Molecular systematics of Malaysian mahseer and phylogeography of Tor douronensis (valenciennes)

Mahseer or commonly known as ‘ikan Kelah’ is an indigenous species of Malaysia. The popularity of this freshwater fish among the locals has made it an economical important aquaculture candidate. This study examines the molecular systematics among Malaysian Mahseers namely Tor douronensis (N=7), Tor tambroides (N=4) and Neolissochilus stracheyi (N=7) and their relationships with other Asian cyprinids (Ctenopharynodon idella, Aristichthys nobilis, Mylopharyngodon piceus, Hypophthalmichthys molitrix, Opsariichthys bidens, Carrasius auratus, Barbonymus gonionotus and Danio rerio) using direct sequencing of mitochondrial DNA genes (cytochrome oxidase subunit II, 12S ribosomal RNA and ATPase6/8) and a nuclear gene (beta-actin). The phylogenetic trees were constructed using Neighbour Joining, Maximum Parsimony and Bayesian analyses. This study also describes the DNA mitochondrial diversity and genetic structure of T. douronensis (N=134) in Sarawak river systems based on cytochrome c oxidase I gene sequences. The nucleotide diversity index was used to estimate within population genetic diversity. While, DNA sequence polymorphism program was used to generate haplotype sequences and later the genetic relationships among haplotypes were determined using the reduced median network and by constructing phylogenetic trees through Neighbour Joining and Maximum Parsimony methods. The test of genetic structuring of T. douronensis in Sarawak was employed using analysis of molecular variance (AMOVA) implemented using ARLEQUIN program. The results of phylogenetic study from these two gene mitochondrial DNA and a nuclear gene strongly support the reciprocally monophyletic status between genus Tor (T. douronensis and T. tambroides) and genus Neolissochilus (represented by N. stracheyi). Thus, the findings have strengthened the current taxonomic status for all three Malaysian indigenous Mahseer. For the Asian cyprinids, an interesting finding was that A. nobilis and H. molitrix were phylogenetically similar and was clustered consistently in the same subclade and was supported with a very low Kimura-2-Parameter distance value (0.000). The mitochondrial DNA diversity and population structure analyses inferred from cytochrome c oxidase I sequences 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 populations which were separated by geographical barrier or river systems. The constructed Neighbour Joining (NJ) and Maximum Parsimony (MP) trees based on haplotypes showed similar topologies, in which the southern Sarawak population was grouped in Cluster I while northern and central Sarawak were clustered in Cluster II. Population structure of the three regions was analysed using Analysis of Molecular Variance (AMOVA). Most of the variations occurred among regions and among subpopulations within a region. The p value after Bonferroni correction revealed that the pairwise FST values for some populations of southern Sarawak (Bau – Terbat, Terbat – Semadang, Bau-Semadang) and population of northern Sarawak (Kg. Pa Puti - Tuyo River) were not significantly different (P>0.05). The sharing of haplotype HapTD1 between samples from Semadang (91.3%), Bakun Dam (25%), Bau (86.4%), Entabai River (6.7%) and Terbat (100%) indicated the historical interconnection of drainages of southern and central Sarawak during the Tertiary and Quaternary Periods via the Sunda River (10-5 mya). Overall, the phylogenetic analyses of the three mitochondrial genes and a nuclear gene have provided better insights into the evolutionary relationships and taxonomy analysis of the Asian cyprinids in relation to Malaysian Mahseer. The phylogeneticresults generated from both types of genes were generally in agreement and concordant with the current classification of the cyprinids based on morphological and meristic characters. The population structure analysis using cytochrome c oxidase I gene sequences has shown high heterogeneity among most of T. douronensis populations in Sarawak which could possibly because of low level of gene flow between the populations. These findings have important implications for aquaculture and fisheries management of this indigenous species of Malaysian Mahseers.

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