Molecular phylogenetic analysis using combined chloroplast ndhF-rpl32 and nuclear ITS sequences included 30 selected Begonia species from Peninsular Malaysia, representing all regional sections and habitat types (ten limestone, thirteen forest, seven granite species). Bayesian inference and molecular dating inferred that Begonia dispersed from continental Asia into Peninsular Malaysia during the mid–late Miocene, with the primary estimate at approximately 10.65 million years ago (reported highest posterior density, HPD, range 9.7–12.12 mya). This timing derives from the combined sequence dataset analyzed in the study.
The early history within Peninsular Malaysia shows an ancestral lineage that split into two major clades early after arrival. These two lineages are reported as clade A and clade B, with divergence times around 9.85 mya (clade A; reported HPD values included in the source) and 8.85 mya (clade B), respectively. Following these splits, multiple subsequent speciation events produced the contemporary diversity observed across limestone and non-limestone habitats.
The two principal clades identified by the analyses display distinct biogeographic and climatic associations. Clade A contains species associated with Indian/continental Asia and a monsoon-influenced climate; this clade includes taxa assigned to Sect. Platycentrum and Sect. Parvibegonia. Clade A is resolved as slightly older in the date estimates presented.
Clade B groups taxa that the authors interpret as forming a Sunda Shelf–centered assemblage, associated with equatorial climate conditions. Examples within clade B include species from Sect. Petermannia, Jackia and Ridleyella. The study frames the difference between clades in terms of climatic histories rather than solely by substrate preference.
Analyses indicate that colonization of limestone substrates by Begonia in Peninsular Malaysia happened on multiple independent occasions; the study reports at least three separate transitions into limestone habitats. These repeated shifts demonstrate that substrate specialization in Begonia is not the result of a single colonization event followed by in situ diversification, but rather of multiple, independent adaptive or dispersal events into karst environments.
Despite the repeated colonizations of limestone, the authors conclude that climate appears to have been a more influential driver of diversification than substrate alone. This inference stems from the recovery of clades that correlate with broader climatic regimes (monsoon vs equatorial) and from the observation that both limestone and non-limestone specialist lineages are distributed across the two major clades.
Strong population structuring by locality is documented among sampled Begonia species, which the authors note is a common pattern in the genus. The paper provides examples of species with marked population differentiation, including Begonia kingiana, B. foxworthyi, B. nurii and B. sinuata. This structuring occurs regardless of whether species have narrow or broader geographic distributions.
For species that are more widespread, notably B. kingiana and B. sinuata, the authors suggest possible explanations for how species cohesion is maintained across their range. Two hypotheses presented in the source are: behavioural or physiological inertia in niche evolution (that is, persistence of ancestral ecological traits) and variation or dynamics in genome size and genome evolution. The paper frames these as potential mechanisms and does not provide experimental validation within the reported analyses.
Overall, the recovered phylogenetic relationships are described as largely concordant with current sectional classifications of Begonia in Peninsular Malaysia. However, exceptions are noted. Sections identified in the study as not forming monophyletic groups include Sect. Parvibegonia and Sect. Diploclinium. Additionally, two species complexes resolved as paraphyletic are highlighted. These findings indicate that some current taxonomic boundaries may not reflect evolutionary history as reconstructed from the combined chloroplast and nuclear markers used in this study.
The authors emphasize conservation concerns for Begonia diversity and the biodiverse tropical limestone karsts of Peninsular Malaysia. They note that these karst systems support many single-site endemic Begonia species due to niche partitioning across varied microhabitats. Major threats identified include large-scale quarrying and mining, and human encroachment. The source states that most limestone karsts remain without legal protection, underscoring the vulnerability of these habitats and their specialist flora.
This summary is drawn solely from the preprint report provided on bioRxiv. The article is a preprint and had not been certified by peer review at the time of posting. Details such as full sampling lists, explicit node age HPD intervals beyond those reported in the abstract, and specifics of molecular-clock calibration or analytical parameters are described in the full preprint but are not reproduced here beyond the information reported in the source abstract and article metadata.