A duplicated amh is the master sex-determining gene for Sebastes rockfish in the Northwest Pacific

Teleost fish are the most diverse group of vertebrates and provide opportunities to study the evolution of sex determination (SD) systems. Using genomic and functional analyses, we identified a male-specific duplication of anti-Müllerian hormone ( amh ) gene as the male master sex-determining (MSD) gene in Sebastes schlegelii . By resequencing 10 males and 10 females, we characterized a 5 kb-long fragment in HiC_Scaffold_12 as a male-specific region, which contained an amh gene (named amhy ). We then demonstrated that amhy is a duplication of autosomal amh that was later translocated to the ancestral Y chromosome. amha and amhy shared high-nucleotide identity with the most significant difference being two insertions in intron 4 of amhy . Furthermore, amhy overexpression triggered female-to-male sex reversal in S. schlegelii , displaying its fundamental role in driving testis differentiation. We developed a PCR assay which successfully identified sexes in two species of northwest Pacific rockfish related to S. schlegelii . However, the PCR assay failed to distinguish the sexes in a separate clade of northeast Pacific rockfish. Our study provides new examples of amh as the MSD in fish and sheds light on the convergent evolution of amh duplication as the driving force of sex determination in different fish taxa.

Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe

Morphology-based identification of North AtlanticSebasteshas long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North AtlanticSebastescomprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicusandS. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification ofSebastesmarket samples.

Separating recruitment and mortality time lags for a delay-difference production model

Many fishery production models implicitly incorporate a single time lag for both recruitment and mortality despite the fact that in populations of breeding adults, deaths occur yearly while the entry of new adults comes from juveniles born potentially many years prior to adulthood. Models that do not account for this difference in timing will overestimate abundance for a decreasing stock and underestimate increases during a recovery period. We investigated the effect of incorporating unequal recruitment and mortality time lags into depletion-based stock reduction analysis (DB-SRA), a stock assessment method for data-poor species. Using both simulated data and catch series of Pacific rockfish (Sebastes spp.), we found that for declining stocks with no mortality delay and a recruitment time lag equal to age-at-maturity, estimated overfishing limits were up to 40% lower than those from the model with both time lags equal to age-at-maturity. Deviation between the two models’ predictions increases with age-at-maturity and natural mortality rate, suggesting that time lag separation is most important for long-lived species. We propose a correction factor for net production models that eliminates stock overestimation due to implicitly equal time lags.

Development and application of an agent-based model to evaluate methods for estimating relative abundance indices for shoaling fish such as Pacific rockfish (Sebastes spp.)

Thorson, J. T., Stewart, I. J., and Punt, A. E. 2012. Development and application of an agent-based model to evaluate methods for estimating relative abundance indices for shoaling fish such as Pacific rockfish (Sebastes spp.). – ICES Journal of Marine Science, 69: 635–647. Many marine fish, including Pacific rockfish (Sebastes spp.), exhibit habitat-selective and shoaling behaviours, which can lead to imprecision when using survey data to estimate an annual index of stock abundance. We develop a spatial agent-based model (ABM) for Pacific rockfish, which generates data similar to those observed in existing bottom-trawl surveys and can represent various spatial and shoaling behaviours. We use the ABM to evaluate the performance of a model that uses mixture distribution methods to account for fish shoals and delta-methods to account for range expansion or contraction. This delta-mixture model is compared with conventional delta-generalized linear models (delta-GLMs) and a quantile regression delta-model. The delta-mixture increases precision by 15% relative to delta-GLMs in estimated abundance indices when shoaling behaviours are present, whereas precision is similar between delta-GLM and delta-mixture models when shoals are absent. The delta-quantile method has similar improvements over conventional delta-GLM methods, and the improved precision from delta-mixture and delta-quantile methods is decreased but not eliminated by decreased sampling intensities. These simulations represent the first evaluation of delta-mixture models for index standardization and show a substantial improvement over conventional delta-GLMs for shoaling species such as Pacific rockfish.