Otolith Shape Analysis Research Articles

Otolith shape analysis of the European sardine Sardina pilchardus from Atlantic and Mediterranean waters: connectivity and population density

Otolith shape analysis of the European sardine Sardina pilchardus from Atlantic and Mediterranean waters: connectivity and population density

Body and otolith shape analyses of the Brazilian sardine, Sardinella brasiliensis, to differentiate population-units in the purse seine fishery off Brazil

Body and otolith shape analyses of the Brazilian sardine, Sardinella brasiliensis, to differentiate population-units in the purse seine fishery off Brazil

Otolith shape and isotopic ratio analyses as a tool to study Spondyliosoma cantharus population structure

Knowledge on population units is critical for understanding population dynamics and providing an adequate fisheries management. Despite its vast distribution and commercial importance, there is no information on black seabream population structure. Different approaches to otolith analysis were used to elucidate on the stock structure of this species. Otoliths from seven areas along the eastern Atlantic: English Channel, Bay of Biscay, Galicia (Spain), Peniche (west coast of Portugal), Algarve (south coast of Portugal), the Canary Islands and Angola were compared through elliptical Fourier analysis and oxygen and carbon stable isotopes ratio. Otolith shape analysis data achieved 80% of correct assigned specimens in discriminant analysis while poor correct assignment levels were achieved with the stable isotopes ratio. However, the PERMANOVA conducted on δ13C and δ18O values revealed significant differences between all areas, with exception of the two Portuguese areas. The results of this study indicate that black seabream spends most of its life in the same area and that the studied populations should probably be considered as different stock units. However, some mixture was detected in the European region pointing for the usefulness of life history parameters and genetic studies to enlighten the stock structure of the species.

Directional bilateral asymmetry in otolith morphology may affect fish stock discrimination based on otolith shape analysis

AbstractOtolith shape analysis is an efficient fish stock identification tool. However, most applications used left and right otoliths or only one of them arbitrarily chosen without testing for biases resulting from potential directional bilateral asymmetry (DA) in otolith shape, i.e. a unimodal population-level deviation form bilateral symmetry between right and left otolith shapes. In this study, 560 bogues (Boops boops) were sampled from 11 geographical locations from the Canary Islands to the Aegean Sea and elliptical Fourier descriptors were used to describe their otoliths’ shape. First, a significant otolith DA was observed at the global scale with an average amplitude of 2.77%. However, at the scale of sampling locations, DA was not always significant and varied in amplitude and direction. Second, population structure was investigated using the shape of either right otoliths or left otoliths or both together. Analyses based on right otoliths or both otoliths together, suggested three stock units: a North-Western Mediterranean Sea stock, an Eastern Mediterranean Sea stock, and a Central-Eastern Atlantic Ocean and South-Western Mediterranean Sea stock. In contrast, no coherent geographical pattern was found based on left otoliths. Our results highlight the importance of accounting for potential otolith DA in otolith shape-based stock identification.

Analyses of egg size, otolith shape, and growth revealed two components of small yellow croaker in Haizhou Bay spawning stock

The geographical variations in life history characteristics of small yellow croaker Larimichthys polyactis, caused by experienced different environmental conditions, have been observed in China seas. Previous studies based on spatial distribution, migration route, and body morphometrics suggested a complex stock structure. In this study, to clarify the source of a spawning stock, we investigated the reproduction strategy and inter-structure of the Haizhou Bay (HZB) spawning stock in the middle Yellow Sea from both egg survey and adult otolith increment analysis. Egg and adult samples were collected from three surveys during spawning season in 2013. Distinct spatial and temporal variations were detected in egg distribution and size, and otolith shape analysis of adult fishes revealed two morphotypes with different increment growth using random forest cluster. The results indicate the existence of two components within the same spawning stock in HZB from different wintering grounds, and accordingly special protection should be required for this stock given the significance to maintain connectivity between adjacent subpopulations.

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.

Differentiation of Freckled Goatfish Upeneus tragula Richardson, 1846 (Mullidae) in the Coastal Zone of Vietnam Based on Otolith Shape Analysis

Abstract—The shape of otoliths (sagittae) is analyzed in freckled goatfish Upeneus tragula from South Vietnam (Gulf of Thailand), southern Central Vietnam (Nha Phu and Nha Trang bays), and North Vietnam (Ha Long Bay). The shape indices, elliptic Fourier analysis, and canonical discriminant analysis are applied. In the Gulf of Thailand, the samples off Hon Thom (Thom Island, An Thoi Archipelago, to the south of Phu Quoc Island) including the red morph and black morph collected during two subsequent years almost do not differ in otolith shape. A comparison of the samples from four regions of the Gulf of Thailand (40 km to the west of Phu Quoc, pooled sample off Hon Thom, coastal zone to the east of Phu Quoc, and 19 km to the west of Ha Tien) shows a discrimination of the stocks from the west to northeast. Substantial differentiation between the samples from Central and North Vietnam is not registered. The results are discussed in relation to the features of life history of U. tragula and possible relative isolation of some stocks.

Size-effect, asymmetry, and small-scale spatial variation in otolith shape of juvenile sole in the Southern North Sea

While otolith shape analysis can provide a valuable tool for discriminating between fish populations, factors which may influence otolith shape, such as the effect of size, directional asymmetry in growth, and local environmental conditions, are often unknown. Here, we analyzed differences in otolith shape across three size classes of age-0 common sole Solea solea L. from nursery grounds off the Belgian coast and in the Wadden Sea. Across size classes, form-factor decreased and roundness remained consistently high in both nursery grounds, while ellipticity increased in the Belgian nursery. Directional asymmetry between left and right otoliths measured by Fourier coefficients accounted for 0.96 and 7.2% of the variance when comparing otoliths overall, and for each size class, respectively. Within the Belgian nursery, results were consistent across sampling years and locations. In addition, otolith shape was marginally different between nursery grounds, but highly variable within nursery grounds. A small divergent group, which seems partly related to fish size, was noted at both spatial and temporal scales. Based on these results and before embarking on a study of population structure using otolith shape in age-0 common sole, we recommend testing for directional asymmetry and fish size effects across the entire region of interest.

Otolith shape analysis for stock discrimination of two Collichthys genus croaker (Pieces: Sciaenidae,) from the northern Chinese coast

The otolith morphology of two croaker species (Collichthys lucidus and Collichthys niveatus) from three areas (Liaodong Bay, LD; Huanghe (Yellow) River estuary, HRE; Jiaozhou Bay, JZ) along the northern Chinese coast were investigated for species identification and stock discrimination. The otolith contour shape described by elliptic Fourier coefficients (EFC) were analysed using principal components analysis (PCA) and stepwise canonical discriminant analysis (CDA) to identify species and stocks. The two species were well differentiated, with an overall classification success rate of 97.8%. And variations in the otolith shapes were significant enough to discriminate among the three geographical samples of C. lucidus (67.7%) or C. niveatus (65.2%). Relatively high mis-assignment occurred between the geographically adjacent LD and HRE samples, which implied that individual mixing may exist between the two samples. This study yielded information complementary to that derived from genetic studies and provided information for assessing the stock structure of C. lucidus and C. niveatus in the Bohai Sea and the Yellow Sea.

Comparison of three methods for identification of redfish (Sebastes mentella and S. norvegicus) from the Greenland east coast

In management of fisheries, knowledge about the species is crucial due to differences in life history traits. The first step is therefore species identification. For many species this task is straightforward, however for some species e.g. the two species of Atlantic redfish Sebastes mentella and Sebastes norvegicus, it can be difficult for an untrained eye. With the goal to separate the two species, we analysed otolith shape variation of S. mentella and S. norvegicus caught on the continental slope of East Greenland using the R package “Shape R”. Results were evaluated against genetic analysis of the same fish, and compared to results of both a visual identification of the two species and a separation based on a linear discriminant analysis on standardised values of fish length, fish weight and otolith weight. It was concluded that the objective otolith shape analysis using the Shape R package analysis achieve a reasonable classification success, however with a clear bias towards S. mentella. Classification using the otolith weight achieved a slightly higher success than the shape analysis making it a promising method. Furthermore, the method is at the same time both objective, less time consuming than the otolith shape analysis and less expensive than genetic analysis. However, the visual classification method of the whole fish had the highest success rate of the three tested methods, which despite the need for trained technicians makes it the most successful method.

Otolith shape analysis as a tool for stock separation of albacore tuna feeding in the Northeast Atlantic

For management purposes, albacore tuna (Thunnus alalunga, Bonnaterre 1788) in the North Atlantic are considered to be from one homogenous stock. However, multiple lines of evidence suggest that there is some degree of stock complexity. In this study, the stock structure of North Atlantic albacore tuna is investigated using otolith shape analysis. Juvenile albacore tunas were collected from the commercial fishery in the Bay of Biscay region over a three-year period (2012–2014). Catches were concentrated in two main areas: within the Bay of Biscay (East) and off the western shelf edge (West). Otolith shape was defined using Elliptical Fourier analysis and was compared between albacore from these two catch locations using generalised canonical discriminant analysis. The results show significant differences in otolith shape between albacore from the Eastern and Western locations using Elliptical Fourier descriptors. The discriminant analysis and jack-knifed cross-validation classification correctly classified East and West samples with a success rate of 72% and 75% respectively. The results suggest that two components with distinct environmental life histories contribute to the fishery in the Northeast Atlantic. It also implies that albacore juveniles display some degree of fidelity to their feeding areas.

Identifying populations of the blue jack mackerel (Trachurus picturatus) in the Northeast Atlantic by using geometric morphometrics and otolith shape analysis

Identifying populations of the blue jack mackerel (Trachurus picturatus) in the Northeast Atlantic by using geometric morphometrics and otolith shape analysis

Otolith Shape Analysis as a Tool for Species Identification and Studying the Population Structure of Different Fish Species

An analysis and a comparison of the methods of geometric morphometrics as applied to fish species identification and to studies on the population structure of fish stocks based on peculiarities of the otolith shape are performed. A review of the geometric morphometric methods used in studies on fish otoliths is provided. The results of our own research on possible utilization of elliptical Fourier analysis for species identification are also described.

Razmerno-vesovoj sostav i nekotorye dannye po otolitometrii segoletok i dvukhletok navagi Eleginus gracilis yugo-zapadnoj chasti Beringova morya

Razmerno-vesovoj sostav i nekotorye dannye po otolitometrii segoletok i dvukhletok navagi Eleginus gracilis yugo-zapadnoj chasti Beringova morya

The use of otolith shape to determine stock structure of Engraulis encrasicolus along the Tunisian coast

Engraulis encrasicolus is of great economic importance in the Mediterranean. However, little is known about its stock structure. Otolith shape analysis has been successfully used for fish stock identification. In this study, the stock structure of anchovy caught off the open sea and the coastal area of the Gulf of Tunis, lagoon of Bizerte and Lake of Ichkeul were investigated using otolith shape. Otolith shape was determined by Fourier analysis and then compared among specimens sampled from different areas with forward stepwise canonical discriminant analysis. Significant differences in otolith shape between the open sea and inshore anchovy groups were detected. Otolith shape of anchovy collected in the Lake of Ichkeul was distinct from the other groups. This finding suggests a clear discreteness of the open sea and the continental groups. The data highlighted the potential for using otolith shape analysis for anchovy stock identification, as well as the role of oceanographic features in determining stock separation. These findings will have major implications for anchovy fisheries management in Tunisia. By using a precautionary approach and considering the three areas as separate stocks, fisheries management strategies should be adjusted to achieve optimum sustainable production from each stock and to avoid decreases in genetic variety.

The use of Fourier analysis as a tool for Oblada melanura (Linnaeus, 1758) stock unit separation in the south central Mediterranean Sea

For the first time, an otolith shape analysis was used to investigate the stocks of saddled bream (Oblada melanura, Linnaeus, 1758) in three fishing zones along the Tunisian coast (Bizerte, Kélibia and Sayada). Otolith shape analysis was used on 30 otoliths for each site, sampled during the spawning period. Using elliptic Fourier descriptors (EFD) the quantization of the shape otolith was investigated by SHAPE and multivariate statistical procedures. Considering the environmental and the genotypic aspects, the preliminary results of the otolith shape analysis showed dissimilarity in silhouette of otoliths of saddled bream stocks collected from the north (Bizerte), the north-east (Kélibia) and the east (Sayada) of the Tunisian coast. Therefore, these three groups could be considered as three sub-units of the Tunisian stock, which should be managed separately.

Combining microsatellite, otolith shape and parasites community analyses as a holistic approach to assess population structure of Dentex dentex

The common dentex, Dentex dentex, is an iconic marine coastal fish of the Mediterranean Sea. Despite its economic and ecological importance, data on the population structure of this species are still very limited. The aim of this study was to identify the stock structure of the common dentex at relatively fine spatial scale around Corsica Island, using a combination of markers that have different spatial and temporal scales of integration: microsatellite DNA markers, otolith shape analysis and parasites communities. Microsatellite analysis indicated that there was no significant genetic differentiation in D. dentex between the four sampling sites around Corsica. Otolith shape analysis suggests one potential distinct population unit of D. dentex centered in one site (Cap Corse) varying in their degree of differentiation from those in the other zones. Multivariate analysis on parasite abundance data highlights to a lower extent two sites (Bonifacio and Galeria) with some connectivity between adjacent zones. The combination of these three markers together highlights the resulting three sites while giving complementary insights and an opportunity to compare their utility and potential to understand population interactions. A complex population structure around Corsican coasts is then proposed, providing a new perspective on common dentex fishery stock conservation and management strategies.

Otolith shape analysis as a tool for stock identification of the southern blue whiting, Micromesistius australis

The southern blue whiting, Micromesistius australis (Norman, 1937), is an important demersal resource associated with the slope and continental shelf of southern Chile, Argentina and the Malvinas/Falkland Islands. Recent studies have reported schools of adult fish from Atlantic waters migrating along the southern Chilean coast in mid-winter, moving northwards to spawn in August (47º-51ºS), and then returning to Atlantic waters, presumably to feed. The migratory pattern suggests the presence of one or more stock units associated with the South American coast. In the present study, “otolith morphometry” is used to determine the stock structure of M. australis based on applications of basic size descriptors (SDs) (area, perimeter and otolith size), shape indices (SIs) (circularity, squareness, shape factor, roundness, ellipticity), and normalised elliptical Fourier descriptors (NEFDs). Samples were collected during the winter and spring of 2010, during the reproductive period, in the economic zone of southern Chile (36º-57ºS), in the Pacific Ocean and around the Falkland Islands economic zone (50º-52ºS) in the Atlantic Ocean. Analyses were conducted to include the effects of size, sex and age. A stepwise canonical discriminant analysis showed that fish were successfully discriminated with SDs, SIs and NEFDs. In this analysis, 86.4% and 70.1% of the fish were correctly classified as belonging to the Atlantic and Pacific stocks, respectively. A multivariate analysis of variance showed that the mean values of the NEFDs, SDs, and SIs did not vary significantly between sexes within areas (P > 0.05), but varied significantly between the Pacific and Atlantic oceans (P < 0.05). These results highlighted that otolith shape analysis can be a useful tool to evaluate the potential level of mixing in feeding areas where both stocks, the Pacific and Atlantic units, are expected to co-occur.

Evaluation of removal of the size effect using data scaling and elliptic Fourier descriptors in otolith shape analysis, exemplified by the discrimination of two yellow croaker stocks along the Chinese coast

Removal of the length effect in otolith shape analysis for stock identification using length scaling is an important issue; however, few studies have attempted to investigate the effectiveness or weakness of this methodology in application. The aim of this study was to evaluate whether commonly used size scaling methods and normalized elliptic Fourier descriptors (NEFDs) could effectively remove the size effect of fish in stock discrimination. To achieve this goal, length groups from two known geographical stocks of yellow croaker, Larimichthys polyactis, along the Chinese coast (five groups from the Changjiang River estuary of the East China Sea and three groups from the Bohai Sea) were subjected to otolith shape analysis. The results indicated that the variation of otolith shape caused by intra-stock fish length might exceed that due to inter-stock geographical separation, even when otolith shape variables are standardized with length scaling methods. This variation could easily result in misleading stock discrimination through otolith shape analysis. Therefore, conclusions about fish stock structure should be carefully drawn from otolith shape analysis because the observed discrimination may primarily be due to length effects, rather than differences among stocks. The application of multiple methods, such as otoliths shape analysis combined with elemental fingering, tagging or genetic analysis, is recommended for sock identification.

Otolith shape analysis and mitochondrial DNA markers distinguish three sand smelt species in the Atherina boyeri species complex in western Mediterranean

Atherina boyeri is a common euryhaline teleost fish in the Mediterranean and adjacent areas, which inhabits coastal and estuarine waters, including coastal lagoons and more rarely inland waters. Several recent studies have pointed the possible existence of three distinct groups or species, one lagoon/freshwater group and two ‘punctuated and unpunctuated on the flanks' marine groups, within an A. boyeri species complex. This study is a combined approach using otolith shape and molecular markers to better define the structure of the species in the western Mediterranean.Genetic differentiation and species delimitation among nine Atherina boyeri populations from several marine and lagoon/brakish habitat sites in Algeria, Tunisia and France were investigated using three mitochondrial (control region, Cyt b and 16S) and one nuclear markers (2nd intron of S7). For further phylogenetic and phylogeographic study, we added sequences from Genbank covering more areas (Ionian Sea, Adriatic Sea, Tyrrhenian Sea, Black Sea, Atlantic). Five groups were found. Two of them perfectly corresponded to two species already recognized Atherina presbyter and Atherina hepsetus, both living in marine waters; and three additional, including Atherina boyeri (brackish and freshwater environments) and two independent groups of marine punctated and unpunctated individuals. Those findings are corroborated by the study of the otolith contour shape of 362 individuals of seven populations from different habitats using Fourier analysis. Individuals could be discriminated into five groups based on the first two functions (Wilk's lambda = 0.07, p < 0.001). Samples from Ziama inlet, marine punctuated individuals and unpunctuated marine specimens from Annaba's Gulf formed three well separated groups. Specimens from Mellah and Mauguio lagoons formed another group. The last one includes individuals from Bizerte and Thau lagoons. The divergences between them strongly support the potential species within the A. boyeri species complex.