Nannoperca Australis Research Articles

Farm dams: A valuable interim step in small‐bodied threatened fish conservation

AbstractFreshwater fish are facing an extinction crisis on a global scale, with increasing demand for human water consumption driving the regulation and degradation of freshwater ecosystems. Flow regulation especially poses a threat to small‐bodied floodplain and creek specialist species through increasing population fragmentation and isolation, loss and degradation of habitats, and interactions with predators and competitors, resulting in reductions in species' range and abundance. Conserving and recovering many small‐bodied fish species will likely require translocation from wild habitats to refuge habitats to reduce extinction risk and provide buffers against catastrophic natural events (e.g., drought, bushfires). We assessed the value of semi‐artificial farm dams, an abundant feature in the Australian landscape, as interim refugia for the threatened southern pygmy perch Nannoperca australis (Percicthyidae). We compared the relative abundance, population size–structure and body condition of fish introduced (3–4 years prior) into three farm dams with those of three nearby creeks to assess the feasibility of farm dams as a resource to assist small‐bodied native fish conservation and recovery. Farm dams had higher abundance of fish, and equivalent size structure and body condition compared with creek populations, highlighting that suitable farm dams are a valuable and underutilized asset for threatened species' conservation globally.

Contemporary Trends in the Spatial Extent of Common Riverine Fish Species in Australia’s Murray–Darling Basin

As one of the world’s most regulated river basins, the semi-arid Murray–Darling Basin (MDB) in south-eastern Australia is considered at high ecological risk, with substantial declines in native fish populations already identified and climate change threats looming. This places great importance on the collection and use of data to document population trends over large spatial extents, inform management decisions, and provide baselines from which change can be measured. We used two medium-term data sets (10 MDB basin-wide fish surveys from 2004–2022) covering the 23 catchments and 68 sub-catchments of the MDB to investigate trends in the distribution of common riverine species at the entire basin scale. Fifteen native species were analysed for changes in their contemporary range, and whilst short-term changes were identified, all species showed no significant continuous trend over the study period. We further analysed the native species extent relative to their historic records, with bony herring and golden perch occurring in 78% and 68% of their historic river kilometres, respectively, whereas southern pygmy perch, northern river blackfish, silver perch, mountain galaxias, and freshwater catfish were all estimated to occur in less than 10% of their historic extent. Six established non-native species were also analysed and were very consistent in extent over the years, suggesting that they are near the available limits of expansion of their invasion. We provide effect sizes for the spatial extent index which can be used as baselines for future studies, especially those aiming to monitor changes in the spatial extent and population status of native species, or changes in the spatial extent of new or existing non-native species.

A community‐driven captive‐breeding and reintroduction program maintains genetic diversity in a threatened freshwater fish

AbstractCollaborative approaches to conservation management are critical to respond to the ongoing biodiversity crisis. However, local community involvement in many conservation actions is lacking, especially within translocation and reintroduction programs. Similarly, rapid integration of genetic information into collaborative programs with local communities is rarely conducted. Here, we describe a community‐based and collaborative reintroduction program for a threatened Australian freshwater fish, the southern pygmy perch (Nannoperca australis). We integrate on‐the‐ground translocation efforts by volunteers from local communities, captive breeding by a private aquarium business, and genetic analyses done by a research institution to provide a holistic framework for the reintroduction of southern pygmy perch. We evaluated genetic diversity, population structure, relatedness, and inbreeding across the duration of the reintroduction program using data from neutral and adaptive genomic markers. This allowed us to assess the ability of such a program to minimize inbreeding and retain genomic variation, and to promote adaptive potential of the reintroduced population. While genetic variation for the source populations was very low, we found no decrease in genetic diversity or increase in inbreeding across the program. These genetic findings support the efforts made by local communities and will further inform future reintroductions as part of a collaborative conservation framework. We expand on our empirical case study by describing a theoretical framework for integrating conservation genomics research with community‐led conservation management programs and identifying the benefits of such a collaboration. Our study highlights the importance of multifaceted and integrated conservation management approaches to effectively protect and manage threatened species.

Characterisation of nematode larvae found in a vulnerable native Australian fish, the southern pygmy perch, Nannoperca australis Günther

Context The southern pygmy perch (Nannoperca australis) is an endemic freshwater fish in Australia that is facing population decline and is listed as endangered or vulnerable in several states. Aims The aim of this study was to investigate the presence of parasites in the southern pygmy perch population and provide insights into their effect on the health and conservation of the species. Methods In total, 81 southern pygmy perch specimens were examined for parasite infections, followed by characterisation of the parasites. Key results The postmortem examination of the fish specimens did not show any visible parasites. However, through the incubation method, nematode larvae were discovered in 14 fish (mean intensity 1.6, mean abundance 0.28). Conclusions This study represents the first report of nematode larvae belonging to the genus Spiroxys in Australia, specifically in the southern pygmy perch. These findings highlighted the presence of parasite infections in the endangered southern pygmy perch and underscored the importance of conducting further research on parasites and their potential effect on the health and conservation of this species. Implications The discovery of nematode larvae in the southern pygmy perch raises concerns about the potential effects of parasites on the population.

Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction.

Restoration programs in the form of ex-situ breeding combined with reintroductions are becoming critical to counteract demographic declines and species losses. Such programs are increasingly using genetic management to improve conservation outcomes. However, the lack of long-term monitoring of genetic indicators following reintroduction prevents assessments of the trajectory and persistence of reintroduced populations. We carried out an extensive monitoring program in the wild for a threatened small-bodied fish (southern pygmy perch, Nannoperca australis) to assess the long-term genomic effects of its captive breeding and reintroduction. The species was rescued prior to its extirpation from the terminal lakes of Australia's Murray-Darling Basin, and then used for genetically informed captive breeding and reintroductions. Subsequent annual or biannual monitoring of abundance, fitness, and occupancy over a period of 11 years, combined with postreintroduction genetic sampling, revealed survival and recruitment of reintroduced fish. Genomic analyses based on data from the original wild rescued, captive born, and reintroduced cohorts revealed low inbreeding and strong maintenance of neutral and candidate adaptive genomic diversity across multiple generations. An increasing trend in the effective population size of the reintroduced population was consistent with field monitoring data in demonstrating successful re-establishment of the species. This provides a rare empirical example that the adaptive potential of a locally extinct population can be maintained during genetically informed ex-situ conservation breeding and reintroduction into the wild. Strategies to improve biodiversity restoration via ex-situ conservation should include genetic-based captive breeding and longitudinal monitoring of standing genomic variation in reintroduced populations.

Variation in intraspecific demography drives localised concordance but species-wide discordance in response to past climatic change

BackgroundUnderstanding how species biology may facilitate resilience to climate change remains a critical factor in detecting and protecting species at risk of extinction. Many studies have focused on the role of particular ecological traits in driving species responses, but less so on demographic history and levels of standing genetic variation. Additionally, spatial variation in the interaction of demographic and adaptive factors may further complicate prediction of species responses to environmental change. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes, the southern (Nannoperca australis) and Yarra (N. obscura) pygmy perches, to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. We described contemporary genetic diversity, phylogenetic histories, demographic histories, and historical species distributions across both species, and statistically evaluated the degree of concordance in co-occurring populations.ResultsMarked differences in contemporary genetic diversity, historical distribution changes and historical migration were observed across the species, with a distinct lack of genetic diversity and historical range expansion suggested for N. obscura. Although several co-occurring populations within a shared climatic refugium demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species. Discordant responses between species were associated with low standing genetic variation in peripheral populations. This might have hindered adaptive potential, as documented in recent demographic declines and population extinctions for the two species.ConclusionOur results highlight both the role of spatial scale in the degree of concordance in species responses to climate change, and the importance of standing genetic variation in facilitating range shifts. Even when ecological traits are similar between species, long-term genetic diversity and historical population demography may lead to discordant responses to ongoing and future climate change.

Experimental increases in detritus boost abundances of small‐bodied fish in a sand‐affected stream

Abstract Restoration projects often rely on the assumption that a local intervention will restore diminished populations, without fully understanding the constraints that limit the target species in the first place. In rivers, one common restoration technique is to place large structures, such as wood and boulders, on the bed, with the assumption that fish will subsequently arrive and use them. Nonetheless, providing large habitat structure may not overcome demographic or resource constraints on fish populations, and thus may not aid recovery. We aimed to test if resource constraints (food and cover) are limiting local densities of fishes in a degraded stream by experimentally alleviating these constraints. If the abundance of one or more species is constrained by resource availability, then local numbers of these species should increase following an increase in resources. To test our prediction, we increased the availability of food and microhabitat complexity (cover) at sites in Hughes Creek, a degraded stream in south‐east Australia that has extensive accumulations of sand and limited in‐stream structure. At treatment sites, we hammered pairs of wooden stakes (25 cm apart) into the stream bed so that the ends of stakes protruded just above the water surface at moderate flows. Stakes effectively trapped passing sticks and leaves, which increased local detrital densities and, subsequently, invertebrate densities, hence providing food and cover for fish. Over the course of a year, we compared the changes in fish abundances at treatment sites to unmanipulated control sites. Fish responded quickly to enhanced retention of detritus, with assemblage differences observed between treatment and control sites. We caught more river blackfish (Gadopsis marmoratus), southern pygmy perch (Nannoperca australis), Macquarie perch (Macquaria australasica), and mountain galaxias (Galaxias olidus) at treatment sites on some occasions, indicating that these species may be subject to resource constraints in this stream. The magnitude of observed positive fish responses was influenced by the life‐stage of individuals and local stream conditions. Importantly, treatment effects varied through time and were no longer observed after a large flood affected the study stream. Our results show that resource constraints limit local species abundances and demonstrate a novel method of overcoming these constraints in a small, degraded stream. This is a necessary first step but future work is needed to examine whether increases in abundance are due to the provided resources increasing growth rates, survivorship, or reproduction. This work also highlights the importance of understanding species’ life histories, the broader landscape setting, and the disturbance regime when undertaking site scale restoration.

Occupancy modelling confirms the first extirpation of a freshwater fish from one of the world's largest river systems

Abstract Numerous human‐induced changes to freshwater ecosystems are implicated in the loss of biodiversity, including fish extinctions. Dams and weirs have profoundly altered the ecological character of the Murray–Darling Basin (MDB), one of the world's largest river systems, which discharges at the mouth of the River Murray in South Australia. These impacts are evident in the Ramsar‐listed final reaches of the river, where regulation, drought, and flow reductions over recent decades have led to the collapse of freshwater fish populations, including Yarra pygmy perch (Nannoperca obscura), which is Endangered on the International Union for Conservation of Nature Red List of Threatened Species. Nannoperca obscura occurs in several major catchments in south‐eastern Australia, but the genetically unique population in the MDB only inhabits wetlands near the terminus of the River Murray where wild populations were last recorded in 2008 approaching the end of a prolonged drought. This study involved repeated surveys targeting N. obscura to evaluate its occupancy in the MDB while accounting for imperfect detection. The surveys failed to find N. obscura despite regular detection of the closely related southern pygmy perch (Nannoperca australis), which provides a proxy for the congener. This study presents strong evidence that N. obscura is absent in the survey region, thereby inferring the first freshwater fish extirpation from the MDB. The outcomes of this study should prompt responses required to aid the species' population recovery and present a reliable approach to confirm the status of freshwater fishes for conservation management.

The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages.

While the influence of Pleistocene climatic changes on divergence and speciation has been well-documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. We investigated the role of hydrological and coastal topographic changes brought about by Plio-Pleistocene climatic changes on the biogeographic history of a small Australian freshwater fish, the southern pygmy perch Nannoperca australis. Using 7958 ddRAD-seq (double digest restriction-site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to assess the various roles of aridification, sea level and tectonics and associated biogeographic changes across southeast Australia. Sea-level changes since the Pliocene and reduction or disappearance of large waterbodies throughout the Pleistocene were determining factors in strong divergence across the clade, including the initial formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic refugia and fragmentation due to lack of connected waterways maintained the identity and divergence of inter- and intraspecific lineages. Our historical findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change might result in markedly different demographic impacts, both spatially and across different landscape types.

Multi-species monitoring of rare wetland fishes should account for imperfect detection of sampling devices

Accuracy in estimating occupancy of a threatened species is important for conservation but false absences bias many monitoring programs. Imperfect detection is especially relevant to surveys of rare wetland fishes which are often small-bodied and cryptic. Many factors influence probability of detection, including fish size and abundance, habitat characteristics and sampling devices. Imperfect detection can be addressed by accounting for probability of detection when estimating occupancy by modelling detection/non-detection data collected in replicate surveys. Three ecological specialists were once common in habitats associated with Lake Alexandrina at the terminus of the Murray–Darling Basin, Australia. The threatened Murray Hardyhead (Craterocephalus fluviatilis), Southern Pygmy Perch (Nannoperca australis) and Yarra Pygmy Perch (N. obscura) are now rare in the region following population collapses during a prolonged drought, and ongoing monitoring aims to assess their statuses for management purposes. This study compares probability of detection of the rare wetland fishes and cohabiting species during 2 years of multi-species monitoring using contrasting sampling devices (fyke and seine). The findings suggest large variations in estimated probability of detection can occur between devices for Murray Hardyhead and Southern Pygmy Perch. Yarra Pygmy Perch was undetected during the study. Overall, the findings show multi-species monitoring programs using a single sampling device may wrongly estimate the occupancy of a target fish. By accounting for imperfect detection, multi-species monitoring programs will improve inferences regarding population status, recovery and habitat quality of fishes to more accurately inform wetland management.

Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish.

Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in nonmodel species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g., dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an anova-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed that variation in water quality is an important factor influencing expression variation for N.australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.

Forgotten fishes: What is the future for small threatened freshwater fish? Population risk assessment for southern pygmy perch, Nannoperca australis

Abstract Fish species that have no commercial or recreational value are often overlooked in conservation management, despite serious threats to their long‐term future. This can be termed the ‘small threatened freshwater fishes’ paradigm. Population viability analysis (PVA) is a useful technique to assess threatened species and conservation management options. While the development and use of population models and population viability analysis is common in conservation, and often used for larger fishes, this has not been so for small threatened freshwater species. This study uses the PVA process to develop a stochastic population model for Nannoperca australis (southern pygmy perch) in temperate south‐eastern Australia. The model was most sensitive to early life‐history survival rates, for which there were no estimates from field data, compared with other model uncertainty. This study also found that the oldest age class had the highest reproductive value, providing unique support to the value of big, old, fat and fecund fish (BOFFFs) in sustaining natural populations. Modelling indicated that a population in stable habitat supporting about 2000 female adults would likely to be viable, able to withstand some disturbance and possibly be used as a source population for reintroductions. In reality, however, there are few populations in the wild of sufficient size to withstand such take for translocations and hence the production of fish through hatchery means may be required. This type of approach should prove useful for the conservation management of many similar species globally.

Heat and hypoxia give a global invader, Gambusia holbrooki, the edge over a threatened endemic fish on Australian floodplains

Deciphering the mechanisms by which climate change interacts with invasive species to affect biodiversity is a major challenge of global change biology. We conducted experiments to determine whether the global invader, Gambusia holbrooki, was more resistant to high water temperature (heat) and low dissolved oxygen (hypoxia) than a threatened native fish, Nannoperca australis. Metabolic experiments conducted at 25 and 29 °C showed that G. holbrooki had at least four times the capacity for metabolic depression during hypoxia than N. australis. An increase in environmental temperature from 25 to 29 °C had no significant impact on the critical oxygen tension, P crit, of G. holbrooki, but significantly and strongly increased P crit of N. australis. Gambusia holbrooki also had a lower Q 10 of standard metabolic rate than N. australis. Our results indicate that G. holbrooki have physiological traits conferring greater resistance to hypoxia than N. australis, and as temperature increases, the resistance of N. australis to hypoxia was more eroded than that of G. holbrooki. Intensive monitoring of the temperature and dissolved oxygen dynamics of wetlands showed that contemporary heat waves are already causing conditions that might give G. holbrooki the edge over N. australis on Australian floodplains. Our study adds weight to recent anecdotal reports of drought and heat waves causing localised extinction of N. australis, but the proliferation of G. holbrooki.

Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin.

Understanding how natural selection generates and maintains adaptive genetic diversity in heterogeneous environments is key to predicting the evolutionary response of populations to rapid environmental change. Detecting selection in complex spatial environments remains challenging, especially for threatened species where the effects of strong genetic drift may overwhelm signatures of selection. We carried out a basinwide riverscape genomic analysis in the threatened southern pygmy perch (Nannoperca australis), an ecological specialist with low dispersal potential. High-resolution environmental data and 5162 high-quality filtered SNPs were used to clarify spatial population structure and to assess footprints of selection associated with a steep hydroclimatic gradient and with human disturbance across the naturally and anthropogenically fragmented Murray-Darling Basin (Australia). Our approach included FST outlier tests to define neutral loci, and a combination of spatially explicit genotype-environment association analyses to identify candidate adaptive loci while controlling for the effects of landscape structure and shared population history. We found low levels of genetic diversity and strong neutral population structure consistent with expectations based on spatial stream hierarchy and life history. In contrast, variables related to precipitation and temperature appeared as the most important environmental surrogates for putatively adaptive genetic variation at both regional and local scales. Human disturbance also influenced the variation in candidate loci for adaptation, but only at a local scale. Our study contributes to understanding of adaptive evolution along naturally and anthropogenically fragmented ecosystems. It also offers a tangible example of the potential contributions of landscape genomics for informing insitu and ex situ conservation management of biodiversity.

Multi-generational evaluation of genetic diversity and parentage in captive southern pygmy perch (Nannoperca australis)

Maintaining genetic diversity within captive breeding populations is a key challenge for conservation managers. We applied a multi-generational genetic approach to the captive breeding program of an endangered Australian freshwater fish, the southern pygmy perch (Nannoperca australis). During previous work, fish from the lower Murray-Darling Basin were rescued before drought exacerbated by irrigation resulted in local extinction. This endemic lineage of the species was captive-bred in genetically designed groups, and equal numbers of F1 individuals were reintroduced to the wild with the return of favourable habitat. Here, we implemented a contingency plan by continuing the genetic-based captive breeding in the event that a self-sustaining wild population was not established. F1 individuals were available as putative breeders from the subset of groups that produced an excess of fish in the original restoration program. We used microsatellite-based parentage analyses of these F1 fish to form breeding groups that minimized inbreeding. We assessed their subsequent parental contribution to F2 individuals and the maintenance of genetic diversity. We found skewed parental contribution to F2 individuals, yet minimal loss of genetic diversity from their parents. However, the diversity was substantially less than that of the original rescued population. We attribute this to the unavoidable use of F1 individuals from a limited number of the original breeding groups. Alternative genetic sources for supplementation or reintroduction should be assessed to determine their suitability. The genetic fate of the captive-bred population highlights the strong need to integrate DNA-based tools for monitoring and adaptive management of captive breeding programs.

Range-wide fragmentation in a threatened fish associated with post-European settlement modification in the Murray–Darling Basin, Australia

Distinguishing the relative influence of historic (i.e. natural) versus anthropogenic factors in metapopulation structure is an important but often overlooked step in management programs of threatened species. Biotas in freshwater wetlands and floodplains, such as those in the Murray–Darling Basin (MDB)—one of Australia’s most impacted ecosystems, are particularly susceptible to anthropogenic fragmentation. Here we present a comprehensive multilocus assessment of genetic variation in the threatened southern pygmy perch Nannoperca australis (578 individuals; 45 localities; microsatellite, allozyme and mitochondrial DNA datasets), an ecological specialist with low dispersal potential. We assess patterns of spatial structure and genetic diversity in populations spanning the highly fragmented MDB and test whether recent anthropogenic modification has disrupted range-wide connectivity. We detected strong and hierarchical population structure, very low genetic diversity and lack of contemporary gene flow across the MDB. In contrast, the apparent absence of pronounced or long-term phylogeographic structure suggests that observed population divergences generally do not reflect deeply historic natural fragmentation. Coalescent-based analyses supported this inference, revealing that divergence times between populations from the upper and lower MDB fall into the period of European settlement. It appears that the observed contemporary isolation of populations is partly explained by the severe modification of the MDB post-dating the onset of European settlement. Our integrated approach substantially improves the interpretation of how fragmentation impacts present-day biodiversity. It also provides novel contributions for risk-assessing management actions in the context of captive breeding and translocations of small freshwater fishes, a group of increasing global conservation concern.

Susceptibility of a number of Australian freshwater fishes to dwarf gourami iridovirus (Infectious spleen and kidney necrosis virus).

Megalocytiviruses cause high mortality diseases that have seriously impacted aquaculture, with the most frequent outbreaks occurring in East and South-East Asia. The international trade of juvenile fish for food and ornamental aquaculture has aided the spread of these viruses, which have spread to Europe and Australia and other regions. Australian freshwater fishes were examined for susceptibility to infection with the exotic megalocytivirus, dwarf gourami iridovirus (DGIV), which belongs to a group with the type species, Infectious spleen and kidney necrosis virus (ISKNV). Fish were held at 23±1°C and challenged by intraperitoneal (IP) injection or by cohabitation with Murray cod, Maccullochella peelii (Mitchell) infected with DGIV. A species was deemed to be susceptible to DGIV based on evidence of viral replication, as determined by qPCR, and megalocytic inclusion bodies observed histologically. Horizontal transmission occurred between infected Murray cod and golden perch, Macquaria ambigua (Richardson), Macquarie perch, Macquaria australasica (Cuvier) and Murray cod. This indicated that DGIV shed from infected fish held at 23°C can survive in fresh water and subsequently infect these naïve fish. Further, DGIV administered IP was highly pathogenic to golden perch, Macquarie perch and Murray cod. Compared to these species, the susceptibility of southern pygmy perch, Nannoperca australis (Gunther) was lower. Freshwater catfish (dewfish), Tandanus tandanus (Mitchell), were not susceptible under the experimental conditions based on the absence of clinical disease, mortality and virus replication. This study showed the potential risks associated with naïve and DGIV-infected fish sharing a common water source.

A novel holistic framework for genetic‐based captive‐breeding and reintroduction programs

Research in reintroduction biology has provided a greater understanding of the often limited success of species reintroductions and highlighted the need for scientifically rigorous approaches in reintroduction programs. We examined the recent genetic-based captive-breeding and reintroduction literature to showcase the underuse of the genetic data gathered. We devised a framework that takes full advantage of the genetic data through assessment of the genetic makeup of populations before (past component of the framework), during (present component), and after (future component) captive-breeding and reintroduction events to understand their conservation potential and maximize their success. We empirically applied our framework to two small fishes: Yarra pygmy perch (Nannoperca obscura) and southern pygmy perch (Nannoperca australis). Each of these species has a locally adapted and geographically isolated lineage that is endemic to the highly threatened lower Murray-Darling Basin in Australia. These two populations were rescued during Australia's recent decade-long Millennium Drought, when their persistence became entirely dependent on captive-breeding and subsequent reintroduction efforts. Using historical demographic analyses, we found differences and similarities between the species in the genetic impacts of past natural and anthropogenic events that occurred in situ, such as European settlement (past component). Subsequently, successful maintenance of genetic diversity in captivity-despite skewed brooder contribution to offspring-was achieved through carefully managed genetic-based breeding (present component). Finally, genetic monitoring revealed the survival and recruitment of released captive-bred offspring in the wild (future component). Our holistic framework often requires no additional data collection to that typically gathered in genetic-based breeding programs, is applicable to a wide range of species, advances the genetic considerations of reintroduction programs, and is expected to improve with the use of next-generation sequencing technology.

Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations.

Genetic diversity is an essential aspect of species viability, and assessments of neutral genetic diversity are regularly implemented in captive breeding and conservation programs. Despite their importance, information from adaptive markers is rarely included in such programs. A promising marker of significance in fitness and adaptive potential is the major histocompatibility complex (MHC), a key component of the adaptive immune system. Populations of Australian freshwater fishes are generally declining in numbers due to human impacts and the introduction of exotic species, a scenario of particular concern for members of the family Percichthyidae, several of which are listed as nationally vulnerable or endangered, and hence subject to management plans, captive breeding, and restoration plans. We used a next-generation sequencing approach to characterize the MHC IIB locus and provide a conservative description of its levels of diversity in four endangered percichthyids: Gadopsis marmoratus, Macquaria australasica, Nannoperca australis, and Nannoperca obscura. Evidence is presented for a duplicated MHC IIB locus, positively selected sites and recombination of MHC alleles. Relatively moderate levels of diversity were detected in the four species, as well as in different ecotypes within each species. Phylogenetic analyses revealed genus specific clustering of alleles and no allele sharing among species. There were also no shared alleles observed between two ecotypes within G. marmoratus and within M. australasica, which might be indicative of ecologically-driven divergence and/or long divergence times. This represents the first characterization and assessment of MHC diversity for Percichthyidae, and also for Australian freshwater fishes in general, providing key genetic resources for a vertebrate group of increasing conservation concern.

Intraspecific variation in the growth and survival of juvenile fish exposed to Eucalyptus leachate

Whilst changes in freshwater assemblages along gradients of environmental stress have been relatively well studied, we know far less about intraspecific variation to these same stressors. A stressor common in fresh waters worldwide is leachates from terrestrial plants. Leachates alter the physiochemical environment of fresh waters by lowering pH and dissolved oxygen and also releasing toxic compounds such as polyphenols and tannins, all of which can be detrimental to aquatic organisms. We investigated how chronic exposure to Eucalyptus leaf leachate affected the growth and survival of juvenile southern pygmy perch (Nannoperca australis) collected from three populations with different litter inputs, hydrology and observed leachate concentrations. Chronic exposure to elevated leachate levels negatively impacted growth and survival, but the magnitude of these lethal and sublethal responses was conditional on body size and source population. Bigger fish had increased survival at high leachate levels but overall slower growth rates. Body size also varied among populations and fish from the population exposed to the lowest natural leachate concentrations had the highest average stress tolerance. Significant intraspecific variation in both growth and survival caused by Eucalyptus leachate exposure indicates that the magnitude (but not direction) of these stress responses varies across the landscape. This raises the potential for leachate-induced selection to operate at an among-population scale. The importance of body size demonstrates that the timing of leachate exposure during ontogeny is central in determining the magnitude of biological response, with early life stages being most vulnerable. Overall, we demonstrate that Eucalyptus leachates are prevalent and potent selective agents that can trigger important sublethal impacts, beyond those associated with more familiar fish kills, and reiterate that dissolved organic carbon is more than just an energy source in aquatic environments.