Stock Discrimination Research Articles

What does external morphometry tell us about stock discrimination of Sardina pilchardus stocks from Türkiye?

The analysis of shape is a fundamental part of much biological research. Morphometrics, which incorporates concepts from biology, geometry, and statistics, is the study of the geometrical form of organisms. In addition, morphometric characteristics can be used to differentiate ‘phenotypic stocks’ as groups with similar growth, mortality, and reproductive rates. In this study, 25 morphometric characters were used to discriminate European pilchard (Sardina pilchardus) stocks from Türkiye. Intraspecific variation of the European pilchard was investigated based on morphometric characters. Samples were collected from the Aegean Sea (AS; N = 54), the Sea of Marmara (MS; N = 50) and the Mediterranean Sea (MEDS; N = 50) during the 2019 fishing season. Principal Component Analysis (PCA) and Canonical Discriminant Analysis (CDA) were used for stock discrimination of the European pilchard. Univariate statistics (ANOVA) showed that 24 of the 25 measurements differed significantly between samples to a varying degree (p < 0.001). According to CDA, an overall classification success rate of 87.7% was achieved using 12 morphometric parameters. All samples were clearly separated from each other in the discriminant space, suggesting that there was no strong intermingling between populations. In addition, we would like to conclude that the morphological difference is not at the genetic level, and would like to emphasize the need for additional stock discrimination methods.

Asymmetrical individual both left and right otoliths of Tuna Scombrini collected from the Java Sea

Otolith can be used as a natural marker of fish stock or anomalies between individuals within fish stock. This research aims to study the relationships between fish length and otolith length and confirm differences in otolith shape between species in the Scombrini tribe and Carangidae family (Decapterus ruselli). Sample used in our analysis were collected around July - September 2023 from three different location, Rastrelliger brachysoma (Lekok waters, Pasuruan), Scomber australasicus (Bali Strait waters) and Decapterus ruselli (Sendang Biru, South Malang). Total 96 specimens were identified based on morphological character as Rastrelliger brachysoma, Scomber australasicus and Decapterus ruselli. Each of following samples were cut horizontally at the frontal head to open the skull and remove sagitta otolith below the hindbrain using dissecting set, then cleaned and stored dry in microtube 1,5 ml separately for left and right to further documented using Celestron Digital Microscope Pro Gray USB 44308. Otolith morphometric data collected includes maximum length using TpsDig and weight using analytical balance. The relationship between Forked Length (FL) and otolith length, length-weight relationship of otolith was determined using simple linear regression on software Statistical Product and Service Solutions (SPSS). Paired sample t-test was applied to determine asymmetrical size of left and right otoliths. In this study, it was found that the shape of the otoliths between species has differences in the rostrum, antirostrum, ventral and dorsal parts. FL-otolith length relationship of S. australasicus, R. brachysoma and D. ruselli are Y=0,725+0,164X, r2= 0,519; Y=0,191+0,230X, r2= 0,911; Y=3,156+0,075X, r2=0,071 respectively. The LW sagitta relationship shows that there is a very strong relationship (P<0,05) between L and W of otoliths. The results of the Paired Sample T-test showed that there was no significant difference in the size of the left and right otoliths (Sig>0.05). Otolith shape is influenced by fish behaviour, diet and environment and it may be used as additional information to distinguish between tribe or even species. Otherwise, its asymmetric relationship and LW relationship may be potential new methods for stock discrimination and have other implications such as stock assessment, understanding natural asymmetry, and its potential applications in fisheries management and conservation.

Use of otolith microchemical and morphological analyses for stock discrimination of Sarpa salpa on two Tunisian islands, Djerba and Kerkennah

Abstract Otolith morphological and microchemical analyses are relatively new scientific research methods used in fish stock evaluation and management. However, in Tunisia, only morphological methods have been used. The objective of this study was the Sarpa salpa stock discrimination of Djerba and Kerkennah by the otoliths morphological and microchemical analysis, while carrying out a fluctuating asymmetry analysis and a stock comparison of males and females for each population. The results revealed significant differences between the Djerba and Kerkennah populations, significant differences between the stocks of males and females in each population, and a highly significant fluctuating asymmetry for both populations. The results of the otolith morphological analysis were similar to those of the microchemical analysis. This result proves that both morphological and microchemical analyses are powerful tools for fish stock discrimination.

Stock discrimination of cleftbelly trevally, Atropus atropos (Bloch and Schneider, 1801) using conventional morphometric technique from South Konkan coast of Maharashtra

Stock discrimination of cleftbelly trevally, Atropus atropos (Bloch and Schneider, 1801) using conventional morphometric technique from South Konkan coast of Maharashtra

Stock discrimination of Paphia malabarica from South Konkan Coast, Maharashtra, India by geometric morphometric shape and size analysis

Stock discrimination of Paphia malabarica from South Konkan Coast, Maharashtra, India by geometric morphometric shape and size analysis

Otolith morphology as a tool for stock discrimination of three rockfish species in the East Sea of Korea

The shape and structure of otoliths play a vital role in studying fish populations because otolith shape indices are often applied to discriminate fish species. This study focused on examining inter- and intra-specific variations in otolith shape and size among three species of rockfish (Sebastes inermis, Sebastiscus marmoratus, and Sebastes zonatus) collected from the Dokdo and Ulleungdo regions of the East Sea in Korea. A total of 35 S. inermis specimens, 19 S. marmoratus specimens, and 59 S. zonatus specimens were collected between April 2021 and August 2022. The otolith shape was visualized using wavelet coefficients in the shapeR package. Otolith size indices, such as length, width, perimeter, and area, and shape indices, including form factor, aspect ratio, ellipticity, circularity, roundness, rectangularity, and squareness, were calculated for each species. Otolith size and shape indices significantly differed among the three rockfish species (p&amp;lt; 0.05). Compared with the other two species, S. marmoratus possessed more elongated otoliths, whereas S. zonatus had the largest otolith area, perimeter, and length. Average shape analysis based on wavelet coefficients revealed significant differences in otolith shape, particularly on the rostrum and posterior sides. A canonical analysis of principal components (CAP) confirmed the complete separation of otolith shapes among the three rockfish species, with 92.5% of the variation explained by the first axis (CAP1). The findings of this study enhance our understanding of the fish species in the Korean East Sea.

Relationships between local variability in parasite communities of the black-spotted croaker (Protonibea diacanthus) (Teleostei: Sciaenidae) and host population structure and seasonality

We evaluated spatial and temporal variability in parasite communities from the commercially important tropical marine fish the black-spotted croaker (Protonibea diacanthus) (Teleostei: Sciaenidae) to examine its population structure off the coast of the Northern Territory, Australia. Differences in parasite assemblage between four locations, across three seasons of the year, were used to evaluate the degree of connectivity of the sciaenid across coastal study areas. Analysis of parasite prevalence and mean intensity in these fish suggested the four sampling sites are distinct host populations. Across time, parasite assemblages at the four sites were distinct during the mid-dry (April–August) and build-up (September–November) seasons. During the wet season (December–March) there was substantial overlap in the parasite assemblages at three of the four sites indicating that fish population mixing may be occurring. Parasite assemblages at one nearshore site remained distinct across spatial and temporal scales. Our findings support the utility of parasitic organisms for elucidating the population structure of host species and reiterate the need to account for both spatial and temporal variability when performing stock discrimination analyses.

Stock Discrimination of Gilthead Seabream (Sparus aurata Linnaeus, 1758) through the Examination of Otolith Morphology and Genetic Structure

Reliable stock identification constitutes an integral component of effective fishery management. Current methods for the identification of putative stock units comprise the analysis of both phenotypic and genetic variability. The present study examined the spatial variation in otolith morphology (shape and asymmetry) and genetic composition of 395 wild-caught Gilthead seabream (Sparus aurata) specimens, collected from the Aegean and Ionian Seas (eastern Mediterranean) between 2014–2018. The degree of scale regeneration (SRD, % of regenerated scales) was used as an indicator to assess the potential presence of aquaculture escapees in the wild-caught samples. Otolith shape and asymmetry analyses showed a phenotypic discrimination between northwestern Aegean and Ionian Gilthead seabream populations. Genetic analyses of nine microsatellite markers revealed higher levels of genetic variation in the wild compared with samples obtained from aquaculture farms. Despite the absence of genetic structure among the wild-caught seabream populations, a low but statistically significant genetic differentiation was found between reared fish and fish collected in the field. The SRD was considered effective in detecting the presence of aquaculture escapees that may have escaped in either early or late rearing phases.

SNP-based discrimination of pink salmon stocks of the Sea of Okhotsk basin: resolution of the approach and possible ways to increase it

In this work, we studied the intraspecific polymorphism of pink salmon, Oncorhynchus gorbuscha (Walbaum, 1792), the least genetically explored species among Pacific salmon and one of the central fisheries objects in the Russian Far East. The most urgent task facing Russian fishery science is to determine the proportion of fish from the main reproduction areas in mixed stocks and, based on these data, predict the number of pink salmon returning to these regions for spawning. Due to the unique feature of the species, which evolved into two allochronous lineages, these lineages have been explored independently in parallel. We designed and used here two sets of outlier SNP markers, and this allowed us to reliably distinguish the most northern (Western Kamchatka and the Magadan coast) and the most southern (Iturup Island) regional stocks as well as intermediate stocks from Sakhalin Island and the Mainland coast in both even and odd lineages of pink salmon. In addition, in odd-year lineage, we discovered pronounced genetic differences between early-run and late-run spawners in Sakhalin Island and the proximity of this early spawning form to the mainland stocks. The created baseline covers the main areas of pink salmon reproduction in the Sea of Okhotsk basin and underlies the regional identification of pink salmon in mixed marine stocks.

Asymmetry of Sagittal Otolith Shape Based on Inner Ear Side Tested on Mediterranean Red Mullet (Mullus barbatus Linnaeus, 1758): Comparative Analysis of 2D and 3D Otolith Shape Data

Sagittal otolith shape analysis is one of the most widespread techniques worldwide to discriminate fish stock units, as this proxy integrates both environmental and genetic factors. All previous otolith shape studies have been carried out using two-dimensional (2D) images, a partial representation of the whole shape of the otolith. However, prior to the identification of stock unit boundaries, the influence of other potential drivers controlling the otolith shape must be analysed to limit their bias. In this study, the presence of asymmetry in otolith shape depending on the inner ear side (i.e., left versus right inner ears) was tested by comparing the approaches of 2D and three-dimensional (3D) sagittal otolith shape analyses. Eighty-two red mullet adults (Mullus barbatus) from three locations in the eastern part of the Mediterranean Sea were studied. Fourier harmonic descriptors computed from 2D outlines and spherical harmonic descriptors computed from 3D meshes were used to evaluate otolith shape variation. The results of a multivariate mixed-effects model from 2D images showed that there was no asymmetry effect of inner ear side on the otolith shape in any location. There was, however, a significant geographical effect for the 2D otolith shape between the Adriatic Sea and the Levantine Sea. In contrast, 3D information showed that both side effects and geographical differences were significant. This is the first study comparing 2D and 3D data showing different results on the same sample of red mullet. These results demonstrate the importance of 3D otolith shape analysis for stock discrimination.

Evaluation of Otolith Shape as an Approach for Stock Discrimination of Sardina pilchardus off the Moroccan Atlantic Coast

Evaluation of Otolith Shape as an Approach for Stock Discrimination of Sardina pilchardus off the Moroccan Atlantic Coast

The combined use of organochlorine contaminant profiles and molecular genetics for stock discrimination of white whales (Delphinapterus leucas) hunted in three communities on southeast Baffin Island

Putative stock differences in white whales (Delphinapterus leucas) landed by hunters between 1992 and 1996 from the southeast Baffin Island communities of Kimmirut (KI), Iqaluit (IQ) and Pangnirtung (PA) were examined using organochlorine contaminant (OC) profiles of 124 whales, the molecular genetics of 270 whales and both types of data from 97 whales. OC concentrations were generally lower in whales hunted in PA than those hunted in KI and IQ, and many OCs were lower in KI than IQ. In canonical discriminant function (CDA) using 13 OC predictor variables (10 OC groups, mirex, octachlorostyrene and endosulfan), the first canonical function accounted for 77% of the variance and separated whales from PA with those from IQ and KI; the second canonical function separated whales from KI with those from IQ. A previous study of the molecular genetics of white whales showed that whales hunted in the three communities were significantly differentiated on the basis of haplotype and/or microsatellite allele frequencies (de March et al., 2002). When the results of two studies were combined, many whales were slightly more strongly associated with a particular source hunting community than they were in the component studies. Using a posteriori crossvalidation probabilities in an analysis with variables from both studies, 72% of white whales were correctly crossvalidated to their source hunting community; 82.5% from PA; 56.5% from IQ; and 58.8% from KI. The highest misclassification rates were KI to IQ (23.5%), IQ to KI and IQ to PA (21.7% in both cases) and the lowest rates were PA to KI (3.5%), PA to IQ (14.0%) and KI to PA (17.6%). This pattern of assignments was not significantly different from those in the genetics or contaminants studies alone. However, the crossvalidation probabilities to the most likely source communities were approximately 20% larger in the combined analysis than in the component studies. Canonical scores in the combined analysis were more strongly correlated with variables from the OC Study than with variables from the genetics study. Whales placed to PA and IQ could be identified primarily by their OC signatures, however many whales from PA also had a strong PA genetics signature. Whales from IQ were identifiable only by their OC signatures. Both a strong KI genetics and OC signature described approximately half of whales from KI. We believe that at least three stocks were sampled from the three communities. Some whales in PA were very distinct, confirming previous beliefs that a separate stock occurs in Cumberland Sound. Whales hunted in IQ and KI differed to a lesser degree, and may be from stocks subject to a gradient or from a mixture of stocks. Some whales from PA are more likely to have genotypes and OC signatures that are also found in IQ and KI than the reverse. It is possible that summering areas of the stocks that were identified in KI and IQ are not consistent from year to year or across generations. The main problems in combining results for individuals used in several studies, particularly when there are many measurements for relatively few individuals, is to find a limited number of relevant predictor variables that can be used in the combined analysis, while avoiding both overparameterisation and results blurred by meaningless variables.

Natal Origin Differentiation Using Eye Lens Stable Isotope Analysis

AbstractNatal origin determination can be critical to understanding the movement, recruitment, and stock discrimination of fish populations. We investigated the utility of eye lens stable isotope analysis as a natural marker to determine natal origins, specifically the differentiation of stocked versus naturally reproduced individuals. We compared isotopic values for stocked and naturally reproduced Rainbow Trout Oncorhynchus mykiss in the North Platte River (Wyoming, USA) and found that the metabolically inert core of the eye lens retained hatchery feed values as the fish grew poststocking. The stable isotope values of eye lens cores from stocked Rainbow Trout were &gt;15‰ higher for δ34S and &gt;4‰ higher for δ13C than naturally reproduced fish. The values for δ15N proved to be a less useful indicator for natal origin than sulfur and carbon. These high carbon and sulfur isotopic values were retained in the core, despite subsequent lens layers showing a dietary shift to natural prey items poststocking. Rainbow Trout formed over 10 layers at age 0, decreasing to an estimated one to two layers during subsequent years. Eye lens stable isotope analysis represents an additional tool for researchers and managers to use natural isotopic markers to accurately assess natal origins and hatchery contributions to fish populations.

Quantifying genetic differentiation and population assignment between two contingents of Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic

In the Northwest Atlantic (NWA), the Atlantic mackerel ( Scomber scombrus) has a northern and a southern contingent, which spawn in Canada and the United States (U.S.), respectively. Both contingents mix mostly along the U.S. shelf during overwintering. The discrimination of individuals from each contingent in fisheries could improve the management of this depleted species in both countries. Here, we used genome-wide markers (&gt;10 000 single nucleotide polymorphisms (SNPs)) to assess genomic differences between mackerel of both contingents, and possibly infer the proportions of each contingent in NWA management units. Small but significant genetic differentiation was observed between the northern and southern contingents ( FST = 0.0010). Genetic assignments to reference samples from the two contingents were performed with predictive accuracy &gt; 85%. Fish from both contingents were present along the U.S. shelf during late winter and early spring but also, without prior evidence of this, likely in Canadian waters from late spring to fall. Genetic assignments could be used as a stock discrimination tool so that fishery removals can be effectively determined and managed on a contingent level.

Stock discrimination of mackerel scad Decapterus macarellus (Cuvier, 1833) in the eastern Indonesia based on metazoan fish parasite composition

Mackerel scad Decapterus macarellus (Cuvier, 1833), a small pelagic species, is the major catch in Asia, particularly in Indonesia. Despite a high catch volume, its utilization status is relatively unknown since stock assessment is mostly conducted for the entire small pelagic group without separating the species. Studies on population biology and stock distribution of mackerel scad in Indonesia so far involved catch-based production models, growth parameter analyses, otoliths, and fish genetics. We herewith discriminate eastern Indonesian fish stocks of D. macarellus by comparing the respective metazoan parasite community. We collected 105 specimens of mackerel scad from three closely connected fishing grounds representing two Indonesian fisheries management areas. Recorded metazoan parasites belonged to the Monogenea (4 species), Digenea (8 species), Acanthocephala (1 species), and Crustacea (2 species), with the two Monogenea Allopseudodiclidophora opelu (Yamaguti, 1965) and Pseudodiclidophora decapteri (Yamaguti, 1965) being the most prevalent. A multidimensional scaling analysis revealed the clustering pattern of the hosts based on the parasites, identifying two major fish stocks, the North Sulawesi group and the North Maluku group. The strength and weaknesses of the so far applied stock assessment methodologies for this small pelagic fish in Indonesia are discussed.

Form identification of purple flying squid (Sthenoteuthis oualaniensis) based on gladius morphology

Stock structure information is an important part of bases for understanding the dynamics of cephalopod populations. Purpleback flying squid Sthenoteuthis oualaniensis is an abundant and highly productive species in tropical and subtropical waters of the Indo-Pacific region. However, it is characterized by a complex stock structure, and the stock discrimination is an urgent priority to understand basic biology and for stock assessment and management purposes. Here, we used gladius morphology to identify and discriminate the dwarf without a dorsal photophore and middle-sized typical forms of S. oualaniensis in the South China Sea. Results showed that both forms had double axes on the gladius and females consistently had a larger gladius than males. Multivariate analyses using the gladius morphometric characteristics indicated that individuals of dwarf form without a dorsal photophore were distinguished from those of middle-sized typical form, which was evidenced by the obvious groups and significant dissimilarity of gladii of these two forms. The discrimination based on the gladius morphometric characteristics showed a high rate of accuracy, in which a global discrimination accuracy was estimated to be 92.36% for both forms without regarding sexes and 65.82% for the discrimination to form and sex. In combination, these lines of evidence indicated that individuals of dwarf without a dorsal photophore and middle-sized typical forms of S. oualaniensis can be accurately distinguished using the gladius morphometric characteristics, and these results will warrant the application of the gladius to study the stock structure of S. oualaniensis and other squid else.

Morphologic, morphometric and contour shape variations of sagittal otoliths of Lepidorhombus spp. in the Aegean Sea.

Otoliths are calcareous anatomical structures in the inner ear of fishes, and they can be used in the discrimination of fish species and stocks due to their species-specific shape. Sagittal otoliths in the Lepidorhombus whiffiagonis and Lepidorhombus boscii, two flatfish species of the same genus distributed in the Aegean Sea, were compared using morphology, morphometry and contour shape analyses. Blind and eyed side otoliths of Lepidorhombus species were evaluated separately due to their morphological features and statistical differences in morphometric measurements (p < 0.05). Four analysis groups were formed: blind side otolith of L. whiffiagonis, eyed side otolith of L. whiffiagonis, blind side otolith of L. boscii and eyed side otolith of L. boscii. Morphometric differences in otolith shape were performed by canonical discriminant analysis, and the first discriminant axis explained 97.4% (Wilks λ=0.270) of the variance between the groups, and the second axis explained 2.3% (Wilks λ=0.620). Classification success between Lepidorhombus species based on CDA is 100%, and the overall CDA classification score between groups is 76.5%. The wavelet functions obtained in the contour analysis showed high variability in the anterior, posterior-dorsal, antero-dorsal and ventral regions of the otoliths among these four analysis groups. Consequently, it is thought that this study will contribute to the taxonomic classification of fish with the morphological and morphometric differences in the blind and eyed side otoliths and the analyses made with the high discrimination success obtained in Lepidorhombus species.

Hidden but revealed: After years of genetic studies behavioural monitoring combined with genomics uncover new insight into the population dynamics of Atlantic cod in Icelandic waters.

Stock structure is of paramount importance for sustainable management of exploited resources. In that context, genetic markers have been used for more than two decades to resolve spatial structure of marine exploited resources and to fully fathom stock dynamics and interactions. While genetic markers such as allozymes and RFLP dominated the debate in the early era of genetics, technology advances have provided scientists with new tools every decade to better assess stock discrimination and interactions (i.e. gene flow). Here, we provide a review of genetic studies performed to understand stock structure of Atlantic cod in Icelandic waters, from the early allozyme approaches to the genomic work currently carried out. We further highlight the importance of the generation of a chromosome-anchored genome assembly together with whole-genome population data, which drastically changed our perception of the possible management units to consider. After nearly 60 years of genetic investigation of Atlantic cod structure in Icelandic waters, genetic (and later genomic) data combined with behavioural monitoring using Data Storage Tags shifted the attention from geographical population structures to behavioural ecotypes. This review also demonstrates the need for future research to further disentangle the impact of these ecotypes (and gene flow among them) on the population structure of Atlantic cod in Icelandic waters. It also highlights the importance of whole-genome data to unravel unexpected within-species diversity related to chromosomal inversions and associated supergenes, which are important to consider for future development of sustainable management programmes of the species within the North Atlantic.

Stock Discrimination of Northern Pike Esox lucius L., 1758 Inhabiting Lakes Simenlik and Ladik (Samsun-Turkey) Using Otolith Biometry and Shape Analysis

This study was carried out to investigate the relationships between total length and otolith dimensions and to detect the otolith shape index values of Northern pike (Esox lucius) which has high economic value, sampled from Ladik and Simenlik Lakes. A total of 140 specimens (Lake Ladik: 82 individuals, Lake Simenlik: 58 individuals) were sampled. Otolith height, length, perimeter, and area were determined by Imaging Software. Nonlinear and linear models were applied to estimate the relationships between the otolith measurements and total length. Form factor, circularity, roundness, rectangularity, aspect ratio, and ellipticity were used for otolith shape analyses. It was found that the relationship between the total length-otolith length was found to have the highest r2 value (Lake Ladik r2=0.949, Lake Simenlik r2=0.914) among the total length-otolith morphometrics at both localities. Otolith shape indices were calculated by using otolith measurements. As a result of comparing shape indices, it was found that there was a significant difference in two localities using roundness, ellipticity, and aspect ratio (P &amp;lt;0.05). The results indicated otolith shape indices could be used as a suitable tool to discriminate Northern pike populations.

Discrimination of the sardine stocks by using a morphometric and meristic analysis along the Moroccan Atlantic coast

Discrimination of the sardine stocks by using a morphometric and meristic analysis along the Moroccan Atlantic coast