Patterns in the distribution and abundance of female eastern king prawns, Melicertus plebejus (Hess, 1865), capable of spawning and reproductive potential in waters off

Linear mixed models were used to test the null hypothesis that there were no differences between seasons and locations in the reproductive potential of female eastern king prawns, Melicertus plebejus along the east coast of Australia. Three samples were collected in each season between autumn 1991 and winter 1992 (inclusive). Females capable of spawning were found at all locations but proportions were greater in lower than higher latitudes. Females capable of spawning were not found at the southern (highest latitude) most location in all seasons. There was a significant interaction in reproductive potential between seasons and locations suggesting that patterns among seasons differed between locations and vice versa. Reproductive potential was greatest amongst the northern (lower latitudes) most locations and was greatest in autumn at these locations. Seasonal patterns were less pronounced further south (higher latitudes). The length composition of females in catches differed between locations with more larger prawns found in samples from northern locations. The challenge that remains is to quantify the oceanic sources of larvae that contribute to recruitment in each nursery area and the estuarine sources of juveniles that contribute adults back to the effective spawning stock. Maintaining the effective spawning stock and important nursery areas are crucial to the sustainability of this resource.

Reproductive ecology and size of sexual maturity in the anomuran crab Aegla parana (Decapoda: Aeglidae)

In Southern Brazil, Aegla parana Schmitt, 1942 is characterized by a broad distribution throughout the Iguacu River basin, particularly between the southern state of Parana and the northern state of Santa Catarina, preferentially inhabiting streams with rocky substrates. Although there has been an increase in the number of studies about the population biology of Aeglidae, many aspects about the reproductive biology of A. parana are still unknown. Therefore, the present study aimed to investigate the size at sexual maturity, reproductive seasonality and recruitment of A. parana from November, 2008 to December, 2009, in a tributary of the Iguacu River located in Uniao da Vitoria, Parana, Brazil. Basic environmental factors were investigated to determine their influence on the reproductive cycle of this species. Gonadal stages were characterized macroscopically, and the presence or absence of embryos in females (ovigerous females) from monthly samples was recorded. The entire sample was composed of 436 males and 211 females. Although the smallest ovigerous female was 16.2 mm, the average size (carapace length, CL) at sexual maturity (CL50%) was calculated at 17.4 mm. The greatest percentage of females with developed (mature, near spawning) gonads stage was observed from January to June, 2009, while ovigerous females were recorded from April to July, 2009, after which the reproductive period ended. Recruitment occurred from October to December, 2009. The presence of ovigerous females was negatively correlated with temperature (Spearman, p < 0.05). Females carrying embryos were generally collected during periods of lower temperatures, whereas recruits entered the population during periods of higher temperatures, when food for them is more abundant in the region studied.

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.

The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus)

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.

Population structure, long-term connectivity, and effective size of mutton snapper (Lutjanus analis) in the Caribbean Sea and Florida Keys

Genetic structure and average long-term connectivity and effective size of mutton snapper (Lutjanus analis) sampled from offshore localities in the U.S. Caribbean and the Florida Keys were assessed by using nuclear-encoded microsatellites and a fragment of mitochondrial DNA. No significant differences in allele, genotype (microsatellites), or haplotype (mtDNA) distributions were detected; tests of selective neutrality (mtDNA) were nonsignificant after Bonferroni correction. Heuristic estimates of average long-term rate of migration (proportion of migrant individuals/generation) between geographically adjacent localities varied from 0.0033 to 0.0054, indicating that local subpopulations could respond independently of environmental perturbations. Estimates of average longterm effective population sizes varied from 341 to 1066 and differed significantly among several of the localities. These results indicate that over time larval drift and interregional adult movement may not be sufficient to maintain population sustainability across the region and that there may be different demographic stocks at some of the localities studied. The estimate of long-term effective population size at the locality offshore of St. Croix was below the minimum threshold size considered necessary to maintain the equilibrium between the loss of adaptive genetic variance from genetic drift and its replacement by mutation. Genetic variability in mutton snapper likely is maintained at the intraregional level by aggregate spawning and random mating of local populations. This feature is perhaps ironic in that aggregate spawning also renders mutton snapper especially vulnerable to overexploitation.

Mitochondrial DNA variation, effective female population size and population history of the endangered Chinese sturgeon, Acipenser sinensis

The anadromous Chinese sturgeon (Acipenser sinensis), mainly endemic to the Yangtze River in China, is an endangered fish species. The natural population has declined since the Gezhouba Dam blocked its migratory route to the spawning grounds in 1981. In the near future, the completion of the Three Gorges Dam, the world's largest hydroelectric project, may further impact this species by altering the water flow of the Yangtze River. Little is currently known about the population genetic structure of the Chinese sturgeon. In this study, DNA sequence data were determined from the control region (D-loop) of the mitochondrial genome of adult sturgeons (n = 106) that were collected between 1995-2000. The molecular data were used to investigate genetic variation, effective female population size and population history of the Chinese sturgeon in the Yangtze River. Our results indicate that the reduction in abundance did not change genetic variation of the Chinese sturgeon, and that the population underwent an expansion in the past. AMOVA analysis indicated that 98.7% of the genetic variability occurred within each year's spawning populations, the year of collection had little influence on the diversity of annual temporary samples. The relative large effective female population size (N-ef) indicates that good potential exists for the recovery of this species in the future. Strikingly, the ratio of N-ef to the census female population size (N-f) is unusually high (0.77-0.93). This may be the result of a current bottleneck in the population of the Chinese sturgeon that is likely caused by human intervention.

Assessment of impact of ten days fishing ban in the major spawning grounds of hilsa (Tenualosa ilisha, Fisher and Bianchi, 1984)

A study was undertaken to find out the impact of ten days fishing ban in the major spawning grounds of hilsa during October to December. The study revealed a positive impact of fishing ban during spawning season on reproduction success of hilsa. Proportionate distribution of male and female hilsa also showed a significant level of distribution in and around the spawning grounds where the ratio was 35:65. Percent of oozing hilsa during fishing ban period in the spawning grounds was observed 1.61%. About 5% spent hilsa was observed in the fish landing centers and was compared with the data of Global Environment Facility (GEF) and Bangladesh Fisheries Research Institute (BFRI) studies and was found about 2.80-3.57 times higher than that of the findings of 2002 and 2003. Estimated egg production value showed about 46,800 Kg of eggs could have been produced that indicating a positive impact of 10 days fishing ban in spawning season. Abundance of higher percentages of gravid hilsa was found which were not available in the same quantity and condition in the non-fishing ban period. During the present investigation, fairly higher amount of spent hilsa and juveniles were also observed in the spawning grounds. Along with the jatka fry, spawn and fries of other fishes were also found in higher quantity than the previous years and thus it is assumed that fishing ban also might have positive impact on the successful breeding of other fishes. Overall, the fishing ban was found effective for successful breeding of hilsa.

Effects of diets, with different levels of n-3 HUFA, designed specifically for gilthead seabream (Sparus auratus L.) broodstock on spawning quality

The effects of dietary lipid levels in the spawning quality has been studied in several cultured fish species. Works like those of Watanabe et al. (1984 a); Mourente et al. (1989); Dhert et al. (1991); Bruce et al. (1993); Navas et al. (1997); Rodriguez et al. (1998); Lavens et al. (1999); Furuita et al. (2002, 2003 b); Mazorra et al. (2003); Fernandez- Palacios (2005) and Aijun et al. (2005) show that lipids and fatty acids are the dietetic components that have more influence in the spawning quality, specially in those species with continuous spawning which display short vitellogenesis periods and are able to incorporate these dietetic components in eggs during the spawning period. Diets for gilthead sea bream (Sparus aurata) broodstock with dietary levels of 2.84% n-3 HUFA, combined with levels of 250 mg/kg vitamine E rasure good spawning quality. Putting so indicative the importance for an effective utilization of essential fatty acids the use of adequate levels of antioxidants.

Spawning and habitat management in salmonid populations at the southern edge of their natural ranges = Reproducción y gestión del hábitat en poblaciones de salmónidos en el extremo meridional de sus distribuciones naturales

Las poblaciones de salmónidos en la Península Ibérica (trucha común, Salmo trutta; y salmón atlántico, Salmo salar) se encuentran cerca del límite meridional de sus distribuciones naturales, y por tanto tienen una gran importancia para la conservación de estas especies. En la presente Tesis se han investigado algunos aspectos de la reproducción y de la gestión del hábitat, con el objeto de mejorar el conocimiento acerca de estas poblaciones meridionales de salmónidos. Se ha estudiado la reproducción de la trucha común en el río Castril (Andalucía, sur de España), donde se ha observado que la freza ocurre desde diciembre hasta abril con el máximo de actividad en febrero. Este hecho representa uno de los periodos reproductivos más tardíos y con mayor duración de toda la distribución natural de la especie. Además, actualmente se sabe que el resto de poblaciones andaluzas tienen periodos de reproducción similares (retrasados y extendidos). Análisis en la escala de la distribución natural de la trucha común, han mostrado que la latitud explica parcialmente tanto la fecha media de reproducción (R2 = 62.8%) como la duración del periodo de freza (R2 = 24.4%) mediante relaciones negativas: a menor latitud, la freza ocurre más tarde y durante más tiempo. Es verosímil que un periodo de freza largo suponga una ventaja para la supervivencia de las poblaciones de trucha en hábitats impredecibles, y por tanto se ha propuesto la siguiente hipótesis, que deberá ser comprobada en el futuro: la duración de la freza es mayor en hábitats impredecibles que en aquellos más predecibles. La elevada tasa de solapamiento de frezaderos observada en el río Castril no se explica únicamente por una excesiva densidad de reproductores. Las hembras de trucha eligieron lugares específicos para construir sus frezaderos en vez de dispersarse aleatoriamente dentro del hábitat adecuado para la freza que tenían disponible. Estas observaciones sugieren que las hembras tienen algún tipo de preferencia por solapar sus frezaderos. Además, en ríos calizos como el Castril, las gravas pueden ser muy cohesivas y difíciles de excavar, por lo que el solapamiento de frezaderos puede suponer una ventaja para la hembra, porque la excavación en sustratos que han sido previamente removidos por frezas anteriores requerirá menos gasto de energía que en sustratos con gravas cohesivas que no han sido alteradas. Por tanto, se ha propuesto la siguiente hipótesis, que deberá ser comprobada en el futuro: las hembras tienen una mayor preferencia por solapar sus frezaderos en ríos con sustratos cohesivos que en ríos con sustratos de gravas sueltas. En el marco de la gestión del hábitat, se han empleado dos enfoques diferentes para la evaluación del hábitat físico, con el objeto de cuantificar los cambios potenciales en la disponibilidad de hábitat, antes de la implementación real de determinadas medidas sobre el hábitat. En primer lugar, se ha evaluado el hábitat físico del salmón atlántico en el río Pas (Cantabria, norte de España), en la escala del microhábitat, empleando la metodología IFIM junto con un modelo hidráulico bidimensional (River2D). Se han simulado una serie de acciones de mejora del hábitat y se han cuantificado los cambios en el hábitat bajo estas acciones. Los resultados mostraron un aumento muy pequeño en la disponibilidad de hábitat, por lo que no sería efectivo implementar estas acciones en este tramo fluvial. En segundo lugar, se ha evaluado el hábitat físico de la trucha común en el río Tajuña (Guadalajara, centro de España), en la escala del mesohábitat, empleando la metodología MesoHABSIM. Actualmente, el río Tajuña está alterado por los usos agrícolas de sus riberas, y por tanto se ha diseñado una restauración para mitigar estos impactos y para llevar al río a un estado más natural. Se ha cuantificado la disponibilidad de hábitat tras la restauración planteada, y los resultados han permitido identificar los tramos en los que la restauración resultaría más eficaz. ABSTRACT Salmonid populations in the Iberian Peninsula (brown trout, Salmo trutta; and Atlantic salmon, Salmo salar) are close to the southern limit of their natural ranges, and therefore they are of great importance for the conservation of the species. In the present dissertation, some aspects of spawning and habitat management have been investigated, in order to improve the knowledge on these southern salmonid populations. Brown trout spawning have been studied in the river Castril (Andalusia, southern Spain), and it has been observed that spawning occurs from December until April with the maximum activity in February. This finding represents one of the most belated and protracted spawning periods within the natural range of the species. Furthermore, it is now known that the rest of Andalusian populations show similar (belated and extended) spawning periods. Broad-scale analyses throughout the brown trout natural range showed that latitude partly explained both spawning mean time (R2 = 62.8%) and spawning duration (R2 = 24.4%) by negative relationships: the lower the latitude, the later the spawning time and the longer the spawning period. It is plausible that a long spawning period would be an advantage for survival of trout populations in unpredictable habitats, and thus the following hypothesis has been proposed, which is yet to be tested: spawning duration is longer in unpredictable than in predictable habitats. High rate of redd superimposition observed in the river Castril was not only caused by high density of spawners. Trout females chose specific sites for redd construction instead of randomly dispersing over the suitable spawning habitat. These observations suggest that female spawners have some kind of preference for superimposing redds. Moreover, in limestone streams such as Castril, unused gravels can be very cohesive and hard to dig, and thus redd superimposition may be an advantage for female, because digging may require less energy expenditure in already used redd sites than in cohesive and embedded unused sites. Hence, the following hypothesis has been proposed, which is yet to be tested: females have a higher preference for superimposing redds in streambeds with cohesive and embedded substrates than in rivers with loose gravels. Within the topic of habitat management, two different approaches have been used for physical habitat assessment, in order to quantify the potential change in habitat availability, prior to the actual implementation of proposed habitat measures. Firstly, physical habitat for Atlantic salmon in the river Pas (Cantabria, northern Spain) has been assessed at the microhabitat scale, using the IFIM approach along with a two dimensional hydraulic model (River2D). Proposed habitat enhancement actions have been simulated and potential habitat change has been quantified. Results showed a very small increasing in habitat availability and therefore it is not worth to implement these measures in this stream reach. Secondly, physical habitat for brown trout in the river Tajuña (Guadalajara, central Spain) has been assessed at the mesohabitat scale, using the MesoHABSIM approach. The river Tajuña is currently impacted by surrounding agricultural uses, and thus restoration was designed to mitigate these impacts and to drive the river to a more natural state. Habitat availability after the planned restoration has been quantified, and the results have permitted to identify in which sites the restoration will be more effective.

Effective Cell-Centred Time-Domain Maxwell's Equations Numerical Solvers

This research work analyses techniques for implementing a cell-centred finite-volume time-domain (ccFV-TD) computational methodology for the purpose of studying microwave heating. Various state-of-the-art spatial and temporal discretisation methods employed to solve Maxwell's equations on multidimensional structured grid networks are investigated, and the dispersive and dissipative errors inherent in those techniques examined. Both staggered and unstaggered grid approaches are considered. Upwind schemes using a Riemann solver and intensity vector splitting are studied and evaluated. Staggered and unstaggered Leapfrog and Runge-Kutta time integration methods are analysed in terms of phase and amplitude error to identify which method is the most accurate and efficient for simulating microwave heating processes. The implementation and migration of typical electromagnetic boundary conditions. from staggered in space to cell-centred approaches also is deliberated. In particular, an existing perfectly matched layer absorbing boundary methodology is adapted to formulate a new cell-centred boundary implementation for the ccFV-TD solvers. Finally for microwave heating purposes, a comparison of analytical and numerical results for standard case studies in rectangular waveguides allows the accuracy of the developed methods to be assessed.