Marker assessment, molecular characterisation, and phylogeny of Peninsular Malaysian Begonia spp. under Section Jackia

Yong, Caylee (2025) Marker assessment, molecular characterisation, and phylogeny of Peninsular Malaysian Begonia spp. under Section Jackia. Final Year Project, UTAR.

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Abstract

Begonia L. encompasses over 2,000 species categorised into 70 sections. Peninsular Malaysia harbours numerous endemic Begonia species, many of which belong to Section Jackia, and are at risk of extinction. Most of these species are poorly identified and documented, with limited genetic and phylogenetic data available. This study employed nuclear (ITS) and chloroplast DNA markers (ndhA intron, ndhF–rpl32, and rpl32–trnL) as recommended by previous Begonia studies. These markers, either in individual or in concatenated form, were used to assess species delimitation and phylogeny of five Begonia samples from Peninsular Malaysia, alongside species from GenBank and earlier studies. The concatenated dataset (ITS+ndhA intron+ndhF–rpl32+rpl32–trnL) successfully delineated species but was unable to resolve the phylogenetic relationships between B. nurii and B. foxworthyi. Species delimitation analyses using ASAP, ABGD, PTP and GMYC revealed at least 14 species of Begonia in the dataset, although the classification of specimens BGNM1 and BGNG1 varied depending on the algorithm. This was further supported by genetic distance data, which recorded an interspecific genetic divergence of 0.51–2.16%. At least two species are potentially novel, while the taxonomic status of others (i.e., B. cf. nurii and B. cf. foxworthyi) remains uncertain due to missing or incorrect genetic data of type specimens. The study provided a preliminary phylogeny of Begonia within Section Jackia and highlights the rich diversity of Begonia in Peninsular Malaysia. Furthermore, the incorporation of floral morphological and genetic data of a wild-collected B. rajah confirmed its identity, establishing that it is extant in the wild after nearly a century of presumed extinction. The performance of each genetic marker (i.e., ease of amplification and sequencing, phylogenetic informativeness, etc.) was assessed, laying valuable groundwork for advancing taxonomic research optimised for the fast-evolving Begonia species of Southeast Asia.

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