A review of the fisheries, life history and stock structure of tropical tuna (skipjack Katsuwonus pelamis, yellowfin Thunnus albacares and bigeye Thunnus obesus) in the Indian Ocean.

Skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares) and bigeye (Thunnus obesus) tuna are the target species of tropical tuna fisheries in the Indian Ocean, with high commercial value in the international market. High fishing pressure over the past three decades has raised concerns about their sustainability. Understanding life history strategies and stock structure is essential to determine species resilience and how they might respond to exploitation. Here we provide a comprehensive review of available knowledge on the biology, ecology, and stock structure of tropical tuna species in the Indian Ocean. We describe the characteristics of Indian Ocean tropical tuna fisheries and synthesize skipjack, yellowfin, and bigeye tuna key life history attributes such as biogeography, trophic ecology, growth, and reproductive biology. In addition, we evaluate the available literature about their stock structure using different approaches such as analysis of fisheries data, genetic markers, otolith microchemistry and tagging, among others. Based on this review, we conclude that there is a clear lack of ocean basin-scale studies on skipjack, yellowfin and bigeye tuna life history, and that regional stock structure studies indicate that the panmictic population assumption of these stocks should be investigated further. Finally, we identify specific knowledge gaps that should be addressed with priority to ensure a sustainable and effective management of these species.

Migration dynamics of juvenile southern bluefin tuna.

Large scale migrations are a key component of the life history of many marine species. We quantified the annual migration cycle of juvenile southern bluefin tuna (Thunnus maccoyii; SBT) and spatiotemporal variability in this cycle, based on a multi-decadal electronic tagging dataset. Behaviour-switching models allowed for the identification of cohesive areas of residency and classified the temporal sequence of movements within a migration cycle from austral summer foraging grounds in the Great Australian Bight (GAB) to winter foraging grounds in the Indian Ocean and Tasman Sea and back to the GAB. Although specific regions within the Indian Ocean were frequented, individuals did not always return to the same area in consecutive years. Outward migrations from the GAB were typically longer than return migrations back to the GAB. The timing of individual arrivals to the GAB, which may be driven by seasonality in prey availability, was more cohesive than the timing of departures from the GAB, which may be subject to the physiological condition of SBT. A valuable fishery for SBT operates in the GAB, as do a number of scientific research programs designed to monitor SBT for management purposes; thus, understanding SBT migration to and from the area is of high importance to a number of stakeholders.

Reliably discriminating stock structure with genetic markers: Mixture models with robust and fast computation.

Delineating naturally occurring and self-sustaining subpopulations (stocks) of a species is an important task, especially for species harvested from the wild. Despite its central importance to natural resource management, analytical methods used to delineate stocks are often, and increasingly, borrowed from superficially similar analytical tasks in human genetics even though models specifically for stock identification have been previously developed. Unfortunately, the analytical tasks in resource management and human genetics are not identical-questions about humans are typically aimed at inferring ancestry (often referred to as "admixture") rather than breeding stocks. In this article, we argue, and show through simulation experiments and an analysis of yellowfin tuna data, that ancestral analysis methods are not always appropriate for stock delineation. In this work, we advocate a variant of a previously introduced and simpler model that identifies stocks directly. We also highlight that the computational aspects of the analysis, irrespective of the model, are difficult. We introduce some alternative computational methods and quantitatively compare these methods to each other and to established methods. We also present a method for quantifying uncertainty in model parameters and in assignment probabilities. In doing so, we demonstrate that point estimates can be misleading. One of the computational strategies presented here, based on an expectation-maximization algorithm with judiciously chosen starting values, is robust and has a modest computational cost.

Absolute abundance of southern bluefin tuna estimated by close-kin mark-recapture.

Southern bluefin tuna is a highly valuable, severely depleted species, whose abundance and productivity have been difficult to assess with conventional fishery data. Here we use large-scale genotyping to look for parent-offspring pairs among 14,000 tissue samples of juvenile and adult tuna collected from the fisheries, finding 45 pairs in total. Using a modified mark-recapture framework where 'recaptures' are kin rather than individuals, we can estimate adult abundance and other demographic parameters such as survival, without needing to use contentious fishery catch or effort data. Our abundance estimates are substantially higher and more precise than previously thought, indicating a somewhat less-depleted and more productive stock. More broadly, this technique of 'close-kin mark-recapture' has widespread utility in fisheries and wildlife conservation. It estimates a key parameter for management-the absolute abundance of adults-while avoiding the expense of independent surveys or tag-release programmes, and the interpretational problems of fishery catch rates.

Spawning Dynamics and Size Related Trends in Reproductive Parameters of Southern Bluefin Tuna, Thunnus maccoyii.

Knowledge of spawning behaviour and fecundity of fish is important for estimating the reproductive potential of a stock and for constructing appropriate statistical models for assessing sustainable catch levels. Estimates of length-based reproductive parameters are particularly important for determining potential annual fecundity as a function of fish size, but they are often difficult to estimate reliably. Here we provide new information on the reproductive dynamics of southern bluefin tuna (SBT) Thunnus maccoyii through the analysis of fish size and ovary histology collected on the spawning ground in 1993-1995 and 1999-2002. These are used to refine previous parameter estimates of spawning dynamics and investigate size related trends in these parameters. Our results suggest that the small SBT tend to arrive on the spawning ground slightly later and depart earlier in the spawning season relative to large fish. All females were mature and the majority were classed as spawning capable (actively spawning or non-spawning) with a very small proportion classed as regressing. The fraction of females spawning per day decreased with fish size, but once females start a spawning episode, they spawned daily irrespective of size. Mean batch fecundity was estimated directly at 6.5 million oocytes. Analysis of ovary histology and ovary weight data indicated that relative batch fecundity, and the duration of spawning and non-spawning episodes, increased with fish size. These reproductive parameter estimates could be used with estimates of residency time on the spawning ground as a function of fish size (if known) and demographic data for the spawning population to provide a time series of relative annual fecundity for SBT.

Demographic structure, sex ratio and growth rates of southern bluefin tuna (Thunnus maccoyii) on the spawning ground.

The demographics of the southern bluefin tuna (SBT) Thunnus maccoyii spawning stock were examined through a large-scale monitoring program of the Indonesian longline catch on the spawning ground between 1995 and 2012. The size and age structure of the spawning population has undergone significant changes since monitoring began. There has been a reduction in the relative abundance of larger/older SBT in the catch since the early 2000s, and a corresponding decrease in mean length and age, but there was no evidence of a significant truncation of the age distribution. Pulses of young SBT appear in the catches in the early- and mid-2000s and may be the first evidence of increased recruitment into the spawning stock since 1995. Fish in these two recruitment pulses were spawned around 1991 and 1997. Size-related variations in sex ratio were also observed with female bias for fish less than 170 cm FL and male bias for fish greater than 170 cm FL. This trend of increasing proportion of males with size above 170 cm FL is likely to be related to sexual dimorphism in growth rates as male length-at-age is greater than that for females after age 10 years. Mean length-at-age of fish aged 8-10 years was greater for both males and females on the spawning ground than off the spawning ground, suggesting that size may be the dominant factor determining timing of maturation in SBT. In addition to these direct results, the data and samples from this program have been central to the assessment and management of this internationally harvested stock.

Maturity ogives for South Pacific albacore tuna (Thunnus alalunga) that account for spatial and seasonal variation in the distributions of mature and immature fish.

Length and age at maturity are important life history parameters for estimating spawning stock biomass and reproductive potential of fish stocks. Bias in estimates of size and age at maturity can arise when disparate distributions of mature and immature fish within a population are not accounted for in the analysis. Here we investigate the spatial and temporal variability in observed size and age at maturity of female albacore tuna, Thunnus alalunga, using samples collected across the South Pacific. Maturity status was identified using consistent histological criteria that were precise enough to allow for mature but regenerating females to be distinguished from immature females during the non-spawning season, permitting year-round sampling for maturity estimation in albacore. Using generalised linear mixed models, we found that the proportion of mature females at length varied significantly with latitude and time of year. Specifically, females at northern latitudes (∼10-20°S, where spawning occurs) were mature at significantly smaller lengths and ages than females at southern latitudes (∼20-40°S), particularly during the spawning season (October-March). This variation was due to different geographic distributions of mature and immature fish during the year. We present a method for estimating an unbiased maturity ogive that takes into account the latitudinal variation in proportion mature at length during a given season (spawning or non-spawning). Applying this method to albacore samples from the western region of the South Pacific gave a predicted length at 50% mature of ∼87 cm fork length (4.5 years).

Reproductive dynamics and potential annual fecundity of South Pacific albacore tuna (Thunnus alalunga).

The reproductive biology of albacore tuna, Thunnus alalunga, in the South Pacific Ocean was investigated with samples collected during broad-scale sampling between 2006 and 2011. Histology was done in a single laboratory according to standard protocols and the data analysed using generalized linear mixed-effects models. The sex ratio of albacore was female biased for fish smaller than approximately 60 cm FL and between 85 and 95 cm, and progressively more male biased above 95 cm FL. Spawning activity was synchronised across the region between 10°S and 25°S during the austral spring and summer where sea surface temperatures were ≥24 °C. The average gonad index varied among regions, with fish in easterly longitudes having heavier gonads for their size than fish in westerly longitudes. Albacore, while capable of spawning daily, on average spawn every 1.3 days during the peak spawning months of October to December. Spawning occurs around midnight and the early hours of the morning. Regional variation in spawning frequency and batch fecundity were not significant. The proportion of active females and the spawning fraction increased with length and age, and mature small and young fish were less active at either end of the spawning season than larger, older fish. Batch fecundity estimates ranged from 0.26 to 2.83 million oocytes with a mean relative batch fecundity of 64.4 oocytes per gram of body weight. Predicted batch fecundity and potential annual fecundity increased with both length and age. This extensive set of reproductive parameter estimates provides many of the first quantitative estimates for this population and will substantially improve the quality of biological inputs to the stock assessment for South Pacific albacore.

Spatial and sex-specific variation in growth of albacore tuna (Thunnus alalunga) across the South Pacific Ocean.

Spatial variation in growth is a common feature of demersal fish populations which often exist as discrete adult sub-populations linked by a pelagic larval stage. However, it remains unclear whether variation in growth occurs at similar spatial scales for populations of highly migratory pelagic species, such as tuna. We examined spatial variation in growth of albacore Thunnus alalunga across 90° of longitude in the South Pacific Ocean from the east coast of Australia to the Pitcairn Islands. Using length-at-age data from a validated ageing method we found evidence for significant variation in length-at-age and growth parameters (L(∞) and k) between sexes and across longitudes. Growth trajectories were similar between sexes up until four years of age, after which the length-at-age for males was, on average, greater than that for females. Males reached an average maximum size more than 8 cm larger than females. Length-at-age and growth parameters were consistently greater at more easterly longitudes than at westerly longitudes for both females and males. Our results provide strong evidence that finer spatial structure exists within the South Pacific albacore stock and raises the question of whether the scale of their "highly migratory" nature should be re-assessed. Future stock assessment models for South Pacific albacore should consider sex-specific growth curves and spatial variation in growth within the stock.