Genetic stock structure and inferred migratory patterns of skipjack tuna (Katsuwonus pelamis) and yellowfin tuna (Thunnus albacares) in Sri Lankan waters

Tuna are the major marine fishery in Sri Lanka, and yellowfin tuna (YFT) (Thunnus albacares) and skipjack tuna (SJT) (Katsuwonus pelamis) represent 94% of all tuna caught. The tuna catch in Sri Lanka has increased rapidly over recent years and this is true generally for the Indian Ocean. Tuna are a major animal protein source for 20 million people in Sri Lanka, while marine fisheries provide the main income source for most Sri Lankan coastal communities. While the importance of the fishery will require effective stock management practices to be employed, to date no genetic studies have been undertaken to assess wild stock structure in Sri Lankan waters as a basis for developing effective stock management practices for tuna in the future. This thesis undertook such a genetic analysis of Sri Lankan T. albacares and K. pelamis stocks. Samples of both YFT and SJT were collected over four years (2001 - 2004) from seven fishing grounds around Sri Lanka, and also from the Laccadive and Maldive Islands in the western Indian Ocean. Partial mitochondrial DNA (mtDNA) ATPase 6 and 8 genes and nuclear DNA (nDNA) microsatellite variation were examined for relatively large samples of each species to document genetic diversity within and among sampled sites and hence to infer stock structure and dispersal behaviour. Data for YFT showed significant genetic differentiation for mtDNA only among specific sites and hence provided some evidence for spatial genetic structure. Spatial Analysis of Molecular Variance (SAMOVA) analysis suggests that three geographically meaningful YFT groups are present. Specifically, one group comprising a single site on the Sri Lankan west coast, a second group comprising a single site on the east coast and a third group of remaining sites around Sri Lanka and the Maldive Islands. Patterns of variation at nDNA loci in contrast, indicate extensive contemporary gene flow among all sites and reflect very large population sizes. For SJT, both mtDNA and nDNA data showed high levels of genetic differentiation among all sampling sites and hence evidence for extensive spatial genetic heterogeneity. MtDNA data also indicated temporal variation within sites, among years. As for YFT, three distinct SJT groups were identified with SAMOVA; The Maldive Islands in the western Indian Ocean comprising one site, a second group comprising a single site on the east coast and a third group of remaining sites around Sri Lanka and the Laccadive Islands. The mtDNA data analyses indicated two divergent (M^ = 1.85% ) SJT clades were present among the samples at all sample sites. SJT nDNA results support the inference that multiple 'sub populations' co-exist at all sample sites, albeit in different frequencies. It appears that variation in the relative frequencies of each clade per site accounts for much of the observed genetic differentiation among sites while effective populations remain extremely large. Based on combined data sets for management purposes therefore, there is no strong evidence in these data to indicate that more than a single YFT stock is present in Sri Lankan waters. For SJT however, evidence exists for two divergent clades that are admixed but not apparently interbreeding around Sri Lanka. The identity of spawning grounds of these two clades is currently unknown but is likely to be geographically distant from Sri Lanka. Spawning grounds of the two distinct SJT clades should be identified and conserved.