Tuna-dolphin-bird feeding assemblages are unique to the Eastern Tropical Pacific Ocean (ETP). These multiple species groups are believed to forage together in response to the physical properties of the near surface ocean as these constrain the distribution of prey. In the Galapagos Marine Reserve (GMR), intra-annual and interannual changes affect the properties of the water column, inducing mesoscale and fine scale temporal variability. Four three-week oceanographic surveys took place, in September 2008, April 2009, October 2009, and September 2010, between the coast of Ecuador and the Galapagos Islands and one small boat survey took place in June 2010 within the GMR. Marine mammal surveys were conducted during daylight hours and Conductivity, Temperature, Depth (CTD) sensor casts were taken throughout the survey. Data were analyzed to determine the types of water masses present and the strength and depth of the thermocline layer. These data were compared with the sightings of marine mammals, bird feeding groups, and tuna-dolphin-bird assemblages. Additionally, these data were used to predict where tuna would be likely to associate with dolphin groups. Results show Equatorial Surface Water was the dominant water mass throughout the archipelago, regardless of season or ENSO index. High salinity, cold water west of Isla Isabela indicated topographic upwelling of the Equatorial Undercurrent. Tropical Surface Waters from the Panama Current were detected north of the Equatorial Front to the east of the islands. Obvious changes in the water column properties were observed between El Niño and La Niña events in the GMR. Most mixed groups were sighted west and south of Isla Isabela during the four oceanographic surveys, as well as north and west of Isla San Cristobal in June 2010. Most sightings were in cool, high salinity waters, and high chlorophyll concentrations. There were a greater number of sightings during the April 2009 survey (ENSO-neutral conditions) than during any of the three fall surveys. Additionally, tuna-dolphin-bird groups were more likely to be seen near Isla Isabela, with the majority of them sighted during the April 2009 survey and a few sighted in each of the September 2008 and October 2009 surveys. No tuna-dolphin-bird groups were sighted during the September 2010 surveys. Results show that the presence and location of these multi-species groups may be controlled by the inter-annual cycles, the intra-annual cycles, or a combination of both types of changes seen within the Galapagos.

Typescript. / Bibliography: leaves 239-263. / Microfiche. / xiii, 263 leaves, bound ill. 29 cm

Various aspects of the biology of the tarwhine Rhabdosargus sarba and western yellowfin bream Acanthopagrus latus were studied. The studies on R. sarba have focused on populations in temperate coastal marine waters at ca 32oS and the lower reaches of an estuary (Swan River Estuary) located at the same latitude and in a subtropical embayment (Shark Bay) at ca 26oS, while those on A. latus were conducted on the population in the latter embayment. A combination of a macroscopic and histological examination of the gonads demonstrated that R. sarba is typically a rudimentary hermaphrodite in Western Australian waters, i.e. the juveniles develop into either a male or female in which the ovarian and testicular zones of the gonads, respectively, are macroscopically undetectable. This contrasts with the situation in the waters off Hong Kong and South Africa, in which R. sarba is reported to be a protandrous hermaphrodite. However, it is possible that a few of the fish that are above the size at first maturity and possess, during the spawning period, ovotestes with relatively substantial amounts of both mature testicular and immature ovarian tissue, could function as males early in adult life and then change to females. Although R. sarba spawns at some time between late winter and late spring in Western Australia, spawning peaks later in the Swan River Estuary than in coastal, marine waters at the same latitude and Shark Bay, in which salinities are always close to or above that of full strength sea water, i.e. 35 ñ . While the males and females attain sexual maturity at very similar lengths in the Swan River Estuary and Shark Bay, i.e. L50s all between 170 and 177 mm, they typically reach maturity at an earlier age in the former environment, i.e. 2 vs 3 years old. Thus, length and consequently growth rate influence the timing of maturity rather than age. During the spawning period, only 9 % of the fish caught between 180 and 260 mm in nearshore, shallow marine waters had become mature, whereas 91 % of those in this length range over reefs were mature, indicating that R. sarba tends to move offshore only when it has become gphysiologically ready to mature. The L50s at first maturity indicate that the current minimum legal length in Western Australia (230 mm) is appropriate for managing this species. Oocyte diameter frequency distributions, stages in oocyte development, duration of oocyte hydration and time of formation of post-ovulatory follicles in mature ovaries of Rhabdosargus sarba in the lower Swan River Estuary (32o 03fS, 115o 44fE) were used, in conjunction with data on tidal cycles, to elucidate specific aspects of the reproductive biology of this sparid in an estuarine environment. The results demonstrated the following. (i) Rhabdosargus sarba has indeterminate fecundity sensu Hunter et al. (1985). (ii) Oocyte hydration commences at about dusk (18:30 h) and is completed by ca 01:30-04:30 h, at which time ovulation, as revealed by the presence of hydrated oocytes in the ovarian duct and appearance of newlyformed post-ovulatory follicles, commences. (iii) The prevalence of spawning was positively correlated with tidal strength and was greatest on days when the tide changed from flood to ebb at ca 06:00 h, i.e. approximately when spawning ceases. Spawning just prior to strong ebb tides would lead to the transport of eggs out of the estuary and thus into salinities that remain at ca 35 ñ . The likelihood of eggs being transported downstream is further enhanced by R. sarba spawning in deeper waters in the estuary, where the flow is greatest. (iv) Although mature ovaries were found in R. sarba in the estuary between early July and December, the prevalence of atretic oocytes was high until September, when salinities started rising markedly from their winter minima. Batch fecundities ranged from 2,416 for a 188 mm fish to 53,707 for a 266 mm fish. The average daily prevalence of spawning amongst mature females during the spawning period of R. sarba caught in the lower estuary, i.e. July to end of October, was 36.5 %. Thus, individual female R. sarba spawned, on average, at intervals of ca 2.7 days in each spawning season. Female R. sarba with total lengths of 200, 250 and 300 mm were estimated to have a batch fecundity of 7,400, 20,100 and 54,800 eggs, respectively and annual fecundities of 332,000, 903,000 and 2,461,000 eggs, respectively. Rhabdosargus sarba is shown to undergo size-related movements in each of the three very different environments in which it was studied. In temperate coastal waters, R. sarba settles in unvegetated nearshore areas and then moves progressively firstly to nearby seagrass beds and then to exposed unvegetated nearshore areas and finally to areas around reefs where spawning occurs. Although R. sarba spawns in the lower Swan River Estuary, relatively few of its early 0+ recruits remain in the estuary and substantial numbers of this species do not start reappearing in the estuary until they are ca 140 mm. In Shark Bay, R. sarba uses nearshore mangroves as a nursery area and later moves into areas around reefs. The maximum ages recorded for R. sarba in coastal marine waters (11 years) and Shark Bay (13 years) were far greater than in the lower Swan River Estuary (6 years). However, the maximum lengths recorded in these three environments were all ca 350 mm. Due to the production by size-related movements of differences amongst the lengths of R. sarba at given ages in different habitats in coastal marine waters, the composite suite of lengths at age was not fully representative of the population of this species as a whole in this environment. A von Bertalanffy growth curve, which was adjusted to take into account size related changes in habitat type, significantly improved the fit to the lengths at age of individuals in the composite samples for the population beyond that provided by the unadjusted von Bertalanffy growth curve. This resulted in the maximum difference between the estimates of length at age from the two growth curves, relative to the L‡ derived from the unadjusted von Bertalanffy curve, reaching a value equivalent to 8 %. However, the maximum differences for the corresponding curves for populations in the lower Swan River Estuary and Shark Bay were far less, i.e. 1.7 and 3.2 %, respectively, and thus not considered biologically significant. Rhabdosargus sarba grew slightly faster in the lower Swan River Estuary than in either coastal marine waters or Shark Bay, possibly reflecting the greater productivity of estuarine environments. Acanthopagrus latus is a protandrous hermaphrodite. Detailed macroscopic and histological examination of the gonads of a wide size range of fish, together with a quantification of how the prevalences of the different categories of gonad change with size and age and during the year, were used to elucidate the sequence of changes that occur in the ovotestes of A. latus during life. The scheme proposed in the present study for the protandrous changes in A. latus differed from those proposed for this species elsewhere, but was similar to that of Pollock (1985) for the congeneric Acanthopagrus australis. The ovotestes of functional males develop from gonads which, as in older juveniles, contain substantial amounts of testicular and ovarian tissue. Such ovotestes, and particularly their testicular component, regress markedly after spawning and then, during the next spawning season, either again become ovotestes in which the testicular zone predominates and contains spermatids and spermatozoa (functional males), or become ovotestes in which the ovarian zone predominates and contains vitellogenic oocytes (functional females). Once a fish has become a functional female, it remains a female throughout the rest of its life. The trends exhibited during the year by reproductive variables demonstrate that A. latus in Shark Bay typically spawns on a very limited number of occasions during a short period in August and September and has determinate fecundity. The potential annual fecundities of 24 A. latus ranged from 764,000 in a 600 g fish to 7,910,000 in a 2,050 g fish and produced a mean }1SE of 1,935,000 } 281,000. The total length at which 50 % of A. latus become identifiable as males (245 mm) is very similar to the current minimum legal length (MLL) of 250 mm, which corresponds to an age of 2.5 years less than the age at which 50 % of males become females. Current spawning potential ratios calculated over a range of alternative values for natural mortality (M) for A. latus in Shark Bay suggests that the present fishing pressure is sustainable, but that the current MLL should be reviewed if recreational fishing pressure continues to increase. The age composition and von Bertalanffy growth parameters for Acanthopagrus latus have been determined. The relevant parameters were inserted into the empirical equations of Pauly (1980) and Ralston (1987) for estimating natural mortality (M). Total mortality (Z) was calculated using Hoenigfs (1983) equations, relative abundance analysis and a simulation based on maximum age and sample size.The two point estimates for M for A. latus, which were both 0.70 year-1, greatly exceeded all estimates for Z (range 0.18 to 0.30 year-1), which is clearly an erroneous result. To resolve this problem of inconsistent estimates, a Bayesian approach was developed, which, through combining the likelihood distributions of the various mortality estimates, produced integrated estimates for M and Z that are more consistent and precise than those produced for these two variables using the above methods individually. This approach now yielded lower values for M than Z and a measure of fishing mortality that appears to be consistent with the current status of the fishery. This approach is equally applicable to other fish species.

The consumption of seafood in the United States has increased rapidly in recent years due to high quality protein and health benefits of seafood. Seafood can be a carrier for bacteria normally distributed in the marine environment and, in some cases, can be contaminated by human pathogens. Therefore, there is a potential health risk if seafood is consumed raw or undercooked. However, information regarding prevalence of foodborne pathogens in retail seafood products and the ability of pathogens to survive in the products during refrigerated and frozen storage is limited. The objective of this study was to generate such information for a better understanding of distribution of foodborne pathogens in seafood products and provide data which might be used for risk assessment of foodborne infection associated with seafood consumption. A total of 45 seafood products were collected from local retail stores and analyzed for aerobic plate counts (APC) and psychrotrophic bacterial counts (PBC) as well as presence of foodborne pathogens, including Escherichia coli O157:H7, Salmonella, Listeria monocytogenes, Staphylococcus aureus, Vibrio parahaemolyticus, and Vibrio vulnificus according to procedures described in the U.S. Food and Drug and Administration Bacteriological Analytical Manual (BAM). Presumptive isolates for each foodborne pathogen were further characterized by biochemical reactions using commercial identification kits and confirmed with polymerase chain reaction (PCR) assay. The samples had bacterial populations ranging from 1.90 to 6.11 CFU/g for APC and from 2.00 to 6.78 CFU/g for PBC. According to the microbiological criteria of International Commission on Microbiological Specifications for Foods (ICMSF), all 45 samples were considered acceptable quality (APC < 10⁷ CFU/g, E. coli < 3 MPN/g) with most samples (93.3%) being good quality (APC < 5 × 10⁵ CFU/g, E. coli < 3 MPN/g). No E. coli O157:H7, Salmonella, S. aureus, V. parahaemolyticus, and V. vulnificus was detected in any samples. Two previously frozen shrimp products (4.4%) were confirmed to carry L. monocytogenes. Studies of growth and survival of L. monocytogenes (3 strains), S. aureus (2 strains), and Salmonella (2 serovars) in raw yellowfin tuna meat stored at 5 - 7 °C for 14 days revealed that L. monocytogenes had the ability to multiply in the tuna meat during refrigerated storage while populations of S. aureus and Salmonella were reduced by 1 to 2 log CFU/g after 14 days at 5 - 7 °C. Studies of holding raw yellowfin tuna meat contaminated with L. monocytogenes, S. aureus, and Salmonella at -18 ± 2 °C for 12 weeks observed that all three pathogens, except Salmonella Newport, in tuna samples survived the frozen storage with less than 2- log of reductions in the populations over 12 weeks of storage. No viable cell of Salmonella Newport was detected in samples after 42 days storage at -18 °C. Raw seafood can be a carrier of foodborne pathogens, particularly L. monocytogenes, and many foodborne pathogens can survive in frozen products for several months. Consumption of raw or undercooked seafood products may lead to human infection if the products are contaminated with pathogens. Therefore, sanitation standard operating procedure (SSOP), good manufacturing practice (GMP) and hazards analysis and critical control points (HACCPs) programs shall all be implemented in the seafood industry to prevent seafood products from being contaminated with foodborne pathogens during handling and processing. Moreover, proper storage of raw seafood products and avoiding cross-contamination during handling at the retail levels also helps to minimize risk of human infection associated with ready-to-eat products. / Graduation date: 2013

Fish populations are regulated by both external environmental factors, e.g., water quality parameters and habitat, and internal reproductive biology and physiology processes. For many species and populations there is often ample external information, while critical internal, i.e., life-history trait (LHT), information is not available. For this study, I determined LHTs and energy allocation patterns for Epinephelus guttatus (red hind), E. striatus (Nassau grouper), and Mycteroperca venenosa (yellowfin grouper) harvested from The Bahamas. I determined age ranges, and how growth patterns and rates differed among the study species. The maximum ages were: 17, E. guttatus; 22, E. striatus; and 13, M. venenosa. Epinephelus striatus was estimated to have the slowest, while M. venenosa had the fastest growth rate. A gonad histological classification system and the ageing data were used to determine the spawning seasons, sex ratios, size and age of sexual maturation and sex change and gonadosomatic indices (GSIs) for the study species. The peak spawning months were January-February for E. guttatus, December-January for E. striatus and March-April for M. venenosa. The fifty-percent sexual maturity estimates were 235 total length mm (Tlmm) (2.05 year old, yo), 435 Tlmm (4.00 yo), and 561 Tlmm (4.66 yo) for E. guttatus, E. striatus and M. venenosa, respectively. The size and age range of sex change for E. guttatus was between 257-401 Tlmm, ~4-5 years old and between 716-871 Tlmm, ~8-9 yo for M. venenosa. I determined protein and lipid concentrations in muscle and gonad tissues to ascertain energy allocation patterns. For all species and sexes except for female E. guttatus, the proportion of energy delegated to somatic growth declines as a fish grows longer, while reproduction energy allocation increases. The results of each study were compared to previous studies conducted throughout the tropical western Atlantic Ocean, and were related to species-specific ecological and spawning behaviors. The findings of each study highlight that the LHTs of the study species greatly differ and these differences will impact population dynamics and need to be considered for management initiatives. In the final chapter, the effects of fishing on LHTs are reviewed and fishery management options are discussed.

Abstract In Taiwan, long-line fishing has been the major technique in fishery. With the enhancement of fishing techniques, the fishing zone of Taiwan has spread all over three of World Oceans, and Taiwan has been regarded as one of five largest pelagic fishing countries. Pelagic long-line fishery plays a crucial role in economic development in Taiwan. In recent years, the fishery environments, whether in domestic or foreign fishing zone, have been dramatically changing. Since the United Nations Convention on the Law of the Sea has been resulted, all of coastal nations have subsequently set up the Exclusive Economic Zone (EEZ) or marine economic development zone, which is stretched out 200 nautical miles from a nation¡¦s coast. However, the establishment of marine economic development zone also brings about the high seas¡¦ largely shrinking. Since the past, the increasing extinction of fish species is mainly resulted from illegal fishing techniques, fishing in the fishing-prohibited zone or during the prohibited period, catching fingerlings and using illegitimate fishing gear. Under such a decreasing fishing circumstance, those Taiwanese long-line fishing vessels under 100 tonnes, mostly fishing in the South Pacific Ocean, are struggling with many changes, such as international fishing limitation, the fishing vessels decreasing policy, the diminishing amount of fish caused by climate changes, the raising oil price and cost. Respecting the situation that most of long-line fishing vessels are managed by ship owners instead of fishery companies, and the fishing-related records are too scarce to provide for reference, this research will explore how the 100-tonne-under long-line fishing vessels owners can manage their business in South Pacific Ocean. All information in this study is acquired from Fisheries Agency in Taiwan and interviews with long-line fishing vessels owners. The questions asked in those interviews mainly target fishing benefit, cost, method of supplies, and the policy on captain and crew management. Based on the analysis of those cases mentioned above, we can figure out the practical operation and management of the 100-tonne-under long-line fishing vessels owners in Taiwan. Furthermore, this study also points out current difficulties in fishery management, providing for those vessels owners as the crucial reference of increasing competitive advantages. Keywords: Long-Line Fishing, South Pacific Ocean, Business Management, Yellowfin Tuna, Cost-Benefit Analysis

Yellowfin tuna Thunnus albacares is a commercially and economically important fisheries species, which comprises the second largest component of South Africa’s catch of tuna and tuna-like species. Catches of the species off South Africa are treated as two discrete stocks by the two tuna Regional Fisheries Management Organisations (tRFMOs) under whose jurisdictions they fall. Individuals caught off the Western Cape, west of the boundary between the tRFMOs at 20°E, are included in assessment and management of the Atlantic Ocean yellowfin tuna stock by the International Commission for the Conservation of Atlantic Tunas (ICCAT), and those caught east of this boundary are assessed and managed as part of the Indian Ocean stock by the Indian Ocean Tuna Commission (IOTC). The boundary between these stocks is based on the confluence of the two oceans in this region and does not incorporate the population structure of species. For sustainable exploitation of fisheries resources, it is important that the definition of management stocks reflects species’ biological population structure; the fine-scale stock structure of yellowfin tuna off South Africa is therefore a research priority which this study aimed to address by means of population genomics analyses. Yellowfin tuna exhibit shallow genetic differentiation over wide geographic areas, and as such traditional population genetic approaches have limited power in resolving fishery significant population structure in the species. Herein, a population genomic approach was employed, specifically, genome-wide analysis of single nucleotide polymorphisms (SNPs) discovered using a next-generation DNA sequencing approach, to confer (i) increased statistical power to detect neutral structuring reflecting population connectivity patterns and (ii) signatures of local adaptation. The mitochondrial Control Region (mtDNA CR) was also sequenced to compare the resolving power of different approaches and to permit coalescent based analyses of the species evolutionary history in the region. Neutral SNP loci revealed significant structure within the dataset (Fst=0.0043; P<0.0001); partitioning of this differentiation within the dataset indicated significant differentiation between yellowfin tuna from the Western Cape and the Gulf of Guinea in the eastern Atlantic Ocean, with no significant differentiation between individuals from the Western Cape and Western Indian Ocean regions. This indicates two population units wherein there is a separation of the Gulf of Guinea from the remaining samples (Indian Ocean including Western Cape) that are largely derived from a single genetic population. This pattern was also supported by assignment tests. Positive outlier SNPs, exhibiting signatures of diversifying selection, suggest that individuals from these regions may be locally adapted, as well as demographically isolated. The mtDNA CR did not reveal any significant genetic structure among samples (Fst=0.0030; P=0.309), demonstrating the increased resolving power provided by population genomics approaches, but revealed signatures of historical demographic fluctuations associated with glacial cycles. Based on the findings of this study, it is suggested that yellowfin tuna caught off the Western Cape of South Africa are migrants from the Indian Ocean population, exhibiting significant genetic differentiation from the Atlantic Ocean Gulf of Guinea individuals, and should thus be included in the assessment and management of the Indian Ocean stock. It is therefore recommended that the boundary between the Atlantic and Indian Ocean yellowfin tuna stocks, under the mandates of ICCAT and the IOTC respectively, should be shifted to approximately 13.35°E to include all individuals caught in South African waters in the Indian Ocean stock.

The population genetic structure of Atlantic yellowfin tuna (Thunnus albacares) has received little attention despite the substantial fishing mortality of juveniles caused by purse seining around fish aggregating devices in the Gulf of Guinea targeting multi-species schools that also include similarly sized skipjack tuna (Katsuwonus pelamis) and bigeye tuna (T. obesus). We used sequence data from 355 bp of the mitochondrial control region I as well as six microsatellite loci to examine: (1) population structure, and (2) to look for evidence of reproductive variance. We analyzed two samples of adults from the Gulf of Mexico (GOM) and one sample of early juveniles (20-50 mm) from the Gulf of Guinea (GOG). We found no evidence of geographic or temporal differentiation among the samples. Accordingly, the null hypothesis of panmixia for yellowfin tuna in the Atlantic Ocean could not be rejected. A sudden expansion analysis based on mtDNA control region I sequence data of yellowfin tuna was highly significant. Time estimates for expansion were between 40,000 and 80,000 years before present. The associated high levels of homoplasy could be masking any existing population structure. Additional sampling from additional locations and across several years will be needed to test the hypothesis of panmixia. We also provide preliminary evidence of the Allendorf-Phelps effect, which may contribute to reproductive variance. This is the first evidence of this effect in any other tuna or pelagic species. Data indicates that early juveniles sharing the same mtDNA control region I haplotype were caught in the same tow and had a significant probability of halfsibship status as calculated from their haplotype and genotype at one microsatellite locus through kinship analysis. Sampling throughout the spawning season and across several years, as well as analysis with additional microsatellite loci that have a more even distribution of alleles, will be needed to more fully identify the sibling status of larvae and early juveniles caught in the same tow as well as the extent of this reproductive variance.

The population genetic structure of Atlantic yellowfin tuna (Thunnus albacares) has received little attention despite the substantial fishing mortality of juveniles caused by purse seining around fish aggregating devices in the Gulf of Guinea targeting multi-species schools that also include similarly sized skipjack tuna (Katsuwonus pelamis) and bigeye tuna (T. obesus). We used sequence data from 355 bp of the mitochondrial control region I as well as six microsatellite loci to examine: (1) population structure, and (2) to look for evidence of reproductive variance. We analyzed two samples of adults from the Gulf of Mexico (GOM) and one sample of early juveniles (20-50 mm) from the Gulf of Guinea (GOG). We found no evidence of geographic or temporal differentiation among the samples. Accordingly, the null hypothesis of panmixia for yellowfin tuna in the Atlantic Ocean could not be rejected. A sudden expansion analysis based on mtDNA control region I sequence data of yellowfin tuna was highly significant. Time estimates for expansion were between 40,000 and 80,000 years before present. The associated high levels of homoplasy could be masking any existing population structure. Additional sampling from additional locations and across several years will be needed to test the hypothesis of panmixia. We also provide preliminary evidence of the Allendorf-Phelps effect, which may contribute to reproductive variance. This is the first evidence of this effect in any other tuna or pelagic species. Data indicates that early juveniles sharing the same mtDNA control region I haplotype were caught in the same tow and had a significant probability of halfsibship status as calculated from their haplotype and genotype at one microsatellite locus through kinship analysis. Sampling throughout the spawning season and across several years, as well as analysis with additional microsatellite loci that have a more even distribution of alleles, will be needed to more fully identify the sibling status of larvae and early juveniles caught in the same tow as well as the extent of this reproductive variance.

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.