Modernising fish and shark growth curves with Bayesian length-at-age models.

Growth modelling is a fundamental component of fisheries assessments but is often hindered by poor quality data from biased sampling. Several methods have attempted to account for sample bias in growth analyses. However, in many cases this bias is not overcome, especially when large individuals are under-sampled. In growth models, two key parameters have a direct biological interpretation: L0, which should correspond to length-at-birth and L∞, which should approximate the average length of full-grown individuals. Here, we present an approach of fitting Bayesian growth models using Markov Chain Monte Carlo (MCMC), with informative priors on these parameters to improve the biological plausibility of growth estimates. A generalised framework is provided in an R package 'BayesGrowth', which removes the hurdle of programming an MCMC model for new users. Four case studies representing different sampling scenarios as well as three simulations with different selectivity functions were used to compare this Bayesian framework to standard frequentist growth models. The Bayesian models either outperformed or matched the results of frequentist growth models in all examples, demonstrating the broad benefits offered by this approach. This study highlights the impact that Bayesian models could provide in age and growth studies if applied more routinely rather than being limited to only complex or sophisticated applications.

Age, growth and maturity of the Australian sharpnose shark Rhizoprionodon taylori from the Gulf of Papua.

Coastal sharks with small body sizes may be among the most productive species of chondrichthyans. The Australian sharpnose shark (Rhizoprionodon taylori) is one of the most productive members of this group based on work in northern and eastern Australia. However, life history information throughout the remainder of its range is lacking. To address this knowledge gap, the age, growth and maturity of R. taylori caught in the Gulf of Papua prawn trawl fishery in Papua New Guinea, were studied. One hundred and eighty six individuals, comprising 131 females (31-66 cm TL) and 55 males (31-53 cm TL) were aged using vertebral analysis and growth was modelled using a multi-model approach. The lack of small individuals close to the size at birth made fitting of growth curves more difficult, two methods (fixed length at birth and additional zero aged individuals) accounting for this were trialled. The von Bertalanffy growth model provided the best fit to the data when used with a fixed length-at-birth (L0 = 26 cm TL). Males (L∞ = 46 cm TL, k = 3.69 yr-1, L50 = 41.7 cm TL and A50 = 0.5 years) grew at a faster rate and matured at smaller sizes and younger ages than females (L∞ = 58 cm TL, k = 1.98 yr-1, L5o = 47.0 cm TL and A50 = 0.93 years). However, none of the methods to account for the lack of small individuals fully accounted for this phenomenon, and hence the results remain uncertain. Despite this, the results reaffirm the rapid growth of this species and suggest that the Gulf of Papua population may grow at a faster rate than Australian populations. Rhizoprionodon taylori is possibly well placed to withstand current fishing pressure despite being a common bycatch species in the Gulf of Papua prawn trawl fishery. However, further research needs to be undertaken to estimate other key life history parameters to fully assess the population status of this exploited shark species and its vulnerability to fishing in the Gulf of Papua.

Refining mortality estimates in shark demographic analyses: a Bayesian inverse matrix approach.

Leslie matrix models are an important analysis tool in conservation biology that are applied to a diversity of taxa. The standard approach estimates the finite rate of population growth (λ) from a set of vital rates. In some instances, an estimate of λ is available, but the vital rates are poorly understood and can be solved for using an inverse matrix approach. However, these approaches are rarely attempted due to prerequisites of information on the structure of age or stage classes. This study addressed this issue by using a combination of Monte Carlo simulations and the sample-importance-resampling (SIR) algorithm to solve the inverse matrix problem without data on population structure. This approach was applied to the grey reef shark (Carcharhinus amblyrhynchos) from the Great Barrier Reef (GBR) in Australia to determine the demography of this population. Additionally, these outputs were applied to another heavily fished population from Papua New Guinea (PNG) that requires estimates of λ for fisheries management. The SIR analysis determined that natural mortality (M) and total mortality (Z) based on indirect methods have previously been overestimated for C. amblyrhynchos, leading to an underestimated λ. Updated distributions of Z and λ were produced for the GBR population and corrected obvious error in the demographic parameters for the PNG population. This approach provides opportunity for the inverse matrix approach to be applied more broadly to situations where information on population structure is lacking.

Effects of Including Misidentified Sharks in Life History Analyses: A Case Study on the Grey Reef Shark Carcharhinus amblyrhynchos from Papua New Guinea.

Fisheries observer programs are used around the world to collect crucial information and samples that inform fisheries management. However, observer error may misidentify similar-looking shark species. This raises questions about the level of error that species misidentifications could introduce to estimates of species' life history parameters. This study addressed these questions using the Grey Reef Shark Carcharhinus amblyrhynchos as a case study. Observer misidentification rates were quantified by validating species identifications using diagnostic photographs taken on board supplemented with DNA barcoding. Length-at-age and maturity ogive analyses were then estimated and compared with and without the misidentified individuals. Vertebrae were retained from a total of 155 sharks identified by observers as C. amblyrhynchos. However, 22 (14%) of these were sharks were misidentified by the observers and were subsequently re-identified based on photographs and/or DNA barcoding. Of the 22 individuals misidentified as C. amblyrhynchos, 16 (73%) were detected using photographs and a further 6 via genetic validation. If misidentified individuals had been included, substantial error would have been introduced to both the length-at-age and the maturity estimates. Thus validating the species identification, increased the accuracy of estimated life history parameters for C. amblyrhynchos. From the corrected sample a multi-model inference approach was used to estimate growth for C. amblyrhynchos using three candidate models. The model averaged length-at-age parameters for C. amblyrhynchos with the sexes combined were L∞ = 159 cm TL and L0 = 72 cm TL. Females mature at a greater length (l50 = 136 cm TL) and older age (A50 = 9.1 years) than males (l50 = 123 cm TL; A50 = 5.9 years). The inclusion of techniques to reduce misidentification in observer programs will improve the results of life history studies and ultimately improve management through the use of more accurate data for assessments.

Rediscovery of the Threatened River Sharks, Glyphis garricki and G. glyphis, in Papua New Guinea.

Recent surveys of the shark and ray catches of artisanal fishers in the Western Province of Papua New Guinea (PNG) resulted in the rediscovery of the threatened river sharks, Glyphis garricki and Glyphis glyphis. These represent the first records of both species in PNG since the 1960s and 1970s and highlight the lack of studies of shark biodiversity in PNG. Two individuals of G. garricki and three individuals of G. glyphis were recorded from coastal marine waters of the Daru region of PNG in October and November 2014. The two G. garricki specimens were small individuals estimated to be 100-105 cm and ~113 cm total length (TL). The three G. glyphis specimens were all mature, one a pregnant female and two adult males. These are the first adults of G. glyphis recorded to date providing a more accurate maximum size for this species, i.e. ~260 cm TL. A single pup which was released from the pregnant female G. glyphis, was estimated to be ~65 cm TL. Anecdotal information from the fishers of pregnant females of G. glyphis containing 6 or 7 pups provides the first estimate of litter size for this species. The jaws of the pregnant female G. glyphis were retained and a detailed description of the dentition is provided, since adult dentition has not been previously documented for this species. Genetic analyses confirmed the two species cluster well within samples from these species collected in northern Australia.