Tunabio: biological traits of tropical tuna and bycatch species caught by purse seine fisheries in the Western Indian and Eastern Central Atlantic Oceans.

Background: Along with the development of the tropical tuna purse-seine fishery from the 1960s in the Atlantic Ocean and from the 1980s in the Indian Ocean, many projects and studies have been conducted to improve knowledge about the biology, migrations and dynamics of the stocks of target and non-target (i.e. bycatch) species taken in these fisheries. Since the 2000s, the European Union (EU) has been supporting Member States in the collection of biological data on species caught by their purse seine and pole and line fisheries, thus making it possible to have a long-term series of data. Biological data have never been saved by the different tuna commissions, unlike the catches by species and sizes by areas and periods. However, these data are essential to monitor the status of the fisheries and fuel the assessment models used by the tuna Regional Fisheries Management Organisations (tRFMOs) for the sustainable management and conservation of the fish stocks under their mandate. New information: We combined historical (1974-1999) and current (2003-2020) datasets on the biology of tropical tunas and bycatch fish caught by large-scale purse seiners in the Eastern Atlantic Ocean (EAO) and Western Indian Ocean (WIO). The resulting Tunabio database is presented in the present data paper and contains all available morphometric and biological data collected on more than 80,000 fish individuals.

NMR-based metabolic profiling and discrimination of wild tropical tunas by species, size category, geographic origin, and on-board storage condition.

Tunas are among the most traded and valued fish species, and good traceability of tuna products in the world market is needed to protect both consumers and tuna stocks. To that purpose, high-resolution proton nuclear magnetic resonance (1H NMR) spectroscopy combined with multivariate data analysis was used to investigate the molecular components of the aqueous extract of white and red muscles in three species of wild tropical tuna species, namely yellowfin tuna (Thunnus albacares), skipjack tuna (Katsuwonus pelamis) and bigeye tuna (T. obesus). Principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) applied to the processed 1H NMR spectra showed significant separation according to the species and size category (i.e., small tunas < 80 cm fork length vs large tunas > 80 cm fork length), the storage conditions on-board the purse-seine vessels (i.e., brine- vs deep-freezing), and the geographical origin (i.e., where the tuna was caught: Mozambique Channel vs western-central Indian Ocean). The major groups of metabolites responsible for differentiation in PLS-DA score plots were the dipeptides (anserine, carnosine) and organic acids (lactate, creatine/phosphocreatine) in the white muscle, and the free amino acids, essential nutrients (choline and its derivatives, phosphatidylethanolamine), dipeptides and organic acids in the red muscle. Our results showed that NMR-based metabolomics is a powerful tool to efficiently discriminate specific profiles among wild tuna species, raw muscle tissues, fish storage conditions and tuna geographical origin.

Fuel consumption and air emissions in one of the world's largest commercial fisheries.

The little information available on fuel consumption and emissions by high seas tuna fisheries indicates that the global tuna fleet may have consumed about 2.5 Mt of fuel in 2009, resulting in the production of about 9 Mt of CO2-equivalent greenhouse gases (GHGs), i.e., about 4.5-5% of the global fishing fleet emissions. We developed a model of annual fuel consumption for the large-scale purse seiners operating in the western Indian Ocean as a function of fishing effort, strategy, and vessel characteristics based on an original and unique data set of more than 4300 bunkering operations that spanned the period 2013-2019. We used the model to estimate the total fuel consumption and associated GHG and SO2 emissions of the Indian Ocean purse seine fishery between 1981 and 2019. Our results showed that the energetic performance of this fishery was characterized by strong interannual variability over the last four decades. This resulted from a combination of variations in tuna abundance but also changes in catchability and fishing strategy. In recent years, the increased targeting of schools associated with fish aggregating devices in response to market incentives combined with the IOTC management measure implemented to rebuild the stock of yellowfin tuna has strongly modified the productivity and spatio-temporal patterns of purse seine fishing. This had effects on fuel consumption and air pollutant emissions. Over the period 2015 to 2019, the purse seine fishery, including its support vessel component, annually consumed about 160,000 t of fuel and emitted 590,000 t of CO2-eq GHG. Furthermore, our results showed that air pollutant emissions can be significantly reduced when limits in fuel composition are imposed. In 2015, SO2 air pollution exceeded 1500 t, but successive implementation of sulphur limits in the Indian Ocean purse seine fishery in 2016 and 2018 have almost eliminated this pollution. Our findings highlight the need for a routine monitoring of fuel consumption with standardized methods to better assess the determinants of fuel consumption in fisheries and the air pollutants they emit in the atmosphere.

Benefit-risk associated with the consumption of fish bycatch from tropical tuna fisheries.

Mercury, omega-3 (docosahexaenoic acid, DHA and eicosapentaenoic acid, EPA) and macronutrients (fat and proteins) were quantified on a wet weight (ww) basis in 20 species of fish taken as bycatch in tropical tuna fisheries. Based on a hazard quotient taking into account mercury and omega-3 contents, a benefit-risk assessment for the consumption of these pelagic species was conducted for three people categories: young children, children and adults. All fish bycatch were found to be an excellent source of proteins (min‒max = 14.4-25.2 g/100 g fillet), had low omega-6/omega-3 ratios (<1, except for silky shark), and had mercury content below the safety limits defined by sanitary agencies. Silky shark and Istiophoridae had the highest mercury contents (min‒max = 0.029-0.317 ppm ww). Omega-3 contents were the lowest in silky shark (0.2 ± 0.2 mg/100 g fillet) and the highest in striped marlin (3.6 ± 3.2 g/100 g fillet). Billfishes (Istiophoridae, including striped marlin), minor tunas (Scombridae), and Carangidae had the highest omega-3 contents (min‒max = 0.68-7.28 g/100 g fillet). The highest hazard quotient values obtained for silky shark and great barracuda reflected a lower nutritional benefit (i.e., low omega-3 source) than risk (i.e., mercury exposure), making them not advisable for consumption. Eight species had low hazard quotients, and among them cottonmouth jack and flat needlefish were found of high health interest (high protein, moderate fat contents, and low omega-6/omega-3 ratio). A daily serving portion of 85-200 g (according to people category) can be recommended for these species. Batfish, and to a lower extent pompano dolphinfish and brassy chub, can also be consumed safely and would provide greater health benefits than risks. These results advocate for a better access of these species to local populations.

The population genomics of yellowfin tuna (Thunnus albacares) at global geographic scale challenges current stock delineation.

Yellowfin tuna, Thunnus albacares, is one of the most important seafood commodities in the world. Despite its great biological and economic importance, conflicting evidence arises from classical genetic and tagging studies concerning the yellowfin tuna population structure at local and global oceanic scales. Access to more powerful and cost effective genetic tools would represent the first step towards resolving the population structure of yellowfin tuna across its distribution range. Using a panel of 939 neutral Single Nucleotide Polymorphisms (SNPs), and the most comprehensive data set of yellowfin samples available so far, we found genetic differentiation among the Atlantic, Indian and Pacific oceans. The genetic stock structure analysis carried out with 33 outlier SNPs, putatively under selection, identified discrete populations within the Pacific Ocean and, for the first time, also within the Atlantic Ocean. Stock assessment approaches that consider genetic differences at neutral and adaptive genomic loci should be routinely implemented to check the status of the yellowfin tuna, prevent illegal trade, and develop more sustainable management measures.

Ecological data for western Indian Ocean tuna.

Tuna are marine apex predators that inhabit the tropical and sub-tropical waters of the Indian Ocean where they support socially and economically important fisheries. Key component of pelagic communities, tuna are bioindicator species of anthropogenic and climate-induced changes through modifications of the structure and related energy-flow of food webs and ecosystems. The IndianEcoTuna dataset provides a panel of ecological tracers measured in four soft tissues (white muscle, red muscle, liver, gonads) from 1,364 individuals of four species, i.e., the albacore (ALB, Thunnus alalunga), the bigeye (BET, T. obesus), the skipjack (SKJ, Katsuwomus pelamis), and the yellowfin (YFT, T. albacares), collected throughout the western Indian Ocean from 2009 to 2015. Sampling was carried out during routine monitoring programs, at sea by observers onboard professional vessels or at landing. For each record, the type of fishing gear, the conservation mode, as well as the fishing date and catch location are provided. Individuals were sampled to span a wide range of body sizes: 565 ALB with fork length from 58 to 118 cm, 155 BET from 29.5 to 173 cm, 304 SKJ from 30 to 74 cm, and 340 YFT from 29 to 171.5 cm. The IndianEcoTuna dataset combines: (1) 9,512 records of carbon and nitrogen stable isotopes (percent element weights, δ13 C and δ15 N values) in 1,185 fish, (2) 887 concentrations of total proteins in 242 fish, (3) 8,356 concentrations of total lipids and three lipid classes (triacylglycerols TAG; phospholipids PL; sterols ST) in 695 fish, and (4) 1,150 and 1,033 profiles of neutral and polar fatty acids in 397 and 342 fish, respectively. Information on sex and weights of the whole fish, gonads, liver and stomach is provided. Because of the essential trophic role and wide-ranging of tuna in marine systems, and the large panel of tropho-energetic tracers and derived-key quantitative parameters provided (e.g., niche width, trophic position, condition indices), the IndianEcoTuna dataset should be of high interest for global and regional research on marine trophic ecology and food web analysis, as well as on the impacts of anthropogenic changes on Indian Ocean marine ecosystems. There are no copyright restrictions for research and/or teaching purposes. Usage of the dataset must include citation of this Data Paper.

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.

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.

Large-Scale Examination of Spatio-Temporal Patterns of Drifting Fish Aggregating Devices (dFADs) from Tropical Tuna Fisheries of the Indian and Atlantic Oceans.

Since the 1990s, massive use of drifting Fish Aggregating Devices (dFADs) to aggregate tropical tunas has strongly modified global purse-seine fisheries. For the first time, a large data set of GPS positions from buoys deployed by French purse-seiners to monitor dFADs is analysed to provide information on spatio-temporal patterns of dFAD use in the Atlantic and Indian Oceans during 2007-2011. First, we select among four classification methods the model that best separates "at sea" from "on board" buoy positions. A random forest model had the best performance, both in terms of the rate of false "at sea" predictions and the amount of over-segmentation of "at sea" trajectories (i.e., artificial division of trajectories into multiple, shorter pieces due to misclassification). Performance is improved via post-processing removing unrealistically short "at sea" trajectories. Results derived from the selected model enable us to identify the main areas and seasons of dFAD deployment and the spatial extent of their drift. We find that dFADs drift at sea on average for 39.5 days, with time at sea being shorter and distance travelled longer in the Indian than in the Atlantic Ocean. 9.9% of all trajectories end with a beaching event, suggesting that 1,500-2,000 may be lost onshore each year, potentially impacting sensitive habitat areas, such as the coral reefs of the Maldives, the Chagos Archipelago, and the Seychelles.

Forecasting the major influences of predation and environment on cod recovery in the northern Gulf of St. Lawrence.

The northern Gulf of St. Lawrence (NGSL) stock of Atlantic cod (Gadus morhua), historically the second largest cod population in the Western Atlantic, has known a severe collapse during the early 1990 s and is currently considered as endangered by the Committee on the Status of Endangered Wildlife in Canada. As for many fish populations over the world which are currently being heavily exploited or overfished, urgent management actions in the form of recovery plans are needed for restoring this stock to sustainable levels. Stochastic projections based on a statistical population model incorporating predation were conducted over a period of 30 years (2010-2040) to assess the expected outcomes of alternative fishing strategies on the stock recovery under different scenarios of harp seal (Pagophilus groenlandicus) abundance and environmental conditions. This sensitivity study shows that water temperature is key in the rebuilding of the NGSL cod stock. Model projections suggest that maintaining the current management practice under cooler water temperatures is likely to maintain the species in an endangered status. Under current or warmer conditions in the Gulf of St. Lawrence, partial recovery might only be achieved by significant reductions in both fishing and predation pressure. In the medium-term, a management strategy that reduces catch could be favoured over a complete moratorium so as to minimize socio-economic impacts on the industry.

Eating up the world's food web and the human trophic level.

Trophic levels are critical for synthesizing species' diets, depicting energy pathways, understanding food web dynamics and ecosystem functioning, and monitoring ecosystem health. Specifically, trophic levels describe the position of species in a food web, from primary producers to apex predators (range, 1-5). Small differences in trophic level can reflect large differences in diet. Although trophic levels are among the most basic information collected for animals in ecosystems, a human trophic level (HTL) has never been defined. Here, we find a global HTL of 2.21, i.e., the trophic level of anchoveta. This value has increased with time, consistent with the global trend toward diets higher in meat. National HTLs ranging between 2.04 and 2.57 reflect a broad diversity of diet, although cluster analysis of countries with similar dietary trends reveals only five major groups. We find significant links between socio-economic and environmental indicators and global dietary trends. We demonstrate that the HTL is a synthetic index to monitor human diets and provides a baseline to compare diets between countries.

Accounting for age uncertainty in growth modeling, the case study of yellowfin tuna (Thunnus albacares) of the Indian Ocean.

Age estimates, typically determined by counting periodic growth increments in calcified structures of vertebrates, are the basis of population dynamics models used for managing exploited or threatened species. In fisheries research, the use of otolith growth rings as an indicator of fish age has increased considerably in recent decades. However, otolith readings include various sources of uncertainty. Current ageing methods, which converts an average count of rings into age, only provide periodic age estimates in which the range of uncertainty is fully ignored. In this study, we describe a hierarchical model for estimating individual ages from repeated otolith readings. The model was developed within a Bayesian framework to explicitly represent the sources of uncertainty associated with age estimation, to allow for individual variations and to include knowledge on parameters from expertise. The performance of the proposed model was examined through simulations, and then it was coupled to a two-stanza somatic growth model to evaluate the impact of the age estimation method on the age composition of commercial fisheries catches. We illustrate our approach using the sagittal otoliths of yellowfin tuna of the Indian Ocean collected through large-scale mark-recapture experiments. The simulation performance suggested that the ageing error model was able to estimate the ageing biases and provide accurate age estimates, regardless of the age of the fish. Coupled with the growth model, this approach appeared suitable for modeling the growth of Indian Ocean yellowfin and is consistent with findings of previous studies. The simulations showed that the choice of the ageing method can strongly affect growth estimates with subsequent implications for age-structured data used as inputs for population models. Finally, our modeling approach revealed particularly useful to reflect uncertainty around age estimates into the process of growth estimation and it can be applied to any study relying on age estimation.

Global marine primary production constrains fisheries catches.

Primary production must constrain the amount of fish and invertebrates available to expanding fisheries; however the degree of limitation has only been demonstrated at regional scales to date. Here we show that phytoplanktonic primary production, estimated from an ocean-colour satellite (SeaWiFS), is related to global fisheries catches at the scale of Large Marine Ecosystems, while accounting for temperature and ecological factors such as ecosystem size and type, species richness, animal body size, and the degree and nature of fisheries exploitation. Indeed we show that global fisheries catches since 1950 have been increasingly constrained by the amount of primary production. The primary production appropriated by current global fisheries is 17-112% higher than that appropriated by sustainable fisheries. Global primary production appears to be declining, in some part due to climate variability and change, with consequences for the near future fisheries catches.