Genetic diversity of captive Tomistoma Schlegelii revealed by microsatellite and mtDNA markers and field survey data at reported sites of occurrence in Peninsular Malaysia

Taranjeet Kaur, Awtar Singh (2026) Genetic diversity of captive Tomistoma Schlegelii revealed by microsatellite and mtDNA markers and field survey data at reported sites of occurrence in Peninsular Malaysia. PhD thesis, UTAR.

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Abstract

To contribute towards the on-going captive management of the Sunda gharial, Tomistoma schlegelii, a population-level genetic study was conducted using microsatellite and mitochondrial DNA (mtDNA) markers, alongside field surveys of confirmed occurrence sites. Microsatellite data identified six clusters (Clusters A to F), while mtDNA data revealed four haplotypes (H1, H2, H5, and the divergent H4 lineage) from 38 individuals. Nuclear genetic diversity within clusters was low (mean 0.25 ± 0.14 to 0.49 ± 0.11), and mtDNA diversity was detected only in Cluster B. Analysis of molecular variance (AMOVA) based on microsatellite data indicated moderate to substantial genetic differentiation. However, AMOVA for mtDNA data showed contrasting results for population differentiation and sex-biased dispersal analyses, depending on whether the divergent H4 haplotype was included or excluded. Coancestry analysis combining both markers identified Clusters B and E as important for breeding purposes. Separately, the daytime field surveys at recent capture of T. schlegelii, namely the Tengi River, Tekah/Nerus River, Sungkai River and Jengka River were carried out to record water parameters and geographical coordinates of capture site. The water parameters, including temperature, pH, salinity, total dissolved solids (TDS), and conductivity, revealed significant differences in pH and temperature between wet and dry seasons. Notably, the pH data aligned with previous studies, which suggested a preference for neutral to mildly acidic rivers. Additionally, terrain analyses and Geographic Information System (GIS)-based assessments indicated that specific river features—such as elevations of 11–16 meters, smaller streams (1–3 Strahler Order), and slopes of 0° to 10°—were consistent across capture sites. These features, reportedly associated with nesting behaviour, combined with mtDNA AMOVA results, suggest potential movement of T. schlegelii females during the breeding season.

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