Academic literature on the topic 'Fish populations – Australia'

Population structure in marine teleosts is often investigated to aid conservation and fisheries management (e.g. to assess population structure to inform restocking programs). We assessed genetic population structure of the important estuary-associated marine fish, mulloway (Argyrosomus japonicus), within Australian waters and between Australia and South Africa. Genetic variation was investigated at 13 polymorphic microsatellite markers. FST values and Bayesian estimates in STRUCTURE suggested population differentiation of mulloway within Australia and confirm strong differentiation between South Africa and Australia. The 12 Australian sample sets fell into one of four spatially separated genetic clusters. Initially, a significant signal of isolation-by-distance (IBD) was evident among Australian populations. However, further investigation by decomposed-pairwise-regression (DPR) suggested five sample sets were influenced more by genetic-drift, rather than gene-flow and drift equilibrium, as expected in strong IBD cases. Cryptic oceanographic and topographical influences may isolate mulloway populations from south-western Australia. The results demonstrate that DPR is suitable to assess population structure of coastal marine species where barriers to gene flow may be less obvious than in freshwater systems. Information on the relative strengths of gene flow and genetic drift facilitates a more comprehensive understanding of the evolutionary forces that lead to population structure, which in turn informs fisheries and assists conservation management. Large-bodied predatory scale-fish may be under increasing pressure on a global scale, owing to a variety of anthropogenic reasons. In southern Australia, the iconic sciaenid A. japonicus (mulloway, jewfish or kob) is no exception. Despite the species supporting important fisheries, much of its ecology is poorly understood. It is possible that a greater understanding of their genetic population structure can help ensure a sustainable future for the only southern Australian sciaenid.

The parasite fauna of gemfish, Rexea solandri, from seven areas off southern Australia, was examined for evidence of isolated gemfish populations. Canonical multivariate analyses of data on larval nematodes (Anisakis spp. and Terranova sp.), cestode plerocercoids (Hepatoxylon trichiuri and Nybelinia sp.), acanthocephalans (Rhadinorhynchus sp. and Corynosoma sp.), and a hemiuroid digenean from a total of 763 gemfish showed that the parasite faunas of fish from eastern Australia were similar except for a sample taken off New South Wales at the end of the spawning season whose affinities are unknown. Fish from South Australia had similar parasite faunas to those collected from eastern Australia, suggesting that fish from the eastern and western Bass Strait belong to the same stock. Fish collected from the Great Australian Bight were distinct from the southern and eastern fish. Differences in parasite fauna were detected between samples taken within the spawning season and those taken from the same locations outside the spawning season, presumably a result of the spawning migration.

The closely related eastern mosquitofish (Gambusia holbrooki) and western mosquitofish (Gambusia affinis) have been introduced into many countries and collectively represent the most widely distributed freshwater fish in the world. We investigated genetic patterns associated with the spread of G. holbrooki in its introduced range in south-eastern Australia, by sampling 60 G. holbrooki populations (n = 1771) from major regions where G. holbrooki was initially introduced into Australia, and characterising the genetic diversity and population structure of G. holbrooki, using five polymorphic nuclear microsatellite loci and sequences from two mitochondrial genetic markers. Results were compared with published data on American and European Gambusia samples and historical records. Low microsatellite diversity and strong population genetic structuring were found within G. holbrooki in south-eastern Australia. Observed heterozygosity and allelic richness declined regionally in the order Sydney, Brisbane, Canberra, Melbourne and Adelaide. Microsatellite variation in Australia was reduced compared with native populations. Two mitochondrial DNA haplotypes of G. holbrooki were found; one was common, whereas the other was detected in one Sydney population and one Melbourne population. Cytochrome b sequence diversity was reduced compared with native and European ranges, and sequences were identical to two haplotypes previously identified. Microsatellite diversity of G. holbrooki in south-eastern Australia validates historical records of its spread, beginning north and moving south. Mitochondrial sequencing confirms that G. holbrooki is present in Australia, but the origins of Australian G. holbrooki populations remain unclear.

AbstractThere is a paucity of information on the diversity and occurrence of freshwater fish parasites in Australia. This study investigates the distribution and occurrence of a parasitic nematode of the genusContracaecumin freshwater fish from south-eastern Australia. Fish (n= 508) belonging to nine species and eight families were collected from eight wetlands associated with the Murrumbidgee River floodplain in the southern Murray–Darling Basin and subjected to laboratory examination. Third-stage nematode larvae were found in eight of the nine fish species. The exception was the fly-specked hardeyhead (Craterocephalus stercusmuscarum), although only one specimen of this species was examined. Nematode larvae were identified asContracaecum bancroftiusing a combined morphological and molecular approach. The parasite was most prevalent in weather loach (Misgurnus anguillicaudatus; 34.8%) and Australian smelt (Retropinna semoni; 21.4%), followed by carp (Cyprinus carpio; 9.5%), of which the former and latter are non-native species.Contracaecumprevalence differed between locations, with Two Bridges having the highest number of infected fish. This may be due to the higher number of suitable host species collected at these localities.Contracaecumspp. are parasites with low host specificity that have also been reported in Australian marine fish, humans and piscivorous birds. The high parasite prevalence in the two abundant non-native fish species in the region suggests that they act as a suitable host for this endemic parasite, resulting in the increase in the parasite population. It would be interesting to study host–parasite interactions in this area, especially if introduced fish populations declined dramatically in the attempt to eradicate them or control their population.

Ranaviral infections have been associated with mass mortality events in captive and wild amphibian, fish, and reptile populations globally. In Australia, two distinct types of ranaviruses have been isolated: epizootic haematopoietic necrosis virus in fish and a Frog virus 3-like ranavirus in amphibians. Experimental studies and serum surveys have demonstrated that several Australian native fish, amphibian, and reptile species are susceptible to infection and supported the theory that ranavirus is naturally circulating in Australian herpetofauna. However, ranaviral infections have not been detected in captive or wild lizards in Australia. Oral-cloacal swabs were collected from 42 wild lizards from northern Queensland and 83 captive lizards from private collections held across three states/territories. Samples were tested for ranaviral DNA using a quantitative PCR assay. This assay detected ranaviral DNA in 30/83 (36.1%) captive and 33/42 (78.6%) wild lizard samples. This is the first time molecular evidence of ranavirus has been reported in Australian lizards.

A summary is given of allozyme, mitochondrial DNA and microsatellite data for commercially important species (13 fish and 7 shellfish) in Australia’s South East Fishery, including contiguous waters and the Tasman Sea. For most fish species, genetic population differentiation was limited and in about half the studies was non-detectable. Striking population differentiation was recorded for gemfish. For fish species, on average only 2–3% of the total genetic variation could be attributed to population differentiation within southern Australian waters. In shellfish, ~5% of variation arose from population differences. The reduced differentiation of fish populations may be due to a longer larval period and greater adult mobility. Although there was evidence that the Tasman Sea acts as a barrier to gene flow, with most fish species showing significant differences between Australia and New Zealand, the degree of differentiation was small (only ~2%). The limited genetic differentiation obserred for most species is attributable to the lack of major oceanographic and environmental barriers to gene flow, together with influential current systems; it necessitates large sample sizes for good genetic tests. However, significant genetic stock structuring is apparent for several fish and shellfish species – particularly for coastal species, where isolation by distance may explain some of the data. Any evidence for genetic stock structure must be factored into plans for sustainable management.

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae:Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cytbgene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overallFSTvalues suggested that both groups exhibit very low dispersal among rivers (SEQ-SFST= 0.13; SEQ-NFST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units along south east Queensland to guide future conservation management. The present findings at least can assist managers to plan for effective conservation and management of different fish species along coastal drainages of south east Queensland, Australia.

Haematology has the potential to be a valuable tool in determining the health status of wild fish populations and wider ecosystem health. However, limited haematological data are available for wild Australian fish species, and the interpretation and nomenclature of leukocytes is variable and inconsistent in fish. The morphology and cytochemical reactions of erythrocytes, thrombocytes and leukocytes of 189 wild eel-tailed catfish (Tandanus tandanus), Wet Tropics tandan (Tandanus tropicanus), Hyrtyl’s tandan (Neosilurus hyrtlii), black catfish (Neosilurus ater), lesser salmon catfish (Neoarius graeffei), and silver cobbler (Neoarius midgleyi) are described. Erythrocytes, thrombocytes, lymphocytes, monocytes and heterophils in all six species are morphologically similar to those reported in other Siluriformes. Basophils and eosinophils are rarely reported in fish; however basophils were observed in peripheral blood smears of T. tropicanus and N. ater, and eosinophils were observed in N. graeffei. Periodic acid Schiff positive granular leukocytes were observed in N. graeffei, N. midgleyi, N. ater and T. tandanus. This is the first report on the leukocyte morphology and cytochemistry of any native Australian catfish species, and provides useful baseline data for future assessments of fish health and ecosystem integrity in Australia.

Abstract Galaxias truttaceus is found in coastal rivers and streams in south-eastern Australia. It spawns at the head of estuaries in autumn and the larvae spend 3 months of winter at sea before returning to fresh water. In Tasmania there are landlocked populations of G. truttaceus in a cluster of geologically young lakes on the recently glaciated Central Plateau. These populations have no marine larval stage and spawn in the lakes in spring. Speciation due to land locking is thought to be a frequent occurrence within Galaxias. To investigate the nature of the speciation event which may be occurring within lake populations of G. truttaceus we studied the mitochondrial DNA (mtDNA) and allozyme diversity of both lake and stream populations. Using the presence or absence of restriction sites recognized by 13 six-base restriction endonucleases, we found 58 mtDNA haplotypes among 150 fish collected from 13 Tasmanian and one south-east Australian mainland stream populations. The most parsimonious network relating the haplotypes by site loss or gain was starlike in shape. We argue that this arrangement is best explained by selection upon slightly beneficial mutations within the mitochondrial genome. Gene diversity analysis under Wright's island model showed that the populations in each drainage were not genetically subdivided. Only two of these stream haplotypes were found among the 66 fish analyzed from four lake populations. Despite the extreme lack of mtDNA diversity in lake populations, the observed nuclear DNA heterozygosity of 40 lake fish (0.10355) was only slightly less than that of 82 stream fish (0.11635). In the short time (3000-7000 years) that the lake fish have been landlocked, random genetic drift in a finite, stable-sized population was probably not responsible for the lack of mtDNA diversity in the lake populations. We infer the lake populations have probably experienced at least one, severe, but transitory bottleneck possibly induced by natural selection for life-history characters essential for survival in the lacustrine habitat. If speciation is occurring in the landlocked populations of G. truttaceus, then it may be driven by genetic transilience.

Phylogeography is a field that has the potential to provide an integrative approach to the conservation of threatened species. The southern purple spotted gudgeon, Mogurnda adspersa, is a small freshwater fish that was once common and widely distributed throughout south-eastern Australia. However, habitat alteration has dramatically reduced the size and the range of Murray–Darling Basin populations, which are now classified as endangered. Here patterns of genetic structure and evolutionary history of M. adspersa in southern Queensland and the Murray–Darling Basin are elucidated using three regions of the mitochondrial DNA, the ATPase 6 and 8 and the control region. Murray–Darling Basin populations are characterised by lineages with highly localised endemism, very low genetic diversity and restricted gene flow. Phylogenetic reconstructions show that Murray–Darling Basin populations comprise a monophyletic clade that possibly originated by range expansion from the coast around 1.6 million years ago. It is proposed that the divergent Murray–Darling Basin clade is of high conservation priority and requires separate management. The present study further exemplifies the role of drainage rearrangement in driving evolutionary diversification in Australian freshwater fishes, an historical process with profound implications for conservation management.

Freshwater systems offer important opportunities to investigate the consequences of intrinsic biological and extrinsic environmental factors on the distribution of genetic variation, and hence population genetic structure. Drainages serve to isolate populations and so preserve historical imprints of population processes. Nevertheless, dispersal between and within drainages is important if the biology of the species confers a good dispersal capability. Knowledge of the population genetic structure or phylogeographic patterns of Australia's freshwater fish fauna is generally depauperate, and the present study aimed to increase this knowledge by investigating patterns of genetic diversity in three Australian species of freshwater fish. I was interested in the relative importance of dispersal capability, the hierarchical nature of stream structure and the consequences of earth history events on patterns of genetic diversity among populations. I examined three species from three families of Australian freshwater fish, Pseudomugil signifer (Pseudomugilidae), Craterocephalus stercusmuscarum (Atherinidae) and Hypseleotris compressa (Gobiidae). These species are abundant, have wide overlapping distributions and qualitatively different dispersal capabilities. I was interested in attempting to unravel how the biological, environmental and historical factors had served to influence the patterns and extent of genetic diversity within each species, thereby inferring some of the important evolutionary processes which have affected Australia's freshwater fauna. I used allozyme and 500-650bp sequences from the ATPase6 mitochondrial DNA (mtDNA) gene to quantify the patterns of genetic variation at several hierarchical levels: within populations, among populations within drainages and among drainages. I collected fish at several spatial scales, from species wide to multiple samples within drainages; samples were collected from the Northern Territory, Queensland and New South Wales. The species with the highest potential for dispersal, H. compressa, exhibited the lowest levels of genetic differentiation as measured at several allozyme loci (H. compressa: FST=0.014; P. signifer FST=0.58; C. stercusmuscarum FST=0.74). Populations of H. compressa also had low levels of mtDNA differentiation, with many recently derived haplotypes which were widespread along the coast of Queensland. This suggested either considerable gene flow occurs or recent demographic change in the populations sampled. As there was no relationship between geographic distance and genetic differentiation, the populations appeared to be out of genetic drift - gene flow equilibrium, assuming the two-dimensional stepping stone model of gene flow. Estimating contemporary gene flow was thus difficult. It was apparent that there has been a recent population expansion and / or contraction of H. compressa populations. It was concluded that there has been considerably more connectivity among populations of H. compressa in the recent past than either of the other study species. Populations of P. signifer showed considerable genetic subdivision at different hierarchical levels throughout the sampled range, indicating gene flow was restricted, especially between separate drainages. Two widely divergent regional groups which had high ATPase6 sequence divergence and approximately concordant patterns at allozyme loci were identified. Interestingly, the groups mirrored previous taxonomic designations. There was also significant subdivision among drainages within regional groups. For example, the adjacent Mulgrave-Russell and Johnstone drainages had individuals with haplotypes that were reciprocally monophyletic and had large allozyme frequency differences. This allowed me to examine the patterns of genetic differentiation among populations within drainages of two essentially independent, but geographically close systems. There was as much allozyme differentiation among populations within subcatchments as there was between subcatchments within drainages, and significant isolation by distance among all populations sampled within a drainage. This suggested that the estuarine confluence between subcatchments was not a barrier to P. signifer, but that distance was an important component in the determination of the distribution of genetic diversity within drainages in P. signifer. There were three main areas of investigation for C. stercusmuscarum: comparing upland and lowland streams of the drainages in north Queensland, investigating the consequences of eustasy on coastal margin populations and examining the intriguing distribution of the two putative sub species, C. s. stercusmuscarum and C. s. fulvus in south east Queensland. First, as populations in upland areas of east coast flowing rivers are above large discontinuities in the river profile, their occurrence is presumably the result of gene flow to and / or from lowland areas, or the result of invasions via the diversion of western flowing rivers. Concordant patterns at both genetic markers revealed that the latter possibility was the most likely, with fixed allozyme differences between upland and lowland populations, and large mtDNA sequence divergence. Indeed, it appeared that there may have been two independent invasions into the upland areas of rivers in North Queensland. Second, lowland east coast populations also had large, although not as pronounced, levels of population subdivision. Lack of isolation by distance, but with a concomitant high level of genetic differentiation among many comparisons, was consistent with a scenario of many small, isolated subpopulations over the range. Interestingly, widespread populations in central Queensland coastal populations (drainages which receive the lowest rainfall) were relatively genetically similar. This was consistent with the widest part of the continental shelf which at periods of lower sea level apparently formed a large interconnected drainage, illustrating the effect of eustatic changes on populations inhabiting a continental margin. Third, putative C. s. fulvus in lowland coastal Queensland drainages were genetically more similar to a population of C. s. fulvus collected from a tributary of the Murray-Darling (western flowing) than they were to adjacent putative C. s. stercusmuscarum. This implied that populations in south east Queensland, north to approximately the Burnett River, appeared to be derived from western flowing streams, and not via dispersal from other lowland east coast populations. Determining the relative importance of intrinsic and extrinsic factors to the development of population genetic structure is a difficult task. The present study demonstrated that the species with the highest dispersal potential had the lowest levels of genetic differentiation, waterfalls can limit gene flow, eustasy acts to join and separate populations leading to complex genetic patterns and that drainage rearrangements are important in determining the distribution of genetic diversity of populations now inhabiting isolated drainages. A difficulty with generalising about population genetic structure in obligate freshwater animals is the unique history of not only each drainage, but also the streams within that drainage and the idiosyncratic biological dynamics of the populations inhabiting those drainages.

Latitudinal patterns in reef fish assemblages reflect the influence of long-term environmental conditions, evolutionary processes and the recent, short-term influence of fishing. Long-term processes generate the typically common latitudinal patterns in reef fish assemblages, such as decreases in diversity and herbivory towards higher latitudes. These patterns reflect the global gradient in water temperature and the isolation of temperate regions from the tropics. Fishing also influences reef fish assemblages in that it decreases the abundance of large-bodied carnivore species on reefs, often leading to over-exploitation, depletion and in some cases the extirpation of populations. Indirectly, the removal of these large-bodied carnivores can influence the abundance of their prey, leading to an increase in non-target species. This study examines the latitudinal patterns in reef fish assemblages across a unique biogeographic region, the temperate Western Australian coast, and incorporates an investigation of the influence of fishing on the structure of these assemblages. Seven regions across seven degrees of latitude and seven degrees of longitude covering approximately 1500 km of coastline were sampled. Fish assemblages were characterised at each region using diver operated stereo-video transects. At each region, four locations, and within each location, four reefs were surveyed totalling 1344 transects. A significant gradient in water temperature exists with latitude and longitude. Along the Western Australian coast, and in contrast to other regions species diversity of reef fish increased towards higher latitudes and there was no evidence for a decrease in the biomass and abundance of herbivorous reef fish. The presence of the poleward flowing warm water Leeuwin current combined with the absence of major extinction events means the temperate Western Australian coast contrasts with global latitudinal trends in reef fish assemblage structure. The unique biogeographic history of temperate Western Australia has also generated a high degree of endemism among reef fish. Nearly 30 % of the species found along the west coast in this study are endemic to Western Australia, with the narrow range of these species playing an important role in the large scale patterns and spatial vi heterogeneity in reef fish assemblage structure. Furthermore, many of these endemic species are large-bodied carnivores and targeted by fishers. The impact of fishing on the abundance of large-bodied carnivores throughout the Western Australian temperate region is clear both spatially and temporally. The distribution of fishing effort is greatest along the west coast and decreases towards the south following the gradient in SST. Along the west coast, high levels of fishing effort have reduced the biomass and abundance of target carnivores to well below the standing biomass of the south coast where a low level of fishing effort occurs. This reduction in biomass is related to the historical declines in catch per unit effort (CPUE) of many key target species. These target species include endemic species such as Choerodon rubescens, Glaucosoma herbraicum, Epinephilides armatus Nemadactylus valenciennesi and Achoerodus gouldii.

The Roe’s abalone (Haliotis roei) fishery near Perth, Western Australia, is uniquely accessible, and highly vulnerable to overexploitation. The sustainability of this intensively utilized fishery requires robust assessment. To facilitate an assessment, this research aimed to provide rigorous and detailed biological information with appropriate interpretation. Four critical aspects of the species’ biology and population dynamics were investigated: (1) the stock structure; (2) the recreational catch; (3) an appropriate growth curve and description of size at age; and (4) abundance measures against which to assess the impact of fishing mortality. Allozyme electrophoresis was used to investigate stock structure across the species’ distribution. Standardized variance in allelic frequencies between 10 sites in south-western Australia indicated high levels of gene flow across the 3000 km sampled (mean FST = 0.009). An isolation-by-distance was evident when pairwise measures of GST were related to geographic distance (r=0.45, P<0.001). The area of complete genetic mixing was estimated from samples within the Perth fishery to be less than the distance between the two nearest sites, or 13 km. Consequently, the Perth fishery comprises numerous discrete stocks, each requiring independent assessment. A possible mechanism for this population structure is the retention of larvae in the wind driven currents oscillating in the near-shore lagoons, with rare pulses of long distance dispersal via the southerly Leeuwin current, running further offshore. The presumed impact of intensive recreational fishing, combined with substantial commercial quotas for the Perth fishery, had led to tight restrictions on fishing effort, without any quantitative measure of the recreational catch. A stratified creel survey was adapted to estimate the effort, catch rate and mean weight of abalone harvested by the recreational sector. Catches were estimated for reef complexes, or stocks, of less than 10 nautical miles (18.5 km) of coast. Between 1997 and 2000 the recreational catch varied from 30 to 45 tonnes whole weight, approximately equivalent to the commercial quota of 36 tonnes. On average 88% of the recreational catch came from two stocks, while 98% of the commercial catch came from these two, and one additional, stocks. The incidental mortality from recreational fishing, measured as the number of abalone left dead on the reef as a proportion of the estimated catch, was approximately 7% and 20% at two sites surveyed. Spatial and temporal patterns of growth were examined on the west coast of Western Australia. Growth increments were measured for abalone larger than about 30 mm from tagging studies at five sites in the Perth fishery, a site at the northern extent of the species’ distribution and a site in the southwest. Mean annual growth increments of the 0+ year class were obtained by fitting components to length frequencies from five sites in the Perth fishery, and combined with growth increments from each Perth tag site for model fitting. A von Bertalanffy growth curve provided a slightly better fit to the tag data, but a Gompertz growth curve was a much better fit when the mean increment from the 0+ to 1+ cohort was included, with the inflection occurring at about 40 mm, the size at sexual maturity. There was no difference in annual growth between the two years studied. There was significant variation in growth between the reef platform and adjacent sub-tidal reef, but this variation was site specific and faster growth rates were not consistently associated with either habitat. There was no latitudinal trend in growth rate. Growth at the Perth sites was the fastest and similar at all five sites with growth increments greater in summer than in winter. Size and abundance of abalone were measured using fixed transects and quadrats. Abalone densities were highest on the outer edge of the platform, intermediate in the middle of the reef platform, and lowest on both the inner platform and the sub-tidal reef. The pattern of mean lengths of abalone was the inverse of the density. Mean length and abundance were driven by the presence of post-settlement juveniles on the outer and middle reef habitats. There was a high spatial variation in abundance, with densities varying between transects at the same site, but the trend between years for each transect at a site was not significantly different. Abalone abundances, by size class, were examined from sites sampled between 1996 and 2002. A low density of post-settlement juveniles at all sites in 1997 was reflected in low densities of the 1+ and 2+ year classes in subsequent years. Abalone abundances at an unfished site were steady over the seven years. Two sites were located within each of the main stocks utilised by the recreational fishery. Abundance was stable or increasing in one stock, corresponding to a stable total catch. In the second stock the total catch increased over time and abundances declined. Perth is the focus of the Roe’s abalone fishery, with recreational and commercial fishers take about equal shares of the annual catch. Stocks are highly subdivided, with most of this catch coming from only 3 stocks occupying about 20 nautical miles of coast. Growth rates were found to be lower than previous estimates, and more similar to other commercial species of abalone. All life history stages are highly habitat specific, particularly the recruits, and the distribution and abundance through time indicate that the main stocks are near, or slightly over, the limit of sustainable fishing.

This study investigated the causes of high level of intra-and inter-population variation known to occur in the morphology of fish in the genus Hypseleotris Eleotride in southern Australia, particularly within the Murray-Darling river system. The three major objectives of the study were, identify the number and distribution of species,determine the genetic structure of the populations and analyse relationships between species and consider the process of speciation in this species complex. The investigation of morphological variation in Hypseleotris confirmed the presence of two well known species i.e. H. compressa and H. galli, in the coastal rivers and also of the inland species H. klunzingeri. Populations of Hypseleotris klunzigeri sensu lato in inland river were found to be very highly variable and analysis using discriminant functions and principle component analysis showed the widespread presence of three forms (A, B1 and B2). The analysis was confused by the presence of north/south clines and upstream/downstream variation in characteristic in each form. After these factors were removed, there was still a great deal of variation in each population. The presence of hybrids between each pair of inland species, identified by both morphological and genetic data, further confused the analysis and makes identification of all specimens to species in the field difficult. Examination of type material of H. Klunzingeri showed that this belonged to form B2. The other forms can be related to the undescribed species, Midgley's carp gudgeon and Lake's carp gudgeon. Keys to the species in the complex in southeastern Australia are given. The morphological and genetic data show that H. compressa and H. klunzingeri are sister species, primarily separated by the eastern uplands. Similarly, the coastal species, H. galli is related to form B1 and more distantly, to form A. Possible scenarios for the complex are given.
Doctor of Philosophy (PhD)

Barramundi (Lates calcarifer) is a centropomid teleost with a wide distribution across the Indo Pacific. In Australia, barramundi are native to the tropical zone from Exmouth Gulf in Western Australia, across the northern part of the continent, to the Mary River in Queensland. Barramundi are protandrous hermaphrodites, and are euryhaline, with a catadromous life history. Barramundi are a valuable Australian resource, with important commercial and recreational fisheries and aquaculture production to the value of $11 million dollars per year. Recent declines in the availability of the fish in some rivers has led to an interest in the possibility of restocking rivers with barramundi from other areas. Determining the genetic structure of barramundi populations in Australia is important for understanding biogeographic history, and appropriate management practices for both aquaculture and recreational and commercial fishing. Previous studies have concentrated on the east coast of Australia, and have largely ignored the western populations. In this study, I obtained DNA data from barramundi populations across the Australian range of the species, as well as populations from Papua New Guinea and Indonesia. The aims of this study were to use the genetic data to determine: 1. if populations in Western Australia show genetic differences between geographic regions 2. if these populations show an ancestral split from populations in the east of Australia and 3. the ancestral origins of Australian barramundi. Previous studies of DNA data from barramundi have discovered an east/west split occurring at the Torres Strait that was assumed to be caused by the closing of the strait during lowered sea levels. However, these studies suffered from a bias in sampling area, concentrating either on the eastern half of the range of barramundi, or on the western tip of the range. Data from these studies were combined and reanalyzed. Two major clades were discovered, with considerable biogeographic structuring, but their geographic locations did not coincide with the reported vicariance event at the Torres Strait. Instead,historical divisions among freshwater drainage systems appeared to have driven the evolutionary history of barramundi in Australia. In order to investigate these historical divisions further, a 290 bp section of the mitochondrial DNA control region was sequenced in 284 barramundi from seven populations across the Australian geographic range of the species and from one population in Papua New Guinea and one population in Indonesia. Analyses of molecular variance within and among populations showed significant geographic structuring, based on biogeographical provinces and drainage divisions. Nested clade analyses indicated that these geographical associations were the result of restricted gene flow, range expansion, and past fragmentation events. I hypothesise that the Ord River area in the west of the continent was the ancestral source population for the rest of the species' range across Australia, with Indonesia being the most likely origin of this source. Populations of barramundi from the Pilbara region are genetically distinct and geographically isolated, with strong evidence of an ancestral divide along geographical barriers to dispersal. There is a strong association between Papua New Guinea and Australia, although further investigations using the cytochrome b region of mitochondrial DNA indicated a more ancestral divide between the two than is currently evident, which could reflect an ancient geographical divide between the two, or could be evidence of a secondary migration route to Australia. For a more detailed study of evolutionary processes acting on populations of barramundi in Western Australia, allelic diversity was examined at five microsatellite loci. All loci were polymorphic and genotypic frequencies conformed to Hardy-Weinberg expectations, with no significant linkage between loci evident in any population. Measures of within population diversity were significantly related to latitude, suggesting southerly migration from a northern source population. The Ord River was the most genetically diverse population, and the most likely ancestral migration source to the area, with diversity decreasing down the west coast. Although there were significant differences among populations, the nuclear microsatellite data do not indicate the same degree of genetic structuring as is evident in the mitochondrial data. This may be a consequence of rapid evolutionary change at microsatellite loci, with past separations or population differences masked by recombination and back mutation of the microsatellite alleles. However, the nature of nuclear and mitochondrial inheritance may also indicate life history differences between the sexes, where significant genetic contribution to gene flow by males and limited female gene flow may lead to preservation of maternally inherited population substructure. The principal findings from this study are: * There is no genetic evidence for an east/west division of barramundi populations in Australia, as suggested by previous research. * Despite barramundi's catadromous life history, and ability to disperse through marine waters, the present genetic structure indicates a division principally among river drainages. From a population genetic viewpoint, the species can be regarded as freshwater, rather than marine. * The most likely origin of barramundi in Australia is the Ord River region, with Indonesia as the route of migration. * Differences in the population structure demonstrated by nuclear and mitochondrial data indicate possible life history differences between the sexes. * Barramundi populations in different biogeographical provinces may have been substantially isolated over a long period of time, and may therefore represent independently evolving populations. This has important implications for fishery management and translocation issues for restocking rivers.

Seagrass is an underwater flowering plant that thrives in clear, sheltered, coastal waters around the world. As well as providing habitat for the marine fauna, seagrass meadows play an important role in the processes and resources of near-shore ecosystems. Coastal degradation of seagrass is prevalent along the metropolitan beaches of Adelaide, a problem common to settled coastal areas around the world, and although evidence from the literature suggests that loss of seagrass beds adversely affects the abundance of some coastal fish species, no quantification of the effect has been attempted. Moreover, although the economic value of seagrass as an 'ecosystem service' has been estimated, its value as a contributor to the productivity of the marine environment has not. In this thesis, mathematical and statistical models are used to explore the relationships that exist between seagrass habitats and the fish, crustacean, and mollusc species that depend upon them. The result is a model which estimates the annual value of seagrass loss to the secondary production in our coastal waters.
thesis (PhDMathematics)--University of South Australia, 2003.

Australia’s nature is exceptional, wonderful and important. But much has been lost, and the ongoing existence of many species now hangs by a thread. Against a relentless tide of threats to our biodiversity, many Australians, and government and non-government agencies, have devoted themselves to the challenge of conserving and recovering plant and animal species that now need our help to survive. This dedication has been rewarded with some outstanding and inspiring successes: of extinctions averted, of populations increasing, of communities actively involved in recovery efforts. Recovering Australian Threatened Species showcases successful conservation stories and identifies approaches and implementation methods that have been most effective in recovering threatened species. These diverse accounts – dealing with threatened plants, invertebrates, fish, reptiles, birds and mammals – show that the conservation of threatened species is achievable: that it can be done and should be done. They collectively serve to inform, guide and inspire other conservation efforts. This is a book of hope and inspiration. It shows that with dedication, knowledge and support, we can retain and restore our marvellous natural heritage, and gift to our descendants a world that is as diverse, healthy and beautiful as that which we have inherited. Joint recipient of the 2018 Whitley Certificate of Commendation for Conservation Zoology

<em>Abstract</em> .—The Murray–Darling basin (MDB) in southeastern Australia, covers 1.1 million km², involves six partner jurisdictions with a myriad of different government agencies, and, hence, provides an excellent example of the complexities of multijurisdictional management across a range of social and political tiers. In the MDB, fish and fisheries compete for water with agriculture, which is the traditional water user and is driven by national economics. Murray–Darling basin rivers are now highly regulated and generally in poor health, with native fish populations estimated to be at only about 10% of their pre-European settlement abundances. All native commercial fisheries are now closed, and the only harvest is by a recreational fishery. The six partner jurisdictions developed a Native Fish Strategy (NFS) to rehabilitate native fish populations to 60% of pre-European settlement levels after 50 years of implementation by addressing priority threats through a coordinated, long-term, whole-of-fish-community (all native fishes) approach. As there are a wide range of stakeholders, broad engagement was needed at a broad range of government and community levels. The NFS funding was discontinued after 10 years, not because of its lack of successes or project governance, but due to jurisdictional political changes and funding cuts that resulted in a failure of the collaborative funding structure. The withdrawal of considerable funding by one jurisdiction led to collective decline in monetary contributions and posed a threat to the multijurisdictional structures for both water and natural resource management (NRM) within the MDB. As a consequence, there was a review and reduction in NRM programs and a subsequent reduction in focus to the core business of water delivery. Reflection on the NFS, however, provides some useful insights as to the successes (many) and failures (funding) of this partnership model. Overall, the strategy and its structure was effective, as exhibited by an audit of outputs, outcomes, and networks; by the evident ongoing advocacy by NRM practitioners and the community; and by the continuation of ideas under other funding opportunities. This has provided a powerful legacy for future management of fishes in the MDB.

<em>Abstract</em> .—The Murray–Darling basin (MDB) in southeastern Australia, covers 1.1 million km², involves six partner jurisdictions with a myriad of different government agencies, and, hence, provides an excellent example of the complexities of multijurisdictional management across a range of social and political tiers. In the MDB, fish and fisheries compete for water with agriculture, which is the traditional water user and is driven by national economics. Murray–Darling basin rivers are now highly regulated and generally in poor health, with native fish populations estimated to be at only about 10% of their pre-European settlement abundances. All native commercial fisheries are now closed, and the only harvest is by a recreational fishery. The six partner jurisdictions developed a Native Fish Strategy (NFS) to rehabilitate native fish populations to 60% of pre-European settlement levels after 50 years of implementation by addressing priority threats through a coordinated, long-term, whole-of-fish-community (all native fishes) approach. As there are a wide range of stakeholders, broad engagement was needed at a broad range of government and community levels. The NFS funding was discontinued after 10 years, not because of its lack of successes or project governance, but due to jurisdictional political changes and funding cuts that resulted in a failure of the collaborative funding structure. The withdrawal of considerable funding by one jurisdiction led to collective decline in monetary contributions and posed a threat to the multijurisdictional structures for both water and natural resource management (NRM) within the MDB. As a consequence, there was a review and reduction in NRM programs and a subsequent reduction in focus to the core business of water delivery. Reflection on the NFS, however, provides some useful insights as to the successes (many) and failures (funding) of this partnership model. Overall, the strategy and its structure was effective, as exhibited by an audit of outputs, outcomes, and networks; by the evident ongoing advocacy by NRM practitioners and the community; and by the continuation of ideas under other funding opportunities. This has provided a powerful legacy for future management of fishes in the MDB.

<i>Abstract</i>.—The population structure of the eastern Australian salmon <i>Arripis trutta </i>stock in the waters of southeastern (SE) Australia was examined using information provided by historical as well as current data sources. An extensive tag-recapture program and aging study undertaken during the 1960s demonstrated widespread mixing of the <i>A. trutta </i>population in SE Australian waters and established a robust model of general movement of fish from Tasmania north to Victoria and NSW with the approach of sexual maturity at ~four years of age. However, this work also hypothesized that the portion of the stock at Flinders Island in Tasmanian waters was resident and did not undergo this northward migration. Otolith chemistry analyses were therefore used as a tool in a ‘weight of evidence’ approach to further examine the population structure of the <i>A. trutta </i>stock in SE Australia. Samples of five year old <i>A. trutta </i>for analysis of otolith chemistry were collected over seven weeks from two sites (10 per site) within each of four locations: northern NSW, southern NSW, Victoria and Tasmania. The cores and edges of otoliths were analyzed using laser ablation inductively coupled plasma mass spectrometry. Univariate analyses did not find spatial differences for any of the elements Li, Na, Mg, Mn, Ba or Sr between locations. Multivariate analyses however, did find differences between the multi-element ‘fingerprints’ of fish from Tasmania compared to each of the other locations (which were similar). This difference was driven by a group of fish collected from Flinders Island in north-eastern Tasmanian waters. The fish collected at this site were also significantly smaller at five years of age than fish from all other sites, indicating reduced growth rates. The lack of consequential and definitive differences in otolith chemistry data combined with the highly migratory nature of <i>A. trutta </i>in this region demonstrated by tagging studies confirm that the most likely stock structure model for <i>A. trutta </i>in SE Australia is of a single well mixed biological stock spanning Tasmania, Victoria and NSW with fish moving north from Tasmania to mainland Australia with the approach of sexual maturity. However, the reduced growth rates and distinct elemental signature for <i>A. trutta </i>from Flinders Island highlights the need for further work to examine the preexisting hypothesis of a potential resident sub-population there.

<em>Abstract</em>.—The flow regime is considered the primary driver of physical processes in riverine ecosystems; thus we expect that the trait composition of fish assemblages might respond similarly to hydrologic variability, even at broad spatial scales. Here, we test the hypothesis that freshwater fish life history strategies on two continents (southern United States and eastern Australia) converge along gradients of hydrologic variability and primary productivity at the drainage scale. Our results show that the fishes of the United States and Australia conform to the three-dimensional adaptive space arising from the trade-offs among three basic demographic parameters of survival, fecundity, and onset and duration of reproductive life. Species from both continents represent the endpoints in adaptive space defining the periodic (19% versus 33% for the United States and Australia, respectively), opportunistic (69% versus 52%), and equilibrium life history strategies (12% versus 15%). We found evidence that fish life history composition of drainage basins in the two continents have converged across similar gradients of hydrologic variability and productivity despite phylogenetic and historical differences. Moreover, these relationships were largely consistent with predictions from life history theory. Increasing hydrologic variability has promoted the greater prevalence of opportunistic strategists (a strategy that should maximize fitness in environmental settings dominated by unpredictable environmental change) while concurrently minimizing the persistence of periodic-type species (a strategy typically inhabits seasonal, periodically suitable environments). Our study provides a conceptual framework of management options for species in regulated rivers because life history strategies are the underlying determinants for population responses to environmental change and therefore can be used to classify typical population responses to flow alteration or mitigation via environmental flow prescriptions.

<em>Abstract</em> .—The collection and use of data to manage the freshwater fisheries of Australia’s Murray–Darling basin (MDB) has a poor history of success. While there was limited assessment data for early subsistence and commercial fisheries, even after more robust data became available during the 1950s its quality varied across jurisdictions and was often poorly collated, assessments were not completed, and the data were underutilized by management. The fishery for Murray Cod <em>Maccullochella peelii </em> is given as an example, where the fishery declined to the point of closure and then the decline continued to the extent that Murray Cod was listed as a threatened species and all harvest now only occurs through the recreational fishery. Lessons from such poor population assessments have not been fully learned, however, as there remains a paucity of harvest data for this recreational fishery. Without a proper assessment, a true economic valuation of this fishery has not been made. As the MDB is Australia’s food bowl, there are competing demands for water use by agriculture, and without a proper assessment of the worth of the fishery, it is difficult for Murray Cod to be truly considered in either economic or sociopolitical discussions. The poor state of MDB rivers and their fish populations (including Murray Cod) has, however, resulted in political pressure for the development of the sustainable rivers audit, a common assessment method for riverine environmental condition monitoring. This audit undertakes standardized sampling for fish and a range of other variables at a number of fixed and randomly selected sites on a 3-year rotating basis. While the sustainable rivers audit has provided a range of data indicating that the condition of rivers is generally very poor, these data have yet to be fully utilized to determine the potential state of the fisheries (such as Murray Cod) or to set targets for rehabilitation, such as for environmental flows. While, to date, data analyses have been somewhat restricted by fiscal constraints, more comprehensive use of data, together with full fishery valuations, should be seen as the way forward for improved management.

<em>Abstract</em> .—The collection and use of data to manage the freshwater fisheries of Australia’s Murray–Darling basin (MDB) has a poor history of success. While there was limited assessment data for early subsistence and commercial fisheries, even after more robust data became available during the 1950s its quality varied across jurisdictions and was often poorly collated, assessments were not completed, and the data were underutilized by management. The fishery for Murray Cod <em>Maccullochella peelii </em> is given as an example, where the fishery declined to the point of closure and then the decline continued to the extent that Murray Cod was listed as a threatened species and all harvest now only occurs through the recreational fishery. Lessons from such poor population assessments have not been fully learned, however, as there remains a paucity of harvest data for this recreational fishery. Without a proper assessment, a true economic valuation of this fishery has not been made. As the MDB is Australia’s food bowl, there are competing demands for water use by agriculture, and without a proper assessment of the worth of the fishery, it is difficult for Murray Cod to be truly considered in either economic or sociopolitical discussions. The poor state of MDB rivers and their fish populations (including Murray Cod) has, however, resulted in political pressure for the development of the sustainable rivers audit, a common assessment method for riverine environmental condition monitoring. This audit undertakes standardized sampling for fish and a range of other variables at a number of fixed and randomly selected sites on a 3-year rotating basis. While the sustainable rivers audit has provided a range of data indicating that the condition of rivers is generally very poor, these data have yet to be fully utilized to determine the potential state of the fisheries (such as Murray Cod) or to set targets for rehabilitation, such as for environmental flows. While, to date, data analyses have been somewhat restricted by fiscal constraints, more comprehensive use of data, together with full fishery valuations, should be seen as the way forward for improved management.