al., 2011). Proponents argued that combining distribution from numerous disjunctions and connecting areas sharing multiple disjunct taxa one could hypothesise historical land connections between areas (e.g. Page, 1987). Dispersal was not considered and vicariance was assumed to have occurred via land bridges prior to the acceptance of plate tectonic theory. Furthermore, phylogenies were ignored, preventing inference about the direction of migration over land bridges. Despite these shortcomings, panbiogeography and its proponents significantly contributed to the advancement of biogeographic theory through their understanding of the importance of comparing the distributions and disjunctions of many taxa (Lomolino et al., 2011).
The combination of the panbiogeographic approach with information derived from phylogenetic systematics led to the cladistic biogeography synthesis. Using the cladistic biogeography approach, the replacement of terminal taxa of phylogenetic trees transforms taxon cladograms into taxon area cladograms. Congruence of multiple taxon area cladograms was assumed to imply distributional homology and numerous congruent taxon area cladograms were combined to represent general area cladograms, which were assumed to represent the biogeographic relationships between regions and their biota (Hennig, 1963; Rosen, 1978). Typically, the relationships of taxa were assumed to have formed through vicariance on a dynamic earth following the acceptance of plate tectonics while deviations from general area cladograms within specific taxa were assumed to be the result of "noise" created by extinction, speciation within areas, and dispersal, which were deemed rare. Introduction to Molecular Biogeography 8
More recently, it has been realised that congruent topologies of taxon area cladograms alone do not imply distributional homology (Donoghue and Moore, 2003). Diversification patterns of numerous clades may achieve congruous topologies through different processes: pseudocongrence. Incongruous topologies may be achieved either through different geographic histories: incongruence; or through shared underlying causes overlaid by secondary processes: pseudoincongruence. Truly congruous general area cladograms can only be produced through distributional homology acting alone. Using taxon area cladograms, congruence, pseudocongruence, incongruence, and pseudoincongruence can only be distinguished by including temporal information in phylogenetic analyses. If two seemingly congruent diversification events occurred on markedly different time scales, distributional homology can be ruled out whereas seemingly incongruent diversification events can be deemed congruent if they occurred concurrently. This logic extends to the timing of geological events, allowing diversification events to be classified as congruent or incongruent with geological events such as the formation of barriers to dispersal. It must be noted however that congruence of diversification and geological events does not imply causation; rather that causation cannot be ruled out. The underlying assumption remains that the more taxa that share congruent topologies once temporal information has been taken into account, the more likely those taxa share dispersal histories and the more confidently their histories can be attributed to concurrent geological events.
The advent of more numerous, larger, and dated phylogenies with a wider taxonomic sample is beginning to transform our understanding of the biogeographic histories of clades and regions alike (Pennington and Dick, 2004; Hughes et al., 2013). Below follows a summary of methods used in modern biogeography, including: the types of data utilised, producing and dating phylogenies, and reconstructing ancestral ranges on phylogenies.
1.2 Phylogenetics for Molecular Biogeography
1.2.1 Types of Data Early theoretical discussions surrounding the derivation of phylogenies were dominated by the relative merits of morphological versus molecular data. The increasing ease and falling cost of producing sequence data has since rendered morphological phylogenies almost obsolete with the debate shifting towards which DNA regions are most appropriate for specific purposes.
As well as primary sequence data, micro- and macro-structural changes provide additional data, which can be utilised during phylogenetic inference (Rokas and Holland, 2000). The most commonly recognised form of structural mutations cause misalignment due to length alterations and are termed 'indels' (insertions and deletions). However, length misalignment can be caused by five categories of microstructural mutation: indels, simple sequence repeats (SSRs), short tandem repeats (STRs), homopolymeric repeats, and inverted repeats (Borsch and Quandt, 2009). Viewed in an alignment, the presence of one of these mutational types is usually evident but without a reconstruction of sequence Introduction to Molecular Biogeography 9 evolution in a phylogenetic context, it can be difficult to determine which. However, the presence of a microstructural mutation can provide valuable phylogenetic information alongside primary sequence data through binary presence-or-absence gap coding (Rokas and Holland, 2000).
Inversions are a further category of structural mutation but can be more difficult to recognise due to their lack of effect upon sequence length; indeed, few automatic aligning algorithms can detect them. Two main methods are used for aligning inverted sequences: inverted and non-inverted motifs can be separated within the alignment or inverted sequences can be reverse-complimented and aligned. If either method is utilised, the presence or absence of each inversion can be coded akin to coding gaps. Reverse-complimenting and aligning inverted sequences has the major benefit of retaining substitution data within inverted regions as informative characters (Borsch and Quandt, 2009; Graham and Reeves, 2000; Löhne and Borsch, 2005). This minimises the impact of inversions on branch length, which is of particular importance in dated phylogenies where branch length is a major determinant of calculated node ages.
1.2.2 Phylogenetic Inference The most commonly applied methods of phylogenetic inference are maximum likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) (Pennington et al., 2006). Of these, BI has a number of advantages over the alternatives. BI and ML methodologies allow incorporation of models of sequence evolution into analyses whereas MP works upon the principle that all possible mutations are equally unlikely. In regions with high levels of homoplasy and uneven distributions of rate variation, MP is liable to give misleading results, often due to long-branch attraction. However, unrealistic model selection is also likely to lead to unrealistic results in both BI and ML analyses. BI and ML's incorporation of models of sequence evolution also allow parsimony uninformative characters (characters unique to a single taxon) to be incorporated into the analysis and thus estimates of branch length. A strength unique to BI is the incorporation of estimates of the probability of nodes into the main analysis rather than through a further analysis such as bootstrapping. This is of particular utility when reconstructing ancestral ranges and estimating divergence dates. Finally, BI allows the incorporation of complex priors into analyses such as the monophyly of certain clades.
1.2.3 Dating Phylogenies Methods of dating phylogenies rely on assumptions about the rate of molecular evolution across a tree (Rutschmann, 2006). Early models assumed fixed, clocklike rates of molecular evolution and calculated node ages as a function of their genetic distance from nodes of known age and a calculated rate of molecular evolution (Renner, 2005). However, few phylogenies exhibit clocklike molecular evolution (Drummond et al., 2006) leading to the development of alternative models. The simplest involve users defining sections of a phylogeny, usually either clades or grades, which conform to a different rate of rate evolution from the remainder of the tree. Rates are calculated independently for each section, corrected for, and ages are calculated as with a clocklike tree (Rutschmann, 2006). Introduction to Molecular Biogeography 10
Despite its simplicity, this method is problematic due to difficulty identifying such clades and is only useful where a robust prior hypothesis exists regarding rate variation (Drummond et al., 2006).
Alternative methods relax the assumption of clocklike molecular evolution in their algorithms, often under the assumption of autocorrelation; namely, that rates before and after nodes will be similar (Renner, 2005). An example is the widely implemented penalised likelihood algorithm, which estimates rates by penalising rate changes and poor rate fits within a likelihood framework. The relative penalties for poorly fitting data and rate changes are defined by prior input of a smoothing parameter (Rutschmann, 2006). Alternative Bayesian approaches to autocorrelation assume changes in rates before and after nodes conform to a parametric distribution such as a lognormal distribution once averaged across a tree (Renner, 2005).
Autocorrelation implies inheritance is a major determinant of rate variation, an assumption that has been challenged (Drummond et al., 2006). A further problem is that all the above methods rely on the prior assumption of a 'true' tree, calculated under a different model of molecular evolution to that implemented while calculating node ages (Rutschmann, 2006); therefore, the optimal tree may vary between analyses, which is not corrected for (Drummond et al., 2006). Bayesian inference methodologies implemented in BEAST assume instead that rates variation is independent of topology, instead conforming to a pre-specified parametric distribution across the tree whose parameters are calculated in tandem with estimates of rate variation. Furthermore, topology is calculated simultaneously, allowing uncertainties in the calculated model of molecular evolution to inform topology and vice versa. Topological uncertainty is indicated via clade posterior probability values while uncertainty in node ages is indicated through a calculated distribution of likely ages. The problem of specifying a realistic parametric distribution of rate evolution remains and the selection of an unrealistic distribution can lead to unreliable estimates of node ages (Drummond et al., 2006).
1.2.4 Ancestral Area Reconstruction Ancestral range reconstruction analyses are a suite of methods implemented to estimate the range of ancestral taxa given their extant descendants' distributions and relationships. Different analytical methods rely upon different assumptions regarding range evolution, the development of a lineage's range over time through vicariance, dispersal, and extinction. The simplest assumptions and therefore analyses are parsimony models, which assume the optimal, most-parsimonious reconstruction is that which minimises the instances of range evolution across a phylogeny. In complex analyses where numerous instances of range evolution are required to explain modern distributions, parsimony analyses often produce a number of equally-parsimonious reconstructions, leaving interpretation problematic (Lamm and Redelings, 2009).
Dispersal-Vicariance (DIVA) analyses differ from parsimony analyses by attributing costs only to dispersal and extinction events. No cost is attributed to range evolution where daughter species inherit Introduction to Molecular Biogeography 11 mutually-exclusive partitions of their parent species' range (Yu et al., 2010). Alternative scenarios are compared in a parsimony framework and the reconstruction with the fewest dispersal and extinction events is considered optimal (Lamm and Redelings, 2009). As with other parsimony analyses, DIVA analyses often interpret multiple reconstructions as optimal. Furthermore, as DIVA analyses do not attribute a cost to vicariance, reconstructions often result in unrealistically-wide ancestral ranges. This can be mitigated by constraining ancestral ranges to a certain number of regions; however, this often results in discontinuous range reconstructions (Yu et al., 2010).
Parsimony and DIVA analyses both fail to take into account short branch lengths and require resolved, bifurcating phylogenies (Nylander et al., 2008), an unrealistic expectation in many cases (Yu et al., 2010). Statistical dispersal-vicariance (S-DIVA) analyses run DIVA analyses on multiple input trees derived from post-burnin Bayesian MCMC processes such as those implemented in MrBayes or BEAST (Yu et al., 2010). The likelihood of reconstructions at each node are weighted by the frequency of their occurrence across the suite of trees (Ree and Smith, 2008). S-DIVA analyses are neither non-parametric analyses, like parsimony analyses, nor true Bayesian analyses and are described as non-parametric empirical Bayesian analyses (Nylander et al., 2008).
An alternative to non-parametric parsimony analyses and their non-parametric empirical Bayesian derivatives are maximum likelihood analyses. Maximum likelihood analyses proceed through a Markov process, estimating the frequency and therefore probability of range evolutionary events across a phylogeny (Lamm and Redelings, 2009). Range evolution is assumed to occur stochastically with the probability of reconstructions on each branch the product of the reconstruction of its parent branch and the calculated rate of range evolution. The optimal reconstruction is that which maximises the likelihood across the phylogeny (Ree et al., 2005). Early maximum likelihood analyses were modified from character state reconstructions that only permitted reconstructions of single ranges, which is unrealistic in ancestral range reconstructions as it implies simultaneous dispersal and extinction accounts for every instance of range evolution. Furthermore, branch lengths and topological uncertainty were not taken into account (Ree and Smith, 2008). The alternative Dispersal- Extinction Cladogenesis (DEC) likelihood model (Ree et al., 2005) implements a biogeographic model in a maximum likelihood framework. Multiple region ancestral ranges are permitted, with dispersal and extinction modelled as stochastic processes. Branch length is taken into account by DEC analyses, with probability of reconstruction calculated per unit of branch length rather than per branch. Range evolution is therefore treated as independent of speciation, which is considered unrealistic in scenarios where speciation and range evolution may be linked, such as dispersal and speciation in island radiations (Ree and Smith, 2008). However, this assumption may be more realistic in radiations through continuous space such as continents. The DEC model does not model vicariance as a cost-free part of the speciation process as in DIVA analyses; daughter species are assumed either to inherit the entirety of their parent species' range or a single part of it. Despite the different Introduction to Molecular Biogeography 12 assumptions of the DEC and DIVA models, they often produces results highly congruent with those of S-DIVA analyses and share the tendency to reconstruct wide ancestral ranges (Lamm and Redelings, 2009). The DEC model as implemented in RASP (Yu et al., 2011) requires either multiple Bayesian MCMC derived trees or a single tree including node Bayesian posterior probability values and branch lengths, thus taking topological uncertainty into account.
The Bayesian Binary Markov-chain Monte Carlo (BBM) method implemented in RASP (Yu et al., 2011) assumes range evolution across a tree conforms to a specified distribution across a phylogeny, rather than occurring in a stochastic fashion. The reconstruction where range evolution events conform most closely to the specified distribution is considered optimal (Ali et al., 2012). The distribution and its degree of conformity are calculated based upon methods implemented in MrBayes (Ronquist and Huelsenbeck, 2003). Topological uncertainty and branch length are both taken into account by the method (Ali et al., 2012).
Introduction to Neotropical Biogeography 13
2 Introduction to Neotropical Biogeography The Neotropics are the most species rich of the world's regions containing perhaps around 100 000 plant species, 37% of the world's total (Hughes et al., 2013). However, the Neotropics are not uniformly rich with a number of diversity hotspots (Myers et al., 2000) and a variety of species-rich (e.g. Lupinus L. [Hughes and Eastwood, 2006]; and Inga Mill. [Richardson et al., 2001]) and species- poor (e.g. Lepechinia Willd. [Drew and Sytsma, 2013]) lineages. Combined with their relative isolation, climatic, and geographical heterogeneity, this led Hughes et al. (2013) to refer to the Neotropics as "an 'evolutionary laboratory' for addressing key questions in evolution and biogeography."
Perhaps the most historically debated question is why Neotropical diversity is so high (Antonelli and Sanmartín, 2011). Two alternative models, the cradle model (Haffer, 1969; Gentry, 1982) and museum model (Stebbins, 1974), suggest recent, rapid diversification or steady accumulation of biodiversity respectively. More recent analyses suggest there is truth to both hypotheses, highlighting episodes of rapid diversification punctuated by relative stasis (Hughes et al., 2013). Furthermore, assessing the hyperdiversity of the Neotropics as a whole neglects important differences between individual clades, ecological, and geographic regions (Hughes et al., 2013). Important differences between clades include their date and mode of arrival in the Americas (Christenhusz and Chase, 2013), their rates of diversification (Bardon and Chamagne, 2013), and the patterns of their diversification throughout Neotropical regions and biomes (Hughes et al., 2013; Olmstead, 2013). Differences between biomes include the diversification dates (Pennington et al., 2010) and geographic of origins (Pennington and Dick, 2004) of their taxa, their dates of origins (Simon et al., 2009), and their climactic histories (Hoorn et al., 2010). Understanding these differences is vital to understanding the overall hyperdiversity of the Neotropics and requires an understanding of the evolutionary histories of a variety of taxa and biomes in the context of the geological, ecological, and climatic history of the Americas (Hughes et al., 2013). Furthermore, comparisons between the histories of Neotropical and Paleotropical biomes and taxa, preferably through direct comparisons afforded by pan-tropical groups and habitats, may highlight fundamental differences between the biogeographic histories of each continent (Bardon and Chamagne, 2013).
2.1 Geology, Geography, and Ecology of the Neotropics
2.1.1 Neotropical Floristic Regions The Neotropics span the majority of Central America from Southern Mexico to Panama, the Antilles, and Northern South America and include all major tropical biomes: lowland rainforest, seasonally dry tropical forest (SDTF), savanna, deserts, mid-elevation montane forests, and high elevation grasslands (Hughes et al., 2013). The definition and delimitation of these biomes is controversial (Antonelli and Sanmartín, 2011), and there remains no standard map of Neotropical biomes (Hughes et al., 2013). Introduction to Neotropical Biogeography 14
However, there is broad agreement on the delimitation Neotropical floristic regions, many of which encompass multiple biomes.
The Atlantic Forests of Brazil or Mata Atlantica form a strip of forest of variable width extending from the north- to south-east Brazilian coast separated from Amazonia by the drier Cerrado and Caatina and from the southern Andes by the wetter Pantanal (Melo Santos et al., 2007). The province consists primarily of evergreen tropical forest but also includes patches of SDTF, shrubby vegetation, and open grassland (Fiaschi and Pirani, 2009). The flora of the Mata Atlantica contains around 20 000 species (Melo Santos et al., 2007), leading Myers et al (2000) to consider the Atlantic Forest a global biodiversity hotspot (Figure 1).
The Amazon phylogeographic region is defined as including the highlands of the Guiana Shield and the Amazon basin (Gentry, 1982; Fiaschi and Pirani, 2009). Crude estimates suggest perhaps 30 000 species occur in Brazilian Amazonia with 76% of these endemic (Gentry, 1982). The majority of the region is characterised by high-canopy evergreen tropical forest on clay substrate
Figure 1: Biodiversity hotspots in the Neotropics deposited since the Andean orogeny including Mesoamerica (red), the Caribbean (green), (Hoorn et al., 2010). Numerous areas of Choco (orange), the tropical Andes (dark blue), the Mata At lantica (light blue), and the Cerrado (yellow). pre-Andean white sand substrate form Adapted from Myers et al (2000). habitat islands throughout the Amazon basin while tepuis or isolated sandstone plateaus form the highlands of the Guiana Shield. White sand and tepuis vegetation is generally comprised of scrubland and low-forest rather than the high-canopy forests of the majority of Amazonia (Fiaschi and Pirani, 2009).
The Andean floristic region is comprised of three floristic types. (1) high-elevation grassland above 3000m (Hughes et al., 2013). (2) SDTF in isolated inter-Andean valleys from 500 to 2 500m (Pennington et al., 2010). (3) Mid-elevation montane and cloud forests at 2 000 to 3 400 m (Särkinen et al., 2012). The four Andean biomes together form a plant diversity hotspot (Figure 1) containing ca. 40 000 plant species or 15% of the world's total, almost half of which are endemic to the region (Myers et al., 2000; Särkinen et al., 2012).
The Mesoamerican hotspot spans Central America from the Panama-Colombia border to southern Mexico (Myers et al., 2000). Mesoamerica is contiguous with the lowland Chocó hotspot and the two Introduction to Neotropical Biogeography 15 are sometimes considered a single floristic region (Londoño-Murcia et al., 2010). Unlike Chocó, Mesoamerica includes montane as well as lowland habitats, including moist montane forests towards the south and montane oak-pine forests further north. Lowland habitats within Mesoamerica are primarily seasonally-dry or broadleaf tropical forest with mangroves on both coastlines (Londoño- Murcia et al., 2010). The Mesoamerican hotspot contains an estimated 5 000 endemic plants, 1.7% of total plant species (Myers et al., 2000).
The majority of the lowland Antilles is comprised of tropical or SDTF, with temperate habitats at higher altitudes (Santiago-Valentin and Olmstead, 2004). Gentry, (1982) considered the size and diversity of the Caribbean flora, which encompasses 12 000 species of which 51% are endemic (Santiago-Valentin and Olmstead, 2004) large enough to merit its consideration as a distinct phytogeographic province within the Neotropics. Together with the Bahamas, the Antilles are now considered a global biodiversity hotspot (Figure 1) (Myers et al., 2000).
2.1.2 'Splendid Isolation' - South American Geography Upon reviewing the biogeographic affinities of the mammalian fauna of South America, Simpson (1980) declared their history one of 'splendid isolation' on an 'island continent'. Following the separation of South America from Africa ca. 100 Ma (Pennington and Dick, 2004), Simpson regarded South America and its biota as isolated until the completion of the Isthmus of Panama. However, the geological evolution of South America is not entirely as simple as suggested by Simpson. Until ca. 35-30 Ma, southern South America remained in contact with pre-glacial Antarctica (Pennington and Dick, 2004). This landbridge allowed the migration of temperate groups (e.g. Myrtaceae Juss. [Sytsma et al., 2004] and Alstroemeriaceae Dumort. [Chacón et al., 2012]) but probably not megathermal taxa between the continents. Furthermore, South America may have been closely associated with the Antilles and Central America prior to the closure of the Isthmus of Panama (Pennington and Dick, 2004).
Following Gondwanan breakup, the ecological zonation and drainage patterns of Tropical South America were markedly different to those exhibited today (Hoorn et al., 2010). A 'pan-Amazonian' rainforest region extended south and west of the current Amazon dominated by westward-draining river systems with the continental divide situated in the east of modern-day Amazonia (Hoorn et al., 2010). Throughout the Palaeogene (65-23 Ma), the continental divide migrated towards the centre of Amazonia, resulting in east- and west-flowing proto-Amazon rivers (Hoorn et al., 2010). The topologically complex Brazilian shield, which forms the bedrock of the modern Mata Atlantica, appears to have been uplifted throughout this period with the long history of erosion accounting for the area's diverse topology (Simpson et al., 2001). Introduction to Neotropical Biogeography 16
2.1.3 North America Geography In contrast to South America, North America is of Laurasian origin. North America was never subject to the 'splendid isolation' of South America and has retained a relatively close association with Eurasia via Greenland and perhaps a proto-Iceland (Hoorn et al., 2010). Unlike South America's connection to Antarctica, this continuous or semi-continuous landbridge may have allowed the migration of tropical lineages during a warm climatic period ca. 30-40 Ma (Zachos et al., 2001). Fossil evidence from this period provides evidence megathermal lineages lived high into modern day temperate latitudes, suggesting a close association between European and North American tropical forests and the potential for migration between the two continents via a North Atlantic Land Bridge (NALB) ca. 55-45 Ma (Morley, 2000). Similarly, a close association between North America and eastern Asia may have facilitated the migration of megathermal taxa between the two continents via a Bering Land Bridge (BLB) in the early to mid Eocene (Hoorn et al., 2010).
2.1.4 Formation of the Antilles The Greater and Lesser Antilles span the northern and eastern margins of the Caribbean plate respectively and together form a sporadic series of terrestrial stepping stones from north-western South America to the Yucatan peninsula. The Caribbean plate is generally accepted to have formed to the west of its current position, having moved eastwards relative to North and South America during the late Cretaceous and Palaeogene (Graham, 2003a). The bedrock of the present day Greater Antillean island arc is believed to have originated on the northern edge of the plate ca. 130 Ma, fragmenting into its current form as it attained its current position (Graham, 2003a). The submersion history of the islands is unclear, leading some authors to suggest the existence of a continuous or semi-continuous landbridge termed GAARlandia between the eastern Greater Antilles and northwest South America ca. 32 Ma (Ali, 2012). This hypothesis is based largely upon the coincidence of several dated fauna disjunctions (e.g. toads [Alonso et al., 2012]) between South America and the Greater Antilles and supported by little or no geological evidence (Ali, 2012). Geological evidence better supports a first emergence of the proto-Greater Antilles ca. 49 Ma with them remaining a discontinuous archipelago throughout their history (Graham, 2003a), which may still have served as a route for "stepping stone" dispersal (Antonelli and Sanmartín, 2011).
The islands of the Lesser Antilles formed on the eastern margin of the Caribbean plate where subduction of the Atlantic plate continues to the present day (Alonso et al., 2012; Kopp et al., 2011). Initial emersion of the northern Lesser Antilles is believed to have begun in the Eocene with the southern Lesser Antilles emerging from the Oligocene (Graham, 2003a).
2.1.5 Formation of Central America Central America consists of four tectonic elements, from north to south these are the Maya, Chortis, Chorotega, and Choco blocks (Gutiérrez-García and Vázquez-Domínguez, 2013). The three northernmost blocks have complex geological histories comprised of pre- and post-Miocene elements Introduction to Neotropical Biogeography 17 whereas the Choco block is primarily of Miocene origins and later. The Maya block comprises the Isthmus of Tehuantepec, Yucatan Peninsula, Chiapas Massif, and Belize Mountains. Of these, the mountains of the Isthmus of Tehuantepec and Chiapas Massif are pre-Miocene, each having partially collapsed and reduced in elevation during the Miocene into the Pliocene. The Belize Mountains are composed of pre-Miocene volcanic and limestone elements, uplifted in the early Pleistocene. The emersion of the lowland Yucatan Peninsula gradually progressed from southwest to northeast beginning ca. 33 Ma. The Chortis block includes southern Guatemala to southern Nicaragua and comprises three volcanic provinces extruded through older material: a widespread area of volcanism dates from the late Miocene to present while two more recent episodes date from the Pliocene and Pleistocene respectively. The lowland Nicaragua depression towards the south of the Chortis block was emerged during the Pliocene and separates the Chortis block highlands from those further south (Gutiérrez-García and Vázquez-Domínguez, 2013). The Costa Rican and northern Panamanian Chorotega block comprises primarily of volcanic deposits extruded during the Quaternary with the Tilaran range extruded during the Miocene and Pleistocene (MacMillan et al., 2004). The emersion history of lowland Central America remains unclear with some authors suggesting it remained an archipelago throughout the Miocene whereas others maintain it was a peninsula (Kirby and MacFadden, 2005). However, it is clear extensive highlands existed in northern Central America by the Miocene with those in mid to southern Central America largely formed in the Pliocene and Pleistocene respectively (Gutiérrez-García and Vázquez-Domínguez, 2013).
2.1.6 Closure of the Isthmus of Panama The connection of North and Central America through the formation of the Isthmus of Panama and the subsequent closure of the Central American Seaway is considered a key global event not just due to its biogeographic consequences but also its affect upon the global climate (Montes et al., 2012a). The closure of the Central American Seaway ceased all oceanic currents flowing from the Caribbean and the Pacific, diverting warm sea currents northwards, resulting in today's Gulf Stream (Bacon et al., 2013), considered by some key to the onset of Pliocene glaciations (Montes et al., 2012a). The formation of the Isthmus of Panama also facilitated migration of flora and fauna between North and South America: the 'Great American Biotic Interchange' (Cody et al., 2010).
The primarily lowland Isthmus of Panama is the only stretch of Central America lacking modern day volcanism and consists of a basement complex of igneous and sedimentary rocks dated at ca. 58-39 Ma (Gutiérrez-García and Vázquez-Domínguez, 2013). Fission track and radiometric dating methodologies suggest the igneous complex of Eastern Panama was subject to rapid cooling consistent with exhumation ca. 47-42 Ma while later successions of sedimentary strata were laid down above sea level, suggesting the area was above sea level ca. 35-20 Ma (Montes et al., 2012b). Fossiliferous deposits from this era suggest a Miocene connection between Panama and mainland Introduction to Neotropical Biogeography 18
Central and therefore North America (Kirby and MacFadden, 2005). However, the date of the closure of the Isthmus between eastern Panama and South America remains controversial (Stone, 2013).
The earliest studies of Isthmus closure were based primarily upon indirect data (Bacon et al., 2013) with the majority only providing minimum dates (Farris et al., 2011). These included studies of diverging oxygen isotopes, Caribbean carbonate sedimentation, and diversification between fossil Pacific and Caribbean taxa, all providing remarkably consistent dates of ca. 3 Ma (Bacon et al., 2013). Until recently, this was the widely accepted date of Isthmus closure (Stone, 2013) and used by the majority of reconstructions of the range of ancestral taxa (Cody et al., 2010). A more recent study of geochemical, radioisotope, and paleomagnetic data from the Isthmus region attempted to discern the position, formation, and emersion dates of the isthmus' geological features by more direct means (Farris et al., 2011; Montes et al., 2012a; Montes et al., 2012b). The results of this study suggest a much earlier closure date for the Isthmus of Panama, with the onset of collision between the South American and Caribbean Plates occurring ca. 25 Ma (Farris et al., 2011). Further reconstruction suggests the final deep-water channels were closed by 10 Ma, leaving North and South America separated by only a few areas of shallow sea until ca. 6 Ma (Montes et al., 2012b). This interpretation is disputed with other authors suggesting Montes' reconstructions are not detailed enough to determine the areas' emersion history (Stone, 2013). Both early and late closure theories are supported by conflicting biological information (Stone, 2013) leading some authors to suggest a hybrid model with an almost-complete Isthmus forming ca. 7 Ma leading to a gradual onset of the Great American Biotic Interchange (Bacon et al., 2013).
2.1.7 The Andean Orogeny The commencement of Andean uplift was triggered by plate subduction along the pacific margins of the South American plate ca. 65-34 Ma (Hoorn et al., 2010). The historical altitude of the Andes cannot be measured directly and indirect indicators such as historical floras and erosion patterns lack accuracy. However, independent estimates show high levels of congruence, particularly for the Central Andes (see review in Gregory-wodzicki, 2000). The Central Andean Antiplano and Eastern Cordillera may have only reached 25-30% of their current height by ca. 14 Ma and subsequent rapid increase in mountain building saw their height increase by 2-3.5km from ca. 10 Ma (Gregory- Wodzicki, 2000; Garzione et al., 2008). The altitudinal history of the Northern Andes is less clear but estimates suggest they reached no more than 40% of their current height by 4 Ma, followed by a period of intense mountain building (Gregory-Wodzicki, 2000; Mora et al., 2008). Evidence from fossil and sediment evidence suggests the northern and central Andes were separated by a marine incursion, termed the West Andean Portal (WAP) until emersion ca. 12 Ma (Antonelli et al., 2009).
The Andean orogeny resulted in the shifting of the South American continental divide from central to eastern South America while the emergence of the first mountains over 2 km resulted in dramatically Introduction to Neotropical Biogeography 19 increased rainfall in eastern South America (Hoorn et al., 2010). The newly formed eastward-flowing alluvial systems resulted in increased deposition in the Andean basin and the formation of the Pebas aquatic system in western Amazonia ca. 24-10 Ma (Antonelli and Sanmartín, 2011), fragmenting the proto-Amazonian rainforest (Hoorn et al., 2010). As mountain building peaked ca. 12 Ma, sedimentation increased further, filling the Pebas basin and resulting in the formation of the modern Amazon River ca. 7 Ma (Hoorn et al., 2010). In parallel, the Amazonian rain forest spread into the area vacated by the Pebas system (Roncal and Kahn, 2013). This resulted in a matrix of Miocene to modern-day clay sediments overlaying older white sand substrates throughout the Amazon basin (Fine et al., 2013).
2.2 Biogeography of the Neotropics
2.2.1 Origins of Neotropical Clades The origin of Neotropical clades was first considered in great detail by Gentry (1982), who classified groups into those of Laurasian and Gondwanan origins by their inferred geographic affinities. Gentry's Gondwanan groups outnumbered Laurasian groups by ten to one, suggesting a much greater contribution to Neotropical hyperdiversity of South American than North American groups. Gentry's Laurasian groups are primarily distributed through the uplands of Central American and to a lesser extent the Andes, with many absent south of Panama of the Nicaraguan lowlands whereas Gondwanan groups dominate Amazonia, the mid- and low-elevation Andes, lowland Central America, and the Mata Atlantica.
The recent profusion of dated phylogenies has allowed the reconstruction of ancestral ranges of numerous Neotropical taxa, testing Gentry's theory that Neotropical groups are primarily of Laurasian or Gondwanan origins. This has revealed a striking scarcity of groups whose diversification predates Laurasian and Gondwanan breakup (Hoorn et al., 2010; Christenhusz and Chase, 2013; Olmstead, 2013). A number of groups previously believed to be of Gondwanan origins have crown ages too young to entertain this hypothesis including the Berberidopsidaceae Takht., Restionaceae R.Br., and Proteaceae Juss. (Christenhusz and Chase, 2013) although the Solanales Juss. ex Bercht & J.Presl. appear to have diversified in Gondwanaland before the isolation of individual families on other post- Gondwanan fragments (Olmstead, 2013). Numerous large Neotropical groups appear to have diversified within the Neotropics following Gondwanan breakup (e.g. Bromeliaceae Juss. [Givnish et al., 2011]; Solanaceae Juss., Bignoniaceae Juss., and Verbenaceae J.St.-Hil. [Olmstead, 2013]; and the Gesnerioideae [Perret et al., 2013]) whereas many groups are believed to have arrived later via the boreotropical NALB and BLB (e.g. Rubiaceae Juss. [Antonelli et al., 2009]; Melastomataceae Juss. [Renner, 2001]; Guatteria Ruiz & Pav., Annonaceae Juss. [Pirie et al., 2006]; Lauraceae Juss. [Chanderbali et al., 2001]; Burseraceae Kunth [Weeks et al., 2005]; and Malpighiaceae Juss. [Davis et al., 2002]), a temperate connection to South America (e.g. Myrtaceae [Sytsma et al., 2004]; and Introduction to Neotropical Biogeography 20
Alstroemeriaceae [Chacón et al., 2012]), overwater sweepstake dispersal (e.g. Renealmia L.f., Zingerberaceae Martinov [Särkinen et al., 2007]; and multiple Legume groups [(Lavin et al., 2004]), or a combination of routes (e.g. Chrysobalanaceae R.Br. [Bardon et al., 2013]). A number of groups also appear to have migrated into the Neotropics from temperate North (e.g. Lupinus [Hughes and Eastwood, 2006]; Valeriana L. [Bell et al., 2012]; and Lepechinia [Drew and Sytsma, 2013]) or South America (e.g. Puya Molina [Jabaily and Sytsma, 2013]; and Oreobolus R.Br. [Chacón et al., 2006]). The surprising prevalence of dispersal has led to a recent synthesis of intercontinental distributions where the importance of vicariance is overshadowed by long distance dispersal (Christenhusz and Chase, 2013).
2.2.2 Effects of the Andean Orogeny The Andean orogeny and its profound effects upon the ecology, hydrology, and climate of South America and further afield have been suggested as one of the key drivers of Neotropical diversification. Gentry (1982) recognised two major patterns in his Gondwanan centred taxa: Amazonian- and Andean-centred taxa later termed the Gentry pattern (Antonelli and Sanmartín, 2011). Andean centred taxa have centres of diversity in the lowlands and mid-elevation forests of Andean and Central America, to a lesser extent in the Antilles and Mata Atlantica, and little or no diversity in Amazonia. They typically comprise of bushes, epiphytes, and herbs whereas Amazonian- centred taxa are primarily trees and lianas. Many Amazonian-centred taxa have representatives in the Cerrado but have lower species richness in Andean and upland Central America. However, Amazonian taxa dominate the Central American lowland forests in number if not diversity. Gentry proposed the uplift of the Andes and the partially concurrent closure of the Isthmus of Panama were responsible for rapid radiations of South American bushes, epiphytes, and herbs throughout Central and Andean America resulting in today's profusion of Andean-centred taxa (Gentry, 1982).
Evaluation of Gentry's hypothesis requires investigation of the diversification of taxa occurring in each of the three Andean vegetation types: montane grasslands, mid-elevation forests, and SDTFs (Särkinen et al., 2012). Few genera occur across all three vegetation types (Gentry, 1982) but all three have areas of high endemism, although overall richness is significantly lower in SDTFs (Hughes and Eastwood, 2006). By ca. 10 Ma the height of the Andes remained relatively modest but was still high enough to result in areas of high rainfall at mid-elevations and consequently rain shadows, leading to the formation of mid-elevation forests and SDTFs respectively (Särkinen et al., 2012). Extensive high elevation grasslands formed much later following the widespread elevation of the Andes above 3 km ca. 2.5 Ma (Hughes and Eastwood, 2006; Rauscher, 2002). Application of dated phylogenetics to a variety of SDTF, MEF, and HEG lineages is beginning to reveal diversification patterns between lineages. The majority of SDTF and MEF lineages and species are significantly older than HEG lineages with the majority of SDTF lineages showing large degrees of phylogenetic structure between geographically separated inter-Andean valleys (Pennington et al., 2010; Särkinen et al., 2012). This Introduction to Neotropical Biogeography 21 suggests geographically-isolated areas of SDTFs have persisted throughout the Andean orogeny, leading to distinct species complexes in each area. MEF lineages appear of a similar age to SDTF lineages but little information is available on their diversification histories; however, Särkinen et al (2012) predict the relatively continuous distribution of MEFs will have resulted in less dispersal- limited and therefore less geographically structured lineages. Irrespective, radiation within primarily MEF lineages such as the core tillandsioids (Bromeliaceae Juss.) appears to have been explosive (Givnish et al., 2011). Dated phylogenetic analyses of HEG lineages have revealed large, recent, and rapid speciation throughout the newly-formed grasslands (Rauscher, 2002; Hughes and Eastwood, 2006; Jabaily and Sytsma, 2013) with diversification rates comparable to oceanic island radiations (Hughes and Eastwood, 2006) contrasting with the older species ages of SDTF lineages (Särkinen et al., 2012). The correlation between the ages of SDTF and HEG lineages and the formation of their respective habitats suggests Gentry's hypothesis of diversification linked to Andean uplift is largely correct; however, the age of diversification differs between individual biomes in tandem with the origins of those biomes. The impact of the WAP upon dispersal between the north and central Andes has rarely been tested although a number of groups appear confined to either side of the proposed barrier (Antonelli et al., 2009).
The diverse geographic origins of Andean clades from all three biomes have been highlighted by the recent application of phylogenetic range reconstruction techniques. The formation of montane ecosystems in tropical South America appears to have facilitated the migration of temperate North American clades intro South America via the uplands of Central America (e.g. Rubiaceae [Antonelli et al., 2009]; Lupinus [Hughes and Eastwood, 2006]; Valeriana [Bell et al., 2012]; and Lepechinia [Drew and Sytsma, 2013]) and the migration of temperate South American clades into the Neotropics (e.g. Puya [Jabaily and Sytsma, 2013]; Oreobolus [Chacón et al., 2006]; the Alstroemeriaceae [Chacón et al., 2012]; and Calceolaria L. [Cosacov et al., 2009]). Furthermore, a number of clades appear to have diversified in the tropical Andes before subsequent northerly and southerly migrations (e.g. Peperomia Ruiz & Pav. subgenus Tildenia Miq. [Symmank et al., 2011]) or colonised the Andes from other South American biomes such as the Guiana Shield (e.g. Pitcairnioideae Harms and Fosterella L.B.Sm., Bromeliaceae [Givnish et al., 2011]) and the Mata Atlantica ( Sinningieae Fritsch, Gesneriaceae Rich. & Juss. [Perret et al., 2006]).
As well as affecting species diversification within Andean biomes, the Andean uplift may have resulted in cessation of gene flow and therefore vicariance within and between lowland areas. High diversification rates in late-Miocene understory Andean-centred Costus L. subgenus Costus (Kay et al., 2005) and Renealmia (Särkinen et al., 2007) have tentatively been ascribed to vicariance caused by these barriers although Andean-influenced climate change and the affects of the closure of the Isthmus of Panama may also have played a role. Furthermore, the alteration of drainage patterns, sedimentation, and climate caused by the Andean uplift presumably had dramatic impacts upon the Introduction to Neotropical Biogeography 22 majority of Neotropical floristic regions. Evidence from dated phylogenies of lowland taxa (e.g. Inga [Richardson et al., 2001]; Guatteria [Erkens et al., 2007]; and Astrocaryum G.Mey. [Roncal et al., 2013]) seems to indicate increased diversification concordant with the most rapid stages of Andean uplift. However, the exact cause of this diversification remains unclear as this time period coincides with changes in sediment type, climate, and the drainage of the Pebas system in Amazonia. Roncal et al (2013) attempted discern whether diversification in Astrocaryum was limited to Western Amazonia and therefore attributable into areas vacated by the drainage of the Pebas system; however, increased diversification appeared to be widespread and predate the drainage and is thus more likely to be due to changes in climate or sedimentation. However, the diversification histories of numerous Amazonian taxa need to be investigated before any patterns can be confirmed (Antonelli and Sanmartín, 2011) A related theory suggesting increased Miocene diversification represents the diversification of newly- fragmented white sand lineages into clay substrates remains untested (Fiaschi and Pirani, 2009).
2.2.3 Crossing the Isthmus of Panama A recent meta-analysis of dated phylogenies of 25 plant and 33 animal groups displaying disjunctions over the Isthmus of Panama attempted to discern whether disjunctions were concordant with Isthmus closure (Cody et al., 2010). The timing of dispersal events were determined as occurring between the maximum stem age and the minimum crown age of the disjunct group, often resulting in considerable uncertainty. Their analyses shows 32% of plant disjunctions have crown nodes over 20 Ma whereas disjunctions of this age have not been observed in animals. Given the recent earlier estimates of Isthmus closure date (Farris et al., 2011; Montes et al., 2012a; Montes et al., 2012b), it is difficult to attribute dates before this date unambiguously to dispersal or migration. However, their results suggest plants were more likely than plants to disperse over the Central American Seaway prior to its closure. The lack of dispersal constraint in plants is highlighted by (Olmstead, 2013), who found a total of 24 groups Neotropical disjunctions across the Isthmus of Panama in the Solanaceae, Verbenaceae, and Bignoniaceae. Disjunctions were not dated, but their varying depth within the phylogeny of the Solanales suggests the existence of both pre-and post-closure disjunctions. The variable ages of disjunctions across the Isthmus of Panama led Bacon et al (2013) to suggest a model whereby the likelihood of dispersal across the Isthmus gradually increased until full closure.
Little work has been done on the relative rates of dispersal across the Isthmus of Panama of Andean- and Amazonian-Centred groups. Reconstructions suggest lowland southern Central America had emerged and was in close proximity with South America by ca. 25 Ma. The two landmasses were possibly connected by 15 Ma (Farris et al., 2011; Montes et al., 2012a; Montes et al., 2012b). Limited uplands were present in southern Central America by this point (MacMillan et al., 2004; Gutiérrez- García and Vázquez-Domínguez, 2013). The relative proximity of lowland Central and South American habitat in the late-Miocene and Pliocene perhaps suggests lowland taxa may have been Introduction to Neotropical Biogeography 23 more prone to early dispersal than upland taxa; however, there remains little data to support this hypothesis.
2.2.4 Colonisation of the Caribbean Gentry (1982) considered the floristic composition of the Caribbean to contain a larger Laurasian component than the remainder of the Neotropics while the Gondwanan component was considered to be comprised of an almost equal number of Andean- and Amazonian-centred lineages. Few studies have reconstructed the ancestral ranges of Caribbean taxa although Santiago-Valentin and Olmstead (2004) were able to identify five groups apparently of Central and North American origin and two of South American origin; however, none of these disjunctions were dated. Subsequent studies have identified further groups of Central American (e.g. Pinus L. [Jardón-Barbolla et al., 2011]) and South American (e.g. Bromeliaceae [Givnish et al., 2011]) origins.
2.2.5 Biogeography of the Mata Atlantica The origins and diversification patterns of the rich Mata Atlantica flora remain poorly studied from a biogeographic perspective (Iganci et al., 2011; Hughes et al., 2013); however, the presence of large numbers of endemic species in some groups suggests large radiations have occurred within the region (Fiaschi and Pirani, 2009). Furthermore, Gentry (1982) suggested the presence of numerous seemingly primitive groups indicates the Mata Atlantica has acted as a source region for groups colonising the remainder of the Americas. This hypothesis is supported by a number of more recent studies although lineages from other areas have also colonised the Mata Atlantica (Fiaschi and Pirani, 2009) such as Amazonia ( Bromelia L.), the Southern Andes (e.g. Brazilian shield bromelioids Burnett.; Alstroemeriaceae), the central Andes (e.g. Dyckia , Schult.f.; Encholirium Mart. ex Schult.) and the Guiana Shield (e.g. Oreobolus ) (Givnish et al., 2011; Chacón et al., 2012). The floristic composition of the northern and southern Mata Atlantica appear distinct with many species and genera occurring only north or south of the Rio Doce basin, correlating with changes in climate and elevation profile (Oliveira-Filho and Fontes, 2000). The northern Atlantic forest shows greatest floristic affinity to Amazonia (Melo Santos et al., 2007) leading to the proposal of several Cenezoic wet-forest links between Amazonia and the northern Mata Atlantica (Fiaschi and Pirani, 2009). In contrast, the flora of southern Mata Atlantica includes numerous Andean-centred taxa, which are largely absent from the northern Atlantic Forests (Fiaschi and Pirani, 2009).
2.2.6 Dispersal throughout the Americas: Niche Conservation or Niche Evolution? Clade diversification throughout a matrix of heterogeneous environments such as the Neotropics may comprise predominantly of dispersal into similar environments: 'niche conservation'; adaptation to disparate environments: 'niche evolution'; or continuum between the two phenomena (Olmstead, 2013). Understanding the relative importance of niche conservation and evolution is paramount to understanding diversification patterns in the Neotropics (Hughes et al., 2013). Large-scale analyses of the Solanaceae, Bignoniaceae, and Verbenaceae have revealed striking correlation between the Introduction to Neotropical Biogeography 24 northern and southern limits of Neotropical clades, suggesting sub-family scale niche conservation despite the ecological diversity of genera within each clade (Olmstead, 2013). The limits of range evolution in each clade appear primarily ecological, with multiple long-distance dispersal events between similar northern and southern hemisphere biomes supported. Similarly, an important role for niche conservation is suggested in Neotropical temperate and upland radiations (e.g. Puya [Jabaily and Sytsma, 2013]; and Lupinus [Hughes and Eastwood, 2006]), radiations of lowland taxa (e.g. Inga [Richardson et al., 2001]), and seasonally-dry tropical forest taxa (Pennington et al., 2010). Indeed, niche conservation may be an important determinant of the Gentry pattern (Olmstead, 2013). However, radiations into the recently-formed Cerrado appear to suggest recruitment from ecologically diverse biomes (Hughes et al., 2013) leading to suggestions there may be no overall trend towards niche conservation or evolution in the Neotropics (Simon et al., 2009).
Introduction to Begonia 25
3 Introduction to Begonia
3.1 Begonia Classification and Phylogeny The Begoniaceae C.Agardh is a member of the Cucurbitales Juss. ex Bercht. & Presl. within Eurosids I, an order also containing the Anisophylleaceae Ridl., Datiscaceae Dum., Coriariaceae Mirb., Corynocarpaceae Engl., Cucurbitaceae Juss., and the Tetramelaceae Airy Shaw (Chase et al., 2009). A sister relationship between the Begoniaceae and Datiscaceae has been proposed; however, support is low (Clement et al., 2004). The majority of families in the Cucurbitales are small (Anisophylleaceae, 34 species; Datiscaceae, 2 species; Coriariaceae, 5 species; Corynocarpaceae, 6 species) with only the Cucurbitaceae (ca. 960 species) and Begoniaceae (ca. 1600 species) considered species rich. Two genera are currently recognised within the Begoniaceae: the species rich genus Begonia L. and the endemic Hawaiian, monotypic genus Hillebrandia Oliv. (Forrest and Hollingsworth, 2003). The relationship between these two genera is well established with a number of studies resolving them as sister (Clement et al., 2004; Goodall-Copestake, 2005; Plana, 2002; Plana, 2003; Plana et al., 2004) confirming earlier hypotheses based upon morphology (Clement et al., 2004). Begonia is one of the ten largest plant genera (Frodin, 2004) and is distributed throughout the tropics of Africa, the Americas, and Asia but absent from Australia and from Samoa to Hawaii (Figure 2). Begonia is divided into 65 sections (Doorenbos et al., 1998; Forrest and Hollingsworth, 2003), each of which is confined to one of these three regions with the exception of the primarily African section Tetraphila A.DC., which has a single Asian species (de Wilde et al., 2011).
The Begoniaceae have been subject to a number of worldwide, regional, and sectional phylogenetic studies utilising sequence data from all three genomes and morphological data in isolation and combination (Table 1). Morphological cladistic studies have produced predominantly unresolved phylogenies (Tebbitt, 1997; Badcock, 1998; Forrest, 2000) with the exception of a study of African Begonia of sections Loasibegonia A.DC. and Scutobegonia Warb. (Sosef, 1994). More recent molecular phylogenetic studies (Goodall-copestake et al., 2009; Plana et al., 2004; Thomas et al., 2012b) have resolved African Begonia as paraphyletic with Asian and Neotropical clades nested within. In analyses of nuclear mitochondrial DNA sequence data (Goodall-Copestake et al., 2010), Neotropical Begonia are resolved as a monophyletic group nested within seasonally-dry African Begonia . This contrasts with analyses of chloroplast data which resolve Neotropical Begonia as two monophyletic clades within seasonally-dry adapted African Begonia (Goodall-Copestake et al., 2009; Goodall-Copestake et al., 2010).
Introduction to Begonia 26
Table 1: Published Phylogenies of Begonia .
Datasets Utilised Coverage Molecular Morphological Nuclear Chloroplast Mitochondrion African Sosef, 1994 (Loasibegonia, - - - Scutobegonia ) Asian Tebbitt, 1997 - - - (Sphenanthera ) American and Asian Badcock, 1998 - - - (Knesebeckia sensu latu ), 86 species Worldwide, 175 Forrest, 2000 - - - species. Predominantly Plana, 2002 ITS trn L intron - Africa, 57 species. Forrest & Worldwide, 35 ITS, Hollingsworth, - - - species. 5.8S, 18S P, 2003 Predominantly Plana, 2003 African, 81 - - trn L intron - species. Predominantly Plana et al., 2004 African, 73 - ITS trn L intron - species. Clement et al., Worldwide, 7 ITS, - - - 2004 species. 5.8S, 18S L. Forrest, Hughes, Worldwide, 64 ITS, Hollingsworth, - - Species. 5.8S, 18S & Zomlefer, 2005 trn K intron, mat K gene; pet B-petD cox 1 gene; mat R gene; spacer, pet D gene, nad 1b-c intron, nad 1 Goodall- Worldwide, 30 18S, pet D intron; psb B gene; nad 7 1-2 intron, - copestake, 2005 species. rbc L gene; psb D gene, nad 7 gene, nad 7 2-3 psb C gene, psb C- intron; rps 14-cob trn S spacer; trn L spacer intron Tebbitt et al., Asian - ITS - - 2006 (Platycentrum , Introduction to Begonia 27
Sphenanthera , Leprosae ), 48 species. Goodall- Worldwide, 21 18S, copestake et al., - - - species. rbc L 2009 trn K intron, mat K gene; pet B-petD cox 1 gene; mat R gene; spacer, pet D gene, nad 1b-c intron, nad 1 Goodall- Worldwide, 30 pet D intron; psb B gene; nad 7 1-2 intron, copestake et al., - - species gene; psb D gene, nad 7 gene, nad 7 2-3 2010 psb C gene, psb C- intron; rps 14-cob trn S spacer; trn L spacer intron ndh A intron, ndh F- Predominantly Thomas, 2010 - - rpl 32 spacer, rpl 32- - Asian: 84 species. trn L spacer African de Wilde, (Tetraphila, Hughes, Rodda, Baccabegonia, - ITS, 5.8S trn L intron - & Thomas, 2011 Squamibegonia ), 22 species. Rajbhandary, Hughes, Predominantly Phutthai, - ITS - - Asian, 111 species. Thomas, & Shresta, 2011 ndh A intron, ndh F- Thomas et al., Predominantly - - rpl 32 spacer, rph 32- - 2011 Asian, 84 species. trn L spacer Predominantly ndh A intron, ndh F- Thomas et al., Asian, - - rpl 32 spacer, rph 32- - 2012 103 species trn L spacer
Recent densely-sampled phylogenies have been published of African (Plana, 2003; Plana et al., 2004; Plana, 2002) and Asian (Thomas, 2010; Rajbhandary et al., 2011; Thomas et al., 2012) Begonia and relationships within both groups are relatively well studied. These phylogenies have facilitated biogeographic studies (Plana et al., 2004; Rajbhandary et al., 2011; Thomas et al., 2012) reconstruction of ancestral morphological states (Thomas et al., 2011), clarified existing sectional relationships (Plana, 2003) and revealed unexpected relationships between sections (Thomas, 2010). A densely-sampled phylogeny of Neotropical Begonia would facilitate similar analyses of American Begonia . Introduction to Begonia 28
3.2 Begonia Biogeography That Begonia and Hillebrandia are sister is surprising considering the range and diversity of Begonia in comparison with Hillebrandia's single species and restricted Hawaiian range (Figure 2). The current islands of Hawaii are roughly 15 million years whereas Begonia and Hillebrandia are estimated to have diverged ca. 45 Ma (Clement et al., 2004; Clement et al., 2005) meaning Hillebrandia cannot have maintained its current range since its split with Begonia . Clement et al. (2004) suggest Hillebrandia is a relict genus, having hopped from older to younger Hawaiian landmasses for perhaps 30 Ma. Hillebrandia may have inhabited other suitable but since-eroded islands prior to 30 Ma such as the Emperor Sea Mounts; however, the continental origins of the genus remain unclear. Plausible hypotheses include an Afro-Eurasian Boreotropical origin of the Begoniaceae with extinction of European and Asian members; a South Pacific-Malaysian origin with colonisation of Africa by Begonia , extinction of Malaysian Begonia , and re-colonisation by African Begonia ; or an American origin with colonisation of Africa, extinction of American Begonia , and re- colonisation of America by African Begonia . A South Pacific-Malaysian origin is perhaps the most likely as many members of the Cucurbitales have centres of diversity in the region (Clement et al., 2004).
Figure 2: Worldwide distribution of the Begoniaceae: Yellow, Hillebrandia , 1 species; Green, African Begonia , ca. 160 species; blue, Asian Begonia , ca. 650 species; red, Neotropical Begonia , ca. 690 species. Adapted from Goodall-Copestake et al (2010).
The age of the MRCA of Begonia has been estimated multiple times (e.g. Clement et al., 2004; Goodall-copestake et al., 2009). The most recent and robust analysis estimates the age of the crown node of Begonia at 24 Ma with a standard deviation of 3.57 Ma (95% probability interval: 17-31 Ma) (Thomas et al., 2012), placing the diversification of Begonia unambiguously on a post-Gondwanan land mass. The basal-most diversification events within Begonia are African and Madagascan; African Begonia are paraphyletic, containing both Asian and Neotropical Begonia (Goodall- Copestake et al., 2009; Plana et al., 2004), strongly suggesting an initial African diversification of Begonia . Early diverging African clades include a Malagasy and Indian Ocean clade, a yellow- Introduction to Begonia 29 flowered western and central African Clade, and a fleshy-fruited mainland African clade (Plana et al., 2004). A further clade contains seasonally-dry adapted African Begonia of the southern and eastern African sections Rostrobegonia Warb., Sexalaria A.DC., and Augustia (Klotzsch) A.DC., and Peltaugustia (Warb.) Barkley (Plana et al., 2004). Seasonally-dry adapted African Begonia are paraphyletic, containing all Neotropical species and a monophyletic radiation of Asian and Socotran Begonia (Plana et al., 2004; Goodall-Copestake et al., 2009; Goodall-Copestake et al., 2010). The split between Asian and African Begonia is dated in the Miocene and the poorly-supported basal-most lineages of the Asian radiation include the two Socotran species Begonia socotrana Hook.f. and Begonia samhaensis M.Hughes & A.G.Mill., leading authors to suggest African Begonia colonised mainland Asia via a hot, wet Miocene Arabian corridor (Plana et al., 2004; Goodall-Copestake et al., 2009; Thomas et al., 2012). Dispersal from mainland Asia to the Sunda shelf has occurred at least five times throughout the Miocene, potentially via continuous land bridges. Further overwater dispersal from western to eastern Malesia over Wallace's line has occurred on at least five occasions since the late Miocene (Thomas et al., 2012). A final Pliocene instance of overwater dispersal is highlighted by the single species of the African section Tetraphila in Laos and Thailand, well after the aridification of the Arabian corridor (de Wilde et al., 2011).
Neotropical Begonia are tentatively dated as diversifying during the Miocene (Goodall-Copestake et al., 2010; Thomas et al., 2012). Although Neotropical taxon sampling in both analyses was poor resulting in unreliable date estimates, the origins of Neotropical Begonia are estimated well after the disappearance of the BLB and NALB. Colonisation of the Americas must therefore be the result of long-distance dispersal. However, the incongruity between the monophyly of Neotropical Begonia in mitochondrial datasets and its well-supported polyphyly in chloroplast datasets (Goodall-Copestake et al., 2010) poses an interesting question: how can the range evolution of Begonia have resulted in this pattern? A single dispersal event could not have produced this pattern as only a single lineage of each genome would have been introduced into the Americas; therefore, at least two colonisations must have introduced chloroplast lineages independently. However, the descendants of the multiple colonisations cannot have persisted in genetic isolation from each other as this would result in multiple lineages of both genomes. Either the original colonisers themselves or the descendants of each lineage must have hybridised, leading to the introgression of the mitochondrial genome from one lineage while its chloroplast genome was maintained. It is likely that introgression involving the nuclear genome also occurred but a signature of this has not been detected so far as the markers used have not generated well supported phylogenies. Independent phylogenies of multiple unlinked nuclear DNA regions or genomic analyses of gene and spacer arrangement may reveal further introgressed markers. Such a scenario is plausible considering the frequency at which artificial Begonia hybrids are produced, with natural interspecific hybrids also being observed (Goodall-Copestake et al., 2010). Introduction to Begonia 30
Within Neotropical Begonia , no phylogenies to date have achieved wide taxonomic or geographic sampling, leaving it impossible to infer the biogeographic history of the genus in the Americas.
3.2.1 Habitats, Ecology, and Sections of Neotropical Begonia The distribution of Begonia in the Neotropics typifies Gentry's Andean-Centred distribution (Figure 3A). The main centres of both species and sectional diversity are the Andes, southern-central Central America, and the Mata Atlantica. Begonia is comparatively poorly represented in Amazonia and the Guiana Shield. At its northernmost range, Neotropical Begonia almost reaches the northern Mexican border with species of sections Quadriperigonia Ziesenh. and Doratometra (Klotzsch) A.DC. and Begonia monophylla Pavon ex A.DC., the single Mexican species of section Eupetalum (Lindl.) A.DC., present. Begonia diversity and abundance is high throughout Central America with the exception of the Yucatan Peninsula and Nicaraguan highlands. The Antilles are primarily populated by species of section Begonia , totalling around 40 species (Acevedo-Rodriguez and Strong, 2012). Begonia diversity is high from the Paria Peninsula in an arc south and east along the Andes through Venezuela, Colombia, Ecuador, Peru, and Bolivia. Begonia is present in northern Argentina but no GBIF records were available thus assessing diversity was not possible. Diversity is high throughout the Mata Atlantica of eastern and south-eastern Brazil. The majority of records in the remainder of the Neotropics are of widespread species or species not included in the analysis.
The majority of Begonia species within the Neotropics and elsewhere are narrow endemics (Tebbitt, 2005), which has been attributed to the poor dispersal ability of their pollen and seeds (Thomas et al., 2012). Most Begonia species practice Batesian auto-mimetic deceit pollination, with males offering a pollen reward and females superficially resembling males. Deceit pollination primarily attracts generalist pollinators so is not an effective long-distance pollination strategy (Castillo et al., 2012). Most Begonia fruits are anemochorous (wind-dispersed) winged capsules. Although wing-fruited species are capable of long-distance dispersal, this is primarily achieved by canopy trees or species in open habitats. Anemochory is not an effective dispersal syndrome in understory plants (Burt-Utley, 1985). The low dispersal ability of Begonia fruit and seeds is reflected in low rates of gene flow between populations, making Begonia an ideal group for studying range evolution over recent and ancient time scales. Seeds in some Neotropical sections may be adapted to wind or water dispersal but the majority of Begonia species appear dispersal limited (de Lange and Bouman, 1999) with low levels of gene flow between populations (Hughes and Hollingsworth, 2008; Twyford, 2012).
Neotropical Begonia are divided into 28 currently recognised sections, although the boundaries between these sections are not always clear (Doorenbos et al., 1998). Well categorised sections include the largest section Pritzelia (Klotzsch) A.DC.; the rhizomatous Central American sections Gireoudia (Klotzsch) A.DC. and Weilbachia (Klotzsch & Oersted ex Klotzsch) A.DC.; the geophytic primarily-Mexican section Quadriperigonia , the horn fruited sections Casparya (Klotzsch) Warb., Introduction to Begonia 31
Semibegoniella (C.DC.) Barkley & Baranov, and Urniformia Houghton ex Ziesenh.; and the peltate- leaved climbing section Gobenia A.DC. The remaining sections are poorly categorised. Species of section Barya are characterised by their pendant flowers, acute slender tepals, and fused, columnar filaments. However, Doorenbos et al. (1998) suggest differences in habit, inflorescence structure, and seed micromorphology may render Barya (Klotzsch) A.DC. an unnatural section. Two species of Barya are tuberous, a characteristic shared with all species of the primarily-Andean section Eupetalum and some species of the Central and Andean American section Knesebeckia (Klotzsch) A.DC., the distinction between which is considered arbitrary (Doorenbos et al., 1998). Furthermore, species of Parietoplacentalia Ziesenh. have been placed in section Eupetalum and Knesebeckia but differ in their female flower and fruit morphology. The sections Begonia , Ruizopavonia A.DC., Hydristyles A.DC. have been described as shading off each other (Doorenbos et al., 1998) with the sections Cyathocnemis (Klotzsch) A.DC., Lepsia (Klotzsch) A.DC., Trendelenbergia (Klotzsch) A.DC., and Doratometra , Donaldia (Klotzsch) A.DC. linked to individual sections within the complex. The affinities and phylogenetic relationships of all sections of Neotropical Begonia are poorly studied and knowledge would be greatly improved by a densely-sampled phylogeny. Abstract 32
4 Abstract
Aim The origin of the Neotropical hyperdiversity is one of the most intriguing questions in modern biogeography, requiring the investigation of biogeographic histories of a variety of lineages. We produced a dated phylogeny and reconstructed ancestral ranges of the species-rich, Andean-centred genus Begonia L. to discern the genus' dispersal history throughout the Neotropics and determine correlates of range evolution.
Location Neotropics, Central America, South America, Antilles
Methods Plastid DNA sequence data from species representing the full geographic range and the majority of sections of Neotropical Begonia were analysed using a secondarily-calibrated uncorrelated-rates relaxed molecular clock to estimate the age of Neotropical crown groups and divergence times within Neotropical Begonia . Ancestral areas were reconstructed within a parsimony framework implemented on Bayesian derived trees under a dispersal-vicariance model, a likelihood framework under a dispersal-extinction-cladogenesis model (DEC), and a Bayesian Binary method.
Results The results indicated two independent overwater long-distance dispersal colonisations of the Neotropics from Africa. Basal lineages of both clades are reconstructed as diversifying in South America with multiple dispersal events between the Mata Atlantica and the Andes, a single radiation within Central America, and a single radiation within the Antilles. Significant co-occurrence of lineages is only observed in the recently-uplifted northern Andes and southern Central America.
Main Conclusions The phylogeny of Begonia displays numerous radiations within regions punctuated by long distance dispersal. Successful colonisation and diversification is predicted by the presence of upland habitat and appears to be mediated by niche pre-emption. Successful colonisation of multiple lineages in the northern Andes and southern Central America may be due to the lack of niche pre-emption in newly- created habitat.
Keywords Ancestral area reconstruction, Andes, Antilles, Central America, dispersal, diversification, Great American Biotic Interchange, historical biogeography, Hybridisation, Mata Atlantica, Neotropical Begonia, Neotropics, South America 33
Figure 3: Neotropical Begonia occurrence records from the Global Biodiversity Information Facility (GBIF): (a) All species. (b) Species included in the analysis*. (c) Neotropical clade 1 (NC1)*. (d) Neotropical clade 2 (NC2). *Excluding the widespread species Begonia glabra .
5 Introduction The Neotropics are the most species rich of the world's regions containing perhaps 100 000 plant species or 37% of the world's total (Hughes et al., 2013). However, the Neotropics are not uniformly rich with a number of biodiversity hotspots (Myers et al., 2000) and a variety of relatively species-rich and species-poor lineages and biomes. Combined with their relative isolation, climatic, and geographic heterogeneity, this led Hughes et al (2013) to refer to the Neotropics as "an 'evolutionary laboratory' for addressing key questions in evolution and biogeography."
Within the Neotropics, two main distribution patterns have been identified. Gentry (1982) recognised a dichotomy between what he termed Amazonian- and Andean-centred taxa, since labelled the Gentry pattern (Antonelli and Sanmartín, 2011). The centres of diversity of Andean-centred taxa are primarily located in the low- to mid-elevation forests of Andean and Central America with moderate representation in the West Indies and Mata Atlantica and little or no representation in lowland Central and Amazonian America. Andean-centred taxa are typically bushes, epiphytes, or understory herbs whereas the majority of Amazonian-centred taxa are trees and lianas. Amazonian-centred taxa Introduction 34 dominate the lowlands of Central and Amazonian America with moderate representation in the Cerrado. Understanding the formation of the Gentry pattern and in particular the diversification of Andean-centred taxa is considered key to explaining the extraordinary diversity of the Neotropics (Pirie et al., 2006).
Andean centred taxa typically inhabit montane ecosystems; hence it is important to consider the geological histories of montane regions. The Guiana Shield of northern South American and Brazilian shield of east and southeast Brazil are both comprised of Precambrian bedrock uplifted through the Palaeogene (ca. 65-23 Ma), are the most ancient uplands in the Americas (Hoorn et al., 2010), and their long history of erosion accounts for their diverse topology (Simpson et al., 2001). In contrast, the Andean orogeny has a history of long periods of relatively slow uplift punctuated by episodes of rapid uplift (Hoorn et al., 2010). The initiation of the orogeny was triggered by subduction along the pacific margins of the South American plate ca. 65-34 Ma (Hoorn et al., 2010) but the central Andes may only have reached 25-30% of their current height by ca. 14 Ma before a period of rapid uplift ca. 10 Ma (Gregory-Wodzicki, 2000; Garzione et al., 2008). The elevation history of the northern Andes is less clear but they may have reached no more than 40% of their current height by ca. 4 Ma followed by exceptionally rapid uplift (Gregory-Wodzicki, 2000; Mora et al., 2008). The Northern and Central Andes may have been separated by a marine incursion, the West Andean Portal (WAP) until ca. 12 Ma (Antonelli et al., 2009), which now forms the Huancamamba depression. The uplands of Central America have diverse histories with some forming through volcanism and others through uplift of older bedrock; however, mountain age generally decreases from north to south (Gutiérrez-García and Vázquez-Domínguez, 2013). The northern Central American mountains of the Isthmus of Tehuantepec and Chiapas Massif are pre-Miocene, each having partially collapsed during the Miocene whereas the uplands of Nicaragua, El Salvador, and Honduras are primarily of Miocene and Pliocene volcanic origin. These mountains are separated from those of Costa Rica by the Nicaragua depression, a lowland corridor stretching from the Pacific to the Caribbean that was at least partially flooded until the Pleistocene (Gutiérrez-García and Vázquez-Domínguez, 2013). Although volcanism in Costa Rica and Panama dates back to the Miocene, Miocene complexes were only uplifted at the beginning of the Pleistocene ca. 2.5 Ma and the majority of the area's volcanism dates from the Pleistocene (MacMillan et al., 2004). The closure date of the Isthmus of Panama between Central America and South America remains controversial (Montes et al., 2012a; Montes et al., 2012b; Farris et al., 2011; Stone, 2013); however, the lack of uplands in southern Panama and recent dates of upland formation south of the Nicaragua depression suggest a significant lowland or oceanic barrier existed between montane Central and South America until the early Pleistocene (Gutiérrez-García and Vázquez-Domínguez, 2013).
Gentry (1982) proposed the recent Andean orogeny and closure of the Isthmus of Panama were responsible for rapid radiations of South American bushes, epiphytes, and herbs throughout Central Introduction 35 and Andean America, resulting in today's Andean-centred taxa. However, the profusion of recent molecular phylogenetic range reconstructions of Andean-centred taxa has highlighted their diverse origins. Andean-centred taxa appear to have diversified through the montane Neotropics from numerous montane tropical and temperate regions including temperate North America and northern Central America (e.g. Rubiaceae Juss. [Antonelli et al., 2009]; Lupinus L. [Hughes and Eastwood, 2006]; Valeriana L. [Bell et al., 2012]; and Lepechinia Willd. [Drew and Sytsma, 2013]), South America (e.g. Puya Molina [Jabaily and Sytsma, 2013]; Oreobolus R.Br. [Chacón et al., 2006]; the Alstroemeriaceae Dumort. [Chacón et al., 2012]; and Calceolaria L. [Cosacov et al., 2009]), the Guiana Shield (e.g. Pitcairnioideae Harms and Fosterella L.B.Sm., Bromeliaceae Juss. [Givnish et al., 2011]), and the Mata Atlantica (Sinningieae Fritsch, Gesneriaceae Rich. & Juss. [Perret et al., 2006]). The majority of diversifications appear to coincide with the Miocene uplift of the central Andes and Quaternary uplift of the northern Andes. We suggest the Andean uplift produced novel montane environments within relatively-short dispersal distances of pre-existing montane and temperate Neotropical habitats. Recent dispersal between older montane Neotropical habitats via the Andes by pre-adapted groups may explain why so many taxa are shared by all Neotropical regions. We predict range reconstructions of Andean-centred taxa will reveal little floristic exchange between older montane habitats prior to Andean uplift followed by increased exchange via the newly-emerged Andes, particularly following the formation of the Northern Andes and southern Central American uplands. Testing this hypothesis requires dated phylogenies with ancestral range reconstructions of Andean-centred taxa throughout the montane Americas.
Our study utilises the mega-diverse (ca. 1600 species), pantropical genus Begonia (Figure 2). The genus is believed to have first diversified in Africa but remains relatively species poor on the continent (ca. 160 species) compared to Asia (ca. 650 species) and the Neotropics (ca. 690 species) making Begonia a model group for investigating biogeographic differences between continents (Goodall-Copestake et al., 2010). Within the Neotropics, Begonia displays a typical Andean-centred Neotropical distribution with diversity of species and sections highest in the tropical Andes, Central America, the Mata Atlantica, and to a lesser extent the West Indies while the genus is almost absent from the Guiana Shield, Amazon Basin, and Chocó (Figure 3A). This reflects the fact the genus is primarily found on slopes in the understory of primary vegetation (Blanc, 2002). The utility of Begonia for the detection of biogeographic patterns is well recognised, with molecular phylogenies of Asian (Thomas et al., 2012) and African (Plana, 2003; Plana et al., 2004) Begonia showing a large degree of geographic structure. This has been attributed to the high numbers of narrow endemics within the genus, possibly due to the low dispersal ability of pollen and seeds of most species (Thomas et al., 2012). Begonia species primarily practice Batesian auto-mimetic deceit pollination with a pollen reward to visitors of male flowers and female flowers superficially resembling male flowers but offering no reward. The lack of a second reward means deceit pollination is not conducive Introduction 36 to long- or medium-distance pollen dispersal (Castillo et al., 2012). The majority of Begonia fruits are winged capsules containing numerous, tiny seeds from 300 to 600 µm (de Lange and Bouman, 1999). Although winged capsules of some species are dispersed long distances, these such primarily live in open habitats or are canopy trees. Anemochory is less likely to result in long-distance dispersal in rainforest understory groups such as Begonia (Burt-Utley, 1985). Seeds in a number of Neotropical sections appear to display adaptations for wind or water dispersal but it appears most Begonia species are dispersal limited (de Lange and Bouman, 1999). Their low dispersal ability is reflected in low rates of gene flow between populations (Hughes and Hollingsworth, 2008; Twyford, 2012), making Begonia an ideal group for studying range evolution over recent and ancient time scales and small or large geographical scales.
No densely-sampled, dated phylogenies of Neotropical Begonia have been published to date. Preliminary insights come from chloroplast and mitochondrial phylogenies of the genus which sampled ten Neotropical species and placed them in a pantropical context (Goodall-Copestake et al., 2009; Goodall-Copestake et al., 2010). In the mitochondrial phylogeny, Neotropical Begonia form a well -supported, monophyletic clade nested within seasonally-dry adapted (SDA) African Begonia ; however, in the chloroplast phylogeny, Neotropical Begonia are polyphyletic, forming two well- supported clades, each sister to a clade of SDA African Begonia .
This study aims to test the cpDNA polyphyly of Neotropical Begonia and produce a well-sampled, dated phylogeny of the genus to address the following questions. (1) When, where, and how were the Neotropics colonised by Begonia ? (2) Did multiple lineages of Begonia colonise the Neotropics and if so how did they interact? (3) What is the dispersal history of Begonia throughout the Neotropics and how have potential lowland and oceanic barriers to dispersal between upland areas affected its colonisation history.
Materials and Methods 37
6 Materials and Methods
6.1 Taxon Sampling The dataset comprised 268 taxa of Begonia , including 137 Neotropical, 30 African, and 101 Asian taxa and data from three non-coding plastid DNA regions ( ndh A intron, ndh F-rpl 32 spacer, rpl 32- trn L spacer). These regions were chosen due to their proven phylogenetic utility within Begonia (Thomas et al., 2011; Thomas et al., 2012). In total, sequences for 131 Neotropical and 23 African taxa were newly generated. The final dataset comprised species representing all major sections of Neotropical Begonia (sections Begonia , Casparya (Klotzsch) Warb., Cyathocnemis (Klotzsch) A.DC., Eupetalum (Lindl.) A.DC., Gireoudia (Klotzsch) A.DC., Knesebeckia (Klotzsch) A.DC., Pritzelia (Klotzsch) A.DC., Quadriperigonia Ziesenh., Ruizopavonia A.DC., and Weilbachia (Klotzsch & Oersted ex Klotzsch) A.DC.), the majority of smaller Neotropical sections (sections Barya (Klotzsch) A.DC., Donaldia (Klotzsch) A.DC., Doratometra (Klotzsch) A.DC., Gaerdtia (Klotzsch) A.DC., Hydristyles A.DC., Lepsia (Klotzsch) A.DC., Scheidweilaria (Klotzsch) A.DC., Solananthera (Klotzsch) A.DC., Tetrachia Brade, Trachelocarpus (C.Müller) A.DC., and Wagneria (Klotzsch) A.DC.), nine African sections (Sections Augusta (Klotzsch) A.DC., Erminea A.DC., Loasibegonia A.DC., Meizaria (Gaud.) Warb., Nerviplacentaria A.DC., Peltaugustia (Warb.) Barkley, Quadrilobaria A.DC., Rostrobegonia Warb., Squamibegonia Warb., and Tetraphila A.DC.), and ten Asian sections (Sections Alcida C.B.Clarke, Bractibegonia A.DC., Coelocentrum Irmscher, Haagea (Klotzsch) A.DC., Parvibegonia A.DC., Petermannia (Klotzsch) A.DC., Platycentrum (Klotzsch) A.DC., Reichenheimia (Klotzsch) A.DC., Ridleyana Irmscher, and Sphenanthera (Hassk.) Warb.).
To ensure selected Neotropical species represented all regions inhabited by Neotropical Begonia , GBIF occurrence data was downloaded for all Neotropical Begonia species (Figure 3A). The distribution of included species (Figure 3B) and all species (Figure 3A) were compared by eye in DIVA-GIS v7.5.0.0 (Hijmans et al., 2001) to ensure the range and diversity hotspots of selected species represented the range and diversity of Neotropical Begonia as a whole.
The inclusion of a number of African species was essential to allow the placement of the ancestors of Neotropical Begonia into phylogenetic context. For this purpose, species of seasonally-dry adapted Begonia of sections Rostrobegonia and Augustia were included due to their proposed close relationships with Neotropical Begonia (Goodall-Copestake, 2005; Goodall-Copestake et al., 2009; Goodall-Copestake et al., 2010). Furthermore, inclusion of closely related groups allows more accurate estimation of branch length by breaking up branches between distantly related taxa, increasing accuracy of dating and decreasing the impact of long-branch attraction.
6.2 Laboratory Methods DNA was extracted from fresh material or silica gel dried material using Qiagen DNeasy Plant Mini Kits (Qiagen, Germantown, MD, USA) following the recommended protocol and all samples were Materials and Methods 38
placed in the Edinburgh DNA bank. Amplification was carried out following one of two 25 µl PCR
protocols depending upon reagent availability. Reactions at RBGE contained 11 µl of ddH 20, 5 µl of 10x reaction buffer, 2.5 µl of dNTPs (2 mM), 4 µl of TBT-PAR, 1 µl of PCR product, 0.2 µl of phusion polymerase (Thermo Fisher Scientific, Waltham, MA, USA), and 0.75 µl of forward and reverse primer solution (10 µM). Reactions carried out at HAST Institute consisted of 16.25 µl of
ddH 20, 5 µl of reaction buffer, 0.5 µl of dNTPs (10 mM), 0.2 µl of DMSO, 1 µl of PCR product, 0.2 µl of phusion polymerase, and 0.75 µl of forward and reverse primer solution (10 µM). Phusion polymerase was used due to its utility in reducing slipping caused by large single nucleotide repeats, which are common in the sampled regions within Begonia (Thomas, 2010). The primers used in this study are shown in Table 2. PCR reactions were carried out with template denaturation at 95˚C for 5 minutes followed by 35 cycles of denaturation at 98˚C for 30 seconds, primer annealing at 50˚C for 30 seconds, primer extension at 72˚C for 30 seconds, and a final primer extension at 72˚C for 5 minutes. Following amplification, samples were separated by electrophoresis on a 1% agarose gel stained with SYBR Safe (Invitrogen/Life Technologies, Carlsbad, CA, USA) and visualised under UV light. PCR products were either sequenced by Genomics BioSci & Tech, Taipei, Taiwan or purified using ExoSAP-IT (Invitrogen/Life Technologies, Carlsbad, CA, USA) and sequenced using 10 µl reactions including 7.18 µl of ddH 20, 1.5 µl of reaction buffer, 0.125 µl of bigdye, 1 µl of cleaned PCR product, and 0.32 µl of primer solution (10 mM). Sequencing PCR reactions were carried out with 24 cycles of denaturation at 95˚C for 30 seconds, primer annealing at 50˚C for 20 seconds, primer extension at 60˚C for 4 minutes, followed by incubation at 4˚C. Samples were sent to GenePool at the University of Edinburgh.
Table 2: Primers used in this study.
DNA Region Primer Primer Sequence (5'-3') Source ndhAx1 GCY CAA TCW ATT AGT TAT GAA ATA CC (Shaw et al., 2007) ndhA intron ndhAx2 GGT TGA CGC CAM ARA TTC CA (Shaw et al., 2007) rpl32-R CCA ATA TCC CTT YYT TTT CCA A (Shaw et al., 2007) ndhF GAA AGG TAT KAT CCA YGM ATA TT (Shaw et al., 2007) ndh F-rpl 32 Beg1-F TGG ATG TGA AAG ACA TAT TTT GCT (Thomas et al., 2011) Beg2-R TTT GAA AAG GGT CAG TTA ATA ACA A (Thomas et al., 2011) trnL CTG CTT CCT AAG AGC AGC GT (Shaw et al., 2007) rpl 32-trn L rpl32-F CAG TTC CAA AA A AAC GTA CTT C (Shaw et al., 2007)
6.3 Alignment Newly created sequences in the Neotropical Begonia dataset were edited using GeneiousPro v6.1.5 (Biomatters, 2013) and aligned using ClustalW algorithms (Sievers et al., 2011) implemented in BioEdit v7.2.0 (Hall, 1999) with the default settings applied. Aligned sequences were then combined with an aligned matrix of previously-produced sequences and the two matrices were manually aligned Materials and Methods 39 in BioEdit . Gaps were automatically coded in SeqState (Müller, 2004) based upon the simple coding method described in Simmons and Ochoterena (2000). Gap characters referring to regions of highly variable length such as homopolymeric repeats were excluded. Inversions were reverse-complimented and their presence or absence was manually coded as a binary character. This method retains substitutions within inverted regions as informative characters (Borsch and Quandt, 2009; Graham and Reeves, 2000; Löhne and Borsch, 2005) while minimising the affect of each inversion upon branch length. This is of particular importance when producing dated phylogenies as branch length is a major determinant of calculated node ages.
6.4 Phylogenetic Analyses Phylogenetic analyses were carried out using Bayesian Inference methodologies implemented in MrBayes v.3.2.1 x86 (Huelsenbeck and Ronquist, 2001; Ronquist and Huelsenbeck, 2003) with computation carried out on the Oslo Bioportal (Kumar et al., 2009). Data was split into four partitions comprising the three cpDNA regions and one of binary indel and inversion data. Models of molecular evolution for each cpDNA partition were determined using jModelTest v.2.1.4 (Guindon and Gascuel, 2003; Darriba et al., 2012) upon a maximum likelihood topology. Eleven models and four substitution schemes were compared using the Akaike Information Criterion (AIC). The results of the AIC analysis was compared with those from a version of the AIC corrected for small sample sizes (AICc), resulting in selection of the same model for each partition. A GTR+G+I model was applied to the ndh A intron, a GTR+G model was applied to the ndh F-rpl 32 and rpl 32-trn L regions, and a Jukes- Cantor model was applied to the binary data. Two runs of four independent Metropolis-coupled Markov Chain Monte Carlo (MCMC) analyses incorporating one cold and three incrementally heated Markov chains were run per search. Four searches were carried out for 5 x 10 6 generations each with two independent runs sampled every 10 000 generations. Time series plots were analysed in TRACER v1.5 (Rambaut and Drummond, 2013) for all parameters to ensure effective sample size and convergence of parameters between runs. Trees were combined and summarised in a majority rule consensus tree in MrBayes with the burnin set at 750 000 generations.
6.5 Bayesian Divergence Age Estimation
6.5.1 Secondary Calibration The ideal method of dating a phylogeny is through applying calibration dates derived from fossils to a number of nodes throughout the tree; however, this is impossible in the Begoniaceae as the only known fossil from the family is too young to provide a useful calibration point (Stults and Axsmith, 2011). A number of previous authors have calibrated Begonia phylogenies through designating island emergence dates as the maximum date of clades confined to those islands (Plana, 2003; Plana et al., 2004); however, this method lacks independence from the geo-temporal context being investigated so produces a circular argument (Rutschmann, 2006). A further method involves producing dated Materials and Methods 40
phylogenies encompassing the wider Cucurbitales and Fagales and thus families with a more complete fossil record to estimate the stem and crown ages of Begonia , which is then secondarily applied to Begonia-specific analyses (Goodall-Copestake et al., 2009; Thomas et al., 2012). Secondary calibration suffers from problems caused by the amplification of any errors and uncertainty within the original analysis (Rutschmann, 2006) but is unavoidable in this case. The age of the Begonia crown group was estimated at 24 Ma (+/- 3.57) (Thomas et al., 2012).
6.5.2 Bayesian Divergence Time Estimation Bayesian divergence time estimation was carried out with an uncorrelated relaxed lognormal clock in BEAST v1.7.5 (Drummond et al., 2012). Two separate analyses were run with identical parameters to determine the affect of missing data upon divergence time estimates, one including all taxa and one excluding taxa with missing regions. Replicate accessions were removed from both analyses to reduce their impact upon ancestral state reconstruction. Data was run in a single partition as multiple partitions over-complicated the analysis, causing aberrant dates. The model of sequence evolution was determined using JModelTest v.2.1.4 (Guindon and Gascuel, 2003; Darriba et al., 2012) under the Akaike Information Criterion. The results of the AIC analysis were compared with a version of the AIC corrected for small sample sizes (AICc), resulting in selection of the same model. The general- time reversible model of DNA sequence evolution was selected with among-site variation modelled with a gamma distribution and a proportion of invariable sites (GTR+Γ+I). Birth-death incomplete sampling was selected as a tree prior. Two searches comprising two MCMC chains were run for 5 x 10 7 generations and sampled every 10 000 generations. Time series plots were analysed in TRACER (Rambaut and Drummond, 2013) for all parameters to ensure adequate sample size and convergence of parameters between runs. Trees were combined in LogCombiner v1.7.5 (Drummond et al., 2012) with the burnin set at 500 000 generations and summarised into a maximum clade credibility (MCC) cladogram in TreeAnnotator v1.7.5 (Drummond et al., 2012).
6.6 Ancestral Area Reconstruction
6.6.1 Area Delimitation Nine areas were delimited and considered in this analysis based upon their ecology, geographic and geological histories, areas of Begonia endemism, and previous analyses of taxa with similar Neotropical distributions (e.g. Rubiaceae [Antonelli et al., 2009]; Bromeliaceae [Givnish et al., 2011]; Gesneriaceae [Perret et al., 2013]): 1) Africa and the Socotran Archipelago, 2) Asia, 3) the West Indies, including the Greater and Lesser Antilles, 4) Central America north of the Nicaragua depression, 5) southern Central America, 6) the Andes north of the Huancabamba depression, 7) the central Andes, 8) southeast South America, including the Mata Atlantica (Figure 5). Materials and Methods 41
6.6.2 Area Coding Species ranges were coded using a combination of Global Biodiversity Information Facility (GBIF) data, protologues, types, checklists, floras, and monograph records (Table 3). GBIF data was downloaded for all Neotropical Begonia and combined into a single dataset totalling 22 374 records. Data was visualised in DIVA-GIS v7.5.0.0 (Hijmans et al., 2001) and coordinates were removed from any records occurring outside the Neotropics. Names were checked for spelling and synonymy against The Plant List (Anon, 2010) to ensure records conformed to correct and accepted names. Names of species included in the biogeographic analyses were further checked against literature records (Table 3). The data included 9 834 records of species included in the biogeographic analyses of which 5 030 included latitude and longitude records and 2 008 text descriptions of collection locality from which latitude-longitude could be estimated using Google Earth (Google Inc, 2013), resulting in 7 358 georeferenced records. Species distributions were visualised in DIVA-GIS and compared to literature records for incongruities. Individual incongruous GBIF records were scrutinised and where possible voucher specimen images were viewed to check determinations. Where unverifiable datapoints occurred outside the expected range, literature records were searched for possible reasons for the incongruity such as misapplied names, introductions, and newly discovered populations and data was included or excluded accordingly. Distributions were coded by the range detailed in the literature plus any extensions indicated by the GBIF data. Where only flora or GBIF records were available, species were coded according to the available data; unidentified accessions and species with no available GBIF and literature records were coded by their collection locality.
Table 3: Literature and online resources describing distributions of Neotropical Begonia .
Reference Title Geographic Coverage Catalogue of Seed Plants of the West Acevedo-Rodriguez and Strong, 2012 The West Indies Indies Blanca & Monsalve, 2006 Endemic Begoniaceae of Peru Peru Burt-Utley, 2001 Flora Novo-Galiciana Western Mexico Burt-Utley, 2012 Flora Mesoamerica Southern Mexico to Southern Panama Golding & Wasshausen, 2002 Begoniaceae Worldwide Jimenez & Schubert, 1997 Flora de Veracruz Mexico (Veracruz) Catalogue of the Vascular Plants of Jorgensen & Leon-Yanez, 1999 Ecuador Ecuador A revision of Central American K. Burt-Utley, 1985 Central America Species of Begonia Section Gireoudia Lindemann and Wasshausen, 1997 Checklist of the Plants of the Guianas Guyana, Surinam, French Guiana Venezuela (Amazonas, Bolivar, Delta Lindemann, Steyermark, & Checklist of the Plants of the Guiana Amacuro), Guyana, Surinam, French Wasshausen, 2007 Shield Guiana Catalogo de Plantas e Fungos dos Machado, 2010 Brazil Brazil Materials and Methods 42
Sierra Calzado, 2000 Flora de Cuba Cuba Revision de la Espicies Argentinas del Smith & Schubert, 1941a Argentina Genero Begonia Smith & Wasshausen, 1986 Flora of Ecuador Ecuador Smith & Wasshausen, 1989 Flora de Venezuela Venezuela Smith and Schubert, 1941 Flora of Peru Peru Smith and Schubert, 1946c; Smith and Schubert, 1946b; Smith and Schubert, The Begoniaceae of Colombia Colombia 1946a Smith and Schubert, 1961 Flora of Guatemala Guatemala, Belize Smith, Wasshausen, Golding, & Begoniaceae Worldwide Karegeannes, 1986 Stevens et al., 2001 Flora de Nicaragua Nicaragua Venezuela (Amazonias, Bolivar, Steyermark, 1997 Flora of the Venezuelan Guayana Amacuro, Delta) Begonias: Cultivation, Identification, Tebbitt, 2005 Worldwide and Natural History Tropicos, 2013 Bolivia Checklist Bolivia Catálogo de las Angiospermas y Zarucchi & Wasshausen, 1994 Peru Gymnospermas del Perú Catalogo de las Plantas Vasculares del Paraguay, Uruguay, Argentina, Chile, Zuloaga, Morrone, & Belgrano, 2009 Cono Sur Southern Brazil
6.6.3 Ancestral Area Reconstructions Ancestral ranges were reconstructed using three methods: a likelihood approach to the dispersal- extinction cladogenesis (DEC) model, a Bayesian approach to dispersal-vicariance analysis (Bayes- DIVA), and a Bayesian Binary model (BBM), all implemented in RASP v2.1beta (Yu et al., 2011). Ancestral ranges were constrained to two regions in all three analyses, reflecting the fact all modern species included in the analysis except Begonia glabra Aubl. are confined to one or two regions. Both the S-DIVA and DEC analyses were run on the 9 000 post-burnin trees from the BEAST analysis with the MCC tree used as the input tree. No dispersal constraints were included and the probability of dispersal between all areas was modelled as equal in the DEC analysis. The BBM analysis was run on the MCC tree from the BEAST analysis with all settings as default.
6.7 Diversification Rate Estimates Diversification rates were estimated for four Neotropical clades, African Begonia , Asian Begonia and the entirety of Neotropical Begonia assuming an equal rate of random diversification Yule model calculated as SR = ( ln n 1 - ln n 0)/ t where t is median time estimate of the clade (Ma), n1 is extant
species diversity, and n2 is initial species diversity, here taken as 1. Estimates of extant Asian, African, and Neotropical extant diversity were taken from Goodall-Copestake et al (2010). Species complements of individual clades were estimated by the number of sections that could be Materials and Methods 43 unambiguously attributed to each clade and the number of species per section (Doorenbos et al., 1998; Burt-Utley and Utley, 2011).
Results 44
7 Results
7.1 Phylogenetics of Neotropical Begonia The majority rule consensus tree produced in MrBayes is shown in Figure 4. Neotropical and Asian species form three well-supported clades within an African grade; however, the rooting of this grade or clade is uncertain due to the lack of a non-Begonia outgroup and the low support values found within basal Begonia clades by previous authors (Plana et al., 2004; Goodall-Copestake et al., 2009; Goodall-Copestake et al., 2010). The monophyly of clade A is well supported (PP: 1) including all Neotropical, Socotran, and Asian sections and all species of the seasonally-dry adapted African sections Augustia and Rostrobegonia . Clade A consists of two well supported sister groups: Clade B (PP: 1), containing SDA African Clade 1 and Neotropical Clade 1 (NC1); and Clade C (PP: 1), containing Asian Clade and Clade D (PP: 1). Within Clade B, SDA Clade 1 (PP: 1) and NC1 (PP: 1) form well supported sister groups. SDA Clade 1 contains Begonia engleri Gilg. and Begonia johnstonii Oliv. ex Hook.f. of section Rostrobegonia . Within NC1, the long stem branch length of clade 33 (PP: 1) suggests a degree of rate acceleration occurred within the clade's ancestry. Clade C (PP: 1) includes the Asian Clade (PP: 1) and Clade D (PP: 1) as well supported sister groups. Clade D includes the sister groups SDA Clade 2 (PP: 1) and Neotropical Clade 2 (NC2) (PP: 1). SDA Clade 2 includes Begonia dregei Otto & Diedr., Begonia sutherlandii Hook.f., and Begonia richardsoniana Houllet of section Augustia . Within NC2, a clade comprising an Andean lineage (Clade 177, PP: 1) is resolved as sister to a clade containing the remainder of NC2 (Clade 185, PP: 0.92). Clade 185 contains two lineages, the first of which includes West Indian and Andean species nested within a southeast South American grade (Clade 186, PP: 1). The basal-most lineages of this clade remain unresolved and the long branches of one clade 196 suggests a degree of rate acceleration. This clade is sister to a northern Andean horn-fruited species and a Central American clade (Clade 211, PP: 0.99).
The majority of Neotropical sections are placed exclusively within NC1 or NC2. All included species of sections Trachelocarpus (clade 193, PP: 1) and Solananthera (clade 190, PP: 1) form monophyletic clades and the sole included species of sections Casparya , Doratometra , and Quadriperigonia sit outside other sections on long branches. All species of section Gireoudia are included within clade 212 (PP: 0.99) with all species of Weilbachia nested within. Similarly, all species of sections Cyathocnemis , Hydristyles , Lepsia , and two species of Ruizopavonia are nested within a paraphyletic section Begonia (clade 196, PP: 1). Of the 33 sampled species of sections Pritzelia , 28 are placed within a single clade 33 (PP: 1) with all species of sections Wagneria , Donaldia , and Tetrachia nested within. The remaining five species are placed throughout both NC1 and NC2. Sections Knesebeckia , Gaerdtia , and Ruizopavonia are also resolved as polyphyletic throughout NC1 and NC2. Results 45
7.2 Molecular Age Estimates The maximum clade credibility phylogenies produced by BEAST of all taxa (Figure 5) and all taxa with all three regions include no well-supported incongruence compared either to the majority rule consensus tree produced in MrBayes (Figure 4) or each other. The major clades (clades A-D, NC1, NC2) show the same topology although there are minor, poorly-supported topological differences within clades. Divergence age estimates from the analysis of all taxa are given in Table 5 and estimates of ages of selected clades from both analyses are compared in Table 4.
Table 4: Comparison of Bayesian Posterior Probability node support and BEAST date estimates between analyses containing all data and analyses with missing data removed.
Analysis of Taxa with Missing Analysis of All Taxa Node Data Removed Number Bayesian Posterior Mean Divergence Bayesian Posterior Mean Divergence Probability (PP) Age (95% HDP) Ma Probability (PP) Age (95% HDP) Ma 1 1.00 22.34 (14.95-29.44) 1.00 22.23 (14.73-29.3) 2 0.81 19.53 (12.24-26.42) 0.83 19.04 (12.05-26.31) 23 1.00 16.93 (10.66-23.3) 1.00 16.98 (10.88-23.73) 25 1.00 14.46 (8.95-20.11) 1.00 14.49 (9.2-20.56) 26 1.00 5.64 (2.64-9.08) 1.00 6.55 (3.09-11.15) 33 1.00 9.94 (6.26-14.02) 1.00 9.69 (5.82-13.59) 34 1.00 8.18 (4.92-11.7) 1.00 7.91 (4.67-11.39) 48 0.65 9.4 (5.9-13.23) 0.63 9.21 (5.59-13.06) 71 1.00 16.78 (10.62-22.99) 1.00 16.81 (10.51-23.36) 72 1.00 13.34 (8.43-18.67) 1.00 13.45 (8.26-18.9) 123 1.00 5.21 (2.92-7.62) 1.00 5.15 (3-7.69) 173 1.00 13.67 (8.69-18.94) 1.00 13.79 (8.5-19.32) 174 1.00 6.73 (2.68-12.05) 1.00 6.81 (2.46-12.21) 176 1.00 12.46 (7.87-17.24) 1.00 12.55 (7.85-17.79) 186 0.85 10.8 (6.9-15.2) 1.00 11.03 (6.7-15.57) 203 0.84 4.79 (2.9-7.03) 0.99 4.81 (2.82-7.09) 212 0.98 9.48 (5.82-13.55) 1.00 9.75 (5.7-14.05) 231 0.61 5.76 (3.47-8.2) 0.97 5.57 (3.24-8.11)
7.3 Ancestral Area Reconstructions The results of range reconstructions under the DEC model, by Bayes-DIVA, and the BBM analysis are presented in Table 5 and the optimal reconstructions under the BBM analysis are presented in Figure 5. Reconstructions under the DEC model and Bayes-DIVA were largely congruent; however, both tended to reconstruct numerous equally-parsimonious or almost equally-parsimonious ancestral reconstructions towards the base of the tree leading to difficulty interpreting hypotheses. A large number of node reconstructions encompassed the maximum of two regions, which was deemed Results 46 unlikely due to the scarcity of widespread Begonia species. This tendency led to both analyses supporting vicariance hypotheses at times and places where such scenarios are unrealistic; for example, vicariance between Africa and Asia in the Miocene (S-DIVA analysis node 71; DEC analysis node 74). Reconstruction under the BBM analysis, which lacks a geographic model, produced many fewer ambiguous or multiple-region reconstructions encompassing more temporally- and geographically-plausible scenarios. The results and discussion presented below are based upon the BBM analysis except where stated otherwise.
Africa is reconstructed as the most likely ancestral area for Clade B (node 23) while southeast South America is reconstructed as the most likely ancestral area for NC1 (node 25) and the majority of internal nodes. Within NC1, a single dispersal to the southern Andes (between node 28 and Begonia leathermaniae O'Reilly & Kareg.) and two dispersals to the northern Andes (between node 36 and B. sp. Venezuela; between node 36 and 37) are supported. Two dispersals from the northern Andes to southern Central America (between node 39 and Begonia ulmifolia Willd.; Begonia guaduensis Kunth) are supported. The widespread species Begonia glabra occurs throughout the Neotropics except in southeast South America but is reconstructed as of southeast South American ancestry.
Africa is reconstructed as the probable ancestral area for clade C (node 71) with a single dispersal to Asia preceding the diversification of the Asian clade (between nodes 71 and 72). The MRCA of clade D is reconstructed as African with a single dispersal to the Neotropics (between node 173 and 176). Reconstructions of the ancestral range of NC2 suggest the northern Andes are the most likely ancestral area (BBM, PP[A]: 0.42; DEC, PP[AF]: 0.84; S-DIVA, PP[F]: 1.00); however, support values are relatively low. An Andean sub-clade (clade 177) contains northern and southern Andean species and is reconstructed as having either northern Andean ancestry (S-DIVA, PP[F]: 0.95) or widespread Andean ancestry (BBM, PP[FG]: 0.50; DEC PP[FG]: 0.51). A second sub-clade (clade 186) is reconstructed with southeast South American (BBM, PP[H]: 0.95; S-DIVA, PP[H]: 0.75) or southeast South American and Northern Andean ancestry (DEC, PP[FH]: 1.00). This reconstruction necessitates a dispersal or vicariance between the Andes and southeast South America. Within clade 186, clade 200 includes Andean and West Indian species. Reconstructions at this node are equivocal with the BBM reconstruction suggesting West Indian (PP[C]: 0.32), southeast South American (PP[E]: 0.28), or north Andean (PP[F]: 0.28), the S-DIVA reconstruction suggests a disjunct West Indian and north Andean distribution (PP[CF]: 0.99), and the DEC analysis suggesting either a disjunct north Andean and south Andean (PP[FG]: 0.54) or West Indian (PP[FC]: 0.46) distribution. All analyses require multiple dispersal, vicariance, and extinction events or a combination to explain modern distributions within this clade. A final sub-clade of NC2 (clade 211) contains a north Andean species as sister to a northern Central American radiation. The BBM reconstruction suggests Central America (PP[D]: 0.47) or the north Andes (PP[F]: 0.40) are the most likely range of the MRCA whereas the S-DIVA and DEC analyses suggests a disjunct north Andean and central American range Results 47 is most likely (PP[DF]: 1.00). Within the Central American radiation, a number of dispersals to southern Central America are reconstructed under all analyses.
Table 5: Bayesian Posterior Probabilities, divergence time estimates, and ancestral range reconstructions for nodes as defined in Figure 5. Regions are coded as follows: A, Africa; B, Asia; C, the West Indies; D, northern Central American; E, southern Central America; F, the northern Andes; G, the Southern Andes; H, southeast South America.
Node Bayesian Mean Bayesian Binary S-DIVA DEC Ancestral Number Posterior Divergence Method Ancestral Ancestral Range Probability Age (95% Range Range Reconstruction (PP) HDP) Ma Reconstruction Reconstruction 22.34 (14.95- HA: 0.54, A: 0.24, 1 1.00 A: 0.99 A: 0.89, HA: 0.11 29.44) BA: 0.15, AF: 0.08 19.53 (12.24- 2 0.81 A: 1.00 A: 1.00 A: 1.00 26.42) 18.34 (11.57- 3 0.79 A: 1.00 A: 1.00 A: 1.00 25.07) 9.87 (5.41- 4 1.00 A: 1.00 A: 1.00 A: 1.00 15.17) 7.03 (3.63- 5 1.00 A: 1.00 A: 1.00 A: 1.00 11.47) 3.88 (1.64- 6 1.00 A: 1.00 A: 1.00 A: 1.00 6.83) 17.26 (10.54- 7 0.43 A: 1.00 A: 1.00 A: 1.00 24.04) 9.12 (4.63- 8 1.00 A: 1.00 A: 1.00 A: 1.00 14.33) 1.49 (0.42- 9 1.00 A: 1.00 A: 1.00 A: 1.00 3.05) 0.54 (0.01- 10 0.67 A: 1.00 A: 1.00 A: 1.00 1.54) 11.84 (7.18- 11 1.00 A: 1.00 A: 1.00 A: 1.00 17.21) 10.13 (5.6- 12 0.44 A: 1.00 A: 1.00 A: 1.00 15.34) 1.72 (0.36- 13 1.00 A: 1.00 A: 1.00 A: 1.00 4.09) 6.52 (3.23- 14 1.00 A: 1.00 A: 1.00 A: 1.00 10.89) 15 1.00 0.35 (0-1.15) A: 1.00 A: 1.00 A: 1.00 9.07 (5.19- 16 1.00 A: 1.00 A: 1.00 A: 1.00 13.57) 17 1.00 3.66 (1.49- A: 1.00 A: 1.00 A: 1.00 Results 48
6.43) 1.21 (0.32- 18 1.00 A: 1.00 A: 1.00 A: 1.00 2.48) 3.73 (1.83- 19 1.00 A: 1.00 A: 1.00 A: 1.00 6.27) 0.44 (0.04- 20 1.00 A: 1.00 A: 1.00 A: 1.00 1.15) 3.15 (1.42- 21 0.42 A: 1.00 A: 1.00 A: 1.00 5.38) 20.73 (13.28- A: 0.95, AH: 0.01, H, AH: 0.55, A: 0.22, 22 1.00 A: 1.00 27.92) 0.01, AB: 0.01, B: 0.01 AB: 0.15, AF: 0.08 16.93 (10.66- A: 0.91, AH: 0.05, H, 23 1.00 HA: 1.00 HA: 1.00 23.3) 0.04 24 1.00 4.7 (2-8.34) A: 1.00 A: 1.00 A: 1.00 14.46 (8.95- H: 0.96, AH: 0.03, A, 25 1.00 H: 1.00 H: 1.00 20.11) 0.01 5.64 (2.64- 26 1.00 H: 0.99, GH: 0.01 H: 1.00 H: 1.00 9.08) 4.64 (1.89- 27 0.72 H: 0.96, GH: 0.03 H: 1.00 H: 0.87, GH: 0.13 7.71) 1.08 (0.15- H: 0.86, GH: 0.11, G, 28 1.00 GH: 1.00 GH: 1.00 2.96) 0.03 2.61 (1.35- 袐 29 1.00 H: 1.00 H: 1.00 H: 1.00 4.44) 1.57 (0.37- 30 0.77 H: 1.00 H: 1.00 H: 1.00 3.2) 1.49 (0.62- 31 1.00 H: 1.00 H: 1.00 H: 1.00 2.59) 1.09 (0.4- 32 0.98 H: 1.00 H: 1.00 H: 1.00 2.05) 9.94 (6.26- 33 1.00 H: 0.98, FH: 0.01 H: 1.00 H: 0.83, HF: 0.17 14.02) 8.18 (4.92- 34 1.00 H: 0.95, FH: 0.04 H: 1.00 H: 0.54, HF: 0.46 11.7) 5.33 (2.61- 35 1.00 H: 0.93, FH: 0.04, F, 0.02 HF: 1.00 HF: 1.00 8.46) 6.06 (3.5- H: 0.93, FH: 0.03, EH, HF: 0.57, HE: 0.29, 36 1.00 HF: 1.00 8.99) 0.01, F: 0.01 F: 0.14 F: 0.5, E: 0.22, EF, 0.18, EF: 0.49, F: 0.4, E: 37 1.00 3.11 (1.59- H: 0.04, FH: 0.04, EH: F: 1.00 0.11 5.06) 0.02 0.59 (0.12- 38 1.00 EF: 0.52, F: 0.45, E, 0.03 F: 1.00 EF: 0.62, F: 0.38 1.37) 39 1.00 1.76 (0.72- F: 0.42, E: 0.38, EF, 0.18 EF: 1.00 EF: 1.00 Results 49
3.22) 1.89 (0.96- 40 1.00 H: 1.00 H: 1.00 H: 0.69, HF: 0.31 3.11) 1.19 (0.42- 41 0.99 H: 1.00 H: 1.00 H: 1.00 2.2) 1.48 (0.71- 42 0.92 H: 1.00 H: 1.00 H: 0.69, HF: 0.31 2.47) H: 0.93, HC: 0.01, H: 0.61, HF: 0.3, 43 1.00 0.98 (0.43- H: 1.00 HG: 0.01, HF: 0.01, HE: 0.09 1.66) HE: 0.01, HD: 0.01 0.67 (0.25- 44 0.98 H: 1.00 H: 1.00 H: 1.00 1.22) 0.47 (0.17- 45 0.99 H: 1.00 H: 1.00 H: 1.00 0.93) H: 0.75, HC: 0.05, H: 0.52, HF: 0.35, 46 0.51 0.7 (0.24- H: 0.98 HG: 0.05, HF: 0.05, HE: 0.13 1.33) HE: 0.05, HD: 0.05 HG: 0.2, HC: 0.2, H: 0.93, GH: 0.01, FH, HF: 0.49, HE: 0.29, 47 0.39 0.47 (0.07- HF: 0.2, HD: 0.2, 0.01, EH: 0.01, DH: 0.01 HD: 0.22 1.02) HE: 0.2 9.4 (5.9- 48 0.65 H: 1.00 H: 1.00 H: 1.00 13.23) 8.33 (4.82- 49 0.96 H: 1.00 H: 1.00 H: 1.00 12.08) 7.36 (4.09- 50 0.68 H: 1.00 H: 1.00 H: 1.00 11.1) 7.46 (4.52- 51 1.00 H: 1.00 H: 1.00 H: 1.00 10.64) 7.26 (4.46- 52 0.16 H: 1.00 H: 1.00 H: 1.00 10.24) 4.82 (2.54- 53 1.00 H: 1.00 H: 1.00 H: 1.00 7.41) 2.83 (1.16- 54 0.99 H: 1.00 H: 1.00 H: 1.00 4.77) 55 1.00 0.08 (0-0.38) H: 1.00 H: 1.00 H: 1.00 6.83 (4.06- 56 0.67 H: 1.00 H: 1.00 H: 1.00 9.76) 3.19 (1.72- 57 1.00 H: 1.00 H: 1.00 H: 1.00 5.25) 2.92 (1.49- 58 0.32 H: 1.00 H: 1.00 H: 1.00 4.77) 2.55 (1.2- 59 0.53 H: 1.00 H: 1.00 H: 1.00 4.35) 60 1.00 1.62 (0.54- H: 1.00 H: 1.00 H: 1.00 Results 50
3.11) 5.46 (3.09- 61 1.00 H: 1.00 H: 1.00 H: 1.00 7.96) 62 1.00 2.16 (0.84-4) H: 1.00 H: 1.00 H: 1.00 4.06 (2.35- 63 1.00 H: 1.00 H: 1.00 H: 1.00 6.07) 3.41 (1.87- 64 1.00 H: 1.00 H: 1.00 H: 1.00 5.28) 65 0.74 0.07 (0-0.33) H: 1.00 H: 1.00 H: 1.00 2.92 (1.42- 66 1.00 H: 1.00 H: 1.00 H: 1.00 4.61) 3.6 (1.85- 67 0.74 H: 1.00 H: 1.00 H: 1.00 5.51) 1.1 (0.31- 68 0.41 H: 1.00 H: 1.00 H: 1.00 2.23) 2.57 (1.21- 69 1.00 H: 1.00 H: 1.00 H: 1.00 4.34) 0.9 (0.24- 70 1.00 H: 1.00 H: 1.00 H: 1.00 1.94) 16.78 (10.62- A: 0.89, B: 0.04, AB, A: 0.46, BA: 0.37, 71 1.00 BA: 0.89, HB: 0.11 22.99) 0.03, H: 0.01 AF: 0.17 13.34 (8.43- B: 0.89, AB: 0.08, A, 72 1.00 B: 0.88, BA: 0.12 BA: 0.8, B: 0.2 18.67) 0.02 5.09 (2.04- 73 1.00 B: 1.00 B: 1.00 B: 1.00 9.22) 12.96 (8.03- 74 1.00 B: 0.99, AB: 0.01 B: 1.00 BA: 0.8, B: 0.2 17.98) 11.96 (7.55- 75 0.15 B: 1.00 B: 1.00 B: 1.00 16.85) 9.82 (5.73- 76 1.00 B: 1.00 B: 1.00 B: 1.00 14.45) 9.04 (4.92- 77 1.00 B: 1.00 B: 1.00 B: 1.00 13.53) 3.37 (1.56- 78 0.64 B: 1.00 B: 1.00 B: 1.00 5.67) 2.31 (1.02- 79 1.00 B: 1.00 B: 1.00 B: 1.00 4.03) 1.77 (0.71- 80 1.00 B: 1.00 B: 1.00 B: 1.00 3.28) 10.76 (6.69- 81 0.94 B: 1.00 B: 1.00 B: 1.00 15.14) 9.65 (5.75- 82 1.00 B: 1.00 B: 1.00 B: 1.00 13.55) 83 1.00 9.08 (5.44- B: 1.00 B: 1.00 B: 1.00 Results 51
12.81) 2.13 (0.81- 84 0.89 B: 1.00 B: 1.00 B: 1.00 4.05) 7.57 (4.56- 85 1.00 B: 1.00 B: 1.00 B: 1.00 10.87) 5.92 (3.45- 86 1.00 B: 1.00 B: 1.00 B: 1.00 8.73) 4.43 (2.44- 87 1.00 B: 1.00 B: 1.00 B: 1.00 6.81) 3.66 (1.82- 88 1.00 B: 1.00 B: 1.00 B: 1.00 5.76) 6.06 (3.55- 89 0.93 B: 1.00 B: 1.00 B: 1.00 8.93) 4.34 (2.64- 90 1.00 B: 1.00 B: 1.00 B: 1.00 6.44) 3.71 (1.96- 91 1.00 B: 1.00 B: 1.00 B: 1.00 5.63) 1.67 (0.75- 92 0.93 B: 1.00 B: 1.00 B: 1.00 2.87) 1.02 (0.36- 93 1.00 B: 1.00 B: 1.00 B: 1.00 1.96) 3.8 (2.25- 94 0.98 B: 1.00 B: 1.00 B: 1.00 5.64) 1.09 (0.36- 95 0.93 B: 1.00 B: 1.00 B: 1.00 2.2) 0.39 (0.08- 96 1.00 B: 1.00 B: 1.00 B: 1.00 0.94) 97 1.00 3.47 (2-5.13) B: 1.00 B: 1.00 B: 1.00 3.13 (1.81- 98 0.98 B: 1.00 B: 1.00 B: 1.00 4.75) 2.52 (1.31- 99 0.94 B: 1.00 B: 1.00 B: 1.00 3.91) 0.94 (0.38- 100 1.00 B: 1.00 B: 1.00 B: 1.00 1.78) 0.41 (0.08- 101 1.00 B: 1.00 B: 1.00 B: 1.00 0.89) 0.23 (0.04- 102 1.00 B: 1.00 B: 1.00 B: 1.00 0.57) 2.33 (1.19- 103 0.50 B: 1.00 B: 1.00 B: 1.00 3.67) 1.42 (0.58- 104 1.00 B: 1.00 B: 1.00 B: 1.00 2.63) 1.31 (0.61- 105 1.00 B: 1.00 B: 1.00 B: 1.00 2.25) Results 52
1.14 (0.53- 106 1.00 B: 1.00 B: 1.00 B: 1.00 2.05) 0.69 (0.23- 107 0.29 B: 1.00 B: 1.00 B: 1.00 1.37) 12.82 (8.14- 108 1.00 B: 0.98, AB: 0.02 B: 1.00 BA: 0.8, B: 0.2 18.1) 10.89 (6.22- 109 0.37 B: 0.95, AB: 0.05 BA: 1.00 BA: 1.00 15.97) 1.54 (0.48- A: 0.84, AB: 0.11, B, 110 1.00 A: 1.00 A: 1.00 3.1) 0.05 10.53 (6.05- 111 1.00 B: 0.99, AB: 0.01 B: 1.00 B: 1.00 14.87) 3.19 (1.15- 112 1.00 B: 0.99 B: 1.00 B: 1.00 5.97) 9.17 (5.45- 113 1.00 B: 1.00 B: 1.00 B: 1.00 13.22) 8.48 (4.99- 114 1.00 B: 1.00 B: 1.00 B: 1.00 12.24) 4.61 (2.53- 115 0.91 B: 1.00 B: 1.00 B: 1.00 7.3) 3.47 (1.72- 116 1.00 B: 1.00 B: 1.00 B: 1.00 5.63) 2.78 (1.2- 117 1.00 B: 1.00 B: 1.00 B: 1.00 4.69) 8.22 (4.81- 118 0.99 B: 1.00 B: 1.00 B: 1.00 11.75) 5.19 (2.68- 119 0.27 B: 1.00 B: 1.00 B: 1.00 8.01) 4.69 (2.46- 120 1.00 B: 1.00 B: 1.00 B: 1.00 7.39) 1.66 (0.62- 121 0.36 B: 1.00 B: 1.00 B: 1.00 3.05) 0.26 (0.02- 122 1.00 B: 1.00 B: 1.00 B: 1.00 0.73) 5.21 (2.92- 123 1.00 B: 1.00 B: 1.00 B: 1.00 7.62) 2.75 (1.37- 124 1.00 B: 1.00 B: 1.00 B: 1.00 4.79) 2.07 (0.92- 125 1.00 B: 1.00 B: 1.00 B: 1.00 3.71) 1.3 (0.44- 126 0.94 B: 1.00 B: 1.00 B: 1.00 2.54) 4.14 (2.43- 127 0.90 B: 1.00 B: 1.00 B: 1.00 6.01) Results 53
2.25 (1.16- 128 1.00 B: 1.00 B: 1.00 B: 1.00 3.56) 1.52 (0.7- 129 1.00 B: 1.00 B: 1.00 B: 1.00 2.58) 0.78 (0.26- 130 1.00 B: 1.00 B: 1.00 B: 1.00 1.57) 1.74 (0.85- 131 1.00 B: 1.00 B: 1.00 B: 1.00 2.94) 0.91 (0.28- 132 0.98 B: 1.00 B: 1.00 B: 1.00 1.77) 0.22 (0.02- 133 1.00 B: 1.00 B: 1.00 B: 1.00 0.61) 134 1.00 0.07 (0-0.29) B: 1.00 B: 1.00 B: 1.00 3.77 (2.23- 135 0.54 B: 1.00 B: 1.00 B: 1.00 5.41) 3.33 (2.05- 136 0.80 B: 1.00 B: 1.00 B: 1.00 4.85) 2.73 (1.43- 137 0.06 B: 1.00 B: 1.00 B: 1.00 4.28) 0.35 (0.04- 138 0.92 B: 1.00 B: 1.00 B: 1.00 0.88) 3.05 (1.62- 139 1.00 B: 1.00 B: 1.00 B: 1.00 4.64) 140 0.18 1.62 (0.58-3) B: 1.00 B: 1.00 B: 1.00 2.29 (0.91- 141 1.00 B: 1.00 B: 1.00 B: 1.00 3.93) 3.36 (2.07- 142 0.89 B: 1.00 B: 1.00 B: 1.00 4.9) 143 0.17 2.73 (1.5-4.2) B: 1.00 B: 1.00 B: 1.00 0.78 (0.21- 144 0.93 B: 1.00 B: 1.00 B: 1.00 1.54) 1.89 (0.8- 145 1.00 B: 1.00 B: 1.00 B: 1.00 3.21) 1.31 (0.44- 146 1.00 B: 1.00 B: 1.00 B: 1.00 2.49) 3.33 (1.99- 147 0.97 B: 1.00 B: 1.00 B: 1.00 4.81) 2.15 (1.13- 148 0.43 B: 1.00 B: 1.00 B: 1.00 3.29) 1.27 (0.46- 149 1.00 B: 1.00 B: 1.00 B: 1.00 2.3) 150 1.00 0.06 (0-0.31) B: 1.00 B: 1.00 B: 1.00 1.43 (0.71- 151 1.00 B: 1.00 B: 1.00 B: 1.00 2.34) Results 54
0.3 (0.03- 152 1.00 B: 1.00 B: 1.00 B: 1.00 0.82) 0.95 (0.41- 153 1.00 B: 1.00 B: 1.00 B: 1.00 1.62) 0.64 (0.23- 154 1.00 B: 1.00 B: 1.00 B: 1.00 1.19) 0.41 (0.07- 155 1.00 B: 1.00 B: 1.00 B: 1.00 0.88) 2.97 (1.81- 156 0.54 B: 1.00 B: 1.00 B: 1.00 4.38) 0.72 (0.26- 157 0.99 B: 1.00 B: 1.00 B: 1.00 1.35) 0.56 (0.22- 158 1.00 B: 1.00 B: 1.00 B: 1.00 1.11) 0.43 (0.12- 159 0.22 B: 1.00 B: 1.00 B: 1.00 0.9) 2.83 (1.69- 160 0.95 B: 1.00 B: 1.00 B: 1.00 4.09) 1.94 (0.86- 161 0.20 B: 1.00 B: 1.00 B: 1.00 3.26) 162 1.00 2.54 (1.5-3.8) B: 1.00 B: 1.00 B: 1.00 163 0.89 1 (0.35-1.94) B: 1.00 B: 1.00 B: 1.00 2.26 (1.32- 164 1.00 B: 1.00 B: 1.00 B: 1.00 3.41) 2.03 (1.13- 165 0.95 B: 1.00 B: 1.00 B: 1.00 3.15) 1.5 (0.65- 166 0.44 B: 1.00 B: 1.00 B: 1.00 2.52) 1.05 (0.51- 167 1.00 B: 1.00 B: 1.00 B: 1.00 1.74) 0.85 (0.39- 168 1.00 B: 1.00 B: 1.00 B: 1.00 1.42) 0.58 (0.21- 169 0.78 B: 1.00 B: 1.00 B: 1.00 1.07) 0.48 (0.1- 170 0.19 B: 1.00 B: 1.00 B: 1.00 0.93) 0.69 (0.31- 171 0.24 B: 1.00 B: 1.00 B: 1.00 1.27) 172 0.12 0.38 (0.1-0.8) B: 1.00 B: 1.00 B: 1.00 A: 0.9, F: 0.03, G, 0.01, AF: 0.84, HA: 0.1, 173 1.00 13.67 (8.69- AF: 0.01, H: 0.01, AG: AF: 1.00 AD: 0.04, AG: 0.03 18.94) 0.01, B: 0.01 6.73 (2.68- 174 1.00 A: 1.00 A: 1.00 A: 1.00 12.05) Results 55
175 1.00 0.59 (0-1.95) A: 1.00 A: 1.00 A: 1.00 F: 0.42, A: 0.26, G, 0.15, H: 0.05, AF: 0.03, D: F: 0.8, HF: 0.1, HG: 176 1.00 0.02, FG: 0.02, AG: 0.01, 0.03, DG: 0.03, FG: F: 1.00 12.46 (7.87- FH: 0.01, B: 0.01, E: 0.02, HD: 0.01 17.24) 0.01 10.09 (5.98- 177 1.00 FG: 0.5, F: 0.35, G, 0.15 F: 0.95, FG: 0.05 FG: 0.51, F: 0.49 14.54) 8.69 (4.88- 178 1.00 FG: 0.38, G: 0.35, F, 0.26 FG: 1.00 FG: 0.88, G: 0.12 12.54) 3.89 (1.88- 179 0.97 G: 0.89, FG: 0.1, F, 0.01 G: 1.00 G: 1.00 6.32) 1.71 (0.59- 180 1.00 G: 0.98, FG: 0.01 G: 1.00 G: 1.00 3.34) 2.17 (0.8- 181 1.00 G: 0.98, FG: 0.02 G: 1.00 G: 1.00 4.03) 7.64 (4.25- 182 1.00 F: 0.69, FG: 0.24, G, 0.06 F: 0.93, FG: 0.07 FG: 1.00 11.42) 4.87 (2.4- 183 0.77 F: 0.62, FG: 0.26, G, 0.12 FG: 1.00 FG: 1.00 7.67) 3.83 (1.69- 184 1.00 G: 0.97, FG: 0.03 G: 1.00 G: 1.00 6.37) F: 0.4, H: 0.33, D, 0.1, G: 0.05, A: 0.04, FH: 0.03, HF: 0.69, F: 0.24, F: 0.74, HF: 0.16, 185 0.88 11.89 (7.59- C: 0.01, DF: 0.01, E: HD: 0.05, DF: 0.01 DF: 0.1 16.62) 0.01, B: 0.01, DH: 0.01 10.8 (6.9- 186 0.85 H: 0.95, FH: 0.02, F, 0.01 H: 0.75, HF: 0.25 HF: 1.00 15.2) 9.89 (5.97- 187 1.00 H: 0.99 H: 1.00 H: 1.00 14.49) 6.1 (2.53- 188 0.51 H: 1.00 H: 1.00 H: 1.00 10.27) 9.37 (5.36- 189 1.00 H: 1.00 H: 1.00 H: 1.00 13.97) 1.89 (0.81- 190 0.26 H: 0.99 H: 1.00 H: 1.00 3.64) 0.89 (0.11- 191 1.00 H: 1.00 H: 1.00 H: 1.00 2.16) 6.58 (3.11- 192 0.26 H: 1.00 H: 1.00 H: 1.00 10.48) 1.27 (0.4- 193 1.00 H: 1.00 H: 1.00 H: 1.00 2.69) 3.61 (1.14- 194 1.00 H: 1.00 H: 1.00 H: 1.00 7.02) Results 56
0.3 (0.02- 195 1.00 H: 1.00 H: 1.00 H: 1.00 0.94) 8.28 (5.22- H: 0.93, FH: 0.02, CH, 196 1.00 HC: 0.5, HF: 0.5 HF: 1.00 11.77) 0.01, F: 0.01, C: 0.01 1.44 (0.55- 197 1.00 H: 0.99 H: 1.00 H: 1.00 2.56) 1.08 (0.42- 198 1.00 H: 1.00 H: 1.00 H: 1.00 2.01) 0.6 (0.18- 199 0.84 H: 1.00 H: 1.00 H: 1.00 1.23) C: 0.32, H: 0.28, F, 0.28, 5.52 (3.33- CH: 0.03, CF: 0.03, FH: 200 1.00 FC: 0.99, FG: 0.01 FG: 0.54, FC: 0.46 7.99) 0.02, G: 0.01, E: 0.01, B: 0.01 2.64 (1.29- 201 1.00 F: 0.99, FG: 0.01 F: 1.00 F: 0.52, FG: 0.48 4.29) 2.24 (0.99- 202 1.00 F: 0.95, FG: 0.04 F: 1.00 F: 0.51, FG: 0.49 3.75) 4.79 (2.9- 203 0.84 C: 0.97, CG: 0.01 C: 0.98, GC: 0.02 GC: 0.67, C: 0.33 7.03) 4.4 (2.62- C: 0.89, CG: 0.06, G, 204 1.00 GC: 1.00 GC: 1.00 6.56) 0.03 3.23 (1.56- G: 0.96, CG: 0.03, C, 205 0.96 G: 1.00 G: 1.00 5.01) 0.01 0.39 (0.04- 206 1.00 C: 0.99 C: 1.00 C: 1.00 1.02) 3.47 (1.9- 207 1.00 C: 1.00 C: 1.00 C: 1.00 5.29) 1.16 (0.37- 208 1.00 C: 1.00 C: 1.00 C: 1.00 2.26) 1.17 (0.46- 209 1.00 C: 1.00 C: 1.00 C: 1.00 2.13) 0.35 (0.07- 210 1.00 C: 1.00 C: 1.00 C: 1.00 0.83) 10.77 (6.7- D: 0.47, F: 0.4, DF, 0.07, 211 1.00 DF: 1.00 DF: 1.00 15.2) H: 0.02, G: 0.01 9.48 (5.82- 212 0.98 D: 1.00 D: 1.00 D: 1.00 13.55) 9.04 (5.47- 213 0.97 D: 0.99 D: 1.00 D: 1.00 12.8) 6.99 (4.36- 214 0.31 D: 0.99 D: 1.00 D: 1.00 10.07) 215 1.00 3.7 (1.9-6.05) D: 1.00 D: 1.00 D: 1.00 216 1.00 0.94 (0.21- D: 1.00 D: 1.00 D: 1.00 Results 57
2.23) 2.79 (1.17- 217 1.00 D: 1.00 D: 1.00 D: 1.00 4.78) 1.74 (0.78- 218 0.54 D: 1.00 D: 1.00 D: 1.00 2.94) 6.38 (3.86- 219 0.21 D: 0.98, DE: 0.02 D: 1.00 D: 1.00 9.12) 5.52 (3.04- 220 0.97 D: 0.77, DE: 0.22 D: 0.57, DE: 0.43 D: 0.86, DE: 0.14 8.01) DE: 0.71, D: 0.22, E, 221 1.00 DE: 0.53, E: 0.47 DE: 1.00 2.03 (1-3.47) 0.06 2.22 (0.89- 222 1.00 E: 0.9, DE: 0.09 DE: 0.54, E: 0.46 E: 0.66, DE: 0.34 4.14) 1.48 (0.58- 223 0.29 E: 0.94, DE: 0.06 E: 0.6, DE: 0.4 E: 0.56, DE: 0.44 2.41) 1.24 (0.47- 224 0.05 E: 0.89, DE: 0.1, D, 0.01 DE: 1.00 DE: 1.00 2.39) 1.88 (0.89- 225 0.17 D: 0.84, DE: 0.15 D: 1.00 D: 0.51, DE: 0.49 3.17) 0.96 (0.31- D: 0.92, DE: 0.07, E, 226 1.00 DE: 1.00 DE: 1.00 1.84) 0.01 1.34 (0.57- 227 1.00 D: 0.9, DE: 0.1 D: 1.00 D: 1.00 2.37) 0.5 (0.11- 228 0.87 D: 0.99 D: 1.00 D: 1.00 1.11) 0.59 (0.14- D: 0.84, DE: 0.15, DF, 229 1.00 D: 1.00 D: 0.79, DE: 0.21 1.31) 0.01 DE: 0.82, D: 0.17, DF, DE: 0.39, D: 0.26, 230 1.00 D: 1.00 0.24 (0-0.7) 0.01 DEF: 0.26, DF: 0.09 5.76 (3.47- 231 0.61 D: 1.00 D: 1.00 D: 1.00 8.2) 4.57 (2.65- 232 0.97 D: 1.00 D: 1.00 D: 1.00 6.7) 1.36 (0.33- 233 1.00 D: 1.00 D: 1.00 D: 1.00 2.84) 4.04 (2.3- 234 1.00 D: 1.00 D: 1.00 D: 1.00 5.95) 1.41 (0.45- 235 0.99 D: 1.00 D: 1.00 D: 1.00 2.79) 3.56 (1.99- 236 1.00 D: 1.00 D: 1.00 D: 1.00 5.42) 2.16 (1.05- 237 0.98 D: 1.00 D: 1.00 D: 1.00 3.61) 238 1.00 0.67 (0.2- D: 1.00 D: 1.00 D: 1.00 Results 58
1.41) 0.4 (0.05- 239 1.00 D: 1.00 D: 1.00 D: 1.00 0.94) 5.25 (3.11- 240 0.56 D: 1.00 D: 1.00 D: 1.00 7.58) 3.77 (1.98- 241 0.84 D: 1.00 D: 1.00 D: 1.00 5.93) 2.86 (1.4- 242 1.00 D: 1.00 D: 1.00 D: 1.00 4.72) 1.85 (0.75- 243 0.98 D: 1.00 D: 1.00 D: 1.00 3.33) 4.61 (2.73- 244 1.00 D: 1.00 D: 1.00 D: 1.00 6.79) 1.61 (0.5- 245 1.00 D: 0.99, DE: 0.01 D: 1.00 D: 0.84, DE: 0.16 3.25) 0.28 (0.03- 246 1.00 D: 0.92, DE: 0.08 D: 1.00 DE: 0.53, D: 0.47 0.81) 3.61 (2.01- 247 1.00 D: 1.00 D: 1.00 D: 1.00 5.34) 2.9 (1.56- 248 1.00 D: 1.00 D: 1.00 D: 1.00 4.46) 2.39 (1.29- 249 1.00 D: 1.00 D: 1.00 D: 1.00 3.87) 1.86 (0.87- 250 0.96 D: 1.00 D: 1.00 D: 1.00 3.06) 1.37 (0.54- 251 0.88 D: 1.00 D: 1.00 D: 1.00 2.36) 252 0.79 0.18 (0-0.77) D: 1.00 D: 1.00 D: 1.00
7.4 Diversification Rates In order to attribute unsampled species to a clade, species of sections Donaldia , Pritzelia , Scheidweilaria , Tetrachia , and Wagneria were unambiguously attributed to NC1 and species of sections Barya , Begonia , Casparya , Cyathocnemis , Doratometra , Eupetalum , Gireoudia , Hydristyles , Lepsia , Quadriperigonia , Solananthera , Trachelocarpus , Urniformia , and Weilbachia were unambiguously attributed to NC2 as all or over 90% of sampled appeared in their respective clades. Species of sections Gaerdtia and Knesebeckia were not attributed to either clade as species of each appear in both clades whereas species of sections Gobenia A.DC., Parietoplacentalia Ziesenh., Rossmannia (Klotzsch) A.DC., and Trendelbergia (Klotzsch) A.DC. were not attributed as no species were included within the analysis. Species of sections Semibegoniella (C.DC.) Barkley & Baranov and Urniformia Houghton ex Ziesenh. were attributed to NC2 due to its presumed close relationship to section Casparya . This resulted in 144 species assigned to clade NC2 and 274 assigned to NC2, Results 59
both likely to be gross underestimates. We therefore estimated total Neotropical diversification rates based on the total Neotropical species complement and a diversification time estimated by averaging the median crown ages of NC1 and NC2.
Two further Neotropical radiations were deemed well categorised enough to allow accurate estimation of species numbers, the northern Central American radiation (clade 212) and the primarily West Indian radiation (clade 205). All West Indian species of section Begonia and all species of sections Cyathocnemis and Ruizopavonia were attributed to the clade 205 while all species of sections Doratometra , Gireoudia , Quadriperigonia , and Weilbachia were assigned to clade 212. This resulted in estimates of 105 species in clade 212 and 89 species in clade 205. Estimates of diversification rates are presented in Table 6.
Table 6: Estimated diversification rates for selected groups of Begonia . *Median crown age an average of NC1 and NC2.
Estimate of Extant Species Median crown Per-Lineage species diversification Rate Group Complement node age (Ma) Estimate (diversification Ma -1) African Begonia 160 22.34 0.2272 Asian Begonia 650 13.34 0.4855 NC1 144 14.46 0.3437 NC2 286 12.46* 0.4539 Neotropical 690 13.46 0.4856 Begonia Clade 205 117 9.48 0.5023 Clade 212 89 4.79 0.9371
Discussion 62
8 Discussion
8.1 Neotropical Begonia Taxonomy The phylogeny provides a framework for future taxonomic work on Neotropical Begonia , primarily through assessing the delimitation of sections. Although some sections of Neotropical Begonia such as Casparya and Semibegoniella (Doorenbos et al., 1998) are well categorised, others are considered to "shade off each other" and the placement of numerous species is uncertain (Doorenbos et al., 1998).
The close affinity of sections Cyathocnemis , Hydristyles , and Lepsia to section Begonia was noted by Doorenbos et al (1998). The placement of all three nested within Begonia suggests further taxonomic work may result in unification or the sections or the splitting of section Begonia . Current delimitation of section Ruizopavonia appears unnatural, with two species occurring within section Begonia and the remainder associated with section Donaldia . Similarity between the two sections was noted by Doorenbos (1998) but their association with Begonia dichotoma Jacq. of section Pritzelia is unexpected. The majority of section Pritzelia forms a well supported clade within NC1 with all sampled species of sections Wagneria , Scheidweilaria , and Tetrachia nested within. The paraphyly of Pritzelia suggests further investigation of the largest Neotropical section of Begonia is warrented. Similarly, doubt is cast upon the status of sections Gaerdtia and Knesebeckia by their polyphyly and representation in both NC1 and NC2. Knesebeckia is considered a morphologically diverse section with numerous doubtful inclusions (Doorenbos et al., 1998). It is likely its current delimitation contains numerous recognisable natural groups. The placement of Begonia metallica W.G.Smith of section Pritzelia is congruent with earlier hypotheses of its cultivated origin (Golding and Wasshausen, 2002). Clade 177 contains species of Knesebeckia and the poorly categorised sections Eupetalum and Barya . None of these sections forms a well-supported clade, supporting Doorenbos' view that Barya may not be a natural section. However, sampling is poor in this part of the phylogeny making rushing to conclusions unwise. All species of sections Solananthera and Trachelocarpus form well supported clades while the single sampled species of sections Casparya , Doratometra , and Quadriperigonia sit outside other sections on long branches, indicating their sectional status may be natural. All species of section Weilbachia are nested within section Gireoudia . Weilbachia and Gireoudia are and separated by locule number (Burt-Utley, 1985; Doorenbos et al., 1998; Burt-Utley and Utley, 2011). This analysis suggests locule number is homoplasious within the clade and re- evaluation of the sections may be required.
8.2 Ancient hybridisation in Neotropical Begonia ? The cpDNA polyphyly of Neotropical Begonia contrasts with the mtDNA monophyly observed by Goodall-Copestake et al (2010). This discrepancy is unlikely to be a sampling artefact as all species included in Goodall-Copestake's analysis except Begonia piurensis L.B.Sm. & B.G.Schub. were included in this study and support values in both studies are high. The mitochondrial lineage Discussion 63 remaining in Neotropical species is sister to Augustia , a characteristic shared with the NC2 chloroplast lineage suggesting the lineages were introduced together. The fate of the mitochondrial lineage presumably introduced with chloroplast lineage NC1 is unclear but can potentially be explained by hybridisation between lineages and the introgression of the NC2 mitochondrial lineage into NC1. This explanation would require sympatric occurrence of both lineages soon after their arrival in the Americas congruent with southeast South America being the likely ancestral range for NC1 and potentially for NC2. Paternal mitochondrial inheritance is the rule rather the exception in the closely related Cucurbitaceae (Calderon et al., 2012) and if this is the case in Begonia , the phylogenetic incongruence we observe could be present as the result of a single cross.
8.3 Colonisation of the Neotropics The existence of two Neotropical cpDNA lineages, each sister to SDA African groups confirms the results of earlier analyses (Goodall-Copestake et al., 2010) and implies two successful colonisations of the Neotropics from Africa via long-distance dispersal. Both dispersal events are dated in the mid- Miocene, at which point no overland dispersal routes existed between the continents, leaving long- distance dispersal the only feasible explanation.
Ancestral range reconstructions at the deepest nodes of NC1 are well supported while those of NC2 remain equivocal. The MRCA of NC1 is reconstructed as southeast South American with high levels of confidence under all methods. Although all methods reconstruct the northern Andes as the most likely ancestral area of NC2, support for these reconstructions is low. Initial dispersal to the northern Andes seems unlikely considering their position relative to Africa. The northern Andean reconstruction at the base of clade 176 is a product both of taxonomic uncertainty at the base of the clade and the reconstruction of possible northern and southern Andean, Central American, and southeast South American ranges at the bases of clades 177, 186, and 211. We consider a southeast South American introduction most likely despite its low levels of support in range reconstruction analyses. Colonisation of this region would also be necessary to be congruent with the hybridisation hypothesis outlined above.
Westerly dispersal of entire plants across the Atlantic by oceanic currents is deemed plausible and may be common (Renner, 2004). NC1 is sister to section Rostrobegonia whereas NC2 is sister to Augustia , both seasonally-dry adapted African sections including tuberous and fleshy stemmed- species (Doorenbos et al., 1998). It is possible these adaptations may aid survival in transoceanic rafts. An alternative dispersal mechanism is wind-transport of the tiny seeds of Begonia (Renner, 2004). Distinguishing between these mechanisms is impossible but it seems likely both would result in southeast South American arrival to the Neotropics due to its relative vicinity to Africa. Although numerous instances of intercontinental dispersal from Africa to the Neotropics have been identified (Renner, 2004), only a single study has identified the region where colonisers are likely to have first Discussion 64 arrived and diversified within the Americas. We add two instances of intercontinental dispersal from Africa to southeast South America to the single study published of Pagamea Aubl. (Rubiaceae) thus far (Fiaschi and Pirani, 2009).
8.4 West Indian Begonia All sampled West Indian Begonia species are members of section Begonia and resolved within clade 203. Of the 42 native species included within the recent Catalogue of Seed Plants of the West Indies (Acevedo-Rodriguez and Strong, 2012), 40 are placed within section Begonia and thus likely belong within clade 203. West Indian Begonia are nested within a southeast South American clade, implying colonisation of the West Indies from the Mata Atlantica. The stem and crown ages of clade 203 are estimated at 5.52 Ma (3.33-7.99) and 4.79 Ma (2.9-7.03), placing dispersal to the West Indies around the Miocene-Pliocene border. The majority of the Greater and Lesser Antilles were above water by this point (Graham, 2003a). The two Antillean species not belonging to section Begonia are the widespread Begonia glabra and Begonia brachyclada Urban & Ekman of section Knesebeckia , the latter not sampled in this study. Section Knesebeckia is polyphyletic so the taxonomic and geographic affinities of Begonia brachyclada remain unclear.
The West Indian flora is comprised of elements from the surrounding North (Santiago-Valentin and Olmstead, 2004), Central (Jardón-Barbolla et al., 2011), and South (Graham, 2003b) American floras. Dispersal from southeast South America has been observed in multiple groups (Santiago-Valentin and Olmstead, 2004) including at least eight instances in the Lythraceae J.St.-Hil. (Graham, 2003b). Dispersal of Begonia from southeast South America and subsequent diversification throughout the Antillean archipelagos adds to the growing body of evidence for floristic links between the two regions. Authors have attributed biogeographic links between eastern South America and the Antilles to the existence of a GAARlandian land bridge between the two regions (Alonso et al., 2012). The lack of geological support for this scenario and the putative Eocene age of the suggested land bridge (Ali, 2012) indicates the hypothesis fails to explain the recent link between southeast South American and West Indian Begonia . We suggest frequent wind or water dispersal, perhaps linked to unpredictable currents in the Caribbean basin (Iturralde-vinent, 1999), offer a more-likely explanation.
8.5 Dispersal to the Andes The origin and diversification patterns of the tropical Andean flora is of particular interest to biogeographers due to its extreme diversity (Gentry, 1982; Myers et al., 2000) and the recent formation of much of the Andes (Garzione et al., 2008). Rapid diversification rates have been observed in Andean clades (Hughes et al., 2013) but the pattern appears to differ between Andean biomes, with highest diversification rates in young high elevation grasslands and lowest rates in older Discussion 65
STDFs (Pennington et al., 2010); however, biogeographic investigation of mid-elevation forest lineages such as Begonia has been neglected (Hughes et al., 2013).
Multiple colonisations of the Andes by Begonia from various geographic origins and ages are supported in this study, although the geographic origins of some are unclear. The MRCA of NC2 is reconstructed as northern Andean but we believe a southeast South American range is more likely (see 8.2). A southeast South American reconstruction necessitates Miocene colonisation of the Andes between the stem and crown nodes of clade 177 12.46 Ma (7.87-17.24) and 10.09 Ma (5.98-14.54) respectively. Current sparse sampling of this clade has led to the reconstruction of a wide Andean ancestral range for the MRCA of clade 177; however, it is unclear whether increased sampling would result in an alternative reconstruction. Colonisation of the Andes between node 211 and Begonia sp. N Andes is Miocene or younger but the lack of sampling in this clade, which likely also contains the horn-fruited species of sections Casparya (24 species), Semibegoniella (13 species), and Urniformia (1 species), prevents more accurate estimation.
The presence of species of sections Cyathocnemis and Hydristyles in the central Andes appears to be the result of dispersal from the West Indies (between nodes 204 and 205). The majority of species of both sections are northern Andean (Doorenbos et al., 1998), although those sampled here are both southern Andean. A colonisation of the Northern Andes, subsequent diversification, and migration to the southern Andes is the most parsimonious explanation for the distribution of the two sections. Three Pliocene or late-Miocene dispersals from southeast South America to the Andes are supported (between node 35 and Begonia sp. Venezuela; between nodes 34 and 35; between nodes 200 and 201), all to the northern Andes. Pliocene dispersal is concordant with rapid uplift in the northern Andes (Gregory-Wodzicki, 2000), perhaps suggesting successful colonisation of the Andes was facilitated by the formation of new upland habitat suitable for Begonia . A final Andean dispersal into the southern Andes in the Pleistocene is reconstructed (between node 18 and Begonia leathermaniae ) whereas the presence of a single unsampled species of the Mexican section Quadriperigonia (Begonia thyrsoidea Irmscher) in Peru (Doorenbos et al., 1998) suggests a final instance of intercontinental dispersal to the Andes as the section is nested within an exclusively northern Central American clade and has no representatives between Mexico and Peru. The multiple instances of Begonia dispersal into the Andes from southeast South America, the West Indies, and southern Central America typify the diverse origins of the Andean flora as a whole.
Dispersal or migration between the northern and central Andes is supported in both clade 177 and 201, containing northern and central Andean clades. As sections Cyathocnemis and Hydristyles both include northern and central Andean species, this suggests migration between the two regions has occurred within both sections. All Andean clades of Begonia are probably younger than the emersion of the Western Andean Portal ca. 13 Ma (Antonelli et al., 2009) but the large degree of migration Discussion 66
between the central and northern Andes suggests little or no impact of the Huancabamba depression on the range evolution of Begonia .
8.6 Colonisation of Central America Investigation of dispersal patterns within Central America have been neglected in comparison with those of South America. The majority of past studies of Neotropical diversification patterns have treated Central America as a single region (Givnish et al., 2011) or focussed primarily on the direction and timing of floristic exchange between North and South America via Central America (Antonelli et al., 2009). This study provides some insight into biogeography within Central America.
All sampled species found within northern Central America fall within clade 212, which has a crown age of 9.48 Ma (5.82-13.55) and a stem age of 10.77 Ma (6.7-15.2). Range reconstructions of nodes within NC2 deeper than clade 212 are ambiguous; however, the ancestors of clade 211 were probably South American. The MRCA of clade 212 is unambiguously reconstructed as northern Central American in all analyses, hence northern Central America was probably colonised by long distance dispersal in the mid-late Miocene. Migration via southern Central America is unlikely due to the lack of upland habitat in the region in the Miocene (MacMillan et al., 2004); in contrast, extensive upland habitats were present in northern Central America by the mid-Miocene (Gutiérrez-García and Vázquez-Domínguez, 2013). Clade 212 likely contains all species of sections Gireoudia , Weilbachia ,
Quadriperigonia , and Doratometra , totalling ca. 117㎔ species (Doorenbos et al., 1998; Burt-Utley and Utley, 2011) and representing a large late-Miocene to present day radiation. Two accessions of section Knesebeckia are nested in clade 212 ( Begonia incarnata Link & Otto, Begonia aff. incarnata ). Four further species from Knesebeckia are included within Flora Mesoamerica (Burt-Utley, 2012). It is possible these are also nested within clade 212 and may represent one or more independent colonisations of northern Central America. No species of the small Mexican to Guatemalan section Parietoplacentalia were sampled so it is unclear whether they represent a further colonisation. The presence of a single species of the Andean section Eupetalum (Begonia monophylla Pavon ex A.DC.) in Mexico almost certainly indicates a further instance of long-distance dispersal to northern Central America.
Only one macrofossil has been attributed to Begonia : a capsule fossilised in Pliocene complexes in Alabama (Stults and Axsmith, 2011). Although the fossil lacks the morphological characters required for reliable placement within modern-day sections, Stults and Axsmith (2011) suggested it is most likely related to northern Central American Begonia , which has since been extirpated from the region by climate change. This hypothesis is supported by the Miocene age of northern Central American clade 212. However, West Indian Begonia had also begun to diversify in the nearby Antilles by this point, suggesting colonisation from the Caribbean as an alternative explanation that cannot be discounted based upon current evidence. Discussion 67
Although the fossil lacks enough morphological characters for it to be assigned to section, we suggest it is likely a member of clade 212 as this clade had already diversified significantly within northern Central America by the Pliocene.
Five separate colonisations of southern Central America are supported, all within the Pleistocene. Two colonisations, both by individual members of section Ruizopavonia , have northern Andean ancestry ( Begonia guaduensis , Begonia cooperi C.DC.). In total, eight species of section Ruizopavonia are known from southern Central America (Doorenbos et al., 1998). The remainder of section Ruizopavonia is northern Andean, primarily Colombian and Venezuelan, congruent with a northerly migration following the closure of the Isthmus of Panama. Three further colonisations of southern Central America are derived from northern Central American ancestry (clade 221, clade 239, some members of section Gireoudia ) and a single back colonisation of northern Central America is supported ( Begonia stigmosa Lindl.). While substantial upland habitat existed in northern Central America throughout the Miocene, significant uplift and volcanism in southern Central America commenced only during the Pleistocene (MacMillan et al., 2004; Gutiérrez-García and Vázquez- Domínguez, 2013). The Plio-Pleistocene age of sampled southern Central American taxa suggests colonisation of the region commenced shortly following the formation of suitable montane habitat. The single unsampled southern Central American species of the sections Begonia (Begonia tiliifolia C.DC), Scheidweilaria (Begonia parviflora Poepp & Endl.), Casparya (Begonia urticae L.f.) may represent further migrations from northern South America into southern Central America. Given these are within-species, we predict that they are also of Pleistocene. The affinities of the endemic southern Central American section Urniformia , not sampled in this study, remain unclear.
8.7 Diversification rates in Begonia The phylogeny presented here presents the first opportunity to estimate diversification rates within Neotropical Begonia in comparison with African and Asian Begonia . Net diversification rates in Africa were estimated at 0.2272 Ma -1, twice as fast as the mean diversification rate of families and genera across the Angiosperms (Magallón and Castillo, 2009). Net diversification rates in Asian Begonia , (0.4855 Ma -1), individual Neotropical clades (NC1, 0.3437 Ma -1; NC2, 0.4539 Ma -1; clade 203, 0.9371 Ma -1, clade 212, 0.5023 Ma -1), and Neotropical Begonia as a whole (0.4856 Ma -1) were estimated as much faster than those in Africa but an order of magnitude lower than those reported in the most rapid highland (Hughes and Eastwood, 2006), island (Baldwin and Sanderson, 1998), and continental radiations (Valente et al., 2010). Higher net diversification in the Neotropics than Africa has also been reported in the Chrysobalanaceae R.Br., which is also of Paleotropical origins (Bardon and Chamagne, 2013). A disparity in net diversification between groups can either be explained by differences in speciation rates, extinction rates, or a combination of the two. Although our analysis does not permit distinction between these scenarios, we suggest both higher African extinction rates and an increased diversification rate following arrival in newly colonised Neotropical upland habitats Conclusions 68
(sensu Moore and Donoghue, 2007), perhaps in some cases linked to the formation of those habitats, may account for the disparity.
8.8 Niche pre-emption Niche pre-emption is the monopolisation of habitat by radiations within that habitat, preventing closely related species from establishing (Silvertown, 2004). The ecological similarity of the majority of Begonia species suggests niche pre-emption may play a role in the genus' distribution. Thomas et al., (2012) suggested the phenomenon accounts for the presence of multiple west-to-east Begonia dispersals in the Malaysian archipelago but limited back-colonisation. We find some support for niche pre-emption in Neotropical Begonia . Firstly, the distributions of NC1 and NC2 (Figure 3A, 3B) are largely mutually exclusive, suggesting radiation within one clade within a region may have prevented establishment by the other. This is particularly evident in the West Indies and northern Central America, which are only inhabited by members of NC2. A complete lack of dispersal to both regions by NC1 is perhaps unlikely considering the prevalence of dispersal within Begonia found here and elsewhere (de Wilde et al., 2011; Thomas et al., 2012). This pattern is replicated in the Andes, with the central Andes primarily populated by NC2 and only a single species of NC1 ( Begonia leathermaniae ) established at the far south of the Andean range of Begonia . Significant co-occurrence of NC1 and NC2 is only observed in the extreme northeast Andes and southern Central America, which were both colonised by multiple lineages of NC1 and NC2 during the Pliocene and Pleistocene. These areas share a geological history characterised by Pliocene and Pleistocene upland formation (MacMillan et al., 2004; Gregory-Wodzicki, 2000). We suggest the recent formation of significant habitat suitable for Begonia may have mitigated the affects of niche pre-emption, allowing colonisation and radiation of both lineages before either could monopolise niche space.
9 Conclusions The availability of suitable habitat limits the number of dispersal pathways open to taxa. Habitat availability is limited both by its physical presence and also the presence of closely related competitors: niche pre-emption (Silvertown, 2004). The fully-resolved phylogeny of Neotropical Begonia shows that such data provides a plausible scenario for the dispersal history of the genus. Estimated stem and crown ages and the well-supported monophyly of two Neotropical clades imply independent Miocene long-distance dispersals from Africa to southeast South America followed by numerous dispersals to montane Neotropical habitats. The prevalence of dispersal within Begonia is consistent with recent observations from the Paleotropics (de Wilde et al., 2011; Thomas et al., 2012) and does not appear to be affected by the environment between suitable habitats; instead, dispersal over water and unsuitable terrestrial habitats appear equally likely. Diversification within habitats appears to be mediated by habitat availability, with diversification most likely in newly-created or competitor-free habitats. Conclusions 69
Further testing of biogeographical hypotheses requires the construction of species-level phylogenies of individual Neotropical clades, including Andean, West Indian, Central American, and southeast South America radiations. Comparisons between Neotropical and Paleotropical Begonia radiations should shed further light on the dynamic processes of diversification within the Neotropics.
References 70
10 References
Acevedo-Rodriguez, P. & Strong, M.T. , 2012. Catalogue of the Seed Plants of the West Indies. Smithsonian Institution Scholarly Press , 98 : 1–1192.
Ali, J.R. , 2012. Colonizing the Caribbean: is the GAARlandia land-bridge hypothesis gaining a foothold? Journal of Biogeography , 39 (3): 431–433.
Ali, S.S., Yu, Y., Pfosser, M. & Wetschnig, W. , 2012. Inferences of biogeographical histories within subfamily Hyacinthoideae using S-DIVA and Bayesian binary MCMC analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies). Annals of Botany , 109 (1): 95–107.
Alonso, R., Crawford, A.J. & Bermingham, E. , 2012. Molecular phylogeny of an endemic radiation of Cuban toads (Bufonidae: Peltophryne) based on mitochondrial and nuclear genes. Journal of Biogeography , 39 (3): 434–451.
Anon , 2010. The Plant List . http://www.theplantlist.org [Accessed August 1, 2013].
Antonelli, A., Nylander, J.A.A., Persson, C. & Sanmartín, I. , 2009. Tracing the impact of the Andean uplift on Neotropical plant evolution. Proceedings of the National Academy of Sciences , 106 (24): 9749–9754.
Antonelli, A. & Sanmartín, I. , 2011. Why are there so many plant species in the Neotropics? Taxon , 60 (2): 403–414.
Bacon, C.D., Mora, A., Wagner, W.L. & Jaramillo, C., 2013. Testing geological models of evolution of the Isthmus of Panama in a phylogenetic framework. Botanical Journal of the Linnean Society , 171 (1): 287–300.
Badcock, Z. , 1998. A Phylogenetic Investigation of Begonia L. Section Knesebeckia (Klotzsch) A.DC. PhD Thesis. University of Glasgow.
Baldwin, B. & Sanderson, M.J. , 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences , 95 (8): 9402–9406.
Bardon, L. & Chamagne, J. , 2013. Origin and evolution of Chrysobalanaceae: insights into the evolution of plants in the Neotropics. Botanical Journal of the Linnean Society : 19–37.
Bell, C.D., Kutschker, A. & Arroyo, M.T.K. , 2012. Phylogeny and diversification of Valerianaceae (Dipsacales) in the southern Andes. Molecular Phylogenetics and Evolution , 63 (3): 724–37. References 71
Biomatters , 2013. Geneious v.6.1.6, Available at: http://www.geneious.com/.
Blanc, P. , 2002. Etre plante à l’ombre des forêts Tropicales , Nathan. 1–428
Blanca, L. & Monsalve, C. , 2006. Endemic Begoniaceae in Peru. Revista Peruana de Biologica , 13 (2): 165–170.
Bohle, U., Hilger, H.H. & Martin, W.F. , 1996. Island colonization and evolution of the insular woody habit in Echium L. (Boraginaceae). Proceedings of the National Academy of Sciences , 93 : 11740–11745.
Borsch, T. & Quandt, D. , 2009. Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Systematics and Evolution , 282 (3-4): 169–199.
Burt-Utley, K. , 1985. A Revision of Central American Species of Begonia Section Gireoudia (Begoniaceae). Tulane studies in zoology and botany , 25 (1): 1–131.
Burt-Utley, K. , 2001. Begoniaceae R. McVaugh & W. R. Anderson, eds. Flora Novo-Galiciana , 3: 653–695.
Burt-Utley, K. , 2012. Begoniaceae. Flora Mesoamerica , 2(2): 1–93.
Burt-Utley, K. & Utley, J.F. , 2011. New Species and Notes on Begonia (Begoniaceae) from Middle America, I. Novon: A Journal for Botanical Nomenclature , 21 (4): 393–401.
Calderon, C.I., Yandell, B.S. & Havey, M.J. , 2012. Genetic mapping of paternal sorting of mitochondria in cucumber. Theoretical and Applied Genetics , 125 (1): 11–18.
Castillo, R.A., Caballero, H., Boege, K., Fornoni, J. & Domínguez, C.A. , 2012. How to cheat when you cannot lie? Deceit pollination in Begonia gracilis. Oecologia , 169 (3): 773–782.
Chacón, J., de Assis, M.C., Meerow, A.W. & Renner, S.S. , 2012. From East Gondwana to Central America: historical biogeography of the Alstroemeriaceae. Journal of Biogeography , 39 (10): 1806–1818.
Chacón, J., Madriñán, S., Chase, M.W. & Bruhl, J.J., 2006. Molecular Phylogenetics of Oreobolus (Cyperaceae) and the Origin and Diversification of the American Species. International Association for Plant Taxonomy , 55 (2): 359–366. References 72
Chanderbali, A.S., Werff, H. Van Der & Renner, S.S., 2001. Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes. Annals of the Missouri Botanical Garden , 88 (1): 104–134.
Chase, M.W., Fay, M.F., Reveal, J.L., Soltis, D.E., Soltis, P.S., Peter, F., Anderberg, A.A., Moore, M.J., Olmstead, R.G., Rudall, P.J. & Kenneth, J. , 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society , 161 : 105–121.
Christenhusz, M.J.M. & Chase, M.W. , 2013. Biogeographical patterns of plants in the Neotropics – dispersal rather than plate tectonics is most explanatory. Botanical Journal of the Linnean Society : 277–286.
Clement, W.L., Tebbitt, M.C., Forrest, L.L., Blair, J.E., Brouillet, L., Eriksson, T. & Swensen, S.M. , 2005. Phylogenetic position and biogeography of Hillebrandia sandwicensis (Begoniaceae): A rare Hawaiian relic. American Journal of Botany , 92 (Errata).
Clement, W.L., Tebbitt, M.C., Forrest, L.L., Blair, J.E., Brouillet, L., Eriksson, T. & Swensen, S.M. , 2004. Phylogenetic position and biogeography of Hillebrandia sandwicensis
(Begoniaceae): a rare Hawaiian relict. Americanꉠ Journal of Botany , 91 (6): 905–917.
Cody, S., Richardson, J.E., Rull, V., Ellis, C. & Pennington, R.T. , 2010. The Great American Biotic Interchange revisited. Ecography , (February): 326–332.
Cosacov, A., Sérsic, A.N., Sosa, V., De-Nova, J.A., Nylinder, S. & Cocucci, A.A. , 2009. New insights into the phylogenetic relationships, character evolution, and phytogeographic patterns of Calceolaria (Calceolariaceae). American Journal of Botany , 96 (12): 2240–2255.
Darriba, D., Taboada, G.L., Doallo, R. & Posada, D., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature methods , 9(8): 772.
Davis, C.C., Bell, C.D., Mathews, S. & Donoghue, M.J. , 2002. Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae. Proceedings of the National Academy of Sciences , 99 (10): 6833–6837.
Donoghue, M.J. & Moore, M.J. , 2003. Toward an Integrative Historical Biogeography. Integrative and Comparative Biology , 270 : 261–270. References 73
Doorenbos, J., Sosef, M, S, M. & de Wilde, J.J.F.E., 1998. The sections of Begonia. Wageningen Agricultural University Papers , 98 (2): 1–266.
Drew, B.T. & Sytsma, K.J. , 2013. The South American radiation of Lepechinia (Lamiaceae): phylogenetics , divergence times and evolution of dioecy. Botanical Journal of the Linnean Society , 171 : 171–190.
Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. , 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology , 4(5): e88.
Drummond, A.J., Suchard, M.A., Dong, X. & Rambaut, A. , 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution , 29 : 1969–1973.
Erkens, R.H.J., Chatrou, L.W., Maas, J.W., van der Niet, T. & Savolainen, V. , 2007. A rapid diversification of rainforest trees (Guatteria; Annonaceae) following dispersal from Central into South America. Molecular Phylogenetics and Evolution , 44 (1): 399–411.
Farris, D., Jaramillo, C., Bayona, G.A., Restrepo-Moreno, S.A., Montes, C., Cardona, A., Mora, A., Speakman, R.J., Glascock, M.D. & Valencia, V. , 2011. Fracturing of the Panamanian Isthmus during initial collision with South America. Geology , 39 (11): 1007–1010. ꉠ
Fiaschi, P. & Pirani, J.R. , 2009. Review of plant biogeographic studies in Brazil. Journal of Systematics and Evolution , 47 (5): 477–496.
Fine, P.V.A., Zapata, F., Daly, D.C., Mesones, I., Misiewicz, T.M., Cooper, H.F. & Barbosa, C.E.A. , 2013. The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist tree species of Protium (Burseraceae) across the Amazon Basin. Journal of Biogeography , 40 (4): 646–661.
Forrest, L.L. , 2000. A Phylogeny of Begoniaceae . PhD Thesis. University of Glasgow.
Forrest, L.L. & Hollingsworth, P.M. , 2003. A recircumscription of Begonia based on nuclear ribosomal sequences. Plant Systematics and Evolution , 241 (3-4): 193–211.
Forrest, L.L., Hughes, M., Hollingsworth, P.M. & Zomlefer, W.B. , 2005. A phylogeny of Begonia using nuclear ribosomal sequence data and morphological characters. Systematic Botany , 30 (3): 671–682.
Frodin, D.G. , 2004. History and concepts of big plant genera. Taxon , 53 (3): 753–776. References 74
Garzione, C.N., Hoke, G.D., Libarkin, J.C., Withers, S., MacFadden, B.J., Eiler, J., Ghosh, P. & Mulch, A. , 2008. Rise of the Andes. Science , 320 (5881): 1304–7.
Gentry, A.H. , 1982. floristic diversity: phytogeographical connections between Central and South America, Pleistocene climatic fluctuations, or an accident of the Andean orogeny? Annals of the Missouri Botanical Garden , 69 (3): 557–593.
Givnish, T.J., Barfuss, M.H.J., Van Ee, B., Riina, R., Schulte, K., Horres, R., Gonsiska, P.A., Jabaily, R.S., Crayn, D.M., Smith, J.A.C., Winter, K., Brown, G.K., Evans, T.M., Holst, B.K., Luther, H., Till, W., Zizka, G., Berry, P.E. & Sytsma, K.J. , 2011. Phylogeny, adaptive radiation, and historical biogeography in Bromeliaceae: insights from an eight-locus plastid phylogeny. American Journal of Botany , 98 (5): 872–95.
Golding, J. & Wasshausen, D.C. , 2002. Begoniaceae. Contributions from the United States National Herbarium , 43 : 1–289.
Goodall-Copestake, W.P. , 2005. Framework Phylogenies for the Begoniaceae . PhD Thesis. University of Glasgow.
Goodall-Copestake, W.P., Harris, D.J. & Hollingsworth, P.M. , 2009. The origin of a mega-diverse genus: dating Begonia (Begoniaceae) using alternative datasets , calibrations and relaxed clock methods. Botanical Journal of the Linnean Society , 159 : 363–380.
Goodall-Copestake, W.P., Pérez-espona, S., Harris, D.J. & Hollingsworth, P.M. , 2010. The early evolution of the mega-diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies. Biological Journal of the Linnean Society , 101 : 243–250.
Google Inc , 2013. Google Earth v.7.1.1.1888, Available From http://www.google.com/earth/download/ge/agree.html.
Graham, A. , 2003a. Geohistory Models and Cenozoic Paleoenvironments of the Caribbean Region Geohistory Models and Cenozoic Paleoenvironments of the. Systematic Botany , 28 (2): 378–386.
Graham, S.A. , 2003b. Biogeographic Patterns of Antillean Lythraceae. Systematic Botany , 28 (2): 410–420.
Graham, S.W. & Reeves, P.A. , 2000. Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. International Journal of Plant Sciences , 161 (S6): S83–S96. References 75
Gregory-Wodzicki, K.M. , 2000. Uplift history of the Central and Northern Andes : A review Uplift history of the Central and Northern Andes: A review. Geological Society of America Bulletin , (7).
Guindon, S. & Gascuel, O. , 2003. A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology , 52 (5): 696–704.
Gutiérrez-García, T.A. & Vázquez-Domínguez, E. , 2013. Consensus between genes and stones in the biogeographic and evolutionary history of Central America. Quaternary Research , 79 (3): 311–324.
Haffer, J. , 1969. Speciation in Amazonian forest birds. Science , 165 (3889): 131–137.
Hall, T.A. , 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series , 41 : 95–98.
Hennig, W. , 1963. Phylogenetic Systematics. Annual Review of Entomology , 10 : 97–116.
Hijmans, R.J., Guarino, L., Cruz, M. & Rojas, E. , 2001. Computer tools for spatial analysis of plant genetic resources data: 1. DIVA-GIS. Plant Genetic Resources Newsletter , 127 : 15–19.
Hoorn, C., Wesselingh, F.P., ter Steege, H., Bermudez, M.A., Mora, A., Sevink, J., Sanmartín, I., Sanchez-Meseguer, A., Anderson, C.L., Figueiredo, J.P., Jaramillo, C., Riff, D., Negri, F.R., Hooghiemstra, H., Lundberg, J., Stadler, T., Särkinen, T.E. & Antonelli, A. , 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science , 330 (6006): 927–931.
Huelsenbeck, J.P. & Ronquist, F. , 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics , 17 (8): 754–745.
Hughes, C.E. & Eastwood, R. , 2006. Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes. Proceedings of the National Academy of Sciences , 103 (27): 10334–10339.
Hughes, C.E., Pennington, R.T. & Antonelli, A. , 2013. Neotropical Plant Evolution: Assembling the Big Picture. Botanical Journal of the Linnean Society , 171 (1): 1–18.
Hughes, M. & Hollingsworth, P.M. , 2008. Population genetic divergence corresponds with species- level biodiversity patterns in the large genus Begonia. Molecular Ecology , 17 (11): 2643–51. References 76
Iganci, J.R. V., Heiden, G., Miotto, S.T.S. & Pennington, R.T. , 2011. Campos de Cima da Serra: the Brazilian Subtropical Highland Grasslands show an unexpected level of plant endemism. Botanical Journal of the Linnean Society , 167 (4): 378–393.
Iturralde-vinent, M.A. , 1999. Paleogeography of the Caribbean Region: Implications for Cenozoic Biogeography. Bulletin of the American Museum of Natural History , 1-87 (238).
Jabaily, R. & Sytsma, K.J. , 2013. Historical biogeography and life history evolution of Andean Puya (Bromeliaceae). Botanical Journal of the Linnean Society , 171 : 201–224.
Jardón-Barbolla, L., Delgado-Valerio, P., Geada-López, G., Vázquez-Lobo, A. & Piñero, D. , 2011. Phylogeography of Pinus subsection Australes in the Caribbean Basin. Annals of Botany , 107 (2): 229–41.
Jimenez, R. & Schubert, B.G. , 1997. Begoniaceae. Flora de Veracruz , 100 : 1–70.
Jorgensen, P.M. & Leon-Yanez, S. , 1999. Catalogue of the Vascular Plants of Ecuador , Monographs in Systematic Botany. 316–319
Kay, K.M., Reeves, P.A., Olmstead, R.G. & Schemske, D.W. , 2005. Rapid Speciation and the Evolution of Hummingbird Pollination in Neotropical Costus Subgenus Costus (Costaceae): Evidnce from nrDNA ITS and ETS Sequences. American Journal of Botany , 92 (11): 1899– 1910.
Kirby, M.X. & MacFadden, B.J. , 2005. Was southern Central America an archipelago or a peninsula in the middle Miocene? A test using land-mammal body size. Palaeogeography, Palaeoclimatology, Palaeoecology , 228 (3-4): 193–202.
Kopp, H., Weinzierl, W., Becel, A., Charvis, P., Evain, M., Flueh, E.R., Gailler, A., Galve, A., Hirn, A., Kandilarov, A., Klaeschen, D., Laigle, M., Papenberg, C., Planert, L. & Roux, E. , 2011. Deep structure of the central Lesser Antilles Island Arc: Relevance for the formation of continental crust. Earth and Planetary Science Letters , 304 (1-2): 121–134.
Kumar, S., Skjæveland, Å., Orr, R.J.S., Enger, P., Ruden, T., Mevik, B., Burki, F., Botnen, A. & Shalchian-Tabrizi, K. , 2009. AIR: A Batch Oriented Web Program Package for Production of Supermatrices Ready for Phylogenetic Analysis. BMC Bioinformatics , 10 : 357.
Lamm, K.S. & Redelings, B.D. , 2009. Reconstructing ancestral ranges in historical biogeography: properties and prospects. Journal of Systematics and Evolution , 47 (5): 369–382. References 77
De Lange, A. & Bouman, F. , 1999. Seed Micromorphology of Neotropical Begonias. Smithsonian Contributions to Botany , (90): 1–49.
Lavin, M., Schrire, B.P., Lewis, G.P., Pennington, R.T., Delgado-Salinas, A., Thulin, M., Hughes, C.E., Matos, A.B. & Wojciechowski, M.F. , 2004. Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes. Philosophical transactions of the Royal Society of London. Series B, Biological sciences , 359 (1450): 1509–1522.
Lindemann, J.C., Steyermark, J.A. & Wasshausen, D.C. , 2007. Begoniaceae. In V. Funk, T. Hollowell, P. Berry, C. Kelloff, & S. N. Alexander, eds. Checklist of the Plants of the Guiana Shield . 213–214.
Lindemann, J.C. & Wasshausen, D.C. , 1997. Begoniaceae J. Boggan, V. Funk, C. Kelloff, M. Hoff, G. Cremers, & C. Feuillet, eds. Checklist of the Plants of the Guianas : 62.
Löhne, C. & Borsch, T. , 2005. Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms. Molecular Biology and Evolution , 22 (2): 317–332.
Lomolino, M. V, Riddle, B.R., Whittaker, R.J. & Brown, J.H. , 2011. Biogeography 4th ed., ꉠ Sinauer. 1–560
Londoño-Murcia, M.C., Tellez-Valdés, O. & Sánchez-Cordero, V. , 2010. Environmental heterogeneity of World Wildlife Fund for Nature ecoregions and implications for conservation in Neotropical biodiversity hotspots. Environmental Conservation , 37 (02): 116–127.
Machado, J. , 2010. Catelogo de Plantas e Fungos do Brasil , Jardim Botânico Rio de Janeiro. 751– 758
MacMillan, I., Gans, P.B. & Alvarado, G. , 2004. Middle Miocene to present plate tectonic history of the southern Central American Volcanic Arc. Tectonophysics , 392 (1-4): 325–348.
Magallón, S. & Castillo, A. , 2009. Angiosperm diversification through time. American Journal of Botany , 96 (1): 349–635.
Melo Santos, A.M., Cavalcanti, D.R., Silva, J.M.C. Da & Tabarelli, M. , 2007. Biogeographical relationships among tropical forests in north-eastern Brazil. Journal of Biogeography , 34 (3): 437–446. References 78
Montes, C., Bayona, G.A., Cardona, A., Buchs, D.M., Silva, C.A., Morón, S., Hoyos, N., Ramirez, D.A., Jaramillo, C. & Valencia, V. , 2012a. Arc-continent collision and orocline formation: Closing of the Central American seaway. Journal of Geophysical Research , 117 (B4): B04105.
Montes, C., Cardona, A., McFadden, R., Moron, S.E., Silva, C.A., Restrepo-Moreno, S.A., Ramirez, D.A., Hoyos, N., Wilson, J., Farris, D., Bayona, G.A., Jaramillo, C., Valencia, V., Bryan, J. & Flores, J.A. , 2012b. Evidence for middle Eocene and younger land emergence in central Panama: Implications for Isthmus closure. Geological Society of America Bulletin , 124 (5-6): 780–799.
Moore, B.R. & Donoghue, M.J. , 2007. Correlates of Diversification in the Plant Clade Dipsacales: Geographic Movement and Evolutionary Innovations. The American Naturalist , 170 (8): S28– S54.
Mora, A., Parra, M., Strecker, M.R., Sobel, E.R., Hooghiemstra, H., Torres, V. & Jaramillo, J. V, 2008. Climatic forcing of asymmetric orogenic evolution in the Eastern Cordillera of Colombia. Geological Society of America Bulletin , 120 (7-8): 930–949.
Morley, R.J. , 2000. Origin and evolution of tropicalꉠ rain forests , Wiley-Blackwell.
Morrone, J.J. , 2001. Homology, biogeography and areas of endemism. Diversity and Distributions , 7(6): 297–300.
Müller, K. , 2004. SeqState: primer design and sequence statistics for phylogenetic DNA datasets. Applied Bioinformatics , 4(1): 65–69.
Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A. & Kent, J. , 2000. Biodiversity hotspots for conservation priorities. Nature , 403 (6772): 853–838.
Nylander, J. a a, Olsson, U., Alström, P. & Sanmartín, I. , 2008. Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). Systematic Biology , 57 (2): 257–268.
Oliveira-Filho, A.T. & Fontes, M.A.L. , 2000. Patterns of Floristic Differentiation among Atlantic Forests in Southeastern Brazil and the Influence of Climate. Biotropica , 32 (March 1999): 793– 810. References 79
Olmstead, R.G. , 2013. Phylogeny and biogeography in Solanaceae, Verbenaceae and Bignoniaceae: a comparison of continental and intercontinental diversification patterns. Botanical Journal of the Linnean Society , 171 (1): 80–102.
Page, R.D.M. , 1987. Graphs and generalized tracks: quantifying Croizat’s panbiogeography. Systematic Biology , 36 (1): 1–17.
Pennington, R.T. & Dick, C.W. , 2004. The role of immigrants in the assembly of the South American rainforest tree flora. Philosophical transactions of the Royal Society of London. Series B, Biological sciences , 359 (1450): 1611–22.
Pennington, R.T., Lavin, M., Särkinen, T.E., Lewis, G.P., Klitgaard, B.B. & Hughes, C.E. , 2010. Contrasting plant diversification histories within the Andean biodiversity hotspot. Proceedings of the National Academy of Sciences , 107 (31): 13783–13787.
Pennington, R.T., Richardson, J.E. & Lavin, M. , 2006. Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure. The New Phytologist , 172 (4): 605–616.
Perret, M., Chautems, A., De Araujo, A.O. & Salamin, N. , 2013. Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences. Botanical Journal of the Linnean Society , 171 (1): 61–79.
Perret, M., Chautems, A. & Spichiger, R. , 2006. Dispersal-Vicariance Analysis in the Tribe Sinningieae (Gesneriaceae): A Clue to Understanding the Biogeographical History of the Brazilian Atlantic Forest. Annals of the Missouri Botanical Garden , 92 (2): 340–358.
Pirie, M.D., Chatrou, L.W., Mols, J.B., Erkens, R.H.J. & Oosterhof, J. , 2006. “Andean-centred” genera in the short-branch clade of Annonaceae: testing biogeographical hypotheses using phylogeny reconstruction and molecular dating. Journal of Biogeography , 33 (1): 31–46.
Plana, V. , 2003. Phylogenetic relationships of the Afro-Malagasy members of the large genus Begonia inferred from trnL intron sequences. Systematic Botany , 28 (4): 693–704.
Plana, V. , 2002. Systematics and Biogeography of the Afro-Malagasy Fleshy-Fruited Begonia (Begoniaceae) . PhD Thesis. University of Glasgow. References 80
Plana, V., Gascoigne, A., Forrest, L.L., Harris, D.J. & Pennington, R.T. , 2004. Pleistocene and pre-Pleistocene Begonia speciation in Africa. Molecular Phylogenetics and Evolution , 31 (2): 449–461.
Rajbhandary, S., Hughes, M., Phutthai, T., Thomas, D.C. & Shresta, K.K. , 2011. Asian Begonia: out of Africa via the Himalayas? Gardens’ Bulletin Singapore , 63 (1-2): 277–286.
Rambaut, A. & Drummond, A.J. , 2013. Tracer v1.5, Available at: http://tree.bio.ed.ac.uk/software/tracer/.
Rauscher, J.T. , 2002. Molecular Phylogenetics of the Espeletia Complex (Asteraceae): Evidence from nrDNA Sequences on the Closest Relatives of an Andean Adaptive Radiation. American Journal of Botany , 89 (7): 1074–1084.
Ree, R.H., Moore, B.R., Webb, C.O. & Donoghue, M.J., 2005. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution , 59 (11): 2299– 2311.
Ree, R.H. & Smith, S.A. , 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology , 57 (1): 4–14.
Renner, S.S. , 2001. Historical biogeography of Melastomataceae: the roles of Tertiary migration and long-distance dispersal. American Journal of Botany , 88 (7): 1290–1300.
Renner, S.S. , 2004. Plant Dispersal across the Tropical Atlantic by Wind and Sea. International Journal of Plant Sciences , 165 (S4): S23–S33.
Renner, S.S. , 2005. Relaxed molecular clocks for dating historical plant dispersal events. Trends in Plant Science , 10 (11): 550–8.
Richardson, J.E., Pennington, R.T., Pennington, T.D. & Peter, M. , 2001. Rapid Diversification of a Species-Rich Genus of Neotropical Rain Forest Trees. Science , 293 (5538): 2242–2245.
Rokas, A. & Holland, P.W. , 2000. Rare genomic changes as a tool for phylogenetics. Trends in Ecology & Evolution , 15 (11): 454–459.
Roncal, J. & Kahn, F. , 2013. Cenozoic colonization and diversification patterns of tropical American palms: evidence from Astrocaryum (Arecaceae). Botanical Journal of the Linnean Society , 171 : 120–139. References 81
Ronquist, F. & Huelsenbeck, J.P. , 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics , 19 (12): 1572–1574.
Rosen, D.E. , 1978. Vicariant patterns and historical explanation in biogeography. Systematic Biology , 27 (2): 159–188.
Rutschmann, F. , 2006. Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times. Diversity and Distributions , 12 (1): 35–48.
Santiago-Valentin, E. & Olmstead, R.G. , 2004. Historical biogeography of Caribbean plants: introduction to current knowledge and possibilities from a phylogenetic perspective. Taxon , 53 (2): 299–319.
Särkinen, T.E., Newman, M.F., Maas, P.J.M., Maas, H., Poulsen, A.D., Harris, D.J., Richardson, J.E., Clark, A., Hollingsworth, M. & Pennington, R.T. , 2007. Recent oceanic long-distance dispersal and divergence in the amphi-Atlantic rain forest genus Renealmia L.f. (Zingiberaceae). Molecular Phylogenetics and Evolution , 44 (3): 968–80.
Särkinen, T.E., Pennington, R.T., Lavin, M., Simon, M.F. & Hughes, C.E. , 2012. Evolutionary islands in the Andes: persistence and isolation explain high endemism in Andean dry tropical forests. Journal of Biogeography , 39 (5): 884–900.
Shaw, J., Lickey, B., Schilling, E. & Small, R.L. , 2007. Comparison of Whole Chloroplast Genome Sequences to Choose Noncoding Regions for Phylogenetic Studies in Angiosperms. American Journal of Botany , 94 (3): 275–288.
Sierra Calzado, J. , 2000. Begoniaceae Gantner, ed. Flora de la República de Cuba, Serie A, Plantas Vasculares , 3(1): 1–27.
Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J.D. & Higgins, D.G. , 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology , 7(539): 1–6.
Silvertown, J. , 2004. The ghost of competition past in the phylogeny of island. Journal of Ecology : 168–173.
Simmons, M. & Ochoterena, H. , 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology , 49 (2): 369–381. References 82
Simon, M.F., Grether, R., de Queiroz, L.P., Skema, C., Pennington, R.T. & Hughes, C.E. , 2009. Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire. Proceedings of the National Academy of Sciences , 106 (48): 20359–20364.
Simpson, C.E., Krapovickas, A. & Valls, J.F.M. , 2001. History of Arachis Including Evidence of A. hypogaea L. Peanut Science , 28 (2): 78–80.
Simpson, G.G. , 1980. Splendid Isolation: The Curious History of South American Mammals , Yale University Press. 1–275
Smith, L.B. & Schubert, B.G. , 1941a. Begoniaceae. Flora of Peru , 13 (4): 181–202.
Smith, L.B. & Schubert, B.G. , 1961. Begoniaceae P. C. Standley & L. O. Williams, eds. Flora of Guatemala , 24 (7-1): 157–185.
Smith, L.B. & Schubert, B.G. , 1941b. Revision de las Especies Argentinas del Genero Begonia. Darwiniana , 5: 78–117.
Smith, L.B. & Schubert, B.G. , 1946a. The Begoniaceae of Colombia. Caldasia , 4(18): 179–209.
Smith, L.B. & Schubert, B.G. , 1946b. The Begoniaceae쟀㏤ of Colombia (cont). Caldasia , 4(17): 77– 107.
Smith, L.B. & Schubert, B.G. , 1946c. The Begoniaceae of Colombia (prim). Caldasia , 4(16): 3–38.
Smith, L.B. & Wasshausen, D.C. , 1986. Begoniaceae G. Harling & Anderson, eds. Flora of Ecuador , 25 : 5–66.
Smith, L.B. & Wasshausen, D.C. , 1989. Begoniaceae. In Flora de Venezuela . 5–78.
Smith, L.B., Wasshausen, D.C., Golding, J. & Karegeannes, C.E. , 1986. Begoniaceae. Smithsonian Contributions to Botany , 60 : 1–584.
Sosef, M, S, M. , 1994. Refuge begonias: Taxonomy, phylogeny, and historical biogeography of Begonia sect. Loasibegonia and sect. Scutobegonia in relation to glacial rain forest refuges in Africa . PhD Thesis. Wageningen Agricultural University.
Stebbins, G.L. , 1974. Flowering Plants: Evolution above the Species Level, Belknap Press. 1–480 References 83
Stevens, W.D., Ulloa Ulloa, C., Pool, A. & Montiel, O.M. , 2001. Flora de Nicaragua. Monographs in Systematic Botany from the Missouri Botanical Garden , 85 (1): i–xlii.
Steyermark, J.A. , 1997. Begoniaceae B. K. Steyermark, J A; Berry, P E; Holst, ed. Flora of the Venezuelan Guayana , 3: 397–403.
Stone, R. , 2013. Battle for the Americas. Science , 341 (6143): 230–233.
Stults, D.Z. & Axsmith, B.J. , 2011. First macrofossil record of Begonia (Begoniaceae). American Journal of Botany , 98 (1): 150–153.
Symmank, L., Samain, M.-S., Smith, J.F., Pino, G., Stoll, A., Goetghebeur, P., Neinhuis, C. & Wanke, S. , 2011. The extraordinary journey of Peperomia subgenus Tildenia (Piperaceae): insights into diversification and colonization patterns from its cradle in Peru to the Trans- Mexican Volcanic Belt. Journal of Biogeography , 38 (12): 2337–2349.
Sytsma, K.J., Litt, A. & Zjhra, M. , 2004. Clades, clocks, and continents: historical and biogeographical analysis of Myrtaceae, Vochysiaceae, and relatives in the southern hemisphere. International Journal of Plant Sciences , 165 (S4): S85–S105.
Tebbitt, M.C. , 1997. A systematic investigation of Begonia section Sphenanthera (Hassk.) Benth. & Hook. F . PhD Thesis. University of Glasgow.
Tebbitt, M.C. , 2005. Begonias: Cultivation, Identification, and Natural History , Timber Press. 1–272
Tebbitt, M.C., Lowe-Forrest, L. & Santoriello, A. , 2006. Phylogenetic relationships of Asian Begonia, with an emphasis on the evolution of rain-ballist and animal dispersal mechanisms in sections Platycentrum, Sphenanthera and Leprosae. Systematic botany , 31 (2): 327–336.
Thomas, D.C. , 2010. Phylogenetics and Historical Biogeography of Southeast Asian Begonia L. (Begoniaceae) . PhD Thesis. University of Glasgow.
Thomas, D.C., Hughes, M., Phutthai, T., Ardi, W.H., Rajbhandary, S., Rubite, R., Twyford, A.D. & Richardson, J.E. , 2012. West to east dispersal and subsequent rapid diversification of the mega-diverse genus Begonia (Begoniaceae) in the Malesian archipelago. Journal of Biogeography , 39 (1): 98–113.
Thomas, D.C., Hughes, M., Phutthai, T., Rajbhandary, S., Rubite, R., Ardi, W.H. & Richardson, J.E. , 2011. A non-coding plastid DNA phylogeny of Asian Begonia References 84
(Begoniaceae): evidence for morphological homoplasy and sectional polyphyly. Molecular Phylogenetics and Evolution , 60 (3): 428–444.
Tropicos , 2013. Bolivia Checklist . http://www.tropicos.org/name/40025930?projectid=13 [Accessed July 27, 2013].
Twyford, A.D. , 2012. Speciation and gene flow in Central American Begonia L. (Begoniaceae) . PhD Thesis. The University of Edinburgh.
Valente, L.M., Savolainen, V. & Vargas, P. , 2010. Unparalleled rates of species diversification in Europe. Proceedings of the Royal Society B , 277 (1687): 1489–1496.
Weeks, A., Daly, D.C. & Simpson, B.B. , 2005. The phylogenetic history and biogeography of the frankincense and myrrh family (Burseraceae) based on nuclear and chloroplast sequence data. Molecular Phylogenetics and Evolution , 35 (1): 85–101.
De Wilde, J.J.F.E., Hughes, M., Rodda, M. & Thomas, D.C. , 2011. Pliocene intercontinental dispersal from Africa to Southeast Asia highlighted by the new species Begonia afromigrata (Begoniaceae). Taxon , 60 : 1685–1692.
ꉠ Yu, Y., Harris, A.J. & He, X. , 2011. RASP (Reconstruct Ancestral State in Phylogenies) 2.1.B, Available at: http:// mnh.scu.edu.cn/soft/blog/RASP.
Yu, Y., Harris, A.J. & He, X. , 2010. S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories. Molecular Phylogenetics and Evolution , 56 (2): 848–50.
Zachos, J.C., Shackleton, N.J., Revenaugh, J.S., Pälike, H. & Flower, B.P. , 2001. Climate response to orbital forcing across the Oligocene-Miocene boundary. Science , 292 (5515): 274– 278.
Zarucchi, J.L. & Wasshausen, D.C. , 1994. Begoniaceae. In L. Braco & J. L. Zarucchi, eds. Catalogue of the Flowering Plants and Gymnosperms of Peru . 191–196.
Zuloaga, F.O., Morrone, O. & Belgrano, M.J. , 2009. Begoniaceae F. O. Zuloaga, O. Morrone, & M. J. Belgrano, eds. Catalogo de las Plantas Vasculares del Cono Sur , 2: 1658–1675.
Appendices 85
11 Appendices
11.1 Appendix 1 - Accession Details Table 7: List of accessions used in analyses. Abbreviations are as follows. RBGE, the Royal Botanic Garden Edinburgh; GBG, Glasgow Botanic Gardens; HAST, HAST Institute, Taipei; DT, Daniel Thomas; RM, Ruth McGregor; PM, Peter Moonlight. Geographic coding is as follows. A, Africa; B, Asia; C, West Indies; D, northern Central America; E, southern Central America; F, northern Andes; G, southern Andes; H, southeast South America.
Species Edinburgh DNA (EDNA) Origin Geographic Extracted Number Coding By acetosella See Thomas (2010) B DT aff. elisabethae See Thomas (2010) B DT aff. multangula See Thomas (2010) B DT aptera See Thomas (2010) B DT areolata See Thomas (2010) B DT argenteomarginata See Thomas (2010) B DT boliviensis See Thomas (2010) G DT bonthainensis See Thomas (2010) B DT bracteata See Thomas (2010) B DT brevirimosa See Thomas (2010) B DT chloroneura See Thomas (2010) B DT chlorosticta See Thomas (2010) B DT cleopatrae See Thomasꉠ (2010) B DT corrugata See Thomas (2010) B DT decora See Thomas (2010) B DT dipetala See Thomas (2010) B DT dregei See Thomas (2010) A DT fenicis See Thomas (2010) B DT flagellaris See Thomas (2010) B DT floccifera See Thomas (2010) B DT goegoensis See Thomas (2010) B DT goudotii See Thomas (2010) A DT grandis See Thomas (2010) B DT guttapila See Thomas (2010) B DT hatacoa See Thomas (2010) B DT hernandioides See Thomas (2010) B DT kingiana See Thomas (2010) B DT koordersii See Thomas (2010) B DT laruei See Thomas (2010) B DT longifolia See Thomas (2010) B DT malabarica See Thomas (2010) B DT masarangensis See Thomas (2010) B DT masoniana See Thomas (2010) B DT morsei See Thomas (2010) B DT Appendices 86
multangula See Thomas (2010) B DT multijugata See Thomas (2010) B DT muricata See Thomas (2010) B DT negrosensis See Thomas (2010) B DT nelumbifolia See Thomas (2010) DE DT nigritarum See Thomas (2010) B DT oxyloba See Thomas (2010) A DT palmata See Thomas (2010) B DT pavonina See Thomas (2010) B DT poculifera See Thomas (2010) A DT poliloensis See Thomas (2010) B DT polygonoides See Thomas (2010) B DT robusta See Thomas (2010) B DT roxburghii See Thomas (2010) B DT samarensis See Thomas (2010) A DT serratipetala See Thomas (2010) B DT siccacaudata See Thomas (2010) B DT sikkimensis See Thomas (2010) B DT silletensis See Thomas (2010) B DT sizemoreae See Thomas (2010) B DT socotrana See Thomas (2010) A DT sp. China 1 See Thomas (2010) B DT sp. China 2 See Thomas쟀 (2010)㏤ B DT sp. Sumbawa 1 See Thomas (2010) B DT strigosa See Thomas (2010) B DT sudjanae See Thomas (2010) B DT sutherlandii See Thomas (2010) A DT symsanguinea See Thomas (2010) B DT tenuifolia See Thomas (2010) B DT varipeltata See Thomas (2010) B DT venusta See Thomas (2010) B DT verecunda See Thomas (2010) B DT versicolor See Thomas (2010) B DT watuwilensis See Thomas (2010) B DT sp. Borneo 1 See Thomas (2010) B DT chiasmogyna See Thomas (2010) B DT mendumiae See Thomas (2010) B DT macintyreana See Thomas (2010) B DT stevei See Thomas (2010) B DT vermeulenii See Thomas (2010) B DT didyma See Thomas (2010) B DT sp. Sumatra1 See Thomas (2010) B DT sp. Papua1 See Thomas (2010) B DT ozotothrix See Thomas (2010) B DT Appendices 87
sp. Philippines 1 See Thomas (2010) B DT resecta See Thomas (2010) B DT pseudolateralis See Thomas (2010) B DT hekensis See Thomas (2010) B DT aff. congesta See Thomas (2010) B DT flacca See Thomas (2010) B DT harauensis See Thomas (2010) B DT sp. Kalimantan 1 See Thomas (2010) B DT sp. Sumbawa 2 See Thomas (2010) B DT sp. New Guinea 1 See Thomas (2010) B DT weigallii See Thomas (2010) B DT comestibilis See Thomas (2010) B DT rantemarioensis See Thomas (2010) B DT prionota See Thomas (2010) B DT torajana See Thomas (2010) B DT aff. mekonggensis See Thomas (2010) B DT lasioura See Thomas (2010) B DT nobiae See Thomas (2010) B DT sanguineopilosa See Thomas (2010) B DT hispidissima See Thomas (2010) B DT capituliformis See Thomas (2010) B DT radicans See Thomas (2010) I DT smithiae See Thomas (2010) B DT sp. Thailand 1 See Thomas (2010) B DT sp. Thailand 2 See Thomas (2010) B DT aceroides See Thomas (2010) B DT sp. Thailand 3 See Thomas (2010) B DT hymenophylla See Thomas (2010) B DT alicida See Thomas (2010) B DT demissa See Thomas (2010) B DT elisabethae See Thomas (2010) B DT brandisiana See Thomas (2010) B DT obovoidea See Thomas (2010) B DT Cultivated Specimen, pinetorum EDNA11-0023923 D RM RBGE Cultivated Specimen, lomensis EDNA11-0023928 C RM RBGE Cultivated specimen, nelumbiifolia EDNA11-0023935 DE RM RBGE Cultivated Specimen, squarrosa EDNA11-0023949 D RM RBGE Cultivated specimen, glandulifera EDNA11-0023950 C RM RBGE bissei EDNA11-0023951 Cultivated Specimen, C RM Appendices 88
RBGE Cultivated specimen, corredorana EDNA11-0023955 E RM RBGE Cultivated Specimen, mazae EDNA11-0023990 D RM RBGE Cultivated specimen, acetosa EDNA12-0025374 H RM RBGE Cultivated Specimen, acutifolia EDNA12-0025375 C RM RBGE Cultivated specimen, angularis EDNA12-0025376 H RM RBGE arborescens var. Cultivated Specimen, EDNA12-0025377 H RM confertflora RBGE Cultivated specimen, bradei EDNA12-0025378 H RM RBGE Cultivated Specimen, boliviensis EDNA12-0025379 G RM RBGE Cultivated specimen, capanemae EDNA12-0025380 H RM RBGE Cultivated Specimen, caroliniifolia EDNA12-0025381 D RM RBGE Cultivated specimen, carrieae EDNA12-0025382 D RM 쟀㏤ RBGE Cultivated Specimen, conchifolia EDNA12-0025383 E RM RBGE Cultivated specimen, convolvulacea EDNA12-0025384 H RM RBGE Cultivated Specimen, crassicaulis EDNA12-0025385 D RM RBGE Cultivated specimen, cubensis EDNA12-0025386 C RM RBGE Cultivated Specimen, dentatiloba EDNA12-0025387 H RM RBGE Cultivated specimen, dietrichiana EDNA12-0025388 H RM RBGE Cultivated Specimen, echinosepala EDNA12-0025389 H RM RBGE Cultivated specimen, egregia EDNA12-0025391 H RM RBGE Cultivated Specimen, fissistyla EDNA12-0025392 G RM RBGE Cultivated specimen, gehrtii EDNA12-0025393 H RM RBGE glabra EDNA12-0025394 Cultivated Specimen, CDEFGH RM Appendices 89
RBGE Cultivated specimen, gracilis EDNA12-0025395 D RM RBGE Cultivated Specimen, hispida var. cucullifera EDNA12-0025397 H RM RBGE Cultivated specimen, holtonis EDNA12-0025398 F RM RBGE Cultivated Specimen, hydrocotylifolia EDNA12-0025399 D RM RBGE Cultivated specimen, imperialis EDNA12-0025400 D RM RBGE Cultivated Specimen, integerrima EDNA12-0025402 H RM RBGE Cultivated specimen, involucrata EDNA12-0025403 E RM RBGE Cultivated Specimen, juliana EDNA12-0025404 H RM RBGE Cultivated specimen, kellermanii EDNA12-0025405 D RM RBGE Cultivated Specimen, lubbersii EDNA12-0025406 H RM RBGE Cultivated specimen, luxurians EDNA12-0025407 H RM RBGE Cultivated Specimen, lyman-smithii EDNA12-0025408 D RM RBGE Cultivated specimen, manicata EDNA12-0025409 D RM RBGE Cultivated Specimen, meridensis EDNA12-0025410 F RM RBGE Cultivated specimen, minor EDNA12-0025411 C RM RBGE Cultivated Specimen, multinervia EDNA12-0025412 E RM RBGE Cultivated specimen, obliqua EDNA12-0025413 C RM RBGE Cultivated Specimen, odorata EDNA12-0025414 C RM RBGE Cultivated specimen, olbia EDNA12-0025415 H RM RBGE Cultivated Specimen, olsoniae EDNA12-0025416 H RM RBGE Cultivated specimen, paranaensis EDNA12-0025417 H RM RBGE petasitifolia EDNA12-0025418 Cultivated Specimen, H RM Appendices 90
RBGE Cultivated specimen, purpusii EDNA12-0025420 D RM RBGE Cultivated Specimen, scharffii EDNA12-0025421 H RM RBGE Cultivated specimen, sericoneura EDNA12-0025422 DEF RM RBGE Cultivated Specimen, stigmosa EDNA12-0025423 D RM RBGE Cultivated specimen, ulmifolia EDNA12-0025425 F RM RBGE Cultivated Specimen, tomentosa EDNA12-0033514 H MH RBGE Cultivated specimen, aff. incarnata EDNA13_0030226 D RM RBGE Cultivated Specimen, engleri EDNA13-0000001 A PM RBGE Cultivated specimen, johnstonii EDNA13-0000002 A PM RBGE Cultivated Specimen, ampla EDNA13-0030222 A RM RBGE Cultivated specimen, aff. barkeri EDNA13-0030223 D RM 쟀㏤ RBGE Cultivated Specimen, cyathophora EDNA13-0030224 G RM RBGE Cultivated specimen, dregei EDNA13-0030225 A RM RBGE Cultivated Specimen, lanceolata EDNA13-0030227 H RM RBGE Cultivated specimen, oxyloba EDNA13-0030228 A RM RBGE Cultivated Specimen, poculifera var. poculifera EDNA13-0030229 A RM RBGE Cultivated specimen, polygonata EDNA13-0030230 D RM RBGE Cultivated Specimen, pustulata EDNA13-0030231 D RM RBGE Cultivated specimen, sarcophylla EDNA13-0030232 D RM RBGE Cultivated Specimen, strigillosa EDNA13-0030233 DE RM RBGE Cultivated specimen, thiemei EDNA13-0030234 D RM RBGE edmundoi EDNA13-0033068 Cultivated Specimen, H PM Appendices 91
GBG Cultivated Specimen, maculata EDNA13-0033069 H PM GBG Cultivated Specimen, radicans EDNA13-0033070 H PM GBG Cultivated Specimen, kuhlmannii EDNA13-0033071 H PM GBG Cultivated Specimen, coccinea EDNA13-0033072 H PM GBG Cultivated Specimen, pseudolubbersii EDNA13-0033073 H PM GBG Cultivated Specimen, meridensis EDNA13-0033074 F PM GBG Cultivated Specimen, dichroa EDNA13-0033075 H PM GBG Cultivated Specimen, pruinata EDNA13-0033076 D PM GBG Cultivated Specimen, solananthera EDNA13-0033077 H PM GBG Cultivated Specimen, fissistyla EDNA13-0033078 G PM GBG Cultivated Specimen, leathermaniae EDNA13-0033079 G PM GBG Cultivated Specimen, polygonata EDNA13-0033080 D PM GBG Cultivated Specimen, odeteiantha EDNA13-0033081 H PM GBG Cultivated Specimen, pringlei EDNA13-0033082 D PM GBG Cultivated Specimen, macduffieana EDNA13-0033083 H PM GBG Cultivated Specimen, mollicaulis EDNA13-0033084 H PM GBG Cultivated Specimen, dominicalis EDNA13-0033085 C PM GBG Cultivated Specimen, metallica EDNA13-0033086 H PM GBG Cultivated Specimen, holtonis EDNA13-0033087 F PM GBG Cultivated Specimen, sp. Panama EDNA13-0033088 E PM GBG Cultivated Specimen, cooperi EDNA13-0033089 E PM GBG dichotoma EDNA13-0033090 Cultivated Specimen, F PM Appendices 92
GBG Cultivated Specimen, valida EDNA13-0033091 H PM GBG Cultivated Specimen, foliosa EDNA13-0033092 FG PM RBGE Cultivated specimen, reniformis EDNA13-0033093 H PM RBGE Cultivated Specimen, alice-clarkea EDNA13-0033094 D PM RBGE Cultivated specimen, schmidtiana EDNA13-0033095 H PM RBGE Cultivated Specimen, fagifolia EDNA13-0033096 H PM RBGE Cultivated specimen, popenoei EDNA13-0033097 D PM RBGE Cultivated Specimen, obscura EDNA13-0033098 H PM RBGE Cultivated specimen, herbacea EDNA13-0033099 H PM RBGE Cultivated Specimen, venosa EDNA13-0033100 H PM RBGE Cultivated specimen, cardiocarpa EDNA13-0033101 DE PM 쟀㏤ RBGE Cultivated Specimen, solimultata EDNA13-0033102 H PM RBGE Cultivated specimen, wallichiana EDNA13-0033103 D PM RBGE Silica Gel specimen, monadeplha EDNA13-0033104 G PM TS2205 (E) Silica Gel specimen, weberbaueri EDNA13-0033105 F PM TS2205 (E) Cultivated Specimen, bogneri EDNA13-0033469 A PM RBGE loranthoides ssp. Cultivated specimen, EDNA13-0033470 A PM Rhoalocarpa RBGE Cultivated Specimen, loranthoides EDNA13-0033471 A PM RBGE Cultivated specimen, gabonensis EDNA13-0033472 A PM RBGE Cultivated Specimen, kisuluana EDNA13-0033473 A PM RBGE Cultivated specimen, breedlovei EDNA13-0033474 D PM HAST epipsila EDNA13-0033475 Cultivated specimen, H PM Appendices 93
HAST Cultivated specimen, jocelinoi EDNA13-0033476 H PM HAST Cultivated specimen, ludwigii EDNA13-0033477 F PM HAST Cultivated specimen, crassipes EDNA13-0033478 A PM HAST Cultivated specimen, longipetiolata EDNA13-0033479 A PM HAST Cultivated specimen, madecassa EDNA13-0033480 A PM HAST Cultivated specimen, lyniciorum EDNA13-0033481 D PM HAST Cultivated specimen, glabra EDNA13-0033482 CDEFG PM HAST Cultivated specimen, guaduensis EDNA13-0033483 EF PM HAST Cultivated specimen, fluminensis EDNA13-0033484 H PM HAST Cultivated specimen, aff. nelumbifolia EDNA13-0033485 D PM HAST Cultivated specimen, subvillosa EDNA13-0033486 H PM HAST Cultivated specimen, crispula EDNA13-0033487 H PM HAST Cultivated specimen, mariti EDNA13-0033488 D PM HAST Cultivated specimen, sp. N Andes EDNA13-0033489 F PM HAST Cultivated specimen, karwinskyana EDNA13-0033490 D PM HAST Cultivated specimen, kautskyana EDNA13-0033491 H PM HAST Cultivated specimen, gehrtii EDNA13-0033492 H PM HAST Cultivated specimen, sanguinea EDNA13-0033493 H PM HAST Cultivated specimen, acida EDNA13-0033494 H PM HAST Cultivated specimen, incarnata EDNA13-0033495 D PM HAST Cultivated specimen, maynensis EDNA13-0033497 FG PM HAST sp. Venezuela EDNA13-0033498 Cultivated specimen, F PM Appendices 94
HAST Cultivated specimen, aconitifolia EDNA13-0033499 H PM HAST Cultivated specimen, barkeri EDNA13-0033500 D PM HAST Cultivated specimen, aff. peltata EDNA13-0033501 D PM HAST Cultivated specimen, sp. Cameroon EDNA13-0033502 A PM HAST Cultivated specimen, microsperma EDNA13-0033503 A PM HAST Cultivated specimen, scutifolia EDNA13-0033504 A PM HAST Cultivated specimen, squamulosa EDNA13-0033505 A PM HAST Cultivated specimen, eminii EDNA13-0033506 A PM HAST Cultivated specimen, nossibea EDNA13-0033507 A PM HAST Cultivated specimen, subscutata EDNA13-0033508 A PM HAST Cultivated specimen, richardsoniana EDNA13-0033509 A PM 쟀㏤ HAST Cultivated specimen, sp. Africa EDNA13-0033510 A PM HAST Cultivated specimen, ludicra EDNA13-0033511 D RM HAST Cultivated specimen, listada EDNA13-0033512 H RM HAST Cultivated specimen, undulata EDNA13-0033513 H RM HAST Silica Gel Specimen, micranthera EDNA13-0033515 G MH TS2029 (E) Silica Gel Specimen, sp. Argentina EDNA13-0033516 G MH TS2043 (E) Silica Gel Specimen, fiebrigii EDNA13-0033517 G MH TS2144 (E) Silica Gel Specimen, sp. Bolivia EDNA13-0033518 G MH TS2058 (E)
Results 61
Figure 4: Bayesian majority rule consensus tree (cpDNA data: ndhA intron, ndh F-rpl 32, rpl 32-trn L partitions). Bayesian posterior probability (PP) support values are indicated at each node. Sectional placement of taxa is indicated following taxon names with the following abbreviations: ALC, Alcida ; AUG, Augustia ; BAR, Barya ; BEG, Begonia ; BRA, Bractibegonia ; CAS, Casparya ; COE, Coelocentrum ; CYA, Cyathocnemis ; DIP, Diploclinum ; DON, Donaldia ; DOR, Doratometra ; ERM, Erminea ; EUP, Eupetalum ; GAE, Gaerdtia ; GIR, Gireoudia ; HAA, Haagea ; HYD, Hydristyles ; KNE, Knesebeckia ; LEP, Lepsia ; LOA, Loasibegonia ; MEZ, Mezierea ; NER, Nerviplacentaria ; PAR, Parvibegonia ; PET, Petermannia ; PLA, Platycentrum ; PRI, Pritzelia ; QUA, Quadriperigonia ; QUAD, Quadrilobaria ; REI, Reichenheimia ; RID, Ridleyella ; RUI, Ruizopavonia ; ROS, Rostrobegonia ; SCH, Scheidweilaria ; SOL, Solananthera ; SQA, Squamibegonia ; SPH, Sphenanthera ; TET, Tetrachia ; TETR, Tetraphila ; TRA, Trachelocarpus ; WAG, Wagneria ; WEI, Weilbachia . Selected clades are labelled at their MRCA or by bars above the cladogram. Results 62
Figure 5: Maximum clade credibility cladogram of BEAST analysis. Node heights indicate mean ages. Numbers at nodes represent clades in Table 5. Branches coloured according to their optimal range reconstructions (Table 5) under the model-free Bayesian Binary Method. Pie charts show the relative likelihood of ancestral state reconstructions at selected nodes. Circles after taxon names indicate taxon distributions. Geological epochs are indicated by background colour: Miocene (5.3-23.0 Ma), light grey; Pliocene (0.26-5.3 Ma), mid-grey; Holocene and Pleistocene (0-0.26 Ma), dark grey. Dotted lines indicate posterior clade probabilities less than 0.95.