--- title: "Phylogenetic history of limestone and non-limestone Begonias in Peninsular Malaysia" id: "biorxiv-16-comparative-phylogenetic-analyses-of-limestone-and-non-limestone-begonias-in" canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-16-comparative-phylogenetic-analyses-of-limestone-and-non-limestone-begonias-in" content_type: "clinical_feed_article" specialty: "General" source_name: "bioRxiv (Biomedical Preprints)" source_url: "https://www.biorxiv.org/content/10.64898/2026.09.10.750513v1?rss=1" published_at: "2026-09-13T12:00:00.000Z" evidence_level: "Verified Feed" license: "CC-BY-NC-4.0 / Informational Use" --- # Phylogenetic history of limestone and non-limestone Begonias in Peninsular Malaysia ## Provenance & Clinical Metadata - **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-16-comparative-phylogenetic-analyses-of-limestone-and-non-limestone-begonias-in - **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md) - **Primary Source:** bioRxiv (Biomedical Preprints) - **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.10.750513v1?rss=1) - **Published At:** 2026-09-13T12:00:00.000Z - **Evidence Rating:** Verified Feed ## Executive GIST (TL;DR) - The study used combined chloroplast ndhF-rpl32 and nuclear ITS sequences to perform molecular phylogenetic analyses on 30 Begonia species from Peninsular Malaysia, representing all regional sections and including **limestone**, forest and granite specialists. - Bayesian inference and molecular dating place the colonization of Peninsular Malaysia by Begonia from continental Asia in the **mid–late Miocene** at approximately 10.65 million years ago (HPD reported in the source: 9.7–12.12 mya). - An early split produced two major ancestral lineages, referred to as **clade A** and **clade B**, dated at about 9.85 mya (clade A) and 8.85 mya (clade B) with reported HPD ranges. - Multiple speciation events followed, producing lineages that colonized both limestone and non-limestone (forest, granite) habitats; limestone colonization occurred at least three times independently. - Clade A groups species associated with Indian/Continental Asia and a monsoon climate (including Sect. Platycentrum and Parvibegonia), and is resolved as slightly older than clade B. - Clade B contains groups centered on the Sunda Shelf equatorial climate, including Sect. Petermannia, Jackia and Ridleyella. - Strong population structuring by locality is common across Begonia species sampled (examples: B. kingiana, B. foxworthyi, B. nurii, B. sinuata), regardless of their geographic distribution. - For more widespread species (B. kingiana, B. sinuata), the authors suggest behavioural/physiological inertia in niche evolution and/or genome size dynamics may contribute to species cohesion; these are presented as potential explanations rather than proven mechanisms. - Phylogenetic results largely agree with existing sectional classifications but indicate exceptions: Sect. Parvibegonia, Sect. Diploclinium and two species complexes are resolved as paraphyletic. - Conservation concern is highlighted: diverse limestone karsts in Malaysia face threats from large-scale quarrying/mining and human encroachment, with most limestone habitats lacking legal protection. ## Clinical Analysis & Structured Key Points Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia | bioRxiv Skip to main content New Results Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia View ORCID Profile Ruth Kiew , View ORCID Profile Fathman Shaman Fareed , LIAN CHEE FOONG , View ORCID Profile Sheh May Tam doi: https://doi.org/10.64898/2026.09.10.750513 Ruth Kiew 1 Forest Research Institute Malaysia (FRIM), 52109 Kepong, Selangor, Malaysia; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Ruth Kiew Fathman Shaman Fareed 2 School of Biosciences, Taylors University, Subang Jaya, Selangor, Malaysia; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Fathman Shaman Fareed LIAN CHEE FOONG 3 ex-School of Biosciences, Taylors University, Subang Jaya, Selangor, Malaysia Find this author on Google Scholar Find this author on PubMed Search for this author on this site Sheh May Tam 3 ex-School of Biosciences, Taylors University, Subang Jaya, Selangor, Malaysia Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Sheh May Tam For correspondence: smtam29{at}gmail.com Abstract Info/History Metrics Supplementary material Preview PDF Abstract Karsts of Southeast Asia cover ~400,000 km2, with tropical limestone karsts possessing highly biodiverse flora in many, varied microhabitats that are unique from lowland- and hill forests. Begonia L. is a pantropical mega-genus with ~1,550 described species to date, ideal for studying evolutionary patterns and factors driving tropical population- diversity and speciation. Begonias grow on multiple substrates including limestone and granite, sandstone, quartzite, on steep earth slopes and near streams in primary forests. Niche partitioning is commonly observed, resulting in many single-site endemic Begonia species especially on limestone karsts. Molecular phylogenetic analyses were performed on combined chloroplast ndhF-rpl32 and nuclear internal transcribed spacer ITS sequences that included 30 selected Begonia species representing all sections from Peninsular Malaysia (Pen. Msia; ten limestone-, thirteen forest- and seven granite species). Results of Bayesian inference and molecular dating showed evolution of Begonia from continental Asia into Pen. Msia during the mid-late Miocene period of ~ 10.65 mya (9.7 - 12.12 mya), with at least two independent dispersal events observed by the early splitting of the ancestral lineage into two major clades i.e. clades A- and B at 9.85 mya (HPD 9.7-10.36 mya) and 8.85 mya (HPD 7.7-11.23 mya) respectively; followed by multiple speciation events colonizing limestone- as well as non-limestone (forest, granite) habitats. Begonia speciation into limestone habitats occurred three times, with climate indicated as more important factor than substrate in diversification - clade A contained the Indian/Continental Asia (monsoon climate) species, i.e. Sect. Platycentrum and Parvibegonia, resolved slightly older than clade B where Sect. Petermannia, Jackia and Ridleyella formed a Sunda Shelf (equatorial climate) centred group. Strong population structuring by locality, common in Begonias, was also observed (e.g. B. kingiana, B. foxworthyi, B. nurii, B. sinuata), regardless of distribution. However, for widespread species (B. kingiana, B. sinuata) behavioural (physiological) inertia on niche evolution, and/or genome size variation and dynamics (genome evolution) may potentially explain species cohesion. Phylogenetics relationships are mostly concordant with current sectional classifications excepting Sect. Parvibegonia, Sect. Diploclinium and two paraphyletic species complexes. Conservation of Begonias and biodiverse limestone karsts in Malaysia remains concerning due to ongoing threats (large-scale quarrying/mining, human encroachment), and most are still without any legal protection. Competing Interest Statement The authors have declared no competing interest. Funder Information Declared Forest Research Institute Malaysia, https://ror.org/01mfdfm52 , “Flora of Peninsular Malaysia Project” (01-04-01-000 Khas) Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . Back to top Previous Next Posted September 13, 2026. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. 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