Mother-embryo isotope fractionation in the pygmy devilray Mobula kuhlii cf. eregoodootenkee.

We determined stable-isotope ratios for replicate muscle tissues in 13 gravid Mobula kuhlii cf. eregoodootenkee (110.4-120.4 cm disc width; WD ) and their embryos (7.0-42.3 cm WD ) and also yolks and histrotroph, to assess the potential implications for juvenile nutrition and habitat use. Irrespective of their development in the uterus, embryos had similar δ13 C values in their muscle tissue as the mothers and both had greater values than in the histotroph. During gestation, δ13 C values increased across all sample types. However, while embryo muscle tissue and the histotroph were associated with increasing 15 N levels during embryonic development, this was depleted in the mothers' muscle tissue and yolk. Although speculative, the observed variation in stable-isotope ratios might imply a dietary shift among gravid females during their early gestation. Irrespective of the underlying mechanisms, the results indicate neonates will have relatively greater δ15 N values than post-partum females, which would probably confound juvenile foraging-ecology estimates.

Reducing the marine debris of recreational hoop nets in south-eastern Australia.

Alternative configurations of Australian recreational portunid hoop nets were investigated to address debris and selectivity issues. Four treatment nets (all comprising 152-mm polyamide-PA mesh) were assessed that differed in their twine (conventional multifilament vs new multi-monofilament) and fishing configuration (conventional conical vs inverted shapes). The conical multifilament design lost means (±SEs) of 130.6±23.1 and 5.3±1.2mm of twine 3-h soak-1 when used to target Scylla serrata and Portunus pelagicus. Inverting this hoop net significantly reduced legal-sized catches (by up to 70%) and with greater twine loss (×5) when targeting P. pelagicus. Conversely, both multi-monofilament configurations maintained legal catches of S. serrata and P. pelagicus, but lost 78 and 95% less twine than the conical multifilament design. Using multi-monofilament hoop nets could reduce PA debris by thousands of m p.a. in south-eastern Australia, without affecting targeted catches. Further, a lower fishing height of inverted multi-monofilament nets might reduce non-portunid bycatch.

A 'simple anterior fish excluder' (SAFE) for mitigating penaeid-trawl bycatch.

Various plastic strips and sheets (termed 'simple anterior fish excluders'-SAFEs) were positioned across the openings of penaeid trawls in attempts at reducing the unwanted bycatches of small teleosts. Initially, three SAFEs (a single wire without, and with small and large plastic panels) were compared against a control (no SAFE) on paired beam trawls. All SAFEs maintained targeted Metapenaeus macleayi catches, while the largest plastic SAFE significantly reduced total bycatch by 51% and the numbers of Pomatomus saltatrix, Mugil cephalus and Herklotsichthys castelnaui by up to 58%. A redesigned SAFE ('continuous plastic') was subsequently tested (against a control) on paired otter trawls, significantly reducing total bycatch by 28% and P. saltatrix and H. castelnaui by up to 42%. The continuous-plastic SAFE also significantly reduced M. macleayi catches by ~7%, but this was explained by ~5% less wing-end spread, and could be simply negated through otter-board refinement. Further work is required to refine the tested SAFEs, and to quantify species-specific escape mechanisms. Nevertheless, the SAFE concept might represent an effective approach for improving penaeid-trawl selectivity.

Angling-induced barotrauma in snapper Chrysophrys auratus: are there consequences for reproduction?

In response to concerns regarding the potential for sub-lethal impacts of barotrauma on reproductively active Chrysophrys auratus during catch and release, 90 males and 90 females representing five reproductive stages (immature or resting--28%, developing--8%, developed--7%, ripe or spawning--23% and spent--34%) were angled from 8-70 m and macroscopically assessed (on-board and then in a laboratory). Irrespective of sex, all fish exhibited various clinical signs of barotrauma, including a prolapsed cloaca (60% of fish); gastric herniation (46%); ruptured swim bladder (73%); organ displacement (48%); and kidney (3%), liver (73%) and coloemic-cavity haemorrhaging (33%); with the frequency of nearly all positively associated with capture depth. Reproductive stage was also an important barotrauma predictor (reflecting related morphological changes) with a general trend towards spent fish least likely to incur the various clinical signs--especially for a prolapsed cloaca (also common among immature or resting fish and significantly affected by food in the digestive tract) and a ruptured swim bladder (common among ripe or spawning fish). The only macroscopically visible gonad damage was haemorrhaging, which was least common among immature or resting and spent fish and, irrespective of reproductive stage, temporally reduced in frequency, and more quickly among males than females. While further research is required to accurately describe the effects of angling at each stage of the reproductive cycle and the physiological consequences of barotrauma on the gonads of C. auratus, given the observed influences of reproductive stage and depth on barotrauma found in this study, any adverse effects might be partially managed by regulating either temporal or spatial fishing effort.

Configuring the mesh size, side taper and wing depth of penaeid trawls to reduce environmental impacts.

The effects of reducing mesh size while concomitantly varying the side taper and wing depth of a generic penaeid-trawl body were investigated to improve engineering performance and minimize bycatch. Five trawl bodies (with the same codends) were tested across various environmental (e.g. depth and current) and biological (e.g. species and sizes) conditions. The first trawl body comprised 41-mm mesh and represented conventional designs (termed the '41 long deep-wing'), while the remaining trawl bodies were made from 32-mm mesh and differed only in their side tapers, and therefore length (i.e. 1N3B or 'long' and ∼28o to the tow direction vs 1N5B or 'short' and ∼35o) and wing depths ('deep'-97 T vs 'shallow'-60 T). There were incremental drag reductions (and therefore fuel savings--by up to 18 and 12% per h and ha trawled) associated with reducing twine area via either modification, and subsequently minimizing otter-board area in attempts to standardize spread. Side taper and wing depth had interactive and varied effects on species selectivity, but compared to the conventional 41 long deep-wing trawl, the 32 short shallow-wing trawl (i.e. the least twine area) reduced the total bycatch by 57% (attributed to more fish swimming forward and escaping). In most cases, all small-meshed trawls also caught more smaller school prawns Metapenaeus macleayi but to decrease this effect it should be possible to increase mesh size slightly, while still maintaining the above engineering benefits and species selectivity. The results support precisely optimizing mesh size as a precursor to any other anterior penaeid-trawl modifications designed to improve environmental performance.

Ocean acidification and fertilization in the antarctic sea urchin Sterechinus neumayeri: the importance of polyspermy.

Ocean acidification (OA), the reduction of the seawater pH as a result of increasing levels of atmospheric CO2, is an important climate change stressor in the Southern Ocean and Antarctic. We examined the impact of OA on fertilization success in the Antarctic sea urchin Sterechinus neumayeri using pH treatment conditions reflective of the current and near-future "pH seascape" for this species: current (control: pH 8.052, 384.1 µatm of pCO2), a high CO2 treatment approximating the 0.2-0.3 unit decrease in pH predicted for 2100 (high CO2: pH 7.830, 666.0 µatm of pCO2), and an intermediate medium CO2 (pH 7.967, 473.4 µatm of pCO2). Using a fertilization kinetics approach and mixed-effect models, we observed significant variation in the OA response between individual male/female pairs (N = 7) and a significant population-level increase (70-100%) in tb (time for a complete block to polyspermy) at medium and high CO2, a mechanism that potentially explains the higher levels of abnormal development seen in OA conditions. However, two pairs showed higher fertilization success with CO2 treatment and a nonsignificant effect. Future studies should focus on the mechanisms and levels of interindividual variability in OA response, so that we can consider the potential for selection and adaptation of organisms to a future ocean.

Beta diversity of demersal fish assemblages in the North-Eastern Pacific: interactions of latitude and depth.

Knowledge of broad-scale global patterns in beta diversity (i.e., variation or turnover in identities of species) for marine systems is in its infancy. We analysed the beta diversity of groundfish communities along the North American Pacific coast, from trawl data spanning 32.57°N to 48.52°N and 51 m to 1200 m depth. Analyses were based on both the Jaccard measure and the probabilistic Raup-Crick measure, which accounts for variation in alpha diversity. Overall, beta diversity decreased with depth, and this effect was strongest at lower latitudes. Superimposed on this trend were peaks in beta diversity at around 400-600 m and also around 1000-1200 m, which may indicate high turnover around the edges of the oxygen minimum zone. Beta diversity was also observed to decrease with latitude, but this effect was only observed in shallower waters (<200 m); latitudinal turnover began to disappear at depths >800 m. At shallower depths (<200 m), peaks in latitudinal turnover were observed at ∼43°N, 39°N, 35°N and 31°N, which corresponded well with several classically observed oceanographic boundaries. Turnover with depth was stronger than latitudinal turnover, and is likely to reflect strong environmental filtering over relatively short distances. Patterns in beta diversity, including latitude-by-depth interactions, should be integrated with other biodiversity measures in ecosystem-based management and conservation of groundfish communities.

Incorporating the intraspecific occupancy-abundance relationship into zero-inflated models.

Zero-inflated versions of standard distributions for count data are often required in order to account for excess zeros when modeling the abundance of organisms. Such distributions typically have as parameters lambda, the mean of the count distribution, and pi, the probability of an excess zero. Implementations of zero-inflated models in ecology typically model lambda using a set of predictor variables, and pi is fit either as a constant or with its own separate model. Neither of these approaches makes use of any relationship that might exist between pi and lambda. However, for many species, the rate of occupancy is closely and positively related to its average abundance. Here, this relationship was incorporated into the model for zero inflation by functionally linking pi to lambda, and was demonstrated in a study of snapper (Pagrus auratus) in and around a marine reserve. This approach has several potential practical advantages, including better computational performance and more straightforward model interpretation. It is concluded that, where appropriate, directly linking pi to lambda can produce more ecologically accurate and parsimonious statistical models of species abundance data.

Much ado about nothings: using zero similarity points in distance-decay curves.

Distance decay is used to describe the (usually exponential) decay in ecological similarity of assemblages between two sites as a function of their distance apart along an environmental gradient. Exponential distance-decay curves are routinely fitted by calculating the ecological similarity between each pair of sites, and fitting a linear regression to the points on a scatter plot of log-similarity vs. distance (x-axis). However, pairs of sites where the assemblages have no species in common pose a problem, because the similarity is zero, and the log transformation cannot be applied. Common fixes to this problem (i.e., either removing or transforming the zero values) are shown to have undesirable consequences and to give widely disparate estimates. A new method is presented as a special case of a generalized dissimilarity model. It is fitted very quickly and easily using existing software, and it does not require removal or transformation of the zero similarity points. Its simplicity makes it convenient for use in conjunction with the resampling methods that are routinely employed to test hypotheses, to obtain standard errors of estimated parameters, or to compare distance-decay curves. A word of caution about standard application of the bootstrap is noted, and modified bootstrap and jackknife alternatives are demonstrated.

Mitigating discard mortality from dusky flathead Platycephalus fuscus gillnets.

The mortalities and contributing parameters were estimated for key species discarded during commercial gillnetting (80 mm mesh) targeting dusky flathead Platycephalus fuscus in a southeastern Australian estuary. Bycatches (1470 individuals from 16 species over 11 deployments) were assessed for their immediate mortalities onboard the gillnetter, before subsamples (570 individuals from 11 species) were discarded into cages and monitored for their short-term fate over 4 d. Appropriate controls were concurrently caged and monitored. Blood samples were taken from some live meshed-and-discarded yellowfin bream Acanthopagrus australis and luderick Girella tricuspidata and analysed for plasma cortisol and glucose. Concomitantly angled fish were similarly sampled (to provide baseline estimates of blood physiology). The immediate mortalities of the abundant species ranged between 0 (undersize blue swimmer crab Portunus pelagicus <6 cm carapace length) and 70% (undersize P. fuscus <36 cm total length [TL]). Water temperature had a statistically significant positive relationship with the immediate mortality of G. tricuspidata and large-tooth flounder Pseudorhombus arsius, and TL had a significant negative relationship with the immediate mortality of black sole Synaptura nigra. Compared to baseline estimates, mean plasma cortsiol concentrations in meshed-and-discarded G. tricuspidata and A. australis were significantly greater, and approached levels comparable to most teleosts after peak stress. Mean glucose concentrations were not concomitantly elevated, possibly reflecting limited time between stress and sampling for some individuals. Short-term mortalities occurred throughout the entire 4 d monitoring period for most species and ranged from 0 (yellowfin leatherjacket Meuschenia trachylepis) to 29% (A. australis). Water temperature and TL were identified as having significant impacts similar to those described above on the delayed fate of A. australis and G. tricuspidata. The partitioned mortalities were combined to provide estimates of overall mortality (+/- SE) for the main species that ranged between 5.9 +/- 3.3% (P. pelagicus) and 76.9 +/- 7.8% (undersize P. fuscus). Discard mortality in this fishery could be mitigated by allowing fishers to retain a small percentage of undersize P. fuscus, restricting the deployment of nets in water temperatures >16 to 17 degrees C, and encouraging the careful removal of catches from meshes.

Comparison of hierarchical Bayesian models for overdispersed count data using DIC and Bayes' factors.

When replicate count data are overdispersed, it is common practice to incorporate this extra-Poisson variability by including latent parameters at the observation level. For example, the negative binomial and Poisson-lognormal (PLN) models are obtained by using gamma and lognormal latent parameters, respectively. Several recent publications have employed the deviance information criterion (DIC) to choose between these two models, with the deviance defined using the Poisson likelihood that is obtained from conditioning on these latent parameters. The results herein show that this use of DIC is inappropriate. Instead, DIC was seen to perform well if calculated using likelihood that was marginalized at the group level by integrating out the observation-level latent parameters. This group-level marginalization is explicit in the case of the negative binomial, but requires numerical integration for the PLN model. Similarly, DIC performed well to judge whether zero inflation was required when calculated using the group-marginalized form of the zero-inflated likelihood. In the context of comparing multilevel hierarchical models, the top-level DIC was obtained using likelihood that was further marginalized by additional integration over the group-level latent parameters, and the marginal densities of the models were calculated for the purpose of providing Bayes' factors. The computational viability and interpretability of these different measures is considered.

Mortality of discards from southeastern Australian beach seines and gillnets.

Two experiments were done in an Australian estuary to quantify the mortalities and contributing factors for key species discarded during 8 and 9 deployments of commercial beach (or shore) seines and gillnets, respectively. In both experiments, bycatches (2347 individuals comprising 16 species) were handled according to conventional practices and assessed for immediate mortalities before live samples of selected species were discarded into replicate cages along with appropriate controls, and monitored for short-term mortalities (< or =10 d). All of the seined or gilled fish were alive prior to discarding. During the beach seine experiment, 20% of caged seined-and-discarded surf bream Acanthopagrus australis (n = 290) were dead after 5 d, with most mortalities occurring between the second and fifth day. In the gillnet experiment, 42 and 11% of gilled-and-discarded A. australis (n = 161) and lesser salmon catfish Neoarius graeffei (n = 67), respectively, died during a 10 d monitoring period, mostly within the first 5 d. There were no deaths in any controls for these fish. Mixed-effects logistic models revealed that the mortality of A. australis discarded from both gears was significantly (p < 0.01) and negatively correlated with their total length, while N. graeffei had a significantly (p < 0.05) greater (5-fold) probability of dying when jellyfish Catostylus sp. were present in the gillnet. Simple modifications to the operations of beach seines and gillnets and/or post-capture handling procedures, such as close regulation of size selectivity for the target species, careful removal of fish from meshes, and abstention from setting during high abundances of jellyfish will maximise the survival of discarded bycatch.

Nonlinear multivariate models of successional change in community structure using the von Bertalanffy curve.

von Bertalanffy curves were used to describe the nonlinear relationship between assemblages inhabiting holdfasts of the kelp Ecklonia radiata and the volume of the holdfast. This was done using nonlinear canonical analyses of principal coordinates (NCAP). The volume of the holdfast is a proxy for the age of the plant and, thus, the canonical axis is a proxy for succession in the marine invertebrate community inhabiting the holdfast. Analyses were done at several different taxonomic resolutions on the basis of various dissimilarity measures. Assemblages in relatively large holdfasts demonstrated ongoing variation in community structure with increasing volume when the dissimilarity used was independent of sample size. Smaller holdfasts had proportionately greater abundances of ophiuroids and encrusting organisms (bryozoans, sponges, ascidians), while larger holdfasts were characterised by proportionately greater abundances of crustaceans, polychaetes and molluscs. Such linear and nonlinear multivariate models may be applied to analyse system-level responses to the growth of many habitat-forming organisms, such as sponges, coral reefs, coralline algal turf or forest canopies.

Sensitivity of Bayes estimators to hyper-parameters with an application to maximum yield from fisheries.

Priors are seldom unequivocal and an important component of Bayesian modeling is assessment of the sensitivity of the posterior to the specified prior distribution. This is especially true in fisheries science where the Bayesian approach has been promoted as a rigorous method for including existing information from previous surveys and from related stocks or species. These informative priors may be highly contested by various interest groups. Here, formulae for the first and second derivatives of Bayes estimators with respect to hyper-parameters of the joint prior density are given. The formula for the second derivative provides a correction to a previously published result. The formulae are shown to reduce to very convenient and easily implemented forms when the hyper-parameters are for exponential family marginal priors. For model parameters with such priors it is shown that the ratio of posterior variance to prior variance can be interpreted as the sensitivity of the posterior mean to the prior mean. This methodology is applied to a nonlinear state-space model for the biomass of South Atlantic albacore tuna and sensitivity of the maximum sustainable yield to the prior specification is examined.

The kinetics of monospermic and polyspermic fertilization in free-spawning marine invertebrates.

The equation of Vogel et al. (1982) is widely used in fertilization studies of free-spawning marine invertebrates to predict the percentage of viable eggs that will be fertilized at any specified levels of gamete concentration and contact time. Here, the random collision model that underlies the Vogel et al. equation is extended to distinguish between monospermic and polyspermic fertilization, and separate equations for the percentages of monospermic and polyspermic fertilization are obtained. These equations provide an explanation for empirical observations which have shown a decreased percentage of successful egg development at high sperm concentrations. Comparison is made with an earlier heuristic attempt (Styan, 1998) to predict the extent of polyspermic fertilization, and it is found that this earlier method can underestimate the percentage of polyspermic fertilization by up to 10 percent. Moreover, the approach used here retains the flexibility to model changes in sperm concentration due to dispersal mechanisms, and is able to model different mechanisms for the block to polyspermy.