Ancestral area reconstructions

Figure 3.7 shows a maximum clade credibility chronogram derived from the Bayesian ancestral area reconstruction in BEAST using the seven area states delimited in 3.2.2.1.

Branches are coloured according to the most probable area state of their descendent nodes, and area state posterior probability (PP) distributions are indicated. Figure 3.8 shows the maximum clade credibility chronogram resulting from the analysis of the Begoniaceae dataset in BEAST (see 3.3.2) with branches coloured according to the area state which received the highest proportional likelihood at their descendent nodes according to likelihood ancestral area reconstructions in Mesquite using the seven main area states plus the five composite area states delimited in 3.2.2.1. Proportional likelihoods (PL) of ancestral area reconstructions are indicated.

Bayesian and likelihood reconstructions produced similar results, and the use of five additional composite area states for the five more widespread taxa had a negligible impact on nodal reconstructions except for the reconstruction at the stem and crown node of a clade comprising taxa in the Begonia longifolia complex (discussed below).

Mean age estimates indicate an area transition from Africa to Asia between the Early and Middle Miocene and the analyses reconstruct continental Asia as most probable ancestral area at the crown node (PP: 0.93; PL: 0.96) of a well supported clade containing Socotran and Asian Begonia species. Within this clade, two early divergent lineages, both of which show only poorly supported phylogenetic relationships, form two clades which comprise species with distributions in South India/Sri Lanka and the Yemenite Socotra Archipelago.

Reconstructions at the crown node of the clade which includes one species from South India and the only two species known from the Socotra Archipelago, indicate continental Asia as the most probable ancestral area (PP: 0.93, PL: 0.96) for this clade.

Continental Asia is also the most probable ancestral area for both Clade A (stem node PP:

0.99, PL: 1) and Clade B (stem node PP: 0.96, PL: 0.96). Within Clade A, most nodal reconstructions indicate continental Asia as most probable ancestral area, with several lineages showing area transitions to the Sunda Shelf and Wallacea. The Wallacean species in Clade A belong to two recently diverged clades comprising some more widespread taxa placed in the polyphyletic section Sphenanthera. The first clade is comprised of Begonia longifolia, and the two subspecies of B. aptera, and ancestral area reconstructions at the

35 30 25 20 15 10 5 0 Millions of years ago

Continental Asia + adjacent islands Sunda Shelf region

Wallacea Philippines

New Guinea + adjacent islands

Holocene + Pleistocene (0-2.6)

Continental Asia + adjacent islands Sunda Shelf region

Wallacea Philippines

New Guinea + adjacent islands

Holocene + Pleistocene (0-2.6)

Fig. 3.7. Bayesian ancestral area reconstructions. Maximum clade credibility chronogram derived from a phylogeographic analysis in BEAST using secondary calibration S1 (see Table 3.5) and seven area states as defined in 3.2.2.1. Branches are coloured according to the most probable area state of their descendent nodes, and area state posterior probability (PP) distributions are indicated for nodes at which the most probable area state received < 0.98 PP. Broken lines indicate branches which lead to nodes with a clade PP < 0.95. Geological periods or epochs are indicated in different shades of grey.

Sectional placement of taxa is indicated by the following abbreviations: AUG: Augustia, BRA: Bracteibegonia, COE:

Coelocentrum, DIP: Diploclinium, HAA: Haagea, IGN: unplaced to section, MEZ: Mezierea, PAR: Parvibegonia, PEL:

Peltaugustia, PET: Petermannia, PLA: Platycentrum, REI: Reichenheimia, RID: Ridleyella, SPH: Sphenanthera, SQU:

Squamibegonia, SYM: Symbegonia.

104

Continental Asia + adjacent islands Sunda Shelf region

New Guinea + adjacent islands Sunda Shelf region + Wallacea

Continental Asia + Sunda Shelf region + Wallacea Continental Asia + Philippines

Wallacea + New Guinea

Wallacea + New Guinea + Philippines

CLADE

A

CLADE

B

Fig. 3.8. Likelihood ancestral area reconstructions. Maximum clade credibility chronogram derived from divergence age estimates in BEAST using secondary calibration S1 (see Table 3.5). Branches are coloured according to the area state which received the highest proportional likelihood at their descendent nodes based on likelihood ancestral area reconstructions in Mesquite using the seven main area states plus the five composite area states defined in 3.2.2.1. Broken lines indicate branches which lead to nodes with a clade PP < 0.95. Geological epochs are indicated in different shades of grey. Sectional placement of taxa is indicated by the following abbreviations: AUG: Augustia, BRA: Bracteibegonia, COE: Coelocentrum, DIP: Diploclinium, HAA: Haagea, IGN: unplaced to section, MEZ: Mezierea, PAR: Parvibegonia, PEL: Peltaugustia, PET: Petermannia, PLA: Platycentrum, REI: Reichenheimia, RID: Ridleyella, SPH: Sphenanthera, SQU: Squamibegonia, SYM: Symbegonia.

crown node of the clade are equivocal, especially in the analyses using five additional composite area states for wider distributions. However, reconstructions at the stem nodes indicate continental Asia as most probable area state (PP: 0.99, PL: 1) for the Begonia longifolia complex. The second clade comprises Begonia multangula and B. robusta, and reconstruction at the crown node (PP: 1, PL: 1) and two subsequent deeper nodes support the Sunda Shelf area as most probable ancestral area. Mean divergence age estimates indicate that the divergences of the stem lineages of these two clades occurred in the Pleistocene.

Within Clade B, only species in section Coelocentrum, which form the sister clade to the rest of the clade, show a continental Asian distribution, while all other clades are predominantly or exclusively Malesian. The reconstructions indicate several area transitions from the Sunda Shelf region to the Philippines and to Wallacea, although statistical support is not always strong: 1. The Sunda Shelf is the most probable ancestral area both for the stem node (PP: 0.90, PL: 0.95) and for the crown node (PP: 0.84, PL:

0.96) of a clade comprising species of section Reichenheimia including two Sumatran and one Javanese species as well as one species from Sumbawa (Lesser Sunda Islands) and one species from Buton Island (Southeast Sulawesi). 2. The Sunda Shelf region is the most probable ancestral area reconstructed for the stem node (PP: 0.89, PL: 0.95) of a clade comprising five Philippine species of section Diploclinium. 3. In the clade comprising species of sections Bracteibegonia and Petermannia s.l. (including section Symbegonia) species in section Bracteibegonia with distribution on the Sunda Shelf form the sister clade to section Petermannia, and within section Petermannia Bornean and Sumatran species form the sister clade to a clade comprising Sulawesian, New Guinean and Philippine species. The Sunda Shelf region is the most probable area reconstruction at the stem node (PP: 0.89, PL: 0.95) and at the crown node (PP: 0.93, PL: 0.97) of the Bracteibegonia-Petermannia clade, as well as at the crown node (PP: 0.84, PL: 0.87) of the Petermannia clade indicating an area transition from the Sunda Shelf region to Wallacea. Within the eastern Malesian Petermannia clade, Wallacea is the most probable ancestral area, and Philippine and New Guinean taxa form a well supported clade, with New Guinea as most probable ancestral area reconstruction at the stem node (PP: 0.98, PL: 0.98) of the clade comprising the Philippine samples. Mean divergence estimates indicate that the two independent transitions to Wallacea in Clade B occurred in the Late Miocene (in section Reichenheimia) and Pliocene (in section Petermannia), respectively.

The predominant trend of area transitions between continental Southeast Asia, the Sunda Shelf region and Wallacea, as well as across Wallacea is from west to east (Table 3.7).

106

Area State Transitions Node Geological

time frame Directionality Reconstruction support [PL]

Africa ↔ Continental Asia

Africa → Continental Asia Asian + Socotran Begonia stem Early Miocene West → East 0.96 Continental Asia → Socotra PEL stem Middle Miocene East → West 0.96 Continental Asia ↔ Sunda Shelf

region

Continental Asia → Sunda Shelf

region Sister clade of COE stem Middle Miocene West → East 0.88 B. tenuifolia divergence Pliocene West → East 0.94 B. venusta/B. decora-B. pavonia

stem Pliocene West → East 0.99

B. aff. multangula/B. areolata/

B. robusta-B. multangula stem Pliocene West → East 0.99 Wallace's Line

Continental Asia → Wallacea B. aptera-B. longifolia stem Pleistocene West → East 1 Sunda Shelf → Wallacea REI (Sulawesi + Sumbawa) stem Late Miocene West → East 0.96

PET (Wallacea + New Guinea +

Philippines) stem Pliocene West → East 0.87 B. aff. multangula divergence Pleistocene West → East 0.51 New Guinea → Philippines PET (Philippines) stem Pliocene East → West 0.95 Huxley's Line

Continental Asia → Wallacea B. aptera-B. longifolia stem Pleistocene West → East 1 Sunda Shelf → Wallacea REI (Sulawesi + Sumbawa) stem Late Miocene West → East 0.95

PET (Wallacea + New Guinea +

Philippines) stem Pliocene West → East 0.87 B. aff. multangula divergence Pleistocene West → East 0.51 Sunda Shelf → Philippines DIP (Philippines) stem Late Miocene West → East 0.95 New Guinea → Philippines PET (Philippines) stem Pliocene East → West 0.98 Lydekker's Line

Wallacea → New Guinea PET (New Guinea + Philippines)

stem Pliocene West → East 0.95

New Guinea → Philippines PET (Philippines) stem Pliocene East → West 0.98

Table 3.7. Area state transitions. Based on likelihood ancestral area reconstructions in Mesquite (see Fig. 3.8).

PL: Proportional likelihood. Taxon abbreviations: COE: Coelocentrum, DIP: Diploclinium, PEL: Peltaugustia, PET: Petermannia, REI: Reichenheimia.

3.4 Discussion

3.4.1 Molecular age estimates for the Begoniaceae and Begonia crown group divergences