Malaysian Mahseer, Tor douronensis, locally known as “kelah” in Peninsular Malaysia or semah in Sarawak is one of the important Mahseers used for food as well as the aquarium industry and game fishing. This species is endemic to Malaysian Borneo river basins. The wild stocks of T. douronensis have declined substantially in recent years, due to over exploitation, pollution and illegal fishing practices. DNA sequencing based on a partial sequence of the cytochrome c oxidase I (COI) gene, was used to determine genetic variation in wild stocks of T. douronensis originated from eight different populations in Sarawak River Basins of Malaysian Borneo. The highest haplotype diversity was found in Entabai river population while the lowest were marked in four populations of Lundu, Terbat, Bau and Kg. Pa Puti. The population structure analyses based on ANOVA or found low level of intra and high level of inter population variations in samples of T. douronensis of Sarawak. The presence of unique haplotype in some populations, along with high FST values indicated that there has been restricted or no migration among the existing population which were separated by geographical barrier or river systems. The population structure of the three regions was also analysed using ANOVA and revealed that most of the variations occurred among regions and among subpopulations within a region. Population structure of T. douronensis showed high degree of genetic heterogeneity and appeared to be significantly structured into geographically discrete population.

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