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Sex-ratio is an important demographic parameter, however, the literature surrounding bird and mammal sex-ratio is incredibly inconsistent. Some bird and mammal species provide strong evidence for sex-ratio adjustment because observed sex-ratio results match the predictions of sex manipulation hypotheses. However, some bird and mammal species exhibit sex-ratio results that conflict with the predictions of sex manipulation hypotheses. The need to rectify bird and mammal sex-ratio inconsistencies is paramount when considering many conserved populations face demographic collapse in the presence of climate change. Therefore, this study has reviewed all known bird and mammal sex manipulation hypotheses, and chosen to examine a species that theoretically displays few sex manipulation hypotheses for a simple study design. Displaying two sex manipulation hypotheses, Little Penguins (Eudyptula minor) were predicted to exhibit an even sex-ratio; whether they possessed the means to adjust sex-ratio or not. To test the above prediction, Little Penguin blood samples were retrieved from chicks nesting on Penguin Island and Garden Island and sexed via the CHDI genetic sexing technique, using the established PL/PR primer pair. Little Penguin chick weight and foot length data were also recorded and examined via the logistic growth curve to determine whether the study’s assumption of ‘equal net costs associated with raising either offspring sex’ was true. The sex-ratio for Little Penguin populations on Penguin Island and Garden Island was marginally female-biased, (P = 0.092 and 0.096 respectively). Possible reasons why the predicted sex-ratio of 1:1 was not observed are;(1) the prediction was based on inaccurate species knowledge as the assumption of ‘equal net costs associated with raising either offspring sex’ was determined false, (2) a small sample size for both Penguin Island and Garden Island (41 and 19 respectively), or (3) aspects beyond those covered in sex manipulation hypo

The number of artificial reef deployments around Australia has increased in recent years due to their popularity amongst recreational fishers. As these reefs modify the environment and its associated fauna, monitoring is required to ensure that any negative impacts to the surrounding area are assessed and minimised. Given this and the high cost of purpose-built artificial reefs, there is a need to develop cost-effective monitoring methods to determine their faunal composition. To address this need, this thesis reviewed methods for monitoring the faunas of artificial reefs and utilised the Baited Remote Underwater Video (BRUV) method to survey the fish faunas of two artificial reefs in Geographe Bay. Fourteen fauna monitoring methods, in their application to artificial reefs, were critically evaluated against five criteria, i.e. deployment, accuracy, precision, time and cost. Not all methods were found to be applicable to the different types of artificial reefs, with the accuracy of each technique depending upon the scale at which monitoring occurs and the type of fauna being targeted. The fastest and cheapest techniques were those that either utilised only minimal equipment and/or did not require observers. Remotely operated underwater video, particularly BRUVs, were found to provide a relatively inexpensive and effective tool for monitoring fish communities of artificial reefs. This finding supported the choice of the BRUV method, which was deployed through citizen science, to monitor the fish communities of the Bunbury and Dunsborough artificial reefs in Geographe Bay, south-western Australia, between October 2015 and July 2016. The resultant videos were analysed, using two-way ANOVA, to determine if the number of taxa, total MaxN, Simpson’s Index, as well as the MaxN of several key recreational species, differed between reefs and over time, whilst PERMANOVA was utilised to identify whether the composition of the fish communities differed spatially and temporally.

The focus of this thesis is on the design and use of artificial reefs and the development of a cost-effective method for monitoring their fish faunas. A review of habitat enhancement structures around the world, focusing primarily on artificial reefs, found that these structures have been used for a wide range of purposes such as sediment stabilization, mitigation of illegal trawling, enhancing recreational fisheries and the provision of additional habitat and nurseries for threatened fish stocks. Over time, there has been a growing trend in the use of purpose built reef modules as opposed to the use of materials of opportunity. Within Australia this has been most evident in the shift away from the use of tyres and steel vessels, to the use of specially designed concrete reef modules. As these structures can require financial investments within the millions, it is important to evaluate their effectiveness through post deployment monitoring. A central part of the citizen science monitoring project being developed by Recfishwest in Western Australia is the use of university students to extract information from the Baited Remote Underwater Video (BRUV) footage collected by recreational fishers. This study found that whilst observers recorded similar numbers of species and abundance (total MaxN), significant differences were present between observers in terms of their faunal compositions. This indicates that if inexperienced observers are used in the future as part of a cost-effective monitoring project, observer bias may be a potential source of error in the data and should be mitigated through observer training. Statistical analysis of footage collected from the Bunbury and Dunsborough artificial reefs using BRUVs found a significant difference in species composition between the footage from the two reefs but not between camera positions. However, increased camera soak time and footage collection over a greater temporal scale are needed to increase the reliability of

This thesis represents the first study into the genetic implications of culturing a marine finfish from wild-caught eggs (the ACAAR technique), for use in stock enhancement. This technique should facilitate the capture of genetic diversity in the cultured fish, while also dispensing with the need to maintain a large broodstock in the hatchery. This study was conducted with Chrysophrys auratus from Cockburn Sound in Western Australia. Nine, polymorphic microsatellite loci were used to compare the genetic composition between a sample of wild adults of C. auratus from spawning aggregations in Cockburn Sound and a sample of juveniles cultured using the ACAAR technique. The levels of genetic diversity present in the wild sample, in terms of allelic richness and heterozygosity, were maintained in the juveniles cultured using this technique and their release would likely pose little risk to genetic diversity in the wild. Overall, the allelic compositions were similar between the wild adult and cultured juveniles samples, although some rare alleles were absent in each population due to sampling bias, and bottleneck effects in the cultured juveniles. The levels of inbreeding and relatedness detected in the cultured juveniles were low, and similar to that of the wild adult sample, suggesting that juvenile releases would be unlikely to increase levels of inbreeding in the wild. It is also likely that a large number of effective breeders ( > 133) contributed to the cultured juveniles, thereby lowering the risk of inbreeding, or reductions to the wild effective population size, upon release. These findings together suggest that the ACAAR technique poses a limited risk to the genetic integrity of the wild population, should these fish be released for stock enhancement. It may also serve as a suitable alternative to traditional culturing for other aggregate spawning marine finfish. Further, suggestions are made for the improvement of the ACAAR culturing technique and for improveme

Pairs of closely related species on either side of a barrier provide an opportunity to test evolutionary hypotheses. In southern Australian seas, many species pairs occur on either side of the Bass Strait, which temporarily becomes an isthmus during glacial stages, yet few evolutionary questions have been explored using these species. This thesis used partial nucleotide sequences from mitochondrial cytochrome b and COI genes and length-polymorphism in several nuclear introns in one such species pair, Arripis trutta (east of Bass Strait) and A. truttaceus (west of Bass Strait), to address some evolutionary questions. Data from the two remaining members of the family Arripidae, A. xylabion and A. georgianus, were included to provide context for interpreting patterns in the focal species pair. This research found no evidence for population subdivision in each of A. trutta, A. truttaceus and A. georgianus across their Australian distributions. This likely reflects panmixia, maintained by highly migratory life cycles and restricted breeding distributions. The molecular data also supported the currently recognised four-species taxonomy of the family. Phylogenetic reconstructions did not support the view of a sister-species relationship between the east-west species pair of A. trutta and A. truttaceus but instead suggested that these two species, together with A. xylabion, likely arose as a trifurcation (some 700,000 years ago), and so can be considered as a trio of sibling-species. All Arripis species were characterised by low genetic diversity and there was evidence for a more recent and/or severe population contraction in A. truttaceus compared to A. trutta. These different demographic signals support the a priori hypothesis that environmental conditions to the west of the Bass Strait were more severe than to the east during glacial stages and, in particular, the last glacial maximum. The results are considered in the context of the historical marine biogeography of tem

Northern Australia is believed to contain the last ‘viable’ populations of the critically endangered Freshwater Sawfish, Pristis microdon, Dwarf Sawfish, Pristis clavata, and Green Sawfish, Pristis zijsron, making these populations of global significance. Mitochondrial and microsatellite markers were used to investigate the population structure, levels of genetic diversity, and evolutionary history of each of these species in northern Australian waters. Pristis microdon, which utilizes freshwater rivers as juveniles and marine waters as adults, has high levels of mtDNA heterogeneity and no nDNA heterogeneity; indicating that this species has female philopatry coupled with male-biased dispersal in northern Australian waters. The conservation plans for this species should, therefore, place a high priority on the protection of females, pupping grounds, and nursery areas to minimize the risk of extirpation. Conservation plans also need to consider the likelihood that a decline in the abundance of this species in one location could have an effect on its abundance and genetic ‘health’ in other locations via male gene flow. In contrast, P. clavata and P. zijsron, which spend their entire lives in marine and/or estuarine waters, each have heterogeneity in the mtDNA and nDNA markers, suggesting that gene flow in both males and females is restricted at large spatial scales in northern Australian waters. Consequently, the risk of extirpation for each of these species is relatively high since a decline in abundance is unlikely to be replenished by immigration from other locations. Therefore, conservation plans for P. clavata and P. zijsron should place a high priority on the protection of males and females, as well as pupping grounds and nursery areas. Most of the assemblages of each of the Pristis species contained moderate and high levels of diversity in mtDNA and nDNA markers, respectively. This suggests that the prognosis for the short and medium-term survival of each of th

The research conducted for this thesis has produced quantitative data on the biology and population genetic structure of the Mulloway Argyrosomus japonicus in Western Australia, where this sciaenid is recreationally and commercially fished. These data were used 1) to test various hypotheses regarding the relationship between key biological characteristics of A. japonicus and both latitude and environmental variables, 2) to investigate the population structure and genetic characteristics of populations of A. japonicus on the west and south coasts of Western Australia and to assess the relationships between these populations and those of A. japonicus in eastern Australia and South Africa, and 3) to consider the implications of the biological and genetic results for management.

Initial feasibility of using PCR-generated DNA vaccines (LEC) was completed as outlined in our proposal of July 21, OS. Specifically we demonstrated that (a) manufacture of milligram amounts of LEC DNA vaccine against H3N2 and H1N1 influenza strains was possible using microplate PCR technology; (b)resulting LEC DNA could be purified and formulated with the cationic lipid delivery system Vaxfectin and (c) vaccination of mice with Vaxfectin-formulated LEC vaccine resulted in protection against a lethal viral challenge. In addition, objectives outlined in our Expanded Aims proposal of Feb 21,06 were met. Specifically, we compared the performance of LEC vaccination to that of pDNA vaccination using the mouse influenza challenge model. These data indicate that Vaxfectin-formulated pDNA outperformed Vaxfectin-formulated LEC at doses between 0.4 and 0.08 ug. Protection data for pDNA vs. LEC at doses 2 ug or above were statistically indistinguishable. We also evaluated one potential scalable PCR device concept Heat transfer characteristics of materials and fluids were determined and PCR amplification was attempted at the 10 and 100 mL reaction volumes. Although DNA amplification was unsuccessful, causes for this outcome were identified and potential solutions have been proposed.