Stock Delineation Research Articles

Half a century of citizen science tag-recapture data reveals stock delineation and cross-jurisdictional connectivity of an iconic pelagic fish

Tag-recapture programs to monitor the movements of fish populations are among some of the longest-running citizen-science datasets to date. Here, using half a century of yellowtail kingfish (Seriola lalandi, Carangidae) tag-recapture data collected through citizen-science projects, we report novel insights into population connectivity in Australia and New Zealand (NZ). Despite the importance of kingfish in commercial and recreational fisheries, substantial knowledge gaps about their stock structure and connectivity between jurisdictions hinder current management efforts. Between 1974 and 2022, 63,432 releases and 4636 recaptures (7.3%) of tagged kingfish were collected in Australia and NZ. Most tagged individuals (51.4%) were recaptured within 10 km of their original release location up to 14 years post-release (mean: 225 days), indicating some degree of site fidelity. However, 656 (14.2%) kingfish were recaptured over 100 km from their release location, with one fish travelling at least 2834 km in 702 days. Seasonal variability was evident for releases and recaptures, with more releases occurring in summer and autumn in most jurisdictions. Network analysis of recaptures revealed no connectivity between tagged kingfish from western and eastern Australia, supporting genetic delineation. By contrast, extensive connectivity exists across eastern Australia and NZ, with 87 kingfish moving between five Australian state jurisdictions, 316 individuals travelling across 15 bioregions and six kingfish moving between Australia and NZ. Our findings provide important new insights into the structure and connectivity of the eastern Australia kingfish stock and suggest increased collaboration between state and international fisheries jurisdictions may support improved stock assessment and management.

Genomic differentiation and interoceanic population structure of two large pelagic scombrid species

Tunas of the family Scombridae are of paramount importance for fisheries and the international seafood trade. In order to ensure a sustainable use of these valuable resources, it is crucial that stock delineation and management plans are in accordance. Here, we examined the population genetic structure of the two data-poor scombrid species wahoo (Acanthocybium solandri) and bigeye tuna (Thunnus obesus), both of growing significance in tuna fisheries. Our study employed whole-genome sequencing methods to conduct the most extensive genomic analysis of wahoo and bigeye tuna samples to date, collected from the Atlantic, Indian and Pacific Oceans. For both species, we observe genome-wide differentiation between samples from the Atlantic and the Indo-Pacific regions with little or no genetic structure within each of the ocean basins, indicative of high gene flow. However, by applying a set of extreme outlier tests, genomic differentiation between locations was identified within the Pacific Ocean for both species, as well as for wahoo within the Atlantic Ocean. Additionally, for bigeye tuna, we uncovered a putative chromosomal inversion with patterns of highly linked loci and strong population divergence, that may be involved in adaptive divergence across the distributional range of the species. Taken together, despite considerable gene flow, the detected substructures – most likely driven by local adaptation – challenge previously held assumptions of panmixia in both species. Our findings show that future stock assessment should consider genetic differences at both neutral and divergent loci to develop sustainable conservation and management actions for these valuable marine resources.

Exploratory stock identification through morphometric trait analysis of the estuarine round herring, Gilchristella aestuaria (Pisces: Clupeidae).

As a first step in stock identification of estuarine round herring Gilchristella aestuaria, a morphometric analysis of multiple standardised traits and body condition was conducted on samples from sites across the distribution range of the species, including freshwater and estuarine populations. Multivariate analyses, including a principal component analysis (PCA), revealed that sites on the same river system and sites in close geographic proximity tend to share morphometric traits. Most of the variation in PCA was due to caudal fin length (CFL). Single traits were analysed with generalised additive models with river system location as the smooth term. CFL was strongly related to river systems, and to a lesser extent salinity and turbidity. Unlike previous local-scale studies, this broad-scale study did not support the notion of ecotypes based on eye diameter. Condition indices like body depth and relative weight were related to climatic conditions, salinity and turbidity, more than to river system. The findings agree with previous studies on phylogenetic history and limited gene flow in G. aestuaria, and suggest variation in environmental productivity that affects body condition in different populations. Subsequent research should examine temporal changes in traits like CFL and body condition based on long-term seasonal sampling. Safeguarding this potential resource may be enabled by adopting appropriate management methods based on delineation of stocks with different levels of productivity and connectivity, before widespread fishing of this species is promoted.

Sample size requirements for genetic studies on yellowfin tuna.

In population genetics, the amount of information for an analytical task is governed by the number of individuals sampled and the amount of genetic information measured on each of those individuals. In this work, we assessed the numbers of individual yellowfin tuna (Thunnus albacares) and genetic markers required for ocean-basin scale inferences. We assessed this for three distinct data analysis tasks that are often employed: testing for differences between genetic profiles; stock delineation, and; assignment of individuals to stocks. For all analytical tasks, we used real (not simulated) data from four sampling locations that span the tropical Pacific Ocean. Whilst spatially separated, the genetic differences between the sampling sites were not substantial, a maximum of approximately Fst = 0.02, which is quite typical of large pelagic fish. We repeatedly sub-sampled the data, mimicking a new survey, and performed the analyses. False positive rates were also assessed by re-sampling and randomly assigning fish to groups. Varying the sample sizes indicated that some analytical tasks, namely profile testing, required relatively few individuals per sampling location (n ≳ 10) and single nucleotide polymorphisms (SNPs, m ≳ 256). Stock delineation required more individuals per sampling location (n ≳ 25). Assignment of fish to sampling locations required substantially more individuals, more in fact than we had available (n > 50), although this sample size could be reduced to n ≳ 30 when individual fish were assumed to belong to one of the groups sampled. With these results, designers of molecular ecological surveys for yellowfin tuna, and users of information from them, can assess whether the information content is adequate for the required inferential task.

MULTIDISCIPLINARY APPROACH TO ASSESS COMMERCIALLY IMPORTANT MARINE STOCKS IN THE COASTAL WATERS OF THE YUCATAN PENINSULA – CONTRIBUTION BY CCBA-UADY

<p><strong>Background. </strong>Since the formation of the research group in marine biology at the CCBA, different aspects of this discipline have been developed. One of them is the identification of populations and possible stocks of fish of commercial importance, using different techniques.<strong> </strong>The stock delineation (or population structure) are central considerations for fishery assessment and strategic management of marine natural resources and have to be addressed from a meta-population perspective where complementary technical approaches meet to enable the best picture to delineate complex stock structures. <strong>Objective.</strong> To review the current knowledge on the stock concept and the use of a multidisciplinary approach to properly assess commercially important marine stocks in the coastal waters of the Yucatan peninsula. <strong>Methodology. </strong>We present the research explored so far by the marine biology laboratory (LABIOMA by its acronym in Spanish) of the Autonomous University of Yucatán regarding the marine resources off the coast of the Yucatan peninsula, and the future lines of investigation pursued by our personnel, from fishing gear selectivity, abundances and catchability estimates, traditional morphometrics, parasitological and life history traits as biological tags, to more precise analyses such as fish otolith shape or even stable isotope analysis, genotypic markers, and marine natural products chemistry. <strong>Main findings. </strong>Single technical approaches are insufficient to delineate complex stock structures, especially in wide marine open access ecosystems, and there is a need to harness the full power of complementary and synergistic multidisciplinary approaches to improve fishery assessment and management efficiency in marine natural resources from the coastal areas of the Yucatan peninsula. <strong>Implications. </strong>Most stock assessment models are based on a single unit stock assumption, however the full impact of management actions, including identifying the complexity of the stock of any marine species subject to fishing, could affect the perpetuity of its abundances if the population subunits are not properly located. <strong>Conclusion. </strong>Identification of stocks is necessary for several reasons including allocation of catches, recognition and protection of nursery and spawning areas, and for development of optimal harvest and monitoring strategies. To this end, the LABIOMA are strengthening the assessments of commercially important marine stocks by using multidisciplinary approaches, whose lines of research represent basic aspects to be known and would be of great help to decision makers at the time of establishing more precisely, catch quotas, fishing areas, closed seasons, and therefore make more efficient the management strategies.</p>

Abundance and demography of common bottlenose dolphins (Tursiops truncatus truncatus) in the Indian River Lagoon, Florida: A robust design capture-recapture analysis.

Common bottlenose dolphins (Tursiops truncatus truncatus) inhabiting the Indian River Lagoon (IRL) estuarine system along the east coast of Florida are impacted by anthropogenic activities and have had multiple unexplained mortality events. Given this, managers need precise estimates of demographic and abundance parameters. Mark-recapture photo-identification boat-based surveys following a Robust Design were used to estimate abundance, adult survival, and temporary emigration for the IRL estuarine system stock of bottlenose dolphins. Models allowed for temporary emigration and included a parameter (time since first capture) to assess evidence for transient individuals. Surveys (n = 135) were conducted along predetermined contour and transect lines throughout the entire IRL (2016–2017). The best fitting model allowed survival to differ for residents and transients and to vary by primary period, detection to vary by secondary session, and did not include temporary emigration. Dolphin abundance was estimated from 981 (95% CI: 882–1,090) in winter to 1,078 (95% CI: 968–1,201) in summer with a mean of 1,032 (95% CI: 969–1,098). Model averaged seasonal survival rate for marked residents was 0.85–1.00. Capture probability was 0.20 to 0.42 during secondary sessions and the transient rate was estimated as 0.06 to 0.07. This study is the first Robust Design mark-recapture survey to estimate abundance for IRL dolphins and provides population estimates to improve future survey design, as well as an example of data simulation to validate and optimize sampling design. Transients likely included individuals with home ranges extending north of the IRL requiring further assessment of stock delineation. Results were similar to prior abundance estimates from line-transect aerial surveys suggesting population stability over the last decade. These results will enable managers to evaluate the impact of fisheries-related takes and provide baseline demographic parameters for the IRL dolphin population which contends with anthropogenic impacts and repeated mortality events.

Stock delineation of striped snakehead, Channa striata using multivariate generalised linear models with otolith shape and chemistry data

Otoliths are commonly used to discriminate between fish stocks, through both elemental composition and otolith shape. Typical studies also have a large number of elemental compositions and shape measures relative to the number of otolith samples, with these measures exhibiting strong mean–variance relationships. These properties make otolith composition and shape data highly suitable for use within a multivariate generalised linear model (MGLM) framework, yet MGLMs have never been applied to otolith data. Here we apply both a traditional distance based permutational multivariate analysis of variance (PERMANOVA) and MGLMs to a case study of striped snakehead (Channa striata) in India. We also introduce the Tweedie and gamma distributions as suitable error structures for the MGLMs, drawing similarities to the properties of Biomass data. We demonstrate that otolith elemental data and combined otolith elemental and shape data violate the assumption of homogeneity of variance of PERMANOVA and may give misleading results, while the assumptions of the MGLM with Tweedie and gamma distributions are shown to be satisfied and are appropriate for both otolith shape and elemental composition data. Consistent differences between three groups of C. striata were identified using otolith shape, otolith chemistry and a combined otolith shape and chemistry dataset. This suggests that future research should be conducted into whether there are demographic differences between these groups which may influence management considerations. The MGLM method is widely applicable and could be applied to any multivariate otolith shape or elemental composition dataset.

Stock structure of Pacific cod (Gadus macrocephalus) around the Korean Peninsula: an otolith microchemical perspective

Sustainable management of fishery resources is predicated on a foundational understanding of the biogeography of fish stocks and the delineation of stocks into appropriate management units. Despite notable fluctuations in the catch of commercially valuable Pacific cod (Gadus macrocephalus) in South Korea, relatively little is known regarding the stock structure and migratory trends of this species in the region. Here, otolith microchemistry was used to evaluate the stock structure and ontogenetic migratory trends of Pacific cod from five spawning grounds around the Korean Peninsula. Statistically significant between-region discrimination was evident and resolved Pacific cod around the Korean Peninsula into two distinct stocks. Specimens were classified to region of capture using quadratic discriminant analysis of age-0 and capture elemental signatures with overall accuracies of 71.12 and 79.1% respectively, lending support to the notion that Pacific cod demonstrate natal philopatry. Analysis of the elemental signatures over the first 2 years of life exhibited clear trends indicative of shifts in habitat use, suggesting that trace elements function well as indicators of ontogenetic migration. Our work provides information that is complementary to other direct and indirect methods of monitoring migratory trends and delineating stocks, which are integral components of effective species and ecosystem management plans.

New genomic resources for three exploited Mediterranean fishes

Extensive fishing has led to fish stock declines throughout the last decades. While clear stock identification is required for designing management schemes, stock delineation is problematic due to generally low levels of genetic structure in marine species. The development of genomic resources can help to solve this issue. Here, we present the first mitochondrial and nuclear draft genome assemblies of three economically important Mediterranean fishes, the white seabream, the striped red mullet, and the comber. The assemblies are between 613 and 785 Mbp long and contain between 27,222 and 32,375 predicted genes. They were used as references to map Restriction-site Associated DNA markers, which were developed with a single-digest approach. This approach provided between 15,710 and 21,101 Single Nucleotide Polymorphism markers per species. These genomic resources will allow uncovering subtle genetic structure, identifying stocks, assigning catches to populations and assessing connectivity. Furthermore, the annotated genomes will help to characterize adaptive divergence.

Recruitment synchrony in spatially structured Newfoundland and Labrador populations of American plaice (Hippoglossoides platessoides)

Appropriate stock delineation is one of the fundamentals for reliable stock assessment. Investigating stock delineation is not a common practice on regularly assessed stocks, yet it is highly desirable prior to extensive investment into new assessment approaches for a stock. Recruitment correlations are an important determinant of stock boundaries, and in this paper, we investigate these correlations between American plaice stocks/components in the Northwest Atlantic Fisheries Organization (NAFO) Divisions 2J3KLMNOPs. Currently, American plaice in 2J3K are managed as part of the Labrador and the northeast coast of Newfoundland stock, 3LNO as the Grand Bank stock, and sub-Division 3Ps as the St Pierre Bank stock. We estimated mixed-effect cohort-strength models using abundance indices from Canadian Research Vessel (RV) surveys conducted every year in the spring (3LNOPs) and fall (2J3KLMNO) and investigated the correlation in the recruitment patterns of American plaice in these NAFO divisions. We performed cluster analysis to assess if the estimated correlations are consistent with the current stock delineations. We further explored causative/correlative relationships between spawning stock biomass (SSB), temperature, and recruitment. Our analyses supported the separation of the 2J3K northeast coast stock from the Grand Bank (3LNO) and St Pierre (3Ps) stocks. Our analysis showed strong synchrony in recruitment patterns between the 3LNO and 3Ps regions indicating either interactions in American plaice populations between the Grand Bank and St Pierre stocks, or strong environmental influences on recruitment success that affect both stocks similarly. Our analyses of recruitment correlations with SSB and temperature did not indicate strong associations except for significant correlations between recruitment and SSB between 3L and 3Ps.

Otolith shape analysis as a tool to infer the population structure of the blue jack mackerel, Trachurus picturatus, in the NE Atlantic

The blue jack mackerel, Trachurus picturatus, is an economically important fishery resource of the NE Atlantic, commonly captured around the Macaronesian islands of Azores, Madeira and Canaries, but also along coastal Portugal mainland. Despite its importance for the fisheries industry, information regarding stock delineation for management and conservation purposes is still scarce. This study examines whether otolith shape is efficient to infer about the population structure of the species and if the obtained data is consistent over time. Individuals of T. picturatus were collected in 2013 and 2016 from six important fishery regions in the NE Atlantic: Azores, Madeira, Canaries and Portugal mainland – Matosinhos, Peniche and Portimão. Otolith shape indices and elliptic Fourier descriptors were investigated by uni and multivariate statistical analyses. Data showed regional differences in the otolith shape analysis, with differences between the years. Fish sampled in 2013 showed an overall low re-classification rate (43%) with a high overlap of individuals within sampling locations, suggesting a single population unit. However, samples from 2016 allowed the discrimination of three distinct spatial groups with a moderate overall correct re-classification (62%) - group 1 with samples from the Azores; group 2 with samples from the Canaries; and group 3 with samples from Madeira and Portugal mainland. The hereby data suggests that fish population structure could be dynamic over time, recommends a year-classes follow-up of the population units in the main fishing areas and stresses the need of holistic methodological approaches to study fish stocks. Furthermore the hereby observed complex spatial dynamic structure of the species demands region-specific requirement actions to ensure a rational management of the fishery.

Stock delineation of the long-whiskered catfish, Sperata aor (Hamilton 1822), from River Ganga by using morphometrics

Long-term isolation of populations and interbreeding can lead to morphometric variations among fish populations. This study was conducted with the objective to delineate stock structure of Sperata aor on the basis of morphometric characters, using truss network of the fish body. In total, 407 S. aor samples were collected from the four sampling locations of the Ganga River, viz. Narora, Kanpur, Varanasi and Bhagalpur. In total, 28 truss distance measurements were created by joining 13 morphometric landmarks on the fish body. MANCOVA showed significant (P<0.001) morphological variance among the sampling locations for the target fish species. Univariate ANOVA showed significant (P<0.001) differences in each of the morphometric measurements among the fish from different sampling locations. Wilk’s lambda test of canonical discriminant function analysis showed significant (P<0.001) differences in morphometric measurements of the fish from all sampling locations. Discriminant function analysis using Jackknife (leave-one-out) cross-validation classification showed 87.5% correct classification of the individuals into their original populations. Mantel test showed an overall good correlation between the genetic and morphometric datasets in the selected fish species. The results of this study can be employed in formulating stock-specific management strategies for S. aor from River Ganga.

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.

Morphological divergence of three-spined stickleback in the Baltic Sea—Implications for stock identification

Morphometrics is a beneficial, straightforward and relatively simple tool for fish stock delineation and identification. Analysis of spatial divergence, and morphological traits in relation to other factors, are of high interest both for management and in ecological studies. Morphology can help to delineate stocks, inform about local adaptations as well as ecological role the species play in the ecosystem. Morphological variation and differentiation of three-spined stickleback (Gasterosteus aculeatus) has been thoroughly studied in small freshwater systems, but less is known about differentiation of the species in an open marine system. The Baltic Sea inherits substantial environmental gradients in salinity, temperature, as well as in the nature and intensity of predation, gradients that all can foster local morphological adaptation and potential population differentiation. Previous studies have revealed some morphological differentiation of the species along the coast, but studies from the offshore are lacking. In this study we used traditional as well as geometric morphometrics to analyse divergence in morphological traits like body plate numbers, body- and otolith shape among sticklebacks from two major genetic clusters inhabiting different parts of the Baltic Sea. Our results show that fish from one area (Curonian Lagoon) representing one of the clusters had significantly higher number of body plates, potentially indicating a response to higher predation pressure compared to the other areas studied. Body shape also significantly differed among locations with deeper bodied fish in the Curonian Lagoon. The most conservative and least plastic trait studied, otolith shape, did, however, not show any divergence among the areas studied. Our results suggest morphological divergence in plastic traits like body plates and body shape in response to local environmental conditions. The lack of divergence in otolith shape further suggests that the degree of population differentiation is weak or rather recent, as also highlighted in earlier studies using molecular markers or synchrony in population abundances. In all, our study shows that at least the number of body plates can serve as an effective stock delineator among genetic clusters of three-spined sticklebacks in the Baltic Sea.

Large-scale genetic panmixia in the blue shark (Prionace glauca): A single worldwide population, or a genetic lag-time effect of the "grey zone" of differentiation?

The blue shark Prionace glauca, among the most common and widely studied pelagic sharks, is a top predator, exhibiting the widest distribution range. However, little is known about its population structure and spatial dynamics. With an estimated removal of 10–20 million individuals per year by fisheries, the species is classified as “Near Threatened” by International Union for Conservation of Nature. We lack the knowledge to forecast the long‐term consequences of such a huge removal on this top predator itself and on its trophic network. The genetic analysis of more than 200 samples collected at broad scale (from Mediterranean Sea, North Atlantic and Pacific Oceans) using mtDNA and nine microsatellite markers allowed to detect signatures of genetic bottlenecks but a nearly complete genetic homogeneity across the entire studied range. This apparent panmixia could be explained by a genetic lag‐time effect illustrated by simulations of demographic changes that were not detectable through standard genetic analysis before a long transitional phase here introduced as the “population grey zone.” The results presented here can thus encompass distinct explanatory scenarios spanning from a single demographic population to several independent populations. This limitation prevents the genetic‐based delineation of stocks and thus the ability to anticipate the consequences of severe depletions at all scales. More information is required for the conservation of population(s) and management of stocks, which may be provided by large‐scale sampling not only of individuals worldwide, but also of loci genomewide.

Shark Interactions With Directed and Incidental Fisheries in the Northeast Pacific Ocean: Historic and Current Encounters, and Challenges for Shark Conservation.

For over 100 years, sharks have been encountered, as either directed catch or incidental catch, in commercial fisheries throughout the Northeast Pacific Ocean. A long-standing directed fishery for North Pacific Spiny Dogfish (Squalus suckleyi) has occurred and dominated shark landings and discards. Other fisheries, mainly for shark livers, have historically targeted species including Bluntnose Sixgill Shark (Hexanchus griseus) and Tope Shark (Galeorhinus galeus). While incidental catches of numerous species have occurred historically, only recently have these encounters been reliably enumerated in commercial and recreational fisheries. In this chapter we present shark catch statistics (directed and incidental) for commercial and recreational fisheries from Canadian waters (off British Columbia), southern US waters (off California, Oregon, and Washington), and northern US waters (off Alaska). In total, 17 species of sharks have collectively been encountered in these waters. Fishery encounters present conservation challenges for shark management, namely, the need for accurate catch statistics, stock delineation, life history parameter estimates, and improved assessments methods for population status and trends. Improvements in management and conservation of shark populations will only come with the further development of sound science-based fishery management practices for both targeted and incidental shark fisheries.

Lack of Spatial Subdivision for the Snapper Lutjanus purpureus (Lutjanidae - Perciformes) from Southwest Atlantic Based on Multi-Locus Analyses.

The Caribbean snapper Lutjanus purpureus is a marine species fish commonly found associated with rocky seabeds and is widely distributed along of Western Atlantic. Data on stock delineation and stock recognition are essential for establishing conservation measures for commercially fished species. However, few studies have investigated the population genetic structure of this economically valuable species, and previous studies (based on only a portion of the mitochondrial DNA) provide an incomplete picture. The present study used a multi-locus approach (12 segments of mitochondrial and nuclear DNA) to elucidate the levels of genetic diversity and genetic connectivity of L. purpureus populations and their demographic history. L. purpureus has high levels of genetic diversity, which probably implies in high effective population sizes values for the species. The data show that this species is genetically homogeneous throughout the geographic region analyzed, most likely as a result of dispersal during larval phase. Regarding demographic history, a historical population growth event occurred, likely due to sea level changes during the Pleistocene.

A biophysical model for simulating early life stages of sardine in the Iberian Atlantic stock

The Iberian sardine (Sardina pilchardus) is a traditional fishery in western Iberia that is economically important in Portugal and in Galicia (NW Spain). The International Council for the Exploration of the Seas (ICES) advice for the sardine in regions VIII and IXa in 2013 indicated that the biomass has decreased since 2006 and recruitment has been below the long term average since 2005. Recruitment is very variable, so it is important to understand the underlying processes driving this variation in order to manage the fishery effectively. In this study, a biophysical model was used to simulate the early life (egg and larval) stages of sardine. A high resolution hydrodynamic model for North and Northwest Iberia was used to force a Lagrangian Individually-Based Model (IBM) that simulated advection and dispersion (both horizontal and vertical) and included some biological behaviour. A Lower Trophic Level (LTL) model coupled to the hydrodynamic model was also used to get some insight on recruitment for years 2006–2007. Additionally, since in this area there are two different spawning grounds that could be associated with two eventually different populations, we have tried to show how the model can be used for giving insight on stock connectivity and therefore can contribute to stock delineation.

Genetic markers in marine fisheries: Types, tasks and trends

Thirty years of industrial fishing have led to overexploitation of many species, triggering the urgent need to better assess and manage marine stocks for sustainability. From the very simple definition of stock as “an exploited fishery unit” to its complex delimitation using ecosystem approaches, genetic approaches provide a large number of potential markers to unveil the underlying molecular background of complex biological phenomena in marine species.The present study is a diagnostic assessment of the number of scientific data published in marine fisheries using genetic technologies since the onset of NGS up to 2014. This state of the art approach would allow to derive causalities of real figures and to hypothesize trends in the use and applications of genetic markers. We first briefly overview pros and cons of current technologies used to delineate fish stocks and address intrapopulation knowledge deficits identified under an open population paradigm. Then, in order to assess the advancement of the application of molecular genetic techniques in “fish stock delineation” we review the work published on spatio-temporal structures of fish stocks. Finally, the datamining effort is enlarged across marine fisheries during the period 2004–20014 to decipher the intensity of use of genetic tools per taxa, the main application of each marker type and the trend of use of classic, modern and new generation techniques in fishery research tasks. Although microsatellites and mitochondrial DNA-based markers have being used at a growing pace in fishery research tasks until 2011, a time when application of gene sequencing and NGS-derived markers to fishery research has significantly grown. NGS technologies are underused in fishery science regarding their wide application in other research fields such as agriculture and aquaculture. So a significant increment of new genetic marker types is expected to be implemented in the near future. Conversely, application of classic marker types such as allozymes, AFLPs, whole mitochondrial genomes, RAPDs and RFLPs on mtDNA has been much less used in the period 2004–2014 following the advent of fast and cheap genotypic screening and NGS-derived markers. Power gain afforded from the combination of different genetic markers to address complex processes is lacking in current fishery research since only 21% of the studies over that period employed two genetic marker types and only 3% employed more than two.Combinations of methods would allow addressing management issues such as distribution shifts and population expansion in response to climatic fluctuations and global change, as well as overfishing and fishery collapses.

Otolith chemistry in stock delineation: A brief overview, current challenges and future prospects

Otolith chemistry has become a key tool to identify and delineate fish stock units. Its successful application as a natural tag in stock discrimination studies is based on the ability to distinguish among different groups due to variation in otolith chemical composition. Here, we briefly summarize the history and the development of otolith chemistry in general and their application in stock delineation studies in particular. A short overview of the major achievements in stock identification using otolith chemistry is provided whilst covering the evolution in methodological and analytical approaches over the last decades. Current and future challenges and research gaps are outlined focusing on the need to provide accurate stock structure estimates for management purposes. Overall, there is still large room for improvement regarding how we overcome these challenges and supersede the current gaps in population structure and connectivity studies using otolith chemistry. The most favorable and practical directions for future research are discussed, and include marker integration, new technological and statistical approaches that may contribute in further advancing otolith chemistry and its application in stock delineation. Ultimately, the continued development of holistic approaches combining otolith chemistry with different and potentially complementary techniques is clearly the course of action to promote interconnection between management actions and biological processes, and unambiguously resolve stock structure and scientifically underpin fisheries management.