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Sex determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, non‐invasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex‐determination systems and corresponding statistical methods for identifying sex‐linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex‐linked SNPs and minor allele frequency. The application of three methods was made here: i) identification of heterozygote excess in one sex, ii) F ST outlier analysis between the two sexes and iii) neuronal net modelling. These methods were applied to a large SNP dataset (4604 SNPs) for 1680 thornback rays (Raja clavata ). Using method i), nineteen putative sex‐linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata ) indicated that all 19 SNPs are likely located on the same chromosome. These results suggest that thornback ray has a XX/XY sex‐determination system. Method ii) identified eight SNPs probably located on different chromosomes. Method i) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).

Sex determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, non‐invasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex‐determination systems and corresponding statistical methods for identifying sex‐linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex‐linked SNPs and minor allele frequency. The application of three methods was made here: i) identification of heterozygote excess in one sex, ii) F ST outlier analysis between the two sexes and iii) neuronal net modelling. These methods were applied to a large SNP dataset (4604 SNPs) for 1680 thornback rays (Raja clavata ). Using method i), nineteen putative sex‐linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata ) indicated that all 19 SNPs are likely located on the same chromosome. These results suggest that thornback ray has a XX/XY sex‐determination system. Method ii) identified eight SNPs probably located on different chromosomes. Method i) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).

Sex determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, non‐invasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex‐determination systems and corresponding statistical methods for identifying sex‐linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex‐linked SNPs and minor allele frequency. The application of three methods was made here: i) identification of heterozygote excess in one sex, ii) F ST outlier analysis between the two sexes and iii) neuronal net modelling. These methods were applied to a large SNP dataset (4604 SNPs) for 1680 thornback rays (Raja clavata ). Using method i), nineteen putative sex‐linked SNPs were identified. Comparison with the reference genome of a related species (Amblyraja radiata ) indicated that all 19 SNPs are likely located on the same chromosome. These results suggest that thornback ray has a XX/XY sex‐determination system. Method ii) identified eight SNPs probably located on different chromosomes. Method i) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).

The thornback ray (Raja clavata) in the Bay of Biscay is presumed to have declined during the 20th Century. To evaluate this decline and estimate biomass trajectories, a hypothetical catch time series was created for the period 1903-2013. A Bayesian state-space biomass production model with a Schaefer production function was fitted to the hypothetical catch time series and to a shorter research vessel Catch Per Unit Eeffort (CPUE) time series (1973-2013, with missing years). A censored likelihood made it possible to obtain biomass estimates without a CPUE time series or only with an estimate of biomass depletion. A simulation-estimation approach showed a high sensitivity of results to the prior for the intrinsic growth rate. The model provided biomass trajectories which corroborated and quantified the decline of the Bay of Biscay population. The estimated biomass corresponding to the maximum sustainable yield, BMSY, was 32 000 tonnes, which is 17 times higher than the estimated biomass in 2014. The biomass estimates obtained without a CPUE time series were highly uncertain. Adding a current biomass depletion observation improved precision, though the biomass time trend was sensitive to this value. Results should be interpreted carefully as several assumptions were necessary to create the long catch time series and to define informative priors, notably for the intrinsic growth rate. Despite this, the results confirm the depleted state of the thornback ray in the Bay of Biscay with the estimated biomass in 2014 being around 3% of carrying capacity.

The thornback ray (Raja clavata) in the Bay of Biscay is presumed to have declined during the 20th Century. To evaluate this decline and estimate biomass trajectories, a hypothetical catch time series was created for the period 1903-2013. A Bayesian state-space biomass production model with a Schaefer production function was fitted to the hypothetical catch time series and to a shorter research vessel Catch Per Unit Eeffort (CPUE) time series (1973-2013, with missing years). A censored likelihood made it possible to obtain biomass estimates without a CPUE time series or only with an estimate of biomass depletion. A simulation-estimation approach showed a high sensitivity of results to the prior for the intrinsic growth rate. The model provided biomass trajectories which corroborated and quantified the decline of the Bay of Biscay population. The estimated biomass corresponding to the maximum sustainable yield, BMSY, was 32 000 tonnes, which is 17 times higher than the estimated biomass in 2014. The biomass estimates obtained without a CPUE time series were highly uncertain. Adding a current biomass depletion observation improved precision, though the biomass time trend was sensitive to this value. Results should be interpreted carefully as several assumptions were necessary to create the long catch time series and to define informative priors, notably for the intrinsic growth rate. Despite this, the results confirm the depleted state of the thornback ray in the Bay of Biscay with the estimated biomass in 2014 being around 3% of carrying capacity.

The thornback ray (Raja clavata) in the Bay of Biscay is presumed to have declined during the 20th Century. To evaluate this decline and estimate biomass trajectories, a hypothetical catch time series was created for the period 1903-2013. A Bayesian state-space biomass production model with a Schaefer production function was fitted to the hypothetical catch time series and to a shorter research vessel Catch Per Unit Eeffort (CPUE) time series (1973-2013, with missing years). A censored likelihood made it possible to obtain biomass estimates without a CPUE time series or only with an estimate of biomass depletion. A simulation-estimation approach showed a high sensitivity of results to the prior for the intrinsic growth rate. The model provided biomass trajectories which corroborated and quantified the decline of the Bay of Biscay population. The estimated biomass corresponding to the maximum sustainable yield, BMSY, was 32 000 tonnes, which is 17 times higher than the estimated biomass in 2014. The biomass estimates obtained without a CPUE time series were highly uncertain. Adding a current biomass depletion observation improved precision, though the biomass time trend was sensitive to this value. Results should be interpreted carefully as several assumptions were necessary to create the long catch time series and to define informative priors, notably for the intrinsic growth rate. Despite this, the results confirm the depleted state of the thornback ray in the Bay of Biscay with the estimated biomass in 2014 being around 3% of carrying capacity.

Several species of rays and skates were common in Dutch territorial waters at the beginning of the century and there was a directed fisheries on these species. During the 1930's a decline in landings was seen and shortly after the Second World War there were few rays left on the Dutch continental shelf. At the present time only two species of ray are caught in Dutch waters (the starry ray, Raja radiata, and the stingray, Dasyatis pastinaca), neither are commercially important. The starry ray has replaced the thornback ray (R. clavata) as the most abundant species. Although total mortality (natural + fisheries) on adult rays is above the theoretical replacement level for a number of species, the same species are still present off the British coast. This area is possibly a source of individuals for other parts of the North Sea. It is as yet unclear which stage in the development (i.e survival of adults, eggs or juveniles) is the one limiting the ecolonisation of Dutch coastal waters by the endemic species.

Several species of rays and skates were common in Dutch territorial waters at the beginning of the century and there was a directed fisheries on these species. During the 1930's a decline in landings was seen and shortly after the Second World War there were few rays left on the Dutch continental shelf. At the present time only two species of ray are caught in Dutch waters (the starry ray, Raja radiata, and the stingray, Dasyatis pastinaca), neither are commercially important. The starry ray has replaced the thornback ray (R. clavata) as the most abundant species. Although total mortality (natural + fisheries) on adult rays is above the theoretical replacement level for a number of species, the same species are still present off the British coast. This area is possibly a source of individuals for other parts of the North Sea. It is as yet unclear which stage in the development (i.e survival of adults, eggs or juveniles) is the one limiting the ecolonisation of Dutch coastal waters by the endemic species.