A simple method for estimating growth parameters from multiple length-frequency data in presence of continuous recruitment

The extended recruitment season for short-lived species such as prawns biases the estimation of growth parameters from length-frequency data when conventional methods are used. We propose a simple method for overcoming this bias given a time series of length-frequency data. The difficulties arising from extended recruitment are eliminated by predicting the growth of the succeeding samples and the length increments of the recruits in previous samples. This method requires that some maximum size at recruitment can be specified. The advantages of this multiple length-frequency method are: it is simple to use; it requires only three parameters; no specific distributions need to be assumed; and the actual seasonal recruitment pattern does not have to be specified. We illustrate the new method with length-frequency data on the tiger prawn Penaeus esculentus from the north-western Gulf of Carpentaria, Australia.

Stock-recruitment relationships of the tiger prawns (Penaeus esculentus and Penaeus semisulcatus) in the Australian Northern Prawn Fishery

This paper investigates the stock-recruitment and equilibrium yield dynamics for the two species of tiger prawns (Penaeus esculentus and Penaeus semisulcatus) in Australia's most productive prawn fishery: the Northern Prawn Fishery. Commercial trawl logbooks for 1970-93 and research surveys are used to develop population models for these prawns. A population model that incorporates continuous recruitment is developed. Annual spawning stock and recruitment indices are then estimated from the population model. Spawning stock indices represent the abundance of female prawns that are likely to spawn; recruitment indices represent the abundance of all prawns less than a certain size. The relationships between spawning stock and subsequent recruitment (SRR), between recruitment and subsequent spawning stock (RSR), and between recruitment and commercial catch were estimated through maximum-likelihood models that incorporated autoregressive terms. Yield as a function of fishing effort was estimated by constraining to equilibrium the SRR and RSR. The resulting production model was then used to determine maximum sustainable yield (MSY) and its corresponding fishing effort (f(MSY)). Long-term yield estimates for the two tiger prawn species range between 3700 and 5300 t. The fishing effort at present is close to the level that should produce MSY for both species of tiger prawns. However, current landings, recruitment and spawning stock are below the equilibrium values predicted by the models. This may be because of uncertainty in the spawning stock-recruitment relationships, a change in carrying capacity, biased estimates of fishing effort, unreliable catch statistics, or simplistic assumptions about stock structure. Although our predictions of tiger prawn yields are uncertain, management will soon have to consider new measures to counteract the effects of future increases in fishing effort.

A new data source for fisheries resource assessment: genetic estimates of the effective number of spawners. Final Report to the Fisheries Research and Development Corporation.

The development of innovative methods of stock assessment is a priority for State and Commonwealth fisheries agencies. It is driven by the need to facilitate sustainable exploitation of naturally occurring fisheries resources for the current and future economic, social and environmental well being of Australia. This project was initiated in this context and took advantage of considerable recent achievements in genomics that are shaping our comprehension of the DNA of humans and animals. The basic idea behind this project was that genetic estimates of effective population size, which can be made from empirical measurements of genetic drift, were equivalent to estimates of the successful number of spawners that is an important parameter in process of fisheries stock assessment. The broad objectives of this study were to 1. Critically evaluate a variety of mathematical methods of calculating effective spawner numbers (Ne) by a. conducting comprehensive computer simulations, and by b. analysis of empirical data collected from the Moreton Bay population of tiger prawns (P. esculentus). 2. Lay the groundwork for the application of the technology in the northern prawn fishery (NPF). 3. Produce software for the calculation of Ne, and to make it widely available. The project pulled together a range of mathematical models for estimating current effective population size from diverse sources. Some of them had been recently implemented with the latest statistical methods (eg. Bayesian framework Berthier, Beaumont et al. 2002), while others had lower profiles (eg. Pudovkin, Zaykin et al. 1996; Rousset and Raymond 1995). Computer code and later software with a user-friendly interface (NeEstimator) was produced to implement the methods. This was used as a basis for simulation experiments to evaluate the performance of the methods with an individual-based model of a prawn population. Following the guidelines suggested by computer simulations, the tiger prawn population in Moreton Bay (south-east Queensland) was sampled for genetic analysis with eight microsatellite loci in three successive spring spawning seasons in 2001, 2002 and 2003. As predicted by the simulations, the estimates had non-infinite upper confidence limits, which is a major achievement for the application of the method to a naturally-occurring, short generation, highly fecund invertebrate species. The genetic estimate of the number of successful spawners was around 1000 individuals in two consecutive years. This contrasts with about 500,000 prawns participating in spawning. It is not possible to distinguish successful from non-successful spawners so we suggest a high level of protection for the entire spawning population. We interpret the difference in numbers between successful and non-successful spawners as a large variation in the number of offspring per family that survive – a large number of families have no surviving offspring, while a few have a large number. We explored various ways in which Ne can be useful in fisheries management. It can be a surrogate for spawning population size, assuming the ratio between Ne and spawning population size has been previously calculated for that species. Alternatively, it can be a surrogate for recruitment, again assuming that the ratio between Ne and recruitment has been previously determined. The number of species that can be analysed in this way, however, is likely to be small because of species-specific life history requirements that need to be satisfied for accuracy. The most universal approach would be to integrate Ne with spawning stock-recruitment models, so that these models are more accurate when applied to fisheries populations. A pathway to achieve this was established in this project, which we predict will significantly improve fisheries sustainability in the future. Regardless of the success of integrating Ne into spawning stock-recruitment models, Ne could be used as a fisheries monitoring tool. Declines in spawning stock size or increases in natural or harvest mortality would be reflected by a decline in Ne. This would be good for data-poor fisheries and provides fishery independent information, however, we suggest a species-by-species approach. Some species may be too numerous or experiencing too much migration for the method to work. During the project two important theoretical studies of the simultaneous estimation of effective population size and migration were published (Vitalis and Couvet 2001b; Wang and Whitlock 2003). These methods, combined with collection of preliminary genetic data from the tiger prawn population in southern Gulf of Carpentaria population and a computer simulation study that evaluated the effect of differing reproductive strategies on genetic estimates, suggest that this technology could make an important contribution to the stock assessment process in the northern prawn fishery (NPF). Advances in the genomics world are rapid and already a cheaper, more reliable substitute for microsatellite loci in this technology is available. Digital data from single nucleotide polymorphisms (SNPs) are likely to super cede ‘analogue’ microsatellite data, making it cheaper and easier to apply the method to species with large population sizes.

Development of a DNA based aging technique for use in fisheries assessments. Final report, Australian Fisheries Research and Development Corporation Project 2007/033.

The productivity of a fisheries resource can be quantified from estimates of recruitment, individual growth and natural and fisheries-related mortality, assuming the spatial extent of the resource has been quantified and there is minimal immigration or emigration. The sustainability of a fisheries resource is facilitated by management controls such as minimum and maximum size limits and total allowable catch. Minimum size limits are often set to allow individuals the opportunity to reproduce at least once before the chance of capture. Total allowable catches are a proportion of the population biomass, which is estimated based on known reproduction, recruitment, mortality and growth rates. In some fisheries, however, management actions are put in place without quantification of the resource through the stock assessment process. This occurs because species-specific information, for example individual growth, may not be available. In these circumstances, management actions need to be precautionary to protect against future resource collapse, but this often means that the resource is lightly exploited. Consequently, the productivity of the resource is not fully realised. Australia’s most valuable fisheries are invertebrate fisheries (Australian Department of Agriculture Fisheries and Forestry, 2008). For example, Australian fisheries (i.e. excluding aquaculture) production of crustaceans (largely prawns, rock lobster and crab) was 41,000 tonnes in 2006/7, worth $778 million. Production from mollusc (largely abalone, scallops, oysters and squid) fisheries was 39,000 tonnes, worth $502 million. Together, in 2006/7 crustacean and mollusc fisheries represented 58% of the total value of Australian wild fisheries production. Sustainable management of Australia’s invertebrate fisheries is frustrated by the lack of data on species-specific growth rates. This project investigated a new method to estimate age, and hence individual growth rates, in invertebrate fisheries species. The principle behind the new aging method was that telomeres (i.e. DNA end-caps of chromosomes) get shorter as an individual gets older. We studied commercial crustacean and molluscan species. A vertebrate fish species (silver perch, Bidyanus bidyanus) was used as a control to standardise our work against the literature. We found a clear relationship between telomere length and shell size for temperate abalone (Haliotis rubra). Further research is recommended before the method can be implemented to assist management of wildharvested abalone populations. Age needs to be substituted for shell size in the relationship and it needs to be studied for abalone from several regions. This project showed that telomere length declined with increasing age in Sydney rock oysters (Saccostrea glomerata) and was affected by regional variation. A relationship was not apparent between telomere length and age (or size as a surrogate for age) for crustacean species (school prawns, Metapenaeus macleayi; eastern rock lobster, Sagmariasus verreauxi; southern rock lobster, Jasus edwardsii; and spanner crabs, Ranina ranina). For school prawns, there was no difference between telomere length in males and females. Further research is recommended, however, as telomeric DNA from crustaceans was difficult to analyse using the terminal restriction fragment (TRF) assay. Telomere lengths of spanner crabs and lobsters were at the upper limit of resolution of the assay used and results were affected by degradation and possible contamination of telomeric DNA. It is possible that telomere length is an indicator of remaining lifespan in molluscan and crustacean individuals, as suggested for some vertebrate species (e.g. Monaghan, 2010). Among abalone of similar shell size and among lobster pueruli, there was evidence of individuals having significantly longer or shorter telomeres than the group average. At a population level, this may be a surrogate for estimates of future natural mortality, which may have usefulness in the management of those populations. The method used to assay telomere length (terminal restriction fragment assay) performed adequately for most species, but it was too expensive and time-consuming to be considered a useful tool for gathering information for fisheries management. Research on alternative methods is strongly recommended.

Recruitment sources of brown trout identified by otolith trace element signatures.

This study examined whether element: Ca ratios within the otoliths of juvenile brown trout could provide accurate trace element signatures for specific natal tributaries, and attempted to match these to trace element natal signatures found within the otoliths of adult trout caught in the main stem rivers of the same catchment. The trace element signatures of juvenile trout otoliths were analysed from a sample of eight tributaries representing the main sub-catchments of the Motueka River catchment, New Zealand. Trace element signatures were determined using laser ablation inductively coupled plasma mass spectrometry, and differentiated using linear discriminant function analysis with an overall cross-validated classification success of 96.8%. Temporal stability in element: Ca ratios was investigated by repeat collections of juvenile fish over two years. Natal signatures from 11 of 23 adult trout sampled from the catchment main stems were matched to one of the eight tributary signatures showing recruitment sources to be spread relatively evenly throughout the catchment. This study demonstrates the potential of using otolith trace element analysis to determine the natal origins of freshwater fish within a catchment.

Doctors’ perspectives on law and life-sustaining treatment: Survey design and recruitment strategies for a challenging cohort

- Background Palliative medicine and other specialists play significant legal roles in decisions to withhold and withdraw life-sustaining treatment at the end of life. Yet little is known about their knowledge of or attitudes to the law, and the role they think it should play in medical practice. Consideration of doctors’ views is critical to optimizing patient outcomes at the end of life. However, doctors are difficult to engage as participants in empirical research, presenting challenges for researchers seeking to understand doctors’ experiences and perspectives. - Aims To determine how to engage doctors involved in end-of-life care in empirical research about knowledge of the law and the role it plays in medical practice at the end of life. - Methods Postal survey of all specialists in palliative medicine, emergency medicine, geriatric medicine, intensive care, medical oncology, renal medicine, and respiratory medicine in three Australian states: New South Wales, Victoria, and Queensland. The survey was sent in hard copy with two reminders and a follow up reminder letter was also sent to the directors of hospital emergency departments. Awareness was further promoted through engagement with the relevant medical colleges and publications in professional journals; various incentives to respond were also used. The key measure is the response rate of doctors to the survey. - Results Thirty-two percent of doctors in the main study completed their survey with response rate by specialty ranging from 52% (palliative care) to 24% (medical oncology). This overall response rate was twice that of the reweighted pilot study (16%). - Conclusions Doctors remain a difficult cohort to engage in survey research but strategic recruitment efforts can be effective in increasing response rate. Collaboration with doctors and their professional bodies in both the development of the survey instrument and recruitment of participants is essential.

Atlas of abundance and distribution patterns of ichthyoplankton from the Northeast Pacific Ocean and Bering Sea ecosystems: based on research conducted by the Alaska Fisheries Science Center (1972–1996)

This regional atlas summarizes and illustrates the distribution and abundance patterns of fish eggs and larvae of 102 taxa within 34 families found in the Northeast Pacific Ocean including the Bering Sea, Gulf of Alaska, and U.S. west coast ecosystems. Data were collected over a 20+ year period (1972–1996) by the Recruitment Processes Program of the Alaska Fisheries Science Center (AFSC). Ichthyoplankton catch records used in this atlas were generated from 11,379 tows taken during 100 cruises. For each taxon, general life history data are briefly summarized from the literature. Published information on distribution patterns of eggs and larvae are reviewed for the study area. Data from AFSC ichthyoplankton collections were combined to produce an average spatial distribution for each taxon. These data were also used to estimate mean abundance and percent occurrence by year and month, and relative abundance by larval length and season. Abundance from each tow was measured as catch per 10 m2 surface area. A larval distribution and abundance map was produced with a geographic information system using ArcInfo software. For taxa with identifiable pelagic eggs, distribution maps showing presence or absence of eggs are presented. Presence or absence of adults in the study area is mapped based on recent literature and data from AFSC groundfish surveys. Distributional records for adults and early life history stages revealed several new range extensions. (PDF file contains 288 pages.)

Kurzinformation zum EU - Projekt: "Mechanisms influencing long term trends in reproductive success and recruitment of Baltic cod : implications for fisheries management"

In July 1994 an internationally coordinated and EU financed multidisciplinary research project about Baltic cod recruitment was started. The primary goals are to identify and describe dominant biotic and abiotic processes affecting the developmental success of early stages and the maturation of cod in the Central Baltic, to incorporate these processes into recruitment models in order to enhance prediction of future stock fluctuations due to environmental pertubations, species interactions and fisheries management directives as a prerequisite for an integrated fish stock assessment in the Central Baltic and to evaluate the feasibility and possible effects of stock enhancement programs on stock and recruitment and providing the biological basis for assessing their economic value.

A review of IATTC research on the early life history and reproductive biology of scombrids conducted at the Achotines Laboratory from 1985 to 2005

English: For nearly a century, fisheries scientists have studied marine fish stocks in an effort to understand how the abundances of fish populations are determined. During the early lives of marine fishes, survival is variable, and the numbers of individuals surviving to transitional stages or recruitment are difficult to predict. The egg, larval, and juvenile stages of marine fishes are characterized by high rates of mortality and growth. Most marine fishes, particularly pelagic species, are highly fecund, produce small eggs and larvae, and feed and grow in complex aquatic ecosystems. The identification of environmental or biological factors that are most important in controlling survival during the early life stages of marine fishes is a potentially powerful tool in stock assessment. Because vital rates (mortality and growth) during the early life stages of marine fishes are high and variable, small changes in those rates can have profound effects on the properties of survivors and recruitment potential (Houde 1989). Understanding and predicting the factors that most strongly influence pre-recruit survival are key goals of fisheries research programs. Spanish: Desde hace casi un siglo, los científicos pesqueros han estudiado las poblaciones de peces marinos en un intento por entender cómo se determina la abundancia de las mismas. Durante la vida temprana de los peces marinos, la supervivencia es variable, y el número de individuos que sobrevive hasta las etapas transicionales o el reclutamiento es difícil de predecir. Las etapas de huevo, larval, y juvenil de los peces marinos son caracterizadas por tasas altas de mortalidad y crecimiento. La mayoría de los peces marinos, particularmente las especies pelágicas, son muy fecundos, producen huevos y larvas pequeños, y se alimentan y crecen en ecosistemas acuáticos complejos. La identificación los factores ambientales o biológicos más importantes en el control de la supervivencia durante las etapas tempranas de vida de los peces marinos es una herramienta potencialmente potente en la evaluación de las poblaciones. Ya que las tasas vitales (mortalidad y crecimiento) durante las etapas tempranas de vida de los peces marinos son altas y variables, cambios pequeños en esas tasas pueden ejercer efectos importantes sobre las propiedades de los supervivientes y el potencial de reclutamiento (Houde 1989). Comprender y predecir los factores que más afectan la supervivencia antes del reclutamiento son objetivos clave de los programas de investigación pesquera.

Recruitment as an evolving random process of aggregation and mortality

The dynamics of the survival of recruiting fish are analyzed as evolving random processes of aggregation and mortality. The analyses draw on recent advances in the physics of complex networks and, in particular, the scale-free degree distribution arising from growing random networks with preferential attachment of links to nodes. In this study simulations were conducted in which recruiting fish 1) were subjected to mortality by using alternative mortality encounter models and 2) aggregated according to random encounters (two schools randomly encountering one another join into a single school) or preferential attachment (the probability of a successful aggregation of two schools is proportional to the school sizes). The simulations started from either a “disaggregated” (all schools comprised a single fish) or an aggregated initial condition. Results showed the transition of the school-size distribution with preferential attachment evolving toward a scale-free school size distribution, whereas random attachment evolved toward an exponential distribution. Preferential attachment strategies performed better than random attachment strategies in terms of recruitment survival at time when mortality encounters were weighted toward schools rather than to individual fish. Mathematical models were developed whose solutions (either analytic or numerical) mimicked the simulation results. The resulting models included both Beverton-Holt and Ricker-like recruitment, which predict recruitment as a function of initial mean school size as well as initial stock size. Results suggest that school-size distributions during recruitment may provide information on recruitment processes. The models also provide a template for expanding both theoretical and empirical recruitment research.

Small-scale spatial and temporal variability in growth and mortality of fish larvae in the subtropical northcentral Gulf of Mexico: implications for assessing recruitment success

Extensive plankton collections were taken during seven September cruises (1990–93) along the inner continental shelf of the northcentral Gulf of Mexico (GOM). Despite the high productivity and availability of food during these cruises, significant small-scale spatial variability was found in larval growth rates for both Atlantic bumper (Chloroscombrus chrysurus, Carangidae) and vermilion snapper (Rhomboplites aurorubens, Lutjanidae). The observed variability in larval growth rates was not correlated with changes in water temperature or associated with conspicuous hydrographic features and suggested the existence of less-recognizable regions where conditions for growth vary. Cruise estimates of mortality coefficients (Z) for larval Atlantic bumper (n=32,241 larvae from six cruises) and vermilion snapper (n= 2581 larvae from four cruises) ranged from 0.20 to 0.37 and 0.19 to 0.29, respectively. Even in a subtropical climate like the GOM, where larval-stage durations may be as short as two weeks, observed variability in growth rates, particularly when combined with small changes in mortality rates, can cause order-of-magnitude differences in cumulative larval survival. To what extent the observed differences in growth rates at small spatial scales are fine-scale “noise” that ultimately is smoothed by larger-scale processes is not known. Future research is needed to further characterize the small-scale variability in growth rates of larvae, particularly with regard to microzooplankton patchiness and the temporal and spatial pattern of potential predators. Small-scale spatial variability in larval growth rates may in fact be the norm, and understanding the implications of this subtle mosaic may help us to better evaluate our ability to partition the causes of recruitment variability.