Nathalie Bodin

Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (Thunnus albacares)

Global population genetic structure of yellowfin tuna (Thunnus albacares) is still poorly understood despite its relevance for the tuna fishery industry. Low levels of genetic differentiation among oceans speak in favour of the existence of a single panmictic population worldwide of this highly migratory fish. However, recent studies indicated genetic structuring at a much smaller geographic scales than previously considered, pointing out that YFT population genetic structure has not been properly assessed so far. In this study, we demonstrated for the first time, the utility of 2b-RAD genotyping technique for investigating population genetic diversity and differentiation in high gene-flow species. Running de novo pipeline in Stacks, a total of 6772 high-quality genome-wide SNPs were identified across Atlantic, Indian and Pacific population samples representing all major distribution areas. Preliminary analyses showed shallow but significant population structure among oceans (FST=0.0273; P-value<0.01). Discriminant Analysis of Principal Components endorsed the presence of genetically discrete yellowfin tuna populations among three oceanic pools. Although such evidence needs to be corroborated by increasing sample size, these results showed the efficiency of this genotyping technique in assessing genetic divergence in a marine fish with high dispersal potential.

Reproductive potential of Yellowfin Tuna (Thunnus albacares) in the western Indian Ocean

The reproductive biology of Yellowfin Tuna (Thunnus albacares) in the western Indian Ocean was investigated from samples collected in 2009 and 2010. In our study, 1012 female Yellowfin Tuna were sampled: 320 fish on board a purse seiner and 692 fish at a Seychelles cannery. We assessed the main biological parameters that describe reproductive potential: maturity, spawning seasonality, fish condition, and fecundity. The length at which 50% of the female Yellowfin Tuna population matures (L50) was estimated at 75 cm in fork length (FL) when the maturity threshold was established at the cortical alveolar stage of oocyte development. To enable comparison with previous studies, L50 also was estimated with maturity set at the vitellogenic stage of oocyte development; this assessment resulted in a higher value of L50 at 102 cm FL. The main spawning season, during which asynchrony in reproductive timing among sizes was observed, was November–February and a second peak occurred in June. Smaller females (<100 cm FL) had shorter spawning periods (December to February) than those (November to February and June) of large individuals, and signs of skip-spawning periods were observed among small females. The Yellowfin Tuna followed a “capital-income” breeder strategy during ovarian development, by mobilizing accumulated energy while using incoming energy from feeding. The mean batch fecundity for females 79–147 cm FL was estimated at 3.1 million oocytes, and the mean relative batch fecundity was 74.4 oocytes per gram of gonad-free weight. Our results, obtained with techniques defined more precisely than techniques used in previous studies in this region, provide an improved understanding of the reproductive cycle of Yellowfin Tuna in the western Indian Ocean.

Methods of lipid-normalization for multi-tissue stable isotope analyses in tropical tuna

RATIONALE The bias associated with lipid contents in fish tissues is a recalcitrant topic for trophic studies using stable isotopes. Lipids are depleted in the heavy carbon isotope ((13)C) and the lipid content varies considerably among species, tissues and in both time and space. We have applied and assessed different correction methods for tropical tuna tissues. METHODS We tested two types of normalization methods to deal with variable lipid content in liver, gonads, and white and red muscles of yellowfin, bigeye and skipjack tuna: a chemical extraction using dichloromethane and a mathematical correction based on three modeling approaches (linear, non-linear and mass balance models). We measured isotopic ratios of bulk and lipid-free tissues and assessed the predictive ability of the correction models with the lipid-free measurements. The parameters of the models were estimated from our dataset and from results from published studies on other species. RESULTS Comparison between bulk, lipid-free and lipid-corrected isotopic ratios demonstrated that (1) chemical extraction using dichloromethane did not affect δ(15)N values; (2) the change in δ(13)C values after extraction was tissue-specific; (3) lipid-normalization models using published parameter estimates failed to predict lipid-corrected δ(13)C values; and (4) linear and non-linear models using parameters estimated for each tissue from our dataset provided accurate δ(13)C predictions for all tissues, and mass balance model for white muscle only. CONCLUSIONS Models using published estimates for parameters from other species cannot be used. Based on a range of lipid content that do not exceed 45%, we recommend the linear model to correct the bulk δ(13)C values in the investigated tissues but the parameters have to be estimated from a proportion of the original data for which chemical extraction is required and the isotopic values of bulk and lipid-free tissues are measured.

Trace elements in oceanic pelagic communities in the western Indian Ocean

The mineral composition of target and non-target pelagic fish caught by purse-seiners and longliners in the western-central Indian Ocean was determined. From the 10 essential elements analysed, selenium and zinc showed the highest concentrations in swordfish and blue marlin while Indian mackerel appeared as a good source of copper, iron and chrome. All catch had levels of lead and cadmium, two toxic elements, below the maximum sanitary limits. Although some concerns were raised regarding mercury concentrations in the largest species (wahoo, swordfish and blue marlin), molar ratios of mercury and selenium indicate that all oceanic pelagic fish from the western-central Indian Ocean are safe for human consumption. This study also gives insights on the relationships between the levels of essential and toxic elements in fish muscle and the size, trophic position and diet sources of the studied pelagic species.

Putting all the pieces together: integrating current knowledge of the biology, ecology, fisheries status, stock structure and management of yellowfin tuna (Thunnus albacares)

Yellowfin tuna (Thunnus albacares; YFT) is an apex marine predator inhabiting tropical and sub-tropical pelagic waters. It supports the second largest tuna fishery in the world. Here, we review the available literature on YFT to provide a detailed overview of the current knowledge of its biology, ecology, fisheries status, stock structure and management, at global scale. YFT are characterized by several peculiar anatomical and physiological traits that allow them to survive in the oligotrophic waters of the pelagic realm. They are opportunistic feeders, which allows fast growth and high reproductive outputs. Globally, YFT fisheries have expanded over the last century, progressively moving from coastal areas into the majority of sub-tropical and tropical waters. This expansion has led to a rapid increase in global commercial landings, which are predominantly harvested by industrial longline and purse seine fleets. For management purposes, YFT is divided into four stocks, each of which is currently managed by a separate tuna Regional Fisheries Management Organization. Our current understanding of YFT stock structure is, however, still uncertain, with conflicting evidence arising from genetic and tagging studies. There is, moreover, little information about their complex life-history traits or the interactions of YFT populations with spatio-temporally variable oceanographic conditions currently considered in stock assessments. What information is available, is often conflicting at the global scale. Finally, we suggest future research directions to manage this valuable resource with more biological realism and more sustainable procedures.

Biological and environmental influence on tissue fatty acid compositions in wild tropical tunas

This study examined the fatty acid composition of three sympatric tropical tuna species (bigeye Thunnus obesus, yellowfin T. albacares and skipjack tuna Kastuwonus pelamis) sampled in the Western Indian Ocean in 2013. The fatty acid compositions of neutral and polar lipids, respectively involved in energy storage and cell membrane structure, were explored and compared in four tissues (red and white muscles, liver and gonads), according to biological (size, sex and maturity) and environmental (season and area) factors. The liver and the red muscle were the fattest tissues (i.e., higher levels of storage lipids) in all species and polar lipids were the lowest in the white muscle. Species and tissue types explained most differences in fatty acid compositions, while environmental factors had limited effects, except in the hepatic cell membrane where fatty acid composition varied with monsoons. Docosahexaenoic acid (22:6n-3) was the major fatty acid in both polar and neutral lipid fractions, especially in muscles. Eicosapentaenoic acid (20:5n-3) and oleic acid (18:1n-9) were in higher proportion in neutral than in polar lipids. Arachidonic acid (20:4n-6) and 22:6n-3, together with docosapentaenoic acid (22:5n-6) and stearic acid (18:0), showed preferential accumulation in polar lipids. 20:4n-6 was particularly involved in cell membranes of ovary and white muscle. Overall, an important inter-individual variability in fatty acid compositions of structural lipids was found within tissue types despite considering biological factors that are most likely to influence this type of lipids. It suggests that fatty acid profiles are influenced by individual-specific behaviors.

Persistent organic pollutants in albacore tuna (Thunnus alalunga) from Reunion Island (Southwest Indian Ocean) and South Africa in relation to biological and trophic characteristics

The contamination of albacore tuna (Thunnus alalunga) by Persistent Organic Pollutants (POPs), namely polychlorinated biphenyls (PCBs) and dichlorodiphenyl-trichloroethane (DDT), was investigated in individuals collected from Reunion Island (RI) and South Africas (SA) southern coastlines in 2013, in relation to biological parameters and feeding ecology. The results showed lower PCB and DDT concentrations than those previously reported in various tuna species worldwide. A predominance of DDTs over PCBs was revealed, reflecting continuing inputs of DDT. Tuna collected from SA exhibited higher contamination levels than those from RI, related to higher dietary inputs and higher total lipid content. Greater variability in contamination levels and profiles was identified in tuna from RI, explained by a higher diversity of prey and more individualistic foraging behaviour. PCB and DDT contamination levels and profiles varied significantly in tuna from the two investigated areas, probably reflecting exposure to different sources of contamination.

Reproductive biology of Albacore tuna (Thunnus alalunga) in the western Indian Ocean

The reproductive biology of albacore tuna, Thunnus alalunga, in the western Indian Ocean was examined through analysis of the sex ratio, spawning season, length-at-maturity (L50), spawning frequency and fecundity. From 2013 to 2015, a total of 923 female and 867 male albacore were sampled. A bias in sex ratio was found in favor of females with fork length (LF) < 100 cm. Using histological analyses and gonadosomatic index, spawning was found to occur between 10°S and 30°S, mainly to the east of Madagascar from October to January. Large females contributed more to reproduction through their longer spawning period compared to small individuals. The L50 (mean ± standard error) of female albacore was estimated at 85.3 ± 0.7 cm LF. Albacore spawn on average every 2.2 days within the spawning region and spawning months, from November to January. Batch fecundity ranged between 0.26 and 2.09 million oocytes and the relative batch fecundity (mean ± standard deviation) was estimated at 53.4 ± 23.2 oocytes g-1 of somatic-gutted weight. The study provides new information on the reproductive development and classification of albacore in the western Indian Ocean. The reproductive parameters will reduce uncertainty in current stock assessment models which will eventually assist the fishery to be sustainable for future generations.

Energy allocation strategy of skipjack tuna Katsuwonus pelamis during their reproductive cycle

The lipid composition of somatic and reproductive tissues was determined for female skipjack tuna Katsuwonus pelamis caught in the western Indian Ocean between latitude 10° N and 20° S and longitude 40° and 70° E. The highest total lipid (TL) contents were in the liver and gonads, with white muscle levels approximately three-fold lower. Three lipid classes dominated: triacylglycerols (TAG), sterol esters and wax esters (SE-WE) and phospholipids (PL). Collectively, these accounted for between 70 and 80% of TLs. Changes in lipid concentrations were evaluated over the maturation cycle. Immature fish had the lowest gonad and liver TL levels; concentrations of TL, TAG, SE-WE and PL accumulated from immature to mature (spawning-capable) phase, reflecting sustained vitellogenic activity of the liver and a transfer of lipids to developing oocytes from the onset of vitellogenesis. Gonado-somatic and hepato-somatic indices were positively correlated with each other and positively related to TL in the gonads and liver. Fultons condition index and lipid concentrations in muscle did not vary significantly over the maturation cycle; fat content in the main storage tissues was undepleted as the ovary developed. Hence, K. pelamis apparently supports reproduction directly from food intake over the breeding season. In the gonads, reserve lipids (SE-WE and TAG) and sterols were related to batch fecundity but this was not the case for somatic and hepatic tissues. These results suggest that K. pelamis utilizes an income breeding strategy.

Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna.

Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87–90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24–27%), low assignment index and significant inbreeding. Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species—Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.