At Batu Caves in Selangor, two Begonia species share one limestone hill but live very different lives. Begonia kingiana clings to vertical cliffs higher up the hill, with thick, succulent, shield-shaped leaves that store water and shed rain. Red striped begonia (Begonia phoeniogramma) grows on the soil near the base, in deep shade.
Biologists call this niche partitioning: species dividing a place between them so they don’t compete. But these two are not close cousins. DNA places them on opposite branches of Malaysia’s Begonia family tree, and each stands for a separate occasion when Begonias moved onto limestone. Their story is a way into a bigger one: how these plants reached Malaysia, why so many species are known from a single site, and why they are disappearing.
A big genus, a small peninsula
Begonia is a “mega-genus” of more than 2,000 described species, the sixth-largest group of flowering plants. Peninsular Malaysia has 53 native types, and about 89% are found nowhere else on Earth.
Ruth Kiew and colleagues at the Forest Research Institute Malaysia and Taylor’s University analysed 30 of these species, including all ten that grow on limestone. They read DNA from two sources: chloroplasts (the photosynthesis compartments, which carry their own small genome) and the cell nucleus. From it they built a family tree and estimated when its branches split.
They came from somewhere else
The tree shows that Malaysia’s Begonias are newcomers. Their ancestors spread from continental Asia into the peninsula about 10.65 million years ago (plausible range 9.7 to 12.1), in the middle to late Miocene, in what scientists call a “west-to-east” movement.
The timing coincides with stronger Asian monsoons, from roughly 15 to 10 million years ago. Some of the peninsula’s limestone is hundreds of millions of years older than that. But the authors point to evidence that limestone exposure may have expanded in this period. Researchers studying begonias in China and Vietnam proposed a mechanism: warm, heavy rain erodes soft sediment and uncovers towers and cliffs, opening new habitats.
The family tree has two big branches
Soon after arrival, the lineage divided into two major groups, which implies at least two separate arrivals. Scientists call such a group a clade: an ancestor together with all its descendants, or in plainer terms, one complete branch of the family tree. The authors label the two big ones Clade A and Clade B. The Sunda Shelf, mentioned below, is the equatorial region that includes Peninsular Malaysia, Borneo and Sumatra.
Clade A is about 9.85 million years old (range 9.7 to 10.4) and has its roots in continental Asia, where the monsoon brings distinct wet and dry seasons. Of its 17 sampled species, 14 are non-limestone species, while the remaining 3 can live on both limestone and non-limestone habitats. It is dominated by two groups. Platycentrum species are rhizomatous and mostly grow on granite beside forest streams. Parvibegonia species are low and tuberous, dying back in dry periods and regrowing from the tuber or from seed when the rains return.
Clade B is about 8.85 million years old (range 7.7 to 11.2) and is centred on the Sunda Shelf, where it is wet all year. Of its 13 sampled species, six grow only on limestone. Most of its plants are perennial and take a range of forms: low rosettes on creeping stems (Jackia), tall canes (Petermannia) and the succulent-leaved B. kingiana (Ridleyella).
A word of caution on the numbers: the age ranges overlap, so which clade is older isn’t firmly settled. The split itself has moderate support (82% posterior probability, below the authors’ own 95% bar for “well supported”).
What is clear is that the main split follows climate, not rock. Plants that grow on rock turn up in both clades, which the authors read as climate mattering more than substrate. The ancestral state was probably non-limestone.
How Limestone Begonia in Malaysia Evolved Three Separate Times
Limestone living evolved independently three times across the family tree:
- In Clade A (Subclade A1): Occurred within Parvibegonia across four species (B. integrifolia, B. variabilis, B. phoeniogramma, and B. elisabethae). B. elisabethae is included because it is closely related to the Malaysian species, but its main range extends into Peninsular Thailand.
- In Clade B (Subclade B1): Occurred in B. jayaensis and B. jiewhoei.
- In Clade B (Subclade B3 & B2): Occurred in the Jackia–Ridleyella group, which includes B. kingiana.
Each lineage found its own way onto the rock.
Limestone isn’t a strict requirement for these plants. No single feature marks a Begonia as a limestone species, and in cultivation they grow well on other soils as long as the soil drains freely. A little calcium carbonate, the mineral limestone is made of, makes them grow even better. That last observation comes from a colleague of the authors rather than a formal experiment.
Peninsular Begonias show three main growth habits. Parvibegonia species are low and tuberous, so they can survive dry spells underground. Jackia species form compact rosettes on creeping stems, which suits vertical rock and steep earth banks. Petermannia species are tall and cane-like, reaching one to three metres.
Why cliffs at all?
Begonia seeds are tiny “dust seeds”, 0.2 to 0.5 mm long, with a rough, sculpted surface that perhaps helps them cling to rock. Seedlings that small can be buried by fallen leaves on level ground, so vertical rock faces and steep earth banks may offer a debris-free foothold.
Small Seeds, Short Trips: Isolation on Limestone Hills
The same seeds help explain why species stay local. Begonias use four kinds of fruit:
- Fleshy fruits, presumably eaten by animals. B. longifolia, which has them, is the most widespread species in the peninsula.
- Dry capsules, which release seeds through slits.
- Splash-cups, where raindrops bounce seeds out.
- Capsules with equal-sized wings, which probably release seeds when shaken, like pepper pots.
In still, shaded forest, seeds rarely travel far. Add geography: karsts are “islands within islands”, cut off from one another, and the peninsula’s north-south mountain belts may add further barriers. Isolated populations drift apart, a process the authors call microallopatry, or speciation on a very small scale.
The DNA shows this at work. Take B. foxworthyi, which grows on both granite and limestone. Plants from granite at Lata Tingkat are closest relatives of limestone plants from the same area of Negeri Sembilan, not of granite plants from Lanchang in Pahang. Even within one species, plants group by where they live rather than by the rock they grow on.
A puzzle: separated but still the same
Two widespread species, B. kingiana (limestone) and B. sinuata (sandstone and granite), are roughly 4 to 4.6 million years old. Plants from different places are genetically distinct, which suggests little gene flow between them. Yet neither has split into new species.
The authors offer two tentative ideas for why these species haven’t split. The first comes from salamander research. Animals that pick habitats that suit their bodies best feel little pressure to change, so they stay the same over long periods. The catch is that this doesn’t explain why some Begonias behave this way and others don’t.
The second idea is about DNA. The Begonia with the most chromosomes has only about twice as many as the one with the fewest, yet the biggest genome holds more than ten times as much DNA as the smallest. That suggests the extra DNA is repetitive, meaning stretches copied over and over. In other organisms, bigger genomes have been linked to fewer new species forming. Whether that applies to Begonias hasn’t been tested, so it remains a hypothesis.
Either way, there is a practical lesson: one named species can hide several genetically distinct local populations.
When the labels don’t match the DNA
The DNA mostly supports the traditional groups, with exceptions:
- B. longifolia, once placed in Sphenanthera, sits inside Platycentrum, so Sphenanthera can’t stand alone.
- Diploclinium is scattered across both clades (B. lowiana in A, B. jayaensis in B) and needs redefining.
- Parvibegonia doesn’t hold together: the “unusual” B. sinuata group sits apart from the typical members.
- Two species complexes are tangled, meaning the species as currently defined aren’t cleanly separated by DNA. In Clade B, B. foxworthyi is interleaved with B. yenyeniae, B. tigrina, B. nurii and B. ignorata. In Clade A, B. integrifolia is tangled with B. variabilis and B. elisabethae. Only B. phoeniogramma comes out as clearly distinct.
Hybridisation, which Begonias do easily, could also be part of the tangle. The authors say it warrants further study. Meanwhile they recommend managing these complexes as separate, location-based units, so unique local populations aren’t lost while the taxonomy is sorted out.
Once the rock is gone: Protecting Limestone Begonia in Malaysia
Limestone karsts cover about 0.2% of Peninsular Malaysia but hold around 14% of its flora, at least 1,216 vascular plant species. There are 445 outcrops.
Quarrying is the biggest threat, and unlike most damage it removes the rock itself, so it can’t be undone. Seventy-five of the 445 karsts are sites of active or former quarries. Fires, encroachment and the loss of the tree buffer around each hill add to the pressure.
Legal protection is sparse. Only seven outcrops (1.6%) lie within totally protected areas. Karsts carry the planning label “Environmentally Sensitive Area Rank 1”, but the authors note there is no national strategy for conserving them or regulating their commercial use. Limestone forest has the highest level of extinction of any vegetation type in the peninsula, including five plant species lost from Batu Caves and six from Perak. B. jayaensis, whose only known limestone home is in Kelantan, faces imminent danger from a hydroelectric dam under construction.
Begonias elsewhere have fared no better. B. eiromischa is extinct, a casualty of lowland forest loss; forest cover across the peninsula was down to about 43.6% in 2018. Assessments differ on how many Begonias are threatened: 45.3% (24 of 53) on IUCN’s threatened categories, and about 60% in another. Either way, 21 species (39%) are known from a single locality.
A network, not a single hill
Because so many endemics live on one karst, and no single karst holds more than about a quarter of the limestone flora, protecting one hill isn’t enough. But protecting everything isn’t necessary either. A separate study of Perak, which the authors highlight, found that protecting 15 of 95 karsts would conserve 89% of the state’s limestone flora, 94% of its endemic species and 92% of its threatened species.
The gaps the authors point to:
- No national strategy for limestone conservation
- No state-level mechanism to legally protect biodiverse karsts. Designations such as the Gombak-Hulu Langat Geopark in Selangor, which includes Batu Caves, offer only some level of protection.
- No formal recognition yet of the tangled species complexes as location-based management units
The takeaway
Malaysia’s Begonias are immigrants that arrived about 10.65 million years ago and diversified. Climate shaped their main family split more than rock did, and they colonised limestone three separate times. Isolation on individual hills made them diverse. It also leaves them exposed, because losing one hill can mean losing a whole species.
The paper is dedicated to its late first author, Dr. Ruth Kiew (1946-2025), remembered for her enthusiasm that there were “many more Begonia (and other) species yet to be discovered and studied.”
Source
Study: Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia
Authors: Ruth Kiew, Fathmath Shaman Fareed, Lian Chee Foong, Sheh May Tam (2026)
Read the full paper: https://www.biorxiv.org/content/10.64898/2026.09.10.750513v1
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