Spatiotemporal shape variation in sagittal otoliths of spotted grunter Pomadasys commersonnii in South African estuaries

Otolith shape has long been known to be species specific, but recent reports have pointed to its value as an indicator of stock identity. To test this hypothesis, all three pairs of otoliths were sampled from 2349 Atlantic cod (Gadus morhua) collected on spawning grounds throughout the northwest Atlantic. Otolith shape was determined with Fourier analysis and combined with measures of otolith area and perimeter. There were highly significant differences in otolith shape among most of the cod samples, but shape also differed among ages, sexes, and year-classes. The sagittal otoliths (largest pair) provided slightly better stock discrimination than did the lapillar or asteriscal otoliths. The first discriminant function was highly correlated with both fish and otolith growth rate, indicating that stock discrimination improved as the difference in stock-specific growth rate increased. Reevaluation of published studies on other species indicated that growth rate contributes more variation to regional differences in otolith shape than does stock origin. Differences in otolith shape among ages, sexes, and year-classes were also attributable to growth rate differences. To the extent that growth rates vary more between than within stocks, otolith shape analysis can provide an easily determined measure of stock identity.

Otolith shape as a tool for species identification of the grenadiers Macrourus caml and M. whitsoni

The influence of feeding history on otolith shape and symmetry was examined in juveniles of 2 species of coral reef fish, Amphiprion akindynos and Pomacentrus amboinensis. Fast Fourier analysis was used to describe the shape of otoliths of fish from a variety of experimental feeding treatments, ranging from starvation, through pulse feeding, to feeding ad libitum. The resulting harmonics from both the left and right otoliths of each individual fish were used in a multivariate analysis to investigate shape differences among feeding treatments in the 2 species. When left and right otoliths were analysed separately, no significant differences between feeding treatments were revealed for either species. In contrast, when left and right otoliths from individuals were analysed together, clear separations in feeding groups were observed in both species. Differences among feeding treatments were largely due to differences in the finer details of the otolith shape, represented by the middle level harmonics. Fish that had been starved had significantly different otolith shapes than fish from all other treatments. Differences in otolith shape could not simply be attributed to differences in fish size or age among treatments. We conclude that differences in otolith shape are influenced by recent feeding history, but processes that influence otolith shape are complex and most likely species-specific. This study presents new evidence that otolith shape of tropical fish may directly reflect body condition of individuals regardless of fish size and age.

Geometric mean regression analysis between log(length) and log(height) of otoliths from lake trout (Salvelinus namaycush) from six lakes revealed that the growth of this structure was negatively allometric, indicating that otolith shape varies throughout the life of the fish. Otolith shape was quantified using harmonic amplitudes 2-10 (A2-A10) extracted from Fourier-series analyses. We found harmonic amplitudes 2 (A2) and 5 (A5) to be associated with the length/height relationship. Some recent studies have suggested that growth of fish otoliths affects their shape. Our results indicate that part of this otolith-growth effect could be due to an intrinsic change in shape associated with allometric nature of the length/height relationship. There were no differences in otolith shape between males and females. Otolith shape was also compared among the six populations. Major differences were observed between Lake Normand (Saint Maurice River watershed) and the five lakes in the Ottawa River watershed, suggesting that genotype could be an important factor affecting otolith shape. The percentage of reclassification using a discriminant function analysis was high (86%) for the Lake Normand population. Among populations from the Ottawa River watershed, differences in otolith shape were more subtle, with reclassification percentages ranging from 50 to 75%. However, one population in the Ottawa River watershed (Lake Duval), which was introduced as hatchery-raised individuals, differed slightly from the other populations from the same watershed, including Lake Trente et un Milles, from which it originated.

Sagittal otoliths from four populations of the Pacific deep slope red snapper Etelis carbunculus Cuvier were compared using Fourier descriptors and other shape indices, linear proportions, and dry weight. Otoliths from Hawaii, Vanuatu, Fiji and French Polynesia and a small number from the Commonwealth of the Northern Marianas Islands (NMI) were examined. Regional shape and weight characteristics were distinguishable, despite the wide range of individual variation and limited available size range from some regions. Size-specific differences in otolith shape were found for the four regions for which a sufficient sample was available. Otoliths from Hawaii, French Polynesia, and NMI showed a significant shape affinity. Otoliths from Fiji and Vanuatu were similarly shaped and were distinct from those from the other three regions. Interregional otolith shape affinities for the stocks examined parallel similarities in maximum size and growth rate from the literature, suggesting that growth rate may influence otolith shape. Observed trends in otolith weight as a function of fish length support growth-related regional differences in otolith shape.

The fishing industry is an important economic sector in Namibia and South Africa, with the shallow-water hake Merluccius capensis being an important target species. Recent genetic studies of M. capensis found two stocks in the Benguela Current Large Marine Ecosystem, one in the north (17–29° S) and one in the south (29–36° S), and a proposed mixed stock in the Orange River area (around 29° S). The present study investigated the use of otolith shape analysis for purposes of stock-structure analysis of M. capensis. Merluccius capensis otolith samples were collected during demersal-trawl surveys along the Benguela, for the years 1992, 2004 and 2005. Different years were selected to investigate temporal stability in otolith shape in the northern Benguela. A total of 1 628 otolith images were analysed using the shapeR library in R. Otolith shape was analysed using wavelet transformation, and ANOVA-like permutation tests indicated no significant differences between the northern (17°31′–25°29′ S) and central (25°30′–29°05′ S) Benguela for all years but showed significant differences between the northern and southern (29°05′–35°50′ S) Benguela. This study therefore demonstrated that otolith shape could be used for stock discrimination of M. capensis. It confirmed one stock of M. capensis in the northern and central Benguela and another in the southern Benguela, which supports the current, separate management approach for this species. It also showed some differences in otolith shape from the 1990s to the 2000s, which could be explained by increased movement of the southern Benguela stock to the northern Benguela and increased hybridisation in the later years.

The effects of sex, stock, and environment on the shape of known-age Atlantic cod (Gadus morhua) otoliths from the Faroe Islands were investigated. Moreover, the feasibility of otolith shape analysis for stock identification was evaluated. The shape was described by using several normalized Fourier descriptors and morphometric variables. There were no consistent differences between the left and right otoliths and between sexes within different age classes, stocks, and environments. With our experimental design, we could evaluate the relative importance of genetic and environmental conditions (water temperature and diet regime) on otolith shape and morphometrics. Using otolith shape, cod individuals were significantly separated into Bank and Plateau stocks. Total classification success was between 79% and 85% between stocks and between 85% and 96% between environments for the different age classes. The significant differences in otolith shape between Faroe Bank and Faroe Plateau cod stocks provided a phenotypic basis for stock separation. Stock and environmental influences were substantial in determining the shape of cod otoliths.

Shape analyses were carried out on otoliths of the common sole, Solea solea (Linnaeus, 1758), in order to discriminate local populations in the North-Western Mediterranean Sea. Samples were collected in various environments like coastal lagoons, the outlet of the Rhone River as well as other marine sites. Morphological analyses highlighted a significant asymmetry between the left and right otoliths. This character could be acquired during or shortly after settlement on soft-bottoms when the individuals really become flatfishes. The otolith shape was described by seven harmonics from elliptic Fourier descriptors and by five indices of shape (coefficient of form, roundness, circularity, rectangularity, and ellipticity). The existence of several local populations of common sole in the NW Mediterranean was demonstrated. In particular, discriminant analyses highlighted significant differences in otolith shape according both to fish size and to the types of environment in which the fish live, i.e. coastal lagoons vs. marine sites, but also between sites belonging to the same type (lagoons, and marine sites). The differences in shape could be linked (1) to the particular environmental conditions of each site, and (2) to changes in metabolic and/or physiological conditions according to the stage of development of the fish which most likely influences the otolith growth.

The Indian mackerel, Rastrelliger kanagurta, is a commercially important resource across Indonesia's archipelagic waters. Despite its essential role in the fisheries industry, information regarding its population structures for management purposes is still limited. The present study investigates the variability of otolith shape as an efficient tool for stock discrimination. A total of 159 pairs of sagittal otolith were sampled at four localities along the southern Java-Bali coastal waters. Otolith outline was modeled by using Wavelet coefficients and was compared between localities using ANOVA-like permutation test, Canonical Analysis of Principal Coordinates (CAP), and classification test performed using linear discriminant analysis. The results showed significant differences in the shape of otolith between populations, reflected explicitly in the morphological feature of the excisura major. The differences in otolith shape were examined from all localities (ANOVA-like, p<0.001, and CAP p>0.05), except those otoliths between Palabuhanratu and Pacitan, thus, a mixed stock may occur in these two locations. These findings were also confirmed by the low classification success rate using LDA 44.26%. These results suggested that at least two distinct stocks potentially contributed to the fishery, impacting species management and conservation.

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.

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.

Otolith morphometrics and shape analyses were used to delineate the sub-population structure and determine the level of mixing of southern garfish in South Australian waters. Adult garfish from the 2+ age class were collected from three sites within each of six regions along the South Australian coast: Northern Gulf St Vincent, Southwest Gulf St Vincent, Kangaroo Island, Northern Spencer Gulf, Southern Spencer Gulf and the West Coast of Eyre Peninsula. This study adopted a multi-stage statistical approach exploring the spatial variation in gross otolith morphology and through elliptical Fourier analysis separately, and in combination, over both broad (regional) and fine (site) spatial scales. Stepwise discriminant function analysis revealed significant separation across both spatial scales; however, overall classification success of garfish to their site of capture was poor (<45%). Despite this, the results indicated some level of structuring within South Australia's southern garfish population, as fish were correctly classified at rates that were 32% better than would be expected by chance. At least six putative regional components with various levels of intermixing were detected based on differences in otolith shape. This result refines the spatial resolution of the fishery and consequently highlights the vulnerability of these regional components to localized depletion, particularly as the resource is currently considered to be over-exploited.

Based on their morphological and genetic similarity, several studies have proposed that Lutjanus campechanus and Lutjanus purpureus are the same species, but there is no confirmed consensus yet. A population-based study concerning otolith shape and genetic analyses was used to evaluate if L. campechanus and L. purpureus are the same species. Samples were collected from populations in the southwestern Gulf of Mexico and the Venezuelan Caribbean. Otolith shape was evaluated by traditional and outline-based geometric morphometrics. Genetic characterization was performed by sequencing the mtDNA control region and intron 8 of the nuclear gene FASD2. The otolith shape analysis did not indicate differences between species. A nested PERMANOVA identified differences in otolith shape for the nested population factor (fishing area) in morphometrics and shape indexes (p = 0.001) and otolith contour (WLT4 anterior zone, p = 0.005 and WLT4 posterodorsal zone, p = 0.002). An AMOVA found the genetic variation between geographic regions to be 10%, while intrapopulation variation was 90%. Network analysis identified an important connection between haplotypes from different regions. A phylogenetic analysis identified a monophyletic group formed by L. campechanus and L. purpureus, suggesting insufficient evolutionary distances between them. Both otolith shape and molecular analyses identified differences, not between the L. campechanus and L. purpureus species, but among their populations, suggesting that western Atlantic red snappers are experiencing a speciation process.

Pacific herring (Clupea pallasii) is divided into three subspecies: two in northeast Europe and one in the north Pacific Ocean. Genetic studies have indicated that the populations in northeast Europe have derived from the northwest Pacific herring recently, or during the last 10–15 kyr, and that they are distinct from the population in the northeast Pacific. In addition, hybridization between the Pacific herring and the Atlantic herring has been documented. Otolith variation has been considered to be largely affected by environmental variation, but here we evaluate whether the genetic differentiation is reflected in otolith shape differences. A clear difference in otolith shape was observed between the genetically differentiated herring species Clupea harengus from the Atlantic and C. pallasii. The otolith shape of C. p. suworowi in the Barents Sea was different from the shape of C. pallasii in northern Norway and C. p. pallasii from the Pacific. Populations of C. p. pallasii, sampled east and west of the Alaska Peninsula, which belong to two genetically different clades of the C. p. pallasii in the Pacific Ocean, show a clear difference in otolith shape. C. p. suworowi and the local C. pallasii peripheral population in Balsfjord in northern Norway are more similar to the northwest Pacific herring (C. p. pallasii) than to the northeast Pacific herring (C. p. pallasii), both genetically and in otolith shape. The Balsfjord population, known to be influenced by introgression of mtDNA from the Atlantic herring, does not show any sign of admixture in otolith shape between the two species. A revised classification, considering the observed genetic and morphological evidence, should rather group the northwest Pacific herring in the Bering Sea together with the European populations of C. pallasii than with the northeast Pacific herring in the Gulf of Alaska.

An analysis of patterns in otolith shape is an effective tool for discriminating among fish stocks. Otolith shapes of Patagonian toothfish (Dissostichus eleginoides) and Antarctic toothfish (D. mawsoni) were investigated for geographic variability within seven regions across the Patagonian Shelf, and South Georgia and the South Sandwich Islands (SGSSI). Otolith shape was characterised by its elliptical Fourier coefficients (EFCs), corrected for fish length before being analysed, using multivariate methods. Non-metric multidimensional scaling analysis suggested the following three main groupings: Patagonian Shelf, SGSSI, and the third for Antarctic toothfish. This result was supported by ANOVA-like permutation tests, indicating significant (P &amp;lt; 0.001) differences in otolith shape among these three groupings. Linear discriminant analysis (LDA) cross-validation analyses of the EFCs resulted in otoliths being correctly classified to the sampling region from which they came, with an accuracy ranging from 78.95 to 100%. LDA cross-validation analyses on sampling regions within SGSSI and the Patagonian Shelf were able to classify individuals back to their sampling region with an accuracy of greater than 89.74 and 78.95% respectively. These results have provided some alternative insights into the stock structure of Patagonian toothfish across southern South America, South Atlantic and SGSSI.