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A M E R I C A N J O U R N A L O F B OTA N Y RESEARCH ARTICLE

THE MIOCENE TO PLEISTOCENE COLONIZATION OF THE

PHILIPPINE ARCHIPELAGO BY BEGONIA SECT. BARYANDRA
(BEGONIACEAE)1
MARK HUGHES2, ROSARIO RIVERA RUBITE3, PATRICK BLANC4, KUO-FANG CHUNG5,
AND CHING-I PENG6,7

2Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, UK, EH3 5LR; 3Department of Biology, College of
Arts and Sciences, University of the Philippines Manila, Padre Faura, Manila, Philippines; 43CNRS, 3 rue Michel-Ange 75794
Paris, France; 5National Taiwan University, School of Forestry and Resource Conservation, Daan, Taipei 106, Taiwan; and
6Biodiversity Research Center, Academia Sinica, Nangang, Taipei 115, Taiwan

• Premise of the study: One third of the species-rich Philippine flora is endemic, and most of the islands in the archipelago have
never been connected to a continental region. We currently lack any well-sampled angiosperm phylogenies that span the archi-
pelago, prohibiting the formation of informed hypotheses as to the evolution of this rich and highly endemic flora.
• Methods: We produced time-calibrated phylogenetic trees from both nuclear (ITS) and chloroplast (ndhA intron, ndhF–rpl32
spacer, rpl32–trnL spacer, trnC–trnD spacer) regions of 41 species of Begonia sect. Baryandra, all except one endemic to the
Philippines. Historical biogeography was reconstructed across the chloroplast phylogeny using a Bayesian binary method of
character optimization. Comparison of phylogenies from the two genomes permitted insight into the prevalence of hybridiza-
tion in the group.
• Key results: The Philippine archipelago was colonized by Begonia sect. Baryandra in the late Miocene, via long-distance
dispersal from western Malesia and a point of entry likely to be in the northwestern region of the archipelago. Palawan, Luzon,
and Panay all bear early-branching lineages from this initial colonization. There have been Plio-Pleistocene dispersals from
these islands into Borneo and Mindanao. Hybridization was common between species as evidenced by haplotype sharing and
phylogenetic incongruence.
• Conclusions: The phylogenies show a high degree of geographic structure, which millions of years of exposure to typhoons
have not blurred, showing long-term species and population stability. The recent dispersals to Mindanao are congruent with the
geologically recent arrival of the island at its current latitude in the southern Philippines.

Key words: dispersal; historical biogeography; hybridization; phylogenetic incongruence.

The thousands of islands comprising the Philippine archi-
pelago have differing continental, oceanic, and volcanic ori-
gins, with many of them having undergone recent rapid tectonic
1 Manuscript received 26 September 2014; revision accepted 24 April
2015.
This research was supported by The University of the Philippines
(System Enhanced Creative Work and Research Grant ECWRG 2014-09),
Academia Sinica, Taiwan, National Science Council, Taiwan (NSC
101-2621-B-001-003-MY3 & NSC 98-2621-B-001-002-MY3), Royal
Botanic Garden Edinburgh (supported by the Scottish Governments Rural
and Environment Science and Analytical Services Division), the M. L.
MacIntyre Begonia Trust and the Royal Society of Edinburgh Bilateral
Program. The authors thank the Palawan Council for Sustainable Development,
the Palawan Protected Areas Management Board, Palawan City Council,
and the Department of Environment and Natural Resources for granting
access and research permits, Annie Yang for support in the laboratory,
Mr. Danilo N. Tandang of the Philippine National Herbarium for support in
the field, and two reviewers for their insightful comments on the manuscript.
7 Author for correspondence (e-mail: bopeng@sinica.edu.tw)
doi:10.3732/ajb.1400428
movement (Hall, 2002). In combination with Pleistocene sea
level fluctuations leading to changing island boundaries (Voris,
2000) and a very rich and highly endemic biota (Heaney et al.,
1998; van Welzen et al., 2005), the archipelago is arguably the
most geologically and biogeographically complex area of the
Malesian region. To date, there are no well-sampled plant phy-
logenies covering the archipelago and hence a dearth of data on
which to build hypotheses regarding colonization and specia-
tion patterns of Philippine angiosperms.
Four main routes have been proposed for the biotic coloniza-
tion of the archipelago, namely from Taiwan in the north, from
Borneo in the east via Palawan or the Sulu archipelago, or from
Sulawesi in the south (Dickerson, 1928; Jones and Kennedy,
2008). These routes have been previously postulated as sub-
merged land bridges (Dickerson, 1928) or “umbilici” (the Bornean
routes; Diamond and Gilpin, 1983). However, the Philippines
are mostly oceanic, and with the exception of Palawan are not
thought to have experienced dry-land connections to the rest of
the Malesian region (Heaney, 1986). The four colonization
routes are best considered as stepping stone routes and also
have to be considered in the light of ongoing massive tectonic

American Journal of Botany 102(5): 695–706, 2015; http://www.amjbot.org/ © 2015 Botanical Society of America

695

696 • V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • A M E R I C A N J O U R N A L O F B O TA N Y
changes in the configuration of the archipelago, with Mindanao
and the Visayas having moved from just south of the equator
to their current position during the Miocene (Hall, 2002). The
strongest evidence for a land bridge is between Borneo and
Palawan, based on bathymetric data (Woodruff, 2010) and
animal distributions (Heaney, 1986), though a connection of
Palawan to Mindoro and Luzon is more doubtful. Phylogenetic
analyses have highlighted animal dispersal routes into the archi-
pelago, with bulbuls (Pycnonotidae) colonizing via the Sulu ar-
chipelago in the south and via the Batanes and Babuyan Islands
in the north (Oliveros and Moyle, 2010), geckos (Gekko) colo-
nizing from Palawan via the Buruanga Peninsula in Panay (Siler
et al., 2012), and frogs (Rana) colonizing from Borneo via Palawan
and Mindoro and via the Sulu archipelago (Brown and Guttman,
2002). Some islands within the archipelago will have been linked
in the past due to Pleistocene sea level fall during glacial periods
(Heaney, 1991; Heaney et al., 1998); these grouped islands have
been termed Pleistocene Aggregate Island Complexes (PAICs;
Esselstyn and Brown, 2009). Colonization by animals within the
archipelago may have been facilitated through such PAIC forma-
tion (Heaney et al., 2005). Gecko dispersal appears to be have
been facilitated this way through the PAIC composed of Panay,
Negros, and Cebu, but contemporary island configuration better
explains the distribution of gecko clades elsewhere in the archi-
pelago (Siler et al., 2010). Similar results have been found for
shrews (Crocidura), in which partitioning of genetic diversity
could be explained in part by PAIC formation, but distributions
were also affected by over-water dispersal among adjacent is-
lands (Esselstyn and Brown, 2009).
A number of angiosperm groups from the Philippines have
been placed phylogenetically in a wider Malesian context using
a small number of placeholders, i.e., with poor Philippine sam-
pling. These give insight into routes and dates of entry into the
Philippines, such as from the western Pacific islands during the
Pleistocene for Aglaia (Grudinski et al., 2014), from Borneo
during the Miocene for Alocasia (Nauheimer et al., 2012), from
the Sunda Shelf, Sulawesi and New Guinea during the Mio-
cene-Pliocene for Begonia (Thomas et al., 2012), and from
Borneo during the Pleistocene for Cyrtandra (Atkins et al.,
2001). However, in contrast to the considerable amount of data
available for animal colonization patterns within the archipel-
ago (Jones and Kennedy, 2008), there are no comparable stud-
ies for plants. To get beyond the broad picture of colonization
routes and consider within-archipelago events, we need much
denser sampling of clades within the Philippines.
Begonia is an ideal genus for investigating biogeography;
species tend to be narrowly endemic and poorly dispersed, with
studies in South Africa (Hughes and Hollingsworth, 2008) and
Mexico (Twyford et al., 2014) showing species in highly dif-
ferentiated populations with low levels of gene flow from both
pollen and seeds. This poor dispersal leads to geographically
restricted monophyletic groups of species, which can be used to
track deeper-time tectonic events and also permit the detection
of recent long-distance dispersal events that give rise to phylo-
genetic/geographic discordance (de Wilde et al., 2011). This
study reconstructs the colonization of the Philippine archipel-
ago by Begonia sect. Baryandra using a dated molecular phy-
logeny and current distribution data. The section has 59 species
of mostly lithophytic rhizomatous herbs, representing a mono-
phyletic radiation with all except four species endemic to the
Philippines (Rubite et al., 2013), and high levels of island ende-
mism within the Philippines (Hughes, 2008). The fruits of sect.
Baryandra are typical for the genus, being trilocular, winged,
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dehiscent capsules suited for anemoballistic or rain-splash dis-
persal of the tiny seeds (de Wilde, 2011). The majority of spe-
cies are found in midaltitude montane forests, with some species
growing at lower altitudes near sea level, often on karst lime-
stone (e.g., B. elnidoensis, B. hughesii, B. taraw, and B. wadei),
and some at higher altitudes in cloud forests (e.g., B. angilogen-
sis, B. klemmei, and B. oxysperma).
The highly endemic nature of Begonia species has implica-
tions for the way in which the historical biogeography of the
genus is reconstructed. The complex nature of the Philippine
archipelago and paucity of previous cross-archipelago studies
also influences the choice of appropriate analytical methods.
The first formalization of historical biogeography in an analyti-
cal framework was built around a vicariance paradigm (Rosen,
1976, 1978), and this approach has fed into currently popular ana-
lytical methods. Dispersal–vicariance analysis (DIVA) (Ronquist,
1997), based on a fairly simple model that gives vicariance a
lower cost than dispersal, became widely used following the
rapid expansion of molecular phylogenetics. Such analysis of
ancestral range reconstruction is most likely to be error-free
only when all speciation is due to vicariance (Kodandaramaiah,
2009), which will not hold true for most groups. In the ab-
sence of a priori constraints, a DIVA analysis can produce ever-
expanding ancestral ranges that are meaningless. In Malesia,
the ongoing accretion rather than divergence of land masses
means a vicariance approach can be particularly misleading
(Webb and Ree, 2012). Refinements have been made to the
dispersal–extinction–cladogenesis model (DEC) of geographic
range evolution by incorporating the fitting of a time-calibrated
phylogeny into a scenario of area connections (Ree et al., 2005;
Ree and Smith, 2008). This modification enables rates of dis-
persal and local extinction to be estimated by maximum like-
lihood. However, this model may also be a poor fit to island
biogeography scenarios where we expect dispersal and lineage
divergence events to coincide (Ree and Smith, 2008). In the
absence of multiple studies to inform a dispersal and vicari-
ance model in an area of highly complex geography with mul-
tiple factors influencing distributions, a model-free approach was
used here, optimizing geographic distributions across a phylog-
eny as character states using a Bayesian binary method as im-
plemented in RASP (Yu et al., 2012), allowing for a stochastic
evolution of range akin to random dispersal. This approach
gives a great deal of insight into the movement of Begonia sect.
Baryandra across the Philippine archipelago following initial
colonization. The results raise a number of hypotheses regard-
ing the development of the Philippine endemic flora and are a
first step toward larger meta-analyses of the plant biogeography
of the region.
MATERIALS AND METHODS
Taxon sampling—A total of 42 species from Begonia sect. Baryandra was
sampled from the Philippine archipelago (40 species) and Borneo (2 species).
An additional seven taxa identified only to section were included from the Phil-
ippines (labeled sp.1–7 in Fig. 1). Voucher information is listed in Appendix 1.
Accounting for samples identified to species level only, this sampling repre-
sents 41/59 (69%) of the species in Begonia sect. Baryandra as circumscribed
in Rubite et al. (2013). Asian Begonia have been supported as monophyletic
based on chloroplast sequence data (Thomas et al., 2012), leading us to choose
one American and two African species as outgroups to root the phylogeny
based on the same genome. An additional 15 Asian species from five other sec-
tions of the genus were added to represent phylogenetic branch length variation
to ensure reliable dating estimates and to further confirm the monophyly of the
ingroup. Alternative outgroups (Appendix 1) were used to root the phylogenies
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HUGHES ET AL.—PHILIPPINE BEGONIA • V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • 697

Fig. 1. Maximum clade credibility chronogram from an analysis of the chloroplast alignment in BEAST. Colours represent Bayesian MCMC optimization of
geographic distributions on the phylogeny; black indicates <90% of runs did not give the same optimization. Begonia sect. Baryandra is strongly supported as
monophyletic (PP = 1) and comprises four main subclades A–D each with PP = 1. Asterisks mark clades with PP <0.95.

698 • V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • A M E R I C A N J O U R N A L O F B O TA N Y
based on nuclear data, as the nuclear ribosomal internal transcribed spacer se-
quences are too divergent to align unambiguously between African and Asian
Begonia species.
The known geographical gaps in sampling of Begonia sect. Baryandra com-
prise Mindoro, Bohol, Leyte, and Samar. There are no records of the section
from Marinduque, Masbate, Negros, or Cebu.
DNA extraction, sequencing, and alignment—Chloroplast and nuclear
DNA sequence data sets were generated. Total genomic DNA was extracted
from young leaves and buds using DNeasy Plant Mini Kits (Qiagen, Manches-
ter, UK). Four chloroplast noncoding regions were chosen (ndhA intron, ndhF–
rpl32 spacer, rpl32–trnL spacer, trnC–trnD spacer) and amplified with PCR
primer sequences taken from Demesure et al. (1995) and Thomas et al. (2011).
PCR amplification was carried out with Phusion High-Fidelity DNA Poly-
merase (New England Biolabs) using the manufacturer’s recommended reagent
concentrations and the following temperature cycle protocol: initial denatur-
ation at 95°C for 5 min, followed by 32 cycles at 98°C for 30 s, 50°C for 30 s,
72°C for 30 s (or 60 s for trnC–trnD). The nuclear data set consists of nuclear
ribosomal internal transcribed spacers (ITS1 and 2) with the 5.8S gene, ampli-
fied using primers from Moller and Cronk (1997) and Taq DNA Polymerase
Mastermix Red (Ampliqon, Odense M, Denmark). Sanger sequencing was per-
formed on the PCR products by Genomics BioScience and Technology Co.
(Taipei, Taiwan). Forward and reverse reads for all regions were assembled and
aligned using Geneious Pro (Biomatters, Aukland, New Zealand), with the
alignments being subsequently manually edited in the program BioEdit 7.1.3
(Hall, 1999); inversions were offset. The following bases were excluded from
the chloroplast alignment because of missing data at the ends of regions, or
alignment uncertainty due to long mononucleotide repeats: 701–712, 751–765,
1390–1515, 1956–1970, 2077–2090, 2505–2516, 2910–3048, 3152–3164,
4520–4570, 5680-5770, 6940-7070. GenBank accession numbers for all se-
quences are listed in Appendix 1.
Phylogenetic analysis and divergence time estimation—The optimal
model of DNA sequence evolution was assessed with the program jModeltest
2.1.3 (Posada et al., 2012) using the Akaike information criterion (AIC) and the
Bayesian information criterion (BIC) to estimate the model with the closest fit
to the data. For the four chloroplast regions, the GRT+G+I model was the most
probable (AIC weight > 0.98 in all cases). Under the AIC, the nuclear data set
had a wide spread of probabilities across different models (none with an AIC
weight > 0.50); the BIC highlighted SYM+G as the most probable (BIC weight
= 0.94), and this model was used for phylogenetic analysis.
Bayesian phylogenetic analyses were carried out separately on the chloroplast
and nuclear data sets using the program MrBayes 3.2.1 (Ronquist et al., 2012).
Each data set was treated as a single partition, analyzed under the appropriate
model of sequence evolution and the default parameters of two runs with four
chains each, run for 10 000 000 generations with a sample tree taken every 10 000.
The first 25% of sampled trees were discarded as burn-in, and the remainder sum-
marized as a maximum clade credibility tree visualized using the program Fig-
Tree v.1.4.0 (Rambaut, 2009). The trees resulting from the two analyses were
compared using the program Dendroscope 3 (Huson and Scornavacca, 2012).
A time-calibrated phylogeny based on the aligned chloroplast matrix was con-
structed using an uncorrelated relaxed lognormal clock in the program BEAST
v.1.7.5 (Drummond et al., 2012) and treating the data as a single partition. A
secondary age calibration was necessary, as the only Begonia macrofossil known
(Stults and Axsmith, 2011) is too young to provide a calibration point. Two cali-
bration points were taken from the broadly sampled phylogeny in Thomas et al.
(2012), one dating the age of all Asian Begonia (18.2 Ma) and one dating the ori-
gin of Malesian Begonia (13.0 Ma) both with a standard deviation of 3.57 Myr.
Five separate runs were carried out, beginning with a random tree and run for
10 000 000 generations under a birth–death model of speciation, sampled every
10 000 generations. Plots of the logged parameters for each run were visualized
using the program Tracer v.1.5. (Rambaut and Drummond, 2007) to confirm con-
vergence between runs. The trees from each run were combined into one file us-
ing the program Logcombiner (Drummond et al., 2012) after a burn-in of 20%
from each run, and were summarized into a single maximum clade credibility tree
using the program TreeAnnotator v.1.7.5 (Drummond et al., 2012).
Biogeographic analysis—The Philippine archipelago and neighboring
islands were divided into nine regions (Fig. 1) based on the islands from
which samples were available and current coastlines; an additional five areas
(Africa+America, India, China, western Sunda Shelf [Peninsular Malaysia +
Sumatra] and Sulawesi) were coded to accommodate the wider sampling.
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Terminals on the tree were scored according to their collection locality; given
the microendemism of most Begonia species, this scoring is an accurate reflec-
tion of biological reality. Three of the taxa sampled have ranges that cover more
than one area: (1) Begonia longiscapa occurs in southern Luzon, Biliran, Leyte,
Bohol, and Mindanao, a sample from Biliran was included in the analysis; (2)
B. mindorensis is known from Palawan and Mindoro, no samples were taken
from the latter island; (3) Begonia nigritarum was sampled from Luzon and
Panay, with no samples from the tentative records in Mindoro, Bohol, and Min-
danao (Hughes, 2008). Given the polyphyly of some species uncovered by this
study, we adhere to the conservative approach of scoring only sampled locali-
ties, as we are not confident species occurrence records from other areas repre-
sent related genotypes.
The historical biogeography of Begonia sect. Baryandra across the Philippine
archipelago was reconstructed using a Bayesian binary method of character state
optimization across the maximum clade credibility tree resulting from the BEAST
analysis of the chloroplast sequence alignment described above. The chloroplast
phylogeny was chosen for the biogeographic analysis to track seed dispersal
across the archipelago rather than gene flow via pollen and to keep the results
comparable with those of Thomas et al. (2012), which were also derived from a
chloroplast phylogeny; chloroplasts in Begonia are maternally inherited (Peng
and Chiang, 2000). The Bayesian binary analysis was implemented in the pro-
gram RASP 2.1b (Yu et al., 2012), which uses Markov chain Monte Carlo
(MCMC) source code from MrBayes 3.1.2 (Ronquist and Huelsenbeck, 2003).
The MCMC analysis was run for 50 000 generations using 10 chains, with an
equal probability of dispersal between all regions, and a root distribution of Af-
rica. The number of regions possible at each node was constrained to two.
RESULTS
Sequence characteristics—The aligned sequence matrix for
the nuclear data set was 894 bases long, with 354 (40%) being
informative, and a further 119 (13%) being autapomorphic. The
concatenated chloroplast sequence matrix was 7435 characters
long after site exclusion, with 606 being informative (8%) and a
further 646 (9%) being autapomorphic. The electropherograms
for the nuclear ITS sequences obtained from B. hernandoides 1,
B. taraw 1, Begonia sp. 2, and Begonia sp. 5 were polymorphic,
whereas the sequences obtained from the chloroplast genome for
those individuals were normal reads. Repeat PCR and sequenc-
ing reactions of the ITS gave the same result, confirming poly-
morphism in the individual plants sequenced. These sequences
were not included in the phylogenetic analysis.
Phylogenetic analyses and divergence time— The phylog-
enies based on chloroplast and nuclear data both show a strongly
supported monophyletic Begonia sect. Baryandra (Fig. 2).
Levels of support are generally quite high across the both anal-
yses, with weakening support toward the base and the terminals
of the trees. The chloroplast tree shows an early branching into
four well-supported clades (A–D in Fig. 1; PP = 1.0 in each
case), with the relationships between these clades given by un-
supported short branches, best considered a four-way poly-
tomy. The two different analyses of the chloroplast alignment
(one Bayesian, Fig. 2; one time-calibrated Bayesian, Fig. 1)
gave similar tree topologies, with only minor unsupported dif-
ferences in resolution toward the terminals.
The ITS phylogeny shows significant amounts of hard in-
congruence in comparison with the chloroplast phylogeny.
Clades A, B, and D are present (labeled A′, B′, and D′ in
Fig. 2), although the composition of clades A′ and D′ differs
slightly from that found in the chloroplast analysis, and in ad-
dition, the internal topology differs significantly. Clade C
from the chloroplast analysis is represented by two clades in
the nuclear analysis C1′ and C2′, with clade C1′ being sister to
clade both B′ and C′ with PP = 1.0. Of particular note in terms
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• 699
• V O L . 1 0 2 , N O. 5 M AY 2 0 1 5

Tanglegram based on a Bayesian analysis of the chloroplast alignment (left) and nrITS (right). Asterisks mark clades with PP <0.95. Outgroups not shown. Fig. 2.
HUGHES ET AL.—PHILIPPINE BEGONIA

700 • V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • A M E R I C A N J O U R N A L O F B O TA N Y
of incongruence is the placement of B. wadei and B. elnidoen-
sis (early branching in clade C in the chloroplast tree, highly
nested in clade B in the ITS tree). These two species are eco-
logically and morphologically distinct, as they occur on
coastal limestone and have erect, succulent stems (Merrill and
Quisumbing, 1932). The placement of B. palawanensis is also
remarkable, as this caulescent species belongs to Begonia
sect. Petermannia and its appearance in the ingroup was unex-
pected. The ITS data place this caulescent species as highly
nested in a clade of Begonia sect. Petermannia from the Phil-
ippines (data not shown), a section well outside our Begonia
sect. Baryandra study group. Several species with more than
one terminal sample appear as polyphyletic in one or both
phylogenies (B. hernandioides, B. hughesii, B. longiscapa,
B. luzonensis, B. nigritarum, B. tagbanua).
The age of the Begonia sect. Baryandra crown group is 8.5
(range 4.8–11.8) Ma (Fig. 3). This age estimate is based on a
secondary calibration and will involve a further magnification
of the error present in the primary calibration of the Bego-
niaceae crown group carried out by Thomas et al. (2012), and
hence the dates should be interpreted with caution. However,
the dates are congruent with the estimates based on a similar
secondary calibration of clade ages in Begoniaceae by Thomas
et al. (2012) who obtained an age of 6.7 (range 3.1–10.1) Myr
for this group. The age of the entire crown group in this study,
including the outgroup, is 16.2 (range 10.2–22.0), again compa-
rable with the age of 18.2 (range 11.3–26.0) Myr for the same
crown group in Thomas et al., (2012). The four well-supported
clades (A–D) comprising Begonia sect. Baryandra are best
considered as having diverged very rapidly from one another in
the late Miocene.
Biogeographic analysis— Nodes giving the same ancestral
area reconstruction in at least 90% of runs were considered reli-
able when in combination with a posterior probability for the
node >0.95 (Fig. 1). The ancestral area reconstruction at the
stem of the Begonia sect. Baryandra clade is equivocal, and due
to the lack of support at the base the clade, the point of entry
into the Philippine archipelago is also uncertain. However, there
is a clearer picture of the geographic range evolution of Begonia
sect. Baryandra within the Philippines. Clade A has an ances-
tral area of Luzon, arriving ca. 8.5 Ma, and the 12 species sam-
pled began to diverge ca. 4.2 Ma, in the early Pliocene. From
this clade, there are three colonizations to other areas during the
Pleistocene; northward to the Batan and Lanyu Islands (B. feni-
cis) and to Panay (B. copelandii) and southward to Mindanao
(B. acuminatissima). Clade B has an ancestral area of Panay
and has been present on the island with no dispersal since its
arrival in the late Miocene. Clades C and D both have an ances-
tral area of Palawan, again with an origin in the late Miocene.
Clade C has dispersed from Palawan to Mindanao (two events:
one in the early Pliocene and another in the late Pleistocene), to
Borneo (one event in the late Pliocene) and to Luzon (one event
in the early Pliocene). Clade D has dispersed across the Philip-
pine archipelago, including to the three relatively small volca-
nic islands Romblon, Biliran, and Camiguin, and to Panay,
potentially in a single event in the Pleistocene that has led to
rapid diversification into six species. The clade has also dis-
persed to Borneo (one event) and Luzon (at least two events) in
the Pleistocene. The exact number of the dispersals to Panay
and Luzon are somewhat uncertain due to the lack of support
toward the terminals of clade D.
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DISCUSSION
Arrival of Begonia sect. Baryandra on the archipelago—The
area of ancestry for Begonia sect. Baryandra remains enigmatic,
as the clade is part of an unresolved four-way split including Be-
gonia sect. Ridleyella (peninsular Malaysia), Begonia sect.
Reichenhemia (western Sunda Shelf), and Begonia sect. Peter-
mannia (Malesia) (Fig. 1). This lack of resolution was also found
by Thomas et al. (2012) and indicates a large and rapid range
expansion for the genus in the late Miocene from continental
Asia across the Malesian region. Although the origin of the Bego-
nia sect. Baryandra clade is somewhat obscure, some informed
speculation regarding its entry into the Philippine archipelago is
possible. First, of the four migration routes proposed by Dicker-
son (1928), none would seem to apply. Begonia sect. Baryandra
is very species poor on Borneo (three species; Rubite et al.
(2013)), and the species sampled here are highly nested in the
phylogeny and represent dispersals westward to Borneo from
Palawan rather than the other way round (Fig. 1). The only spe-
cies in the section to occur north of the Philippines, B. fenicis, is
also highly nested in the phylogeny and represents a northward
dispersal from Luzon to Batan and Lanyu. There is no evidence
for colonization from a southern route, as the four species sam-
pled from Mindanao and environs are nested within clades with a
Palawan or Luzon origin. As the Philippines is a center of diver-
sity for the monophyletic Begonia sect. Baryandra, with samples
from surrounding areas highly nested, the most likely scenario
for its arrival on the archipelago is a long-distance dispersal event
from western Malesia rather than a migration and subsequent ex-
tinction across the migration route.
Further pinpointing the arrival locality of the ancestor of Be-
gonia sect. Baryandra in the Philippines is hampered by the
lack of resolution at the base of the clade, geographically speak-
ing a three-way split between Luzon, Panay, and Palawan. This
lack of resolution represents a rapid range expansion into those
areas following dispersal to the Philippines. Panay and Luzon
were contiguous at the time of arrival of Begonia sect. Baryan-
dra in the late Miocene to ca. 5 Ma, with Luzon then continuing
on a rapid northward trajectory relative to Panay, Mindoro, and
Palawan, leaving Panay isolated in its current form as a large
island in the western Visayas (Hall, 2002). The most likely sce-
nario is that the long-distance dispersal event leading to the
colonization of the Philippines between 11.2 and 8.5 Ma en-
tered on one of the islands then comprising the near-contiguous
northern western edge of the archipelago (Palawan, Panay, and
Luzon), then rapidly dispersed to the other two.
Colonization of the Philippines—Several factors will have in-
fluenced the way Begonia sect. Baryandra colonized the Philippines
following the first successful dispersal to the northwest of the
archipelago in the late Miocene: (1) lateral tectonic movement,
(2) tectonic uplift and volcano building, (3) sea level changes,
and (4) typhoon patterns. All of these elements interact with the
biology of the species in Begonia sect. Baryandra.
The geographic configuration of the archipelago has under-
gone huge change since the late Miocene, and the varying prox-
imity of each island will have affected how likely it is to be
colonized. The early branching of B. culasiensis is consistent
with the lineage becoming isolated following the geological
evolution of Panay and with its increasing separation from Lu-
zon. The other six species on Panay are likely the result of two
colonizations by dispersal from either Luzon or Palawan in the
Pleistocene, followed by speciation in situ.
15372197, 2015, 5, Downloaded from https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1400428 by Cochrane Philippines, Wiley Online Library on [02/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License

Fig. 3. Maximum clade credibility chronogram from an analysis of the chloroplast alignment in BEAST. Node bars indicate 95% highest posterior den-
• 701
• V O L . 1 0 2 , N O. 5 M AY 2 0 1 5
HUGHES ET AL.—PHILIPPINE BEGONIA

sity date ranges.


702 • V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • A M E R I C A N J O U R N A L O F B O TA N Y
Mindanao was much farther south during the late Miocene,
near the equator and hence out of the typhoon belt. The island
reached its current latitude during the Pliocene-Pleistocene
(Hall, 2002) and is now on the edge of the typhoon belt, and
although it experiences typhoons, they are less frequent than in
the Visayas and Luzon (Wu et al., 2014). The relatively late ar-
rival of Mindanao into the typhoon belt is congruent with its
Begonia flora being species poor and highly nested in the phy-
logeny. However, the island remains underexplored botanically
relative to the rest of the Philippines and further work may
change this view.
The Mount St. Paul limestone ridge is the youngest geologi-
cal formation in northern Palawan, being the result of uplift
since the mid-Miocene (Piccini and Iandelli, 2011). It has three
endemic Begonia species (B. taraw, B. hughesii, and B. tag-
banua). The time of the split between these taxa (1.9–5.5 Ma)
overlaps with the later phase of this uplift. The ongoing geo-
logical development of the Philippine archipelago, especially
limestone karst uplift such as this, provides new habitats and
the niche space for the evolution of new taxa.
Sea level falls during the Pleistocene climatic fluctuations
will have caused parts of the archipelago, which are currently
islands, to become connected by dry land to form Pleistocene
Aggregate Island Complexes (PAICs; Esselstyn and Brown,
2009). The extent to which these connections may have facili-
tated the dispersal of Begonia species across the aggregate is-
lands is not likely to be large. For example, the proximity of
Negros to Panay has not led to its colonization by Begonia sect.
Baryandra, despite the linkage of the two in a PAIC along with
Cebu and Masbate, which also lack any records for the section.
The distribution of B. longiscapa in the southern Philippines
conforms to the PAIC comprising Biliran, Leyte, Samar, and
Mindanao. However, this is a midaltitude lithophytic species,
and the type of lowland forest that would have colonized the
soils of the exposed sea floor are unlikely to have formed suit-
able habitat. Another member of this clade, B. gitingensis, is
endemic to the volcanic island of Sibuyan at altitudes of ca.
500 m a.s.l.; Romblon does not form part of a PAIC covering
the distribution of other clade members, and hence the occur-
rence of B. gitingensis must be the result of over-sea disper-
sal. It is important to remember that for abiotically dispersed
plants such as Begonia, their distribution is completely the re-
sult of dispersal over different scales, not migration: plants do
not walk. Begonia populations are usually restricted to small
areas of suitable microhabitat (Hughes and Hollingsworth,
2008; Hughes et al., 2011; Nakamura et al., 2013; Sang et al.,
2013), and hence from a begonia’s “eye view” in the Philip-
pines, we have a scenario of islands within islands. Chance
events can play a disproportionately large role in determining
the distributions of clades and species (Higgins et al., 2003;
de Wilde et al., 2011).
Genome incongruence— Comparison of the phylogenies
derived from the nuclear and chloroplast data reveal consider-
able hard incongruence. The differing positions of B. wadei and
B. elnidoensis (isolated and early branching in the chloroplast
phylogeny, highly nested in the nuclear phylogeny) indicates
hybridization. The position of the two species in the chloroplast
phylogeny likely represents their true phylogenetic position, as
they have an unusual fleshy-stemmed morphology and are re-
stricted to coastal karst limestone in contrast with the morphol-
ogy and ecology of the other species in the ITS phylogeny clade
15372197, 2015, 5, Downloaded from https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1400428 by Cochrane Philippines, Wiley Online Library on [02/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
D′, which are rhizomatous forest lithophytes. We conclude the
ITS sequences in B. wadei and B. elnidoensis are likely to have
been introgressed from the B. mindorensis lineage, which has
an overlapping distribution in northern Palawan and the adja-
cent islands, with the hybridization event predating the split
between B. wadei and B. elnidoensis. In the case of B. palawa-
nensis, the position in the chloroplast phylogeny is incongruent
with the taxonomy and morphology of the species and, hence,
probably represents a case of chloroplast capture. In combina-
tion with the other incongruences and polyphyletic species
observed in this study, there is considerable evidence for hy-
bridization being fairly extensive in Begonia sect. Baryandra.
For the ITS genotype in the nuclear genome of one species to
become introgressed into the genome of another may indicate
selection for genes linked to the nucleolar organizing regions
where the nrITS reside. For chloroplast genotypes to become
introgressed into another species may also indicate selection,
either relative, i.e., due to genome incompatibilities leading to
reduced male fitness in hybrids (Tsitrone et al., 2003), or abso-
lute, i.e., the invading chloroplast genotype being fitter than the
one it replaces leading to a selective sweep (Percy et al., 2014).
If the latter, the ease with which Begonia species can swap
chloroplast genomes would allow them access to a “plastid
pool” of various genotypes from neighboring species. Some of
the phylogenetic incongruence may also be due to incomplete
lineage sorting. Begonia species have been reported to exist as
long-term stable entities even through Pleistocene climatic cy-
cles in Central America (Twyford et al., 2013) and the Ryuku
Islands (Nakamura et al., 2014). Such isolated, long-lived pop-
ulations with poor gene flow may make Begonia species prone
to harboring between-population polymorphism and taking a
relatively long time to reach monophyly.
Influences on the origins of the Philippine flora—The arrival
of the Philippines by Begonia sect. Baryandra by a single suc-
cessful long-distance dispersal event and subsequent archipel-
ago-wide radiation highlights the role of chance in shaping
patterns of biodiversity. The colonization of much of the archi-
pelago has been predominantly due to dispersal, although tec-
tonic change may be responsible for early vicariance between
Panay and Luzon. The predominantly young, isolated lineages of
Begonia in Mindanao are consistent with the early, isolated posi-
tion of the island to the south. Further investigations into the phy-
logenetic placement of Mindanao endemics would allow the
testing of hypotheses as to the buildup of the Mindanao flora. If
the tectonic position of the island has been a strong influence on
floristic composition, we would expect older elements of the flora
to be nested within clades from southern Malesia (the Moluccas
and New Guinea) and younger elements nested with northern or
western clades (the northern Philippines or Borneo). A pattern of
younger clades being found in Mindanao than in Luzon has been
reported for rodents (Jansa et al., 2006).
No colonization of Palawan has been detected from other
Philippine islands, which is contradictory to the prevailing ty-
phoon track running east to west. Further, the phylogeny is
highly geographically structured across the Philippines, and
in that respect, comparable to that for Begonia in Sulawesi
(Thomas et al., 2012), which is near the equator and hence
out of the typhoon belt. This high degree of geographic struc-
ture is rather surprising and may indicate that typhoons
have not had as much impact on Begonia distribution as one
might expect given their dust-like seeds. The apparent lack

HUGHES ET AL.—PHILIPPINE BEGONIA
of typhoon-influenced dispersal on the Philippine flora needs
to be further tested with groups having a similar dispersal syn-
drome to Begonia (e.g., Gesneriaceae) and differing dispersal
syndromes (e.g., Asteraceae).
PAIC formation has had a negligible influence on range ex-
pansion by Begonia sect. Baryandra, but this influence may be
larger for other angiosperm groups. The influence of island
linkage during sea-level fall on plant distributions is likely to
depend heavily on the ecology of the plants in question and on
their altitudinal range and soil preference. We would expect
lowland and in particular coastal lowland species to be much
more prone to range expansion via PAIC formation than mon-
tane species. Further studies are needed to test this hypothesis,
either through comparative phylogenetic studies of genera with
high endemism from different habitats, or through phylogeo-
graphic studies within species or species complexes.
LITERATURE CITED
ATKINS, H., J. PRESTON, AND Q. C. B. CRONK. 2001. A molecular test
of Huxley’s line: Cyrtandra (Gesneriaceae) in Borneo and the
Philippines. Biological Journal of the Linnean Society 72: 143–159.
BROWN, R. M., AND S. I. GUTTMAN. 2002. Phylogenetic systematics of
the Rana signata complex of Philippine and Bornean stream frogs:
Reconsideration of Huxley’s modification of Wallace’s Line at the
Oriental–Australian faunal zone interface. Biological Journal of the
Linnean Society 76: 393–461.
DE WILDE, J. J. F. E. 2011. Begoniaceae. In K. Kubitzki [ed.], The fami-
lies and genera of vascular plants, 56–71. Springer, Berlin, Germany.
DE WILDE, J. J. F. E., M. HUGHES, M. RODDA, AND D. C. THOMAS. 2011.
Pliocene intercontinental dispersal from Africa to Southeast Asia
highlighted by the new species Begonia afromigrata (Begoniaceae).
Taxon 60: 1685–1692.
DEMESURE, B., N. SODZI, AND R. J. PETIT. 1995. A set of universal prim-
ers for amplification of polymorphic non-coding regions of mito-
chondrial and chloroplast DNA in plants. Molecular Ecology 4:
129–131.
DIAMOND, J. M., AND M. E. GILPIN. 1983. Biogeographic umbilici and the
origin of the Philippine avifauna. Oikos 41: 307–321.
DICKERSON, R. E. 1928. Distribution of life in the Philippines. Monographs
of the Bureau of Science, Manila 2: 1–322.
DRUMMOND, A. J., M. A. SUCHARD, D. XIE, AND A. RAMBAUT. 2012.
Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular
Biology and Evolution 29: 1969–1973.
ESSELSTYN, J. A., AND R. M. BROWN. 2009. The role of repeated sea-level
fluctuations in the generation of shrew (Soricidae: Crocidura) di-
versity in the Philippine Archipelago. Molecular Phylogenetics and
Evolution 53: 171–181.
GRUDINSKI, M., L. WANNTORP, C. M. PANNELL, AND A. N. MUELLNER-RIEHL.
2014. West to east dispersal in a widespread animal-dispersed woody
angiosperm genus (Aglaia, Meliaceae) across the Indo-Australian
Archipelago. Journal of Biogeography 41: 1149–1159.
HALL, R. 2002. Cenozoic geological and plate tectonic evolution of SE
Asia and the SW Pacific: Computer-based reconstructions, model and
animations. Journal of Asian Earth Sciences 20: 353–431.
HALL, T. A. 1999. BioEdit: A user-friendly biological sequence align-
ment editor and analysis program for Windows 95/98/NT. Nucleic
Acids Symposium Series 41: 95–98 Available at http://www.mbio.
ncsu.edu/bioedit/bioedit.html.
HEANEY, L. 1991. A synopsis of climatic and vegetational change in
Southeast Asia. Climatic Change 19: 53–61.
HEANEY, L. R. 1986. Biogeography of mammals in SE Asia: Estimates of
rates of colonization, extinction and speciation. Biological Journal of
the Linnean Society 28: 127–165.
HEANEY, L. R., D. S. BALETE, M. L. DOLAR, A. C. ALCALA, A. T. L. DANS, P.
C. GONZALES, N. R. INGLE, ET AL. 1998. A synopsis of the mammalian
fauna of the Philippine Islands. Fieldiana Zoology 88: 1–61.
15372197, 2015, 5, Downloaded from https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1400428 by Cochrane Philippines, Wiley Online Library on [02/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
• V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • 703
HEANEY, L. R., J. S. WALSH, AND A. T. PETERSON. 2005. The roles of geo-
logical history and colonization abilities in genetic differentiation be-
tween mammalian populations in the Philippine archipelago. Journal
of Biogeography 32: 229–247.
HIGGINS, S., R. NATHAN, AND M. CAIN. 2003. Are long-distance dispersal
events in plants usually caused by nonstandard means of dispersal?
Ecology 84: 1945–1956.
HUGHES, M. 2008. An annotated checklist of Southeast Asian Begonia.
Royal Botanic Garden Edinburgh, Edinburgh, UK.
HUGHES, M., AND P. M. HOLLINGSWORTH. 2008. Population genetic diver-
gence corresponds with species-level biodiversity patterns in the large
genus Begonia. Molecular Ecology 17: 2643–2651.
HUGHES, M., R. R. RUBITE, Y. KONO, AND C. PENG. 2011. Begonia blan-
cii (sect. Diploclinium, Begoniaceae), a new species endemic to the
Philippine island of Palawan. Botanical Studies (Taipei, Taiwan) 52:
203–209.
HUSON, D. H., AND C. SCORNAVACCA. 2012. Dendroscope 3: An interactive
tool for rooted phylogenetic trees and networks. Systematic Biology
61: 1061–1067.
JANSA, S. A., F. K. BARKER, AND L. R. HEANEY. 2006. The pattern and tim-
ing of diversification of Philippine endemic rodents: Evidence from
mitochondrial and nuclear gene sequences. Systematic Biology 55:
73–88.
JONES, A. W., AND R. S. KENNEDY. 2008. Evolution in a tropical archi-
pelago: Comparative phylogeography of Philippine fauna and flora re-
veals complex patterns of colonization and diversification. Biological
Journal of the Linnean Society. 95: 620–639.
KODANDARAMAIAH, U. 2009. Use of dispersal–vicariance analysis in bio-
geography—A critique. Journal of Biogeography 37: 3–11.
MERRILL, E. D., AND E. QUISUMBING. 1932. Begonia wadei. Addisonia 17:
57–58.
MOLLER, M., AND Q. CRONK. 1997. Origin and relationships of Saintpaulia
(Gesneriaceae) based on ribosomal DNA internal transcribed spacer
(ITS) sequences. American Journal of Botany 84: 956–965.
NAKAMURA, K., G. KOKUBUGATA, R. R. RUBITE, C.-J. HUANG, Y. KONO,
H.-A. YANG, M. YOKOGATA, AND C.-I. PENG. 2014. In situ glacial
survival at the northern limit of tropical insular Asia by a lowland
herb Begonia fenicis (Begoniaceae). Botanical Journal of the Linnean
Society 174: 305–325.
NAKAMURA, K., R. R. RUBITE, Y. KONO, J. R. CALLADO, AND C.-I. PENG.
2013. Begonia tandangii (Begoniaceae, section Baryandra), a
new species from Luzon Island, the Philippines. Phytotaxa 145:
27–37.
NAUHEIMER, L., P. C. BOYCE, AND S. S. RENNER. 2012. Giant taro and its
relatives: A phylogeny of the large genus Alocasia (Araceae) sheds
light on Miocene floristic exchange in the Malesian region. Molecular
Phylogenetics and Evolution 63: 43–51.
OLIVEROS, C. H., AND R. G. MOYLE. 2010. Origin and diversification
of Philippine bulbuls. Molecular Phylogenetics and Evolution 54:
822–832.
PENG, C.-I., AND T.-Y. CHIANG. 2000. Molecular confirmation of unidirec-
tional hybridization in Begonia × taipeiensis Peng (Begoniaceae)
from Taiwan. Annals of the Missouri Botanical Garden 87:
273–285.
PERCY, D. M., G. W. ARGUS, Q. C. CRONK, A. J. FAZEKAS, P. R. KESANAKURTI,
K. S. BURGESS, B. C. HUSBAND, ET AL. 2014. Understanding the spec-
tacular failure of DNA barcoding in willows (Salix): Does this re-
sult from a trans-specific selective sweep? Molecular Ecology 23:
4737–4756.
PICCINI, L., AND N. IANDELLI. 2011. Tectonic uplift, sea level changes and
Plio-Pleistocene evolution of a coastal karst system: The Mount Saint
Paul (Palawan, Philippines). Earth Surface Processes and Landforms
36: 594–609.
POSADA, D., G. L. TABOADA, R. DOALLO, AND D. DARRIBA. 2012. jModel-
Test 2: More models, new heuristics and parallel computing. Nature
Methods 9: 772–772.
RAMBAUT, A. 2009. FigTree, a graphical viewer of phylogenetic trees.
Institute of Evolutionary Biology University of Edinburgh. Available
at http://tree.bio.ed.ac.uk/software/figtree/.

704 • V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • A M E R I C A N J O U R N A L O F B O TA N Y
RAMBAUT, A., AND A. J. DRUMMOND. 2007. Tracer v1.5. Available at http://
beast.bio.ed.ac.uk/Tracer.
REE, R. H., B. R. MOORE, C. O. WEBB, AND M. J. DONOGHUE. 2005. A
likelihood framework for inferring the evolution of geographic range
on phylogenetic trees. Evolution 59: 2299–2311.
REE, R. H., AND S. A. SMITH. 2008. Maximum likelihood inference of
geographic range evolution by dispersal, local extinction, and clado-
genesis. Systematic Biology 57: 4–14.
RONQUIST, F. 1997. Dispersal–vicariance analysis: A new approach to
the quantification of historical biogeography. Systematic Biology 46:
195–203.
RONQUIST, F., AND J. P. HUELSENBECK. 2003. MrBayes 3: Bayesian phylo-
genetic inference under mixed models. Bioinformatics 19: 1572–1574.
RONQUIST, F., M. TESLENKO, P. VAN DER MARK, D. L. AYRES, A. DARLING,
S. HÖHNA, B. LARGET, ET AL. 2012. MrBayes 3.2: Efficient Bayesian
phylogenetic inference and model choice across a large model space.
Systematic Biology 61: 539–542.
ROSEN, D. E. 1976. A vicariance model of Caribbean biogeography.
Systematic Zoology 24: 431–464.
ROSEN, D. E. 1978. Vicariant patterns and historical explanation in bioge-
ography. Systematic Zoology 27: 159.
RUBITE, R. R., M. HUGHES, G. J. ALEJANDRO, AND C.-I. PENG. 2013.
Recircumscription of Begonia sect. Baryandra (Begoniaceae): evi-
dence from molecular data. Botanical Studies (Taipei, Taiwan) 54: 38.
SANG, J., R. KIEW, AND C. GERI. 2013. Revision of Begonia (Begoniaceae)
from the Melinau Limestone in Gunung Mulu National Park and
Gunung Buda National Park, Sarawak, Borneo, including thirteen
new species. Phytotaxa 99: 1–34.
SILER, C. D., AND J. R. OAKS, J. A. ESSELSTYN, A. C. DIESMOS, AND R. M.
Brown. 2010. Phylogeny and biogeography of Philippine bent-toed
geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of
Pleistocene diversification. Molecular Phylogenetics and Evolution
55: 699–710.
SILER, C. D., J. R. OAKS, L. J. WELTON, C. W. LINKEM, J. C. SWAB, A. C.
DIESMOS, AND R. M. BROWN. 2012. Did geckos ride the Palawan raft
to the Philippines? Journal of Biogeography 39: 1217–1234.
STULTS, D. Z., AND B. J. AXSMITH. 2011. First macrofossil record of
Begonia (Begoniaceae). American Journal of Botany 98: 150–153.
THOMAS, D. C., M. HUGHES, T. PHUTTHAI, W. H. ARDI, S. RAJBHANDARY,
R. RUBITE, D. TWYFORD, AND J. E. RICHARDSON. 2012. West to east
15372197, 2015, 5, Downloaded from https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1400428 by Cochrane Philippines, Wiley Online Library on [02/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
dispersal and subsequent rapid diversification of the mega-diverse ge-
nus Begonia (Begoniaceae) in the Malesian archipelago. Journal of
Biogeography 39: 98–113.
THOMAS, D. C., M. HUGHES, T. PHUTTHAI, S. RAJBHANDARY, R. RUBITE, W.
H. ARDI, AND J. E. RICHARDSON. 2011. A non-coding plastid DNA
phylogeny of Asian Begonia (Begoniaceae): evidence for morpho-
logical homoplasy and sectional polyphyly. Molecular Phylogenetics
and Evolution 60: 428–444.
TSITRONE, A., M. KIRKPATRICK, AND D. A. LEVIN. 2003. A model for chlo-
roplast capture. Evolution 57: 1776–1782.
TWYFORD, A., C. KIDNER, AND R. ENNOS. 2014. Genetic differentiation and
species cohesion in two widespread Central American Begonia spe-
cies. Heredity 112: 382–390.
TWYFORD, A., C. KIDNER, N. HARRISON, AND R. ENNOS. 2013. Population
history and seed dispersal in widespread Central American Begonia
species (Begoniaceae) inferred from plastome-derived microsatellite
markers. Botanical Journal of the Linnean Society 171: 260–276.
VAN WELZEN, P. C., J. W. F. SLIK, AND J. ALAHUHTA. 2005. Plant distribution
patterns and plate tectonics in Malesia. Biologiske Skrifter 55: 199–217.
Available at http://www.cabdirect.org/abstracts/20073082423.html.
VORIS, H. K. 2000. Maps of Pleistocene sea levels in Southeast Asia:
Shorelines, river systems and time durations. Journal of Biogeography
27: 1153–1167.
WEBB, C. O., AND R. REE. 2012. Historical biogeography inference in
Southeast Asia. In D. J. Gower, K. G. Johnson, J. E. Richardson, B. R.
Rosen, L. Rüber, and S. T. Williams [eds.], Biotic evolution and envi-
ronmental change in Southeast Asia, 191–215. Cambridge University
Press, Cambridge, UK.
WOODRUFF , D. S. 2010. Biogeography and conservation in Southeast
Asia: How 2.7 million years of repeated environmental fluc-
tuations affect today’s patterns and the future of the remaining
refugial-phase biodiversity. Biodiversity and Conservation 19:
919–941.
WU, L., C. CHOU, C.-T. CHEN, R. HUANG, T. R. KNUTSON, J. J. SIRUTIS, S.
T. GARNER, ET AL. 2014. Simulations of the present and late-twenty-
first-century western North Pacific tropical cyclone activity using a
regional model. Journal of Climate 27: 3405–3424.
YU, Y., A. J. HARRIS, AND X. J. HE. 2012. RASP (Reconstruct Ancestral
State in Phylogenies) 2.1b. Available at http://mnh.scu.edu.cn/soft/
blog/RASP.
 15372197, 2015, 5, Downloaded from https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1400428 by Cochrane Philippines, Wiley Online Library on [02/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
HUGHES ET AL.—PHILIPPINE BEGONIA • V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • 705

APPENDIX 1. Table of GenBank accession numbers and herbarium vouchers used in the molecular phylogenetic analysis (E, Royal Botanic Garden Edinburgh,
Scotland; HAST, Biodiversity Research Center, Academia Sinica, Taiwan; PNH, National Museum, Manila, Philippines).

Taxon ndhA intron ndhF–rpl32 rpl32–trnL trnC–ycf6 ycf6–psbM psbM–trnD ITS Voucher

B. ×dinglensis ined. KR186444 KR186531 KR186705 KR186791 KR186878 KR186618 KR186970 Peng P23859 (HAST)
B. acuminatissima Merr. KR186445 KR186532 KR186706 KR186792 KR186879 KR186619 KR186965 Rubite R321 (PNH)
B. aff. gueritziana Gibbs KR186446 KR186533 KR186707 KR186793 KR186880 KR186620 KR186976 Peng P22344 (HAST)
B. albococcinea Hook. KR186447 KR186534 KR186708 KR186794 KR186881 KR186621 no data Peng P23302 (HAST)
B. anisoptera Merr. KR186448 KR186535 KR186709 KR186795 KR186882 KR186622 KR186987 Rubite R479 (PNH)
B. biliranensis Merr. KR186449 KR186536 KR186710 KR186796 KR186883 KR186623 KR186997 Rubite R311 (PNH)
B. blancii KR186450 KR186537 KR186711 KR186797 KR186884 KR186624 KR187008 Peng P22545 (HAST)
M. Hughes & C.-I Peng
B. bonthainensis Hemsl. KR186451 KR186538 KR186712 KR186798 KR186885 KR186625 no data Peng P22531 (HAST)
B. calcicola Merr. KR186452 KR186539 KR186713 KR186799 KR186886 KR186626 JX656719 Peng P20761 (HAST)
B. camiguinensis Elmer KR186453 KR186540 KR186714 KR186800 KR186887 KR186627 JX656702 Rubite R506 (PNH)
B. castilloi Merr. KR186454 KR186541 KR186715 KR186801 KR186888 KR186628 no data Rubite R98 (PNH)
B. chingipengii Rubite KR186455 KR186542 KR186716 KR186802 KR186889 KR186629 JX656704 Peng P23368 (HAST)
B. chloroneura KR186456 KR186543 KR186717 KR186803 KR186890 KR186630 KR186966 Wilkie et al., 29015 (E)
P.Wilkie & Sands
B. cleopatrae Coyle KR186457 KR186544 KR186718 KR186804 KR186891 KR186631 KR186967 Wilkie et al., 25373 (E)
B. culasienesis ined. KR186458 KR186545 no data KR186805 KR186892 KR186632 KR186968 Peng P23793 (HAST)
B. culasiensis ined. KR186459 KR186546 KR186719 KR186806 KR186893 KR186633 KR186969 Rubite R234 (PNH)
B. dipetala Graham KR186460 KR186547 KR186720 KR186807 KR186894 KR186634 no data Peng P22520 (HAST)
B. dregei Otto & A.Dietr. KR186461 KR186548 KR186721 KR186808 KR186895 KR186635 no data Peng P20868 (HAST)
B. elmeri Merr. KR186462 KR186549 KR186722 KR186809 KR186896 KR186636 KR186971 Rubite R319 (PNH)
B. elnidoensis ined. KR186463 KR186550 KR186723 KR186810 KR186897 KR186637 KR186972 Peng P23508 (HAST)
B. fenicis Merr. KR186464 KR186551 KR186724 KR186811 KR186898 KR186638 KR186973 Peng P10794 (HAST)
B. fenicis Merr. KR186465 KR186552 KR186725 KR186812 KR186899 KR186639 KR186974 Unknown NK11979 (HAST)
B. floccifera Bedd. KR186466 KR186553 KR186726 KR186813 KR186900 KR186640 no data Peng P21216 (HAST)
B. forbesii King KR186467 KR186554 KR186727 KR186814 KR186901 KR186641 JX656718 Peng P22685 (HAST)
B. foxworthyii KR186468 KR186555 KR186728 KR186815 KR186902 KR186642 KF636487 Peng P22721 (HAST)
Burkill ex Ridl.
B. gabaldonensis ined. KR186469 KR186556 KR186729 KR186816 KR186903 KR186643 no data Peng P23356 (HAST)
B. gitingensis Elmer KR186470 KR186557 KR186730 KR186817 KR186904 KR186644 KR186975 Rubite R255 (PNH)
B. gueritziana Gibbs KR186471 KR186558 KR186731 KR186818 KR186905 KR186645 KR186977 Peng P22311 (HAST)
B. gueritziana Gibbs KR186472 KR186559 KR186732 KR186819 KR186906 KR186646 KR186978 Peng P22342 (HAST)
B. gutierrezii Coyle KR186473 KR186560 KR186733 KR186820 KR186907 KR186647 Blanc s.n. (E)
B. hernandioides Merr. KR186474 KR186561 KR186734 KR186821 KR186908 KR186648 KR186980 Peng P21006 (HAST)
B. hernandioides Merr. KR186475 KR186562 KR186735 KR186822 KR186909 KR186649 no data Rubite R106 (PNH)
B. hughesii ined. KR186476 KR186563 KR186736 KR186823 KR186910 KR186650 KR186981 Peng P23466 (HAST)
B. hughesii ined. KR186477 KR186564 KR186737 KR186824 KR186911 KR186651 KR186982 Peng P23475 (HAST)
B. ignorata Irmsch. KR186478 KR186565 KR186738 KR186825 KR186912 KR186652 no data Peng P22725 (HAST)
B. kingiana Irmsch. KR186479 KR186566 KR186739 KR186826 KR186913 KR186653 no data Peng P21226 (HAST)
B. klemmei Merr. KR186480 KR186567 KR186740 KR186827 KR186914 KR186654 KR186983 Rubite R182 (PNH)
B. laruei M.Hughes KR186481 KR186568 KR186741 KR186828 KR186915 KR186655 no data Hughes et al. MH1398 (E)
B. longiscapa Warb. KR186482 KR186569 KR186742 KR186829 KR186916 KR186656 KR186984 Rubite R298 (PNH)
B. longiscapa Warb. KR186483 KR186570 KR186743 KR186830 KR186917 KR186657 KR186985 Rubite R309 (PNH)
B. longiscapa Warb. KR186484 KR186571 KR186744 KR186831 KR186918 KR186658 KR186986 Rubite R316 (PNH)
B. longiscapa Warb. KR186485 KR186572 KR186745 KR186832 KR186919 KR186659 KR186988 Rubite R420 (PNH)
B. manillensis A.DC. KR186486 KR186573 KR186746 KR186833 KR186920 KR186660 KR186989 Rubite R256 (PNH)
B. masoniana Irmsch. KR186487 KR186574 KR186747 KR186834 KR186921 KR186661 no data Peng P21411 (HAST)
B. merrilliana ined. KR186488 KR186575 KR186748 KR186835 KR186922 KR186662 KR186990 Peng P23765 (HAST)
B. mindorensis Merr. KR186489 KR186576 KR186749 KR186836 KR186923 KR186663 KR186991 Rubite R326 (PNH)
B. mindorensis Merr. KR186490 KR186577 KR186750 KR186837 KR186924 KR186664 KR187006 Peng P23456 (HAST)
B. nelumbifolia KR186491 KR186578 KR186751 KR186838 KR186925 KR186665 no data Peng P20879 (HAST)
Schltdl. & Cham.
B. nigritarum KR186492 KR186579 KR186752 KR186839 KR186926 KR186666 KR186995 Rubite R419 (PNH)
(Kamel) Steud.
B. nigritarum KR186493 KR186580 KR186753 KR186840 KR186927 KR186667 KR186996 Rubite R406 (PNH)
(Kamel) Steud.
B. nigritarum KR186494 KR186581 KR186754 KR186841 KR186928 KR186668 KR186998 Peng P23855 (HAST)
(Kamel) Steud.
B. nigritarum KR186495 KR186582 KR186755 KR186842 KR186929 KR186669 no data Peng P23373 (HAST)
(Kamel) Steud.
B. nigritarum KR186496 KR186583 KR186756 KR186843 KR186930 KR186670 KR187000 Peng P23451 (HAST)
(Kamel) Steud.
B. nigritarum KR186497 KR186584 KR186757 KR186844 KR186931 KR186671 KR187001 Peng P23372 (HAST)
(Kamel) Steud.
B. nigritarum KR186498 KR186585 KR186758 KR186845 KR186932 KR186672 KR187002 Peng P23586 (HAST)
(Kamel) Steud.
i (Kamel) Steud. KR186499 KR186586 KR186759 KR186846 KR186933 KR186673 no data Peng P23858 (HAST)
 15372197, 2015, 5, Downloaded from https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1400428 by Cochrane Philippines, Wiley Online Library on [02/02/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
706 • V O L . 1 0 2 , N O. 5 M AY 2 0 1 5 • A M E R I C A N J O U R N A L O F B O TA N Y

APPENDIX 1. Continued.

Taxon ndhA intron ndhF–rpl32 rpl32–trnL trnC–ycf6 ycf6–psbM psbM–trnD ITS Voucher
B. ningmingensis KR186500 KR186587 KR186760 KR186847 KR186934 KR186674 no data Peng P20322 (HAST)
D. Fang, Y. G.
Wei & C.-I Peng
B. obtusifolia Merr. KR186501 KR186588 KR186761 KR186848 KR186935 KR186675 KR186992 Peng P23828 (HAST)
B. oxysperma A.DC. KR186502 KR186589 KR186762 KR186849 KR186936 KR186676 KR186993 Rubite R213 (PNH)
B. oxysperma A.DC. KR186503 KR186590 KR186763 KR186850 KR186937 KR186677 KR186994 Peng P23015 (HAST)
B. palawanensis Merr. KR186504 KR186591 KR186764 KR186851 KR186938 KR186678 no data Peng P23453 (HAST)
B. rubiteae M.Hughes KR186505 KR186592 KR186765 KR186852 KR186939 KR186679 KR187004 Rubite R356 (PNH)
B. rufipila Merr. KR186506 KR186593 KR186766 KR186853 KR186940 KR186680 KR187005 Rubite R265 (PNH)
B. sect. Reichenheimea KR186507 KR186594 KR186767 KR186854 KR186941 KR186681 no data Girmansyah et al.
DEDEN1490 (E)
B. sp. 1 KR186508 KR186595 KR186768 KR186855 KR186942 KR186682 KR187007 Peng P23566 (HAST)
B. sp. 2 KR186509 KR186596 KR186769 KR186856 KR186943 KR186683 no data Kokubagata GK71 (HAST)
B. sp. 3 KR186510 KR186597 KR186770 KR186857 KR186944 KR186684 KR187009 Rubite R136 (PNH)
B. sp. 4 KR186511 KR186598 KR186771 KR186858 KR186945 KR186685 KR187010 Rubite R290 (PNH)
B. sp. 5 KR186512 KR186599 KR186772 KR186859 KR186946 KR186686 no data Peng P23452 (HAST)
B. sp. 6 KR186513 KR186600 KR186773 KR186860 KR186947 KR186687 no data Peng P23418 (HAST)
B. sp. 7 KR186514 KR186601 KR186774 KR186861 KR186948 KR186688 no data Rubite R238 (PNH)
B. sublobata Jack KR186515 KR186602 KR186775 KR186862 KR186949 KR186689 no data Girmansyah et al.
DEDEN1486 (E)
B. subnummarifolia Merr. KR186516 KR186603 KR186776 KR186863 KR186950 KR186690 KR187012 no voucher
B. suborbiculata Merr. KR186517 KR186604 KR186777 KR186864 KR186951 KR186691 KR187013 Rubite R353 (PNH)
B. sutherlandii Hook.f. KR186518 KR186605 KR186778 KR186865 KR186952 KR186692 no data Jasper 1200-5 (HAST)
B. sykakiengii ined. KR186519 KR186606 KR186779 KR186866 KR186953 KR186693 JX656720 Peng P23856 (HAST)
B. sykakiengii ined. KR186520 KR186607 KR186780 KR186867 KR186954 KR186694 no data Peng P23890 (HAST)
B. tagbanua ined. KR186521 KR186608 KR186781 KR186868 KR186955 KR186695 JX656708 Blanc s.n. (E)
B. tagbanua ined. KR186522 KR186609 KR186782 KR186869 KR186956 KR186696 JX656721 Peng P23472 (HAST)
B. taraw ined. KR186523 KR186610 KR186783 KR186870 KR186957 KR186697 KR186979 Blanc s.n. taraw2 (E)
B. taraw ined. KR186524 KR186611 KR186784 KR186871 KR186958 KR186698 JX656714 Blanc s.n. taraw1 (E)
B. tayabensis Merr. KR186525 KR186612 KR186785 KR186872 KR186959 KR186699 JX656709 Rubite R360 (PNH)
B. tigrina Kiew KR186526 KR186613 KR186786 KR186873 KR186960 KR186700 JX656716 Peng P22720 (HAST)
B. trichocheila Warb. KR186527 KR186614 KR186787 KR186874 KR186961 KR186701 JX656710 Peng P20764 (HAST)
B. wadei Merr. & Quisumb. KR186528 KR186615 KR186788 KR186875 KR186962 KR186702 KF636465 Rubite R699 (PNH)
B. woodii Merr. KR186529 KR186616 KR186789 KR186876 KR186963 KR186703 JX656712 Peng P23479 (HAST)
B. woodii Merr. KR186530 KR186617 KR186790 KR186877 KR186964 KR186704 JX656722 Peng P23496 (HAST)