Integrating different approaches in the definition of biological stocks: A northern Australian multi-jurisdictional fisheries example using grey mackerel, Scomberomorus semifasciatus

A holistic approach to stock structure studies utilises multiple different techniques on the same individuals sampled from selected populations and combines results across spatial and temporal scales to produce a weight of evidence conclusion. It is the most powerful and reliable source of information to use in formulating resource management and monitoring plans. Few examples of the use of a holistic approach in stock structure studies exist, although more recently this is changing. Using such an approach makes integration of results from each technique challenging. An integrated stock definition (ISD) approach for holistic stock structure studies was developed in this study to aid in the appropriate interpretation of stock structure results to guide the determination of fishery management units. The ISD approach is applied herein to a study of the northern Australian endemic grey mackerel, Scomberomorus semifasciatus (Scombridae). Analyses of genetic (mitochondrial DNA and microsatellites), parasite, otolith stable isotope, and growth data are synthesised to determine the stock structure of S. semifasciatus across northern Australia. Integration of the results from all techniques identified at least six S. semifasciatus stocks for management purposes. Further, the use of the ISD approach provided a simple basis for integrating multiple techniques and for their interpretation. The use of this holistic approach was a powerful tool in providing greater certainty about the appropriate management units for S. semifasciatus. Future stock structure studies investigating spatial management questions in the fisheries context should adopt a holistic approach and apply the ISD approach for a more accurate definition of biological stocks to improve fisheries management.

Selecting and assessing social objectives for Australian fisheries management

This paper details Australian research that developed tools to assist fisheries managers and government agencies in engaging with the social dimension of industry and community welfare in fisheries management. These tools are in the form of objectives and indicators. These highlight the social dimensions and the effects of management plans and policy implementation on fishing industries and associated communities, while also taking into account the primacy of ecological imperatives. The deployment of these objectives and indicators initially provides a benchmark and, over the life of a management plan, can subsequently be used to identify trends in effects on a variety of social and economic elements that may be objectives in the management of a fishery. It is acknowledged that the degree to which factors can be monitored will be dependent upon resources of management agencies, however these frameworks provide a method for effectively monitoring and measuring change in the social dimension of fisheries management.Essentially, the work discussed in this paper provides fisheries management with the means to both track and begin to understand the effects of government policy and management plans on the social dimension of the fishing industry and its associated communities. Such tools allow the consideration of these elements, within an evidence base, into policy arrangements, and consequently provide an invaluable contribution to the ability to address resilience and sustainability of fishing industries and associated communities.

Bayesian fisheries stock assessment: integrating and updating knowledge

In this thesis the use of the Bayesian approach to statistical inference in fisheries stock assessment is studied. The work was conducted in collaboration of the Finnish Game and Fisheries Research Institute by using the problem of monitoring and prediction of the juvenile salmon population in the River Tornionjoki as an example application. The River Tornionjoki is the largest salmon river flowing into the Baltic Sea. This thesis tackles the issues of model formulation and model checking as well as computational problems related to Bayesian modelling in the context of fisheries stock assessment. Each article of the thesis provides a novel method either for extracting information from data obtained via a particular type of sampling system or for integrating the information about the fish stock from multiple sources in terms of a population dynamics model. Mark-recapture and removal sampling schemes and a random catch sampling method are covered for the estimation of the population size. In addition, a method for estimating the stock composition of a salmon catch based on DNA samples is also presented. For most of the articles, Markov chain Monte Carlo (MCMC) simulation has been used as a tool to approximate the posterior distribution. Problems arising from the sampling method are also briefly discussed and potential solutions for these problems are proposed. Special emphasis in the discussion is given to the philosophical foundation of the Bayesian approach in the context of fisheries stock assessment. It is argued that the role of subjective prior knowledge needed in practically all parts of a Bayesian model should be recognized and consequently fully utilised in the process of model formulation.

Improving the effectiveness of age-abundance indicators in the management of fisheries in Queensland, Australia

The development of fishery indicators is a crucial undertaking as it ultimately provides evidence to stakeholders about the status of fished species such as population size and survival rates. In Queensland, as in many other parts of the world, age-abundance indicators (e.g. fish catch rate and/or age composition data) are traditionally used as the evidence basis because they provide information on species life history traits as well as on changes in fishing pressures and population sizes. Often, however, the accuracy of the information from age-abundance indicators can be limited due to missing or biased data. Consequently, improved statistical methods are required to enhance the accuracy, precision and decision-support value of age-abundance indicators.

Otolith morphology of four mackerel species (Scomberomorus spp.) in Australia: Species differentiation and prediction for fisheries monitoring and assessment

Four species of large mackerels (Scomberomorus spp.) co-occur in the waters off northern Australia and are important to fisheries in the region. State fisheries agencies monitor these species for fisheries assessment; however, data inaccuracies may exist due to difficulties with identification of these closely related species, particularly when specimens are incomplete from fish processing. This study examined the efficacy of using otolith morphometrics to differentiate and predict among the four mackerel species off northeastern Australia. Seven otolith measurements and five shape indices were recorded from 555 mackerel specimens. Multivariate modelling including linear discriminant analysis (LDA) and support vector machines, successfully differentiated among the four species based on otolith morphometrics. Cross validation determined a predictive accuracy of at least 96% for both models. An optimum predictive model for the four mackerel species was an LDA model that included fork length, feret length, feret width, perimeter, area, roundness, form factor and rectangularity as explanatory variables. This analysis may improve the accuracy of fisheries monitoring, the estimates based on this monitoring (i.e. mortality rate) and the overall management of mackerel species in Australia.

Increasing Australian impoundment fisheries potential - Habitat enhancement to improve angling and productivity in impoundments

To investigate strategies for increasing Australian impoundment fisheries productivity and improving recreational angling and regional economic growth

Multijurisdictional fisheries performance reporting: How Australia’s nationally standardised approach to assessing stock status compares

Australian marine wild-capture fisheries are managed by eight separate jurisdictions. Traditionally, fishery status reports have been produced separately by most of these jurisdictions, assessing the fish stocks they manage, and reporting on the effectiveness of their fisheries management. However, the format, the type of stock status assessments, the thresholds and terminology used to describe stock status and the classification frameworks have varied over time and among jurisdictions. These differences complicate efforts to understand stock status on a national scale. They also create potential misunderstanding among the wider community about how to interpret information on the status of fish stocks, and the fisheries management and science processes more generally. This is especially true when considering stocks that are shared across two or more jurisdictional boundaries. A standardised approach was developed in 2011 leading to production of the first national Status of key Australian fish stocks reports in 2012, followed by a second edition in 2014 (www.fish.gov.au). Production of these reports was the first step towards a broader national approach to reporting on the performance of Australian fisheries for target species and for wider ecosystem and socioeconomic consequences. This paper outlines the challenges associated with moving towards national performance reporting for target fish stocks and Australia’s successes so far. It also outlines the challenges ahead, in particular those relating to reporting more broadly on the status of entire fisheries. Comparisons are drawn between Australia and New Zealand and more broadly between Australia and other countries.

Environmental factors and uncertainty in fisheries management in the northern Baltic Sea

The Baltic Sea is a geologically young, large brackish water basin, and few of the species living there have fully adapted to its special conditions. Many of the species live on the edge of their distribution range in terms of one or more environmental variables such as salinity or temperature. Environmental fluctuations are know to cause fluctuations in populations abundance, and this effect is especially strong near the edges of the distribution range, where even small changes in an environmental variable can be critical to the success of a species. This thesis examines which environmental factors are the most important in relation to the success of various commercially exploited fish species in the northern Baltic Sea. It also examines the uncertainties related to fish stocks current and potential status as well as to their relationship with their environment. The aim is to quantify the uncertainties related to fisheries and environmental management, to find potential management strategies that can be used to reduce uncertainty in management results and to develop methodology related to uncertainty estimation in natural resources management. Bayesian statistical methods are utilized due to their ability to treat uncertainty explicitly in all parts of the statistical model. The results show that uncertainty about important parameters of even the most intensively studied fish species such as salmon (Salmo salar L.) and Baltic herring (Clupea harengus membras L.) is large. On the other hand, management approaches that reduce uncertainty can be found. These include utilising information about ecological similarity of fish stocks and species, and using management variables that are directly related to stock parameters that can be measured easily and without extrapolations or assumptions.

Invertebrate predation and trophic cascades in a pelagic food web : The multiple roles of Chaoborus flavicans (Meigen) in a clay-turbid lake

In lake ecosystems, both fish and invertebrate predators have dramatic effects on their prey communities. Fish predation selects large cladocerans while invertebrate predators prefer prey of smaller size. Since invertebrate predators are the preferred food items for fish, their occurrence at high densities is often connected with the absence or low number of fish. It is generally believed that invertebrate predators can play a significant role only if the density of planktivorous fish is low. However, in eutrophic clay-turbid Lake Hiidenvesi (southern Finland), a dense population of predatory Chaoborus flavicans larvae coexists with an abundant fish population. The population covers the stratifying area of the lake and attains a maximum population density of 23000 ind. m-2. This thesis aims to clarify the effects of Chaoborus flavicans on the zooplankton community and the environmental factors facilitating the coexistence of fish and invertebrate predators. In the stratifying area of Lake Hiidenvesi, the seasonal succession of cladocerans was exceptional. The spring biomass peak of cladocerans was missing and the highest biomass occurred in midsummer. In early summer, the consumption rate by chaoborids clearly exceeded the production rate of cladocerans and each year the biomass peak of cladocerans coincided with the minimum chaoborid density. In contrast, consumption by fish was very low and each study year cladocerans attained maximum biomass simultaneously with the highest consumption by smelt (Osmerus eperlanus). The results indicated that Chaoborus flavicans was the main predator of cladocerans in the stratifying area of Lake Hiidenvesi. The clay turbidity strongly contributed to the coexistence of chaoborids and smelt at high densities. Turbidity exceeding 30 NTU combined with light intensity below 0.1 μE m-2 s-1provides an efficient daytime refuge for chaoborids, but turbidity alone is not an adequate refuge unless combined with low light intensity. In the non-stratifying shallow basins of Lake Hiidenvesi, light intensity exceeds this level during summer days at the bottom of the lake, preventing Chaoborus forming a dense population in the shallow parts of the lake. Chaoborus can be successful particularly in deep, clay-turbid lakes where they can remain high in the water column close to their epilimnetic prey. Suspended clay alters the trophic interactions by weakening the link between fish and Chaoborus, which in turn strengthens the effect of Chaoborus predation on crustacean zooplankton. Since food web management largely relies on manipulations of fish stocks and the cascading effects of such actions, the validity of the method in deep clay-turbid lakes may be questioned.

Benthic-pelagic coupling in the northern Baltic Sea: importance of bioturbation and benthic predation

Benthic-pelagic coupling describes processes that operate across and between the seafloor and open-water ecosystems. In soft-sediment communities, bioturbation by sediment-dwelling and epibenthic organisms may strongly shape habitat characteristics and influence processes, e.g. biogeochemical cycling, which supplies bioavailable nutrients to pelagic primary producers. In addition, benthic fauna may mediate benthic-pelagic coupling by affecting the survival and hatching of zooplankton dormant eggs in the sediment. In the shallow waters and seasonally fluctuating environment of the Baltic Sea, emergence from the seafloor essentially contributes to the dynamics of zooplankton pelagic populations. In this thesis, I examine how benthic organisms with different functional traits affect the link between the benthic and pelagic systems in the northern Baltic Sea. By means of experimental laboratory studies, the effects of sediment-dwelling (Monoporeia affinis, Macoma balthica and Marenzelleria spp.) and nectobenthic (Mysis spp.) taxa on the survival and hatching of zooplankton benthic eggs and on benthic nutrient fluxes and sediment structure were investigated. In the predation studies, the nectobenthic mysids Mysis spp. preyed upon benthic eggs of the cladoceran Bosmina longispina maritima (syn. B. coregoni maritima), both in pelagic and benthic environments. Of the sediment-dwelling species, the amphipod M. affinis and the bivalve M. balthica reduced the number of cladoceran eggs in the sediment, whereas the polychaetes Marenzelleria spp. had no effects on cladoceran eggs. Both M. balthica and M. affinis also increased the mortality rates of benthic eggs of copepods and rotifers. It was estimated that zooplankton eggs provide an additional carbon source for food-limited benthic communities. The results indicate that predation pressure on zooplankton benthic eggs may be strong, but varies widely depending on the season and the functional characteristics of the macrofauna. Macoma balthica buried cladoceran eggs and a fluorescent tracer from the sediment surface to a depth of 3 4 cm, indicating efficient sediment mixing. In contrast, the other taxa had fewer effects on particle distributions. In addition to organic matter mineralization, particle mixing is crucial to the success of benthic recruitment of zooplankton, since only eggs close to the sediment surface may hatch. Macoma balthica and M. affinis altered the patterns of zooplankton emergence from the sediment. In general, the highest emergence rates were observed in the absence of macroscopic fauna, and M. balthica exerted a stronger suppressive effect than M. affinis. Moreover, copepods were less severely affected than cladocerans, while only one species (Temora longicornis) clearly benefited from the presence of the macrofauna. These differences probably result from species-specific differences in the resistance of eggs to disturbances. The results show that benthic fauna may considerably alter the patterns of zooplankton emergence from the seafloor, thereby shaping zooplankton pelagic populations. The semi-motile M. balthica and Marenzelleria spp. increased the fluxes of phosphate and ammonium from the sediment to the water, whereas the motile M. affinis and Mysis mixta had a contrasting effect. In the eutrophied Baltic Sea, efficient internal cycling of bioavailable nutrients forms a strong feedback inhibiting the recovery of the ecosystem. Based on the results, a change in species dominance from the two motile taxa, susceptible to oxygen deficiency, to the more tolerant semi-motile taxa provides additional feedback, strengthening internal nutrient cycling and accelerating eutrophication, with deteriorating near-bottom oxygen conditions and changes in the benthic communities. In shallow-water ecosystems, benthic nutrient regeneration plays a key role in determining the overall productivity of the ecosystem. In addition, the results of this study show that the communities in the benthos may essentially contribute to the structure of those in the plankton.

Conference Report: International Institute of Fisheries Economics and Trade Conference (IIFET) 2014

The 17th Biennial Conference of the International Institute of Fisheries Economics and Trade (IIFET) was held in Brisbane in July 2014. IIFET is the principal international association for fisheries economics, and the biennial conference is an opportunity for the best fisheries economists in the world to meet and share their ideas. The conference was organised by CSIRO, QUT, UTAS, University of Adelaide and KG Kailis Ltd. This is the first time the conference has been held in Australia. The conferences covered a wide range of topics of relevance to Australia. These included studies of fishery management systems around the world, identified key issues in aquaculture and marine biodiversity conservation, and provided a forum for new modelling and theoretical approaches to analysing fisheries problems to be presented. The theme of the conference was Towards Ecosystem Based Management of Fisheries: What Role can Economics Play? Several sessions were dedicated to modelling socio-ecological systems, and two keynote speakers were invited to present the latest thinking in the area. In this report, the key features of the conference are outlined.