Stakeholders increasingly expect ecosystem assessments as part of advice on fisheries management. Quantitative models to support fisheries decision‐making may be either strategic (‘big picture’, direction‐setting and contextual) or tactical (focused on management actions on short timescales), with some strategic models informing the development of tactical models. We describe and review ‘Models of Intermediate Complexity for Ecosystem assessments’ (MICE) that have a tactical focus, including use as ecosystem assessment tools. MICE are context‐ and question‐driven and limit complexity by restricting the focus to those components of the ecosystem needed to address the main effects of the management question under consideration. Stakeholder participation and dialogue is an integral part of this process. MICE estimate parameters through fitting to data, use statistical diagnostic tools to evaluate model performance and account for a broad range of uncertainties. These models therefore address many of the impediments to greater use of ecosystem models in strategic and particularly tactical decision‐making for marine resource management and conservation. MICE are capable of producing outputs that could be used for tactical decision‐making, but our summary of existing models suggests this has not occurred in any meaningful way to date. We use a model of the pelagic ecosystem in the Coral Sea and a linked catchment and ocean model of the Gulf of Carpentaria, Australia, to illustrate how MICE can be constructed. We summarize the major advantages of the approach, indicate opportunities for the development of further applications and identify the major challenges to broad adoption of the approach.

The genus Glyphis comprises a group of rare and poorly known species. G. glyphis and G. garricki are found in northern Australia, and both species are listed as Critically Endangered C2a(i) on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. We collated all available records of G. glyphis and G. garricki in Australia to gain an understanding of the species' distribution and biology. All records of G. glyphis (n = 106) were confined to 9 tropical rivers and estuaries north of 15°S. G. garricki (n = 32) were captured in 4 rivers and estuaries as well as in marine environments north of 18°S. Both species can be classified as euryhaline elasmobranchs. Parturition is thought to occur in October to December, and size at birth for both species is around 50 to 65 cm total length (TL). Two male G. garricki were mature at 142 and 144 cm TL, 2 females of 177 and 251 cm TL were mature, with the smaller animal having 9 early-stage embryos in utero. No mature G. glyphis have been recorded to date. Short-term movement patterns of 3 G. glyphis were investigated in the Adelaide River (Northern Territory) using acoustic tags. Animals were tracked for 27.8, 27.0 and 50.2 h respectively and displayed up-and downstream tidally assisted movement, moving on average 10 to 12 km per tide. The limited distribution, specific habitat requirements and repeated use of available habitat make Glyphis species particularly vulnerable to localised overfishing and habitat degradation. These findings highlight the need for additional research and the implementation of national recovery plans for both species.

The biology of elasmobranchs makes them very vulnerable to fishing pressure and there is increasing international concern over their exploitation. In northern Australia the stocks of some species may be shared with those in southern Indonesia. Indonesia has the highest landings of elasmobranchs worldwide ([100,000 t p.a.) and millions of Indonesian artisanal fishers rely heavily on elasmobranchs taken in target fisheries. They are also taken by industrial trawlers and as bycatch in pelagic tuna fisheries. This paper, resulting from a collaborative project between Australia and Indonesia, summarises the elasmobranch fisheries; the characteristics of the fisheries are outlined, the status of the stocks are assessed, and management options described and discussed. The project focussed on representative markets and fish landing sites in southern Indonesia from 2001 to 2005. Data were from market surveys, the records of the Indonesian Directorate General of Capture Fisheries, and from research cruises. Data from the ongoing tuna monitoring programme showed that shark bycatch from the tuna fleets forms about 11% of shark landings in Indonesia. Yield per recruit and related analyses were used to integrate biological information to indicate the productivity of each species to allow for management policy options and constraints. Research cruise data show that catch rates of elasmobranchs in the Java Sea declined by at least one order of magnitude between 1976 and 1997. The results indicate strongly that many of the shark and ray species in Indonesia are overfished and that the most effective management strategy may need to involve capacity control, such as licencing, gear restrictions and catch limits, together with controls on the fin trade.

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This study examined the osmoregulatory status of the euryhaline elasmobranch Carcharhinus leucas acclimated to freshwater (FW) and seawater (SW). Juvenile C. leucas captured in FW (3 mOsm l(-1) kg(-1)) were acclimated to SW (980-1,000 mOsm l(-1) kg(-1)) over 16 days. A FW group was maintained in captivity over a similar time period. In FW, bull sharks were hyper-osmotic regulators, having a plasma osmolarity of 595 mOsm l(-1) kg(-1). In SW, bull sharks had significantly higher plasma osmolarities (940 mOsm l(-1) kg(-1)) than FW-acclimated animals and were slightly hypo-osmotic to the environment. Plasma Na(+), Cl(-), K(+), Mg(2+), Ca(2+), urea and trimethylamine oxide (TMAO) concentrations were all significantly higher in bull sharks acclimated to SW, with urea and TMAO showing the greatest increase. Gill, rectal gland, kidney and intestinal tissue were taken from animals acclimated to FW and SW and analysed for maximal Na(+)/K(+)-ATPase activity. Na(+)/K(+)-ATPase activity in the gills and intestine was less than 1 mmol Pi mg(-1) protein h(-1) and there was no difference in activity between FW- and SW-acclimated animals. In contrast Na(+)/K(+)-ATPase activity in the rectal gland and kidney were significantly higher than gill and intestine and showed significant differences between the FW- and SW-acclimated groups. In FW and SW, rectal gland Na(+)/K(+)-ATPase activity was 5.6+/-0.8 and 9.2+/-0.6 mmol Pi mg(-1) protein h(-1), respectively. Na(+)/K(+)-ATPase activity in the kidney of FW and SW acclimated animals was 8.4+/-1.1 and 3.3+/-1.1 Pi mg(-1) protein h(-1), respectively. Thus juvenile bull sharks have the osmoregulatory plasticity to acclimate to SW; their preference for the upper reaches of rivers where salinity is low is therefore likely to be for predator avoidance and/or increased food abundance rather than because of a physiological constraint.

Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river shark found only in tropical northern Australia and southern Papua New Guinea. Contemporary adult and juvenile shark movements, estimated with the spatial distribution of kin pairs across and within three river systems, was contrasted with historical long-term connectivity patterns, estimated from mitogenomes and genome-wide SNP data. We found strong support for river fidelity in juveniles with the within-cohort relationship analysis. Male breeding movements were highlighted with the cross-cohort relationship analysis, and female reproductive philopatry to the river systems was revealed by the mitogenomic analysis. We show that accounting for juvenile river fidelity and female philopatry is important in population structure analysis and that targeted sampling in nurseries and juvenile aggregations should be included in the genomic toolbox of threatened species management.

BackgroundMitochondrial DNA markers have long been used to identify population boundaries and are now a standard tool in conservation biology. In elasmobranchs, evolutionary rates of mitochondrial genes are low and variation between distinct populations can be hard to detect with commonly used control region sequencing or other single gene approaches. In this study we sequenced the whole mitogenome of 93 Critically Endangered Speartooth Shark Glyphis glyphis from the last three river drainages they inhabit in northern Australia.ResultsGenetic diversity was extremely low (π =0.00019) but sufficient to demonstrate the existence of barriers to gene flow among river drainages (AMOVA ΦST =0.28283, P <0.00001). Surprisingly, the comparison with single gene sub-datasets revealed that ND5 and 12S were the only ones carrying enough information to detect similar levels of genetic structure. The control region exhibited only one mutation, which was not sufficient to detect any structure among river drainages.ConclusionsThis study strongly supports the use of single river drainages as discrete management units for the conservation of G. glyphis. Furthermore when genetic diversity is low, as is often the case in elasmobranchs, our results demonstrate a clear advantage of using the whole mitogenome to inform population structure compared to single gene approaches. More specifically, this study questions the extensive use of the control region as the preferential marker for elasmobranch population genetic studies and whole mitogenome sequencing will probably uncover a large amount of cryptic population structure in future studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0232-x) contains supplementary material, which is available to authorized users.

The feeding ecology of longtail tuna was studied in northern and eastern Australia. Diet biomass data were used to estimate daily ration and consumption of individual prey taxa, particularly penaeids targeted by Australia's valuable Northern Prawn Fishery (NPF). Overall, the 497 stomachs contained 101 prey taxa. In both regions, small pelagic and demersal fishes comprised the majority of the diet biomass. Fish in both regions showed a marked increase in prey diversity, variation in prey composition and stomach fullness index in autumn and winter (March-August). This increase in apparently opportunistic feeding behaviour and feeding intensity showed an inverse relationship with reproductive activity, indicating a possible energy investment for gonad development. Daily ration decreased with increasing fish size, while annual consumption by fish increased with size. Total prey consumption in the Gulf of Carpentaria was estimated at 148 178 t year −1 . This includes 599 t year −1 of penaeids, equivalent to 11% of the annual NPF catch. This study demonstrated that longtail tuna play an important ecological role in neritic ecosystems. Their interaction with commercial fisheries highlights the need for targeted dietary studies of high order predators to better understand trophic pathways to facilitate ecosystem-based fisheries management.