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AimAnthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. This issue is likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to a biodiversity hotspot.LocationSouthwest Western Australia (SWWA).TaxaWestern pygmy perch (Nannoperca vittata) and little pygmy perch (Nannoperca pygmaea).MethodsWe sampled 33 individuals from nine populations spanning the range of both study taxa to explore their phylogeographic history. Using a combination of genomic (ddRAD-seq) and environmental approaches, we investigated population divergence and phylogenetic relationships, delimited species and estimated changes in species distributions since the Pliocene.ResultsWe identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability.Main conclusionsOur results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.

Under climate change, species unable to track their niche via range shifts are largely reliant on genetic variation to adapt and persist. Genomic vulnerability predictions are used to identify populations that lack the necessary variation, particularly at climate-relevant genes. However, hybridization as a source of novel adaptive variation is typically ignored in genomic vulnerability studies. We estimated environmental niche models and genomic vulnerability for closely related species of rainbowfish (Melanotaenia spp.) across an elevational gradient in the Australian Wet Tropics. Hybrid populations between a widespread generalist and several narrow range endemic species exhibited reduced vulnerability to projected climates compared to pure narrow endemics. Overlaps between introgressed and adaptive genomic regions were consistent with a signal of adaptive introgression. Our findings highlight the often-underappreciated conservation value of hybrid populations and indicate that adaptive introgression may contribute to evolutionary rescue of species with narrow environmental ranges.

Flathead gobies (genus Glossogobius) include c. 40 small- to medium-sized benthic fishes found primarily in freshwater habitats across the Indo-Pacific, having biodiversity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger-growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of individuals from the waterways of tropical northern Australia. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris, which included a cryptic species. Genetic divergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical biodiversity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.

The rediscovery of presumed extirpated populations provides a second chance opportunity for species and habitat conservation. This study details the redetection of a westerly outlying population of a secretive wetland fish, the Australian Mudfish Neochanna cleaveri, as a positive note in the face of major environmental change. It also documents the basic ecology of the population to inform natural resource management and better understand the needs of similar habitat specialists. Nuclear genetic markers (allozymes) revealed the rediscovered population to be closely related to those in other parts of the range. Targeted sampling in the south east of South Australia indicated a robust population, occupying vegetated ephemeral wetlands and drains across two fragmented and contrasting systems. Movement sampling failed to detect migrating juveniles, which was supported by otolith trace elemental chemistry, that implied a wholly freshwater or at least non-marine lifecycle. Together these data indicate specific conservation management is warranted for a regionally disjunct and independent population and emphasises the importance of both remnant ephemeral wetlands and some artificial habitats for maintaining freshwater biodiversity across heavily altered landscapes.

Aim: Despite the influence of sea-level changes on biogeographic/phylogeographic patterns in freshwater ecosystems being well documented, studies that explicitly link the influence of sea-level change with speciation are rare. We aim to test the hypothesis that sea-level changes during the Pliocene and Pleistocene have driven speciation in north-western Australia's (NWA’s) largest freshwater fish family, Terapontidae, building upon a body of evolutionary literature focussed on the family. Location: North-western Australian rivers including those draining the Kimberley Plateau. Taxon: Grunters (Family: Terapontidae, Genera: Hannia, Hephaestus, Leiopotherapon, Syncomistes). Methods: A GIS was used to reconstruct palaeodrainages during lowered sea levels and to delineate regions of high connectivity during low and high (current) sea-level conditions. For seven species, the degree of phylogenetic divergence among river basins in different regions was evaluated using a maximum likelihood phylogeny and analyses of the proportion of genetic divergence expressed with 601 base pairs of the mtDNA cytochrome b (cytb) gene. Results: A low proportion of cytb haplotypes were shared among catchments not connected by the same receiving waters (e.g. estuaries) under current (high) sea levels, indicating that contemporary dispersal is limited over fine spatial scales. Deeper phylogeographic patterns were largely congruent with reconstructed low sea-level (LSL) drainage arrangements indicating that historic among-catchment connectivity was far more widespread under LSL conditions. Main Conclusions: The NWA landscape represents a geographic template that has shaped patterns of broad dispersal under low sea levels, and fine-scale isolation under high sea levels. The weight of evidence from recent literature on species boundaries and evolutionary patterns within the terapontids suggests that most NWA species were derived rapidly and recently from a series of spatio-temporal vicariant events caused by such sea-level fluctuations during the late Pliocene and Pleistocene. Together, the findings provide a rare, comprehensively tested example of sea-level change driving speciation in the tropics.

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.Monitoreo Longitudinal de la Diversidad Genómica Neutral y Adaptativa en una Reintroducción Marshall et al. 21-643 Resumen Los programas de restauración a manera de reproducción ex situ combinada con reintroducciones se están volviendo críticos para contrarrestar las declinaciones demográficas y la pérdida de especies. Dichos programas usan cada vez más la gestión genética para mejorar los resultados de conservación. Sin embargo, la falta de monitoreo a largo plazo de los indicadores genéticos posteriores a la reintroducción evita que se realicen evaluaciones de la trayectoria y la persistencia de las poblaciones reintroducidas. Se rescató un pez de talla pequeña (percha pigmea del sur [Nannoperca australis]) previo a su extirpación de los lagos terminales de la Cuenca Murray-Darling en Australia para después reproducirlo en cautiverio con información genética y reintroducirlo. Realizamos monitoreos anuales o bianuales de la abundancia, aptitud y ocupación en vida silvestre durante once años, además de un muestreo genético posterior a la reintroducción. Analizamos los datos genómicos de los grupos originales rescatados, los nacidos en cautiverio y los reintroducidos. Nuestro objetivo era evaluar los efectos genómicos a largo plazo de la reproducción en cautiverio y la reintroducción de esta especie. Esto reveló baja endogamia y el sólido mantenimiento de la diversidad genómica neutral y adaptativa durante varias generaciones. Encontramos una coherencia entre la tendencia creciente en el tamaño de la población efectiva de la población reintroducida y los datos de campo que demostraron el restablecimiento exitoso de la especie. Nuestro estudio proporciona un raro ejemplo empírico de cómo el potencial adaptativo de una población localmente extinta puede mantenerse durante la reproducción de conservación ex situ genéticamente informada y su reintroducción. Las estrategias para mejorar la restauración de la biodiversidad por medio de la conservación ex situ deberían incluir la reproducción en cautiverio basada en la genética y el monitoreo longitudinal de la variación genómica actual de las poblaciones reintroducidas.

Understanding 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. We used environmental and genomic datasets to reconstruct the phylogeographic histories of two ecologically similar and largely co-distributed freshwater fishes to assess the degree of concordance in their responses to Plio-Pleistocene climatic changes. Although several co-occurring populations 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 population declines and extinctions of the two species. Our 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.

Biological invasions are a prominent example of human-induced environmental change that pose a significant threat to worldwide biodiversity. Recent evidence suggests that behavioural traits play a key role in mediating invasion success. However, little research has investigated how rapidly behavioural traits can change during the initial stages of invasion. We investigated the influence of invasion on behaviour in a recent aquatic invader, the Siamese fighting fish (Betta splendens), in northern Australia. These fish represent a recent introduction (ca. 2010) and are thought to be descended from ornamental varieties released into the wild from the aquarium trade. Using fish reared under captive conditions, we measured differences in three ecologically relevant behaviours (activity, foraging, and aggression) across invasive and domestic fighting fish. We found that fish descended from the recent invasive population were more active and consumed fewer food items than their domestic counterparts. Furthermore, foraging latency was repeatable in invasive, but not domestic fish, and this seemed to be driven by an increase in among-individual variation in the invasive population. Finally, while we detected a positive relationship between activity and number of food items eaten in domestic fish, this relationship was absent in the invasive population, suggesting that invasion may have disrupted this behavioural syndrome. Our results highlight that invasion can alter ecologically important behavioural traits and behavioural syndromes, even during the initial stages of invasion, and emphasise the importance of incorporating behaviour into our understanding of invasion biology. Alien species must rapidly adapt to novel environmental conditions in order to establish a successful invasive population. As behaviour mediates how organisms interact with their environment, behavioural traits may play a key role in facilitating invasion success. We investigated rapid changes in behavioural traits in a recently introduced (ca. 2010) ornamental fish, the Siamese fighting fish. We found that invasive fish differed from their domestic source population in two key behavioural traits—activity and foraging behaviour. Furthermore, we extend previous work by showing that invasion not only causes changes in average-level behavioural traits but can also result in changing patterns of behavioural variation and repeatability in newly established populations. Overall, our findings highlight that invasion can induce shifts in ecologically relevant behaviours, even during the early, crucial stages of invasion.

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. Here, we investigate 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 perchNannoperca australis. Using 7,958 ddRAD-seq (double digest restriction-site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to investigate the relative roles of aridification, sea level and tectonics and their 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.

Siamese Fighting Fish Betta splendens is a well-known and popular aquarium fish. The species has recently invaded the Adelaide River floodplain, near Darwin in northern Australia. A very large and extensive population has persisted over consecutive years, with potential for further spread. This represents the first serious alien fish species incursion in the Northern Territory, with reports previously limited mainly to livebearers and cichlids in isolated habitats, some of which have been controlled by specific actions reviewed herein. The invasion highlights the need to maintain and strengthen proactive management, community engagement, and coordinated strategies for vectors of introduction including aquarium fishes.

Two species that had previously been referred to as Glossogobius giuris from Australia are redescribed and tentatively treated as Glossogobius giuris and Glossogobius laticeps. The two species are largely allopatric in Australia with G. laticeps found on the east coast of Queensland and some rivers of the Northern Territory, while G. giuris is distributed from the Northern Territory to rivers of the west coast of Western Australia. The two species are known to be genetically distinct and with some differences in colour patterns. Morphological features separating the species are minor and there is considerable overlap in many of the characters separating them. High variation in the Hammersley Ranges and Kimberley region of Western Australia further complicates separation of the species. The status of the Glossogobius giuris group from India is discussed as a key area to resolving an overall “giuris” species complex. Information is provided on the current identity of a number of species that had previously been considered synonyms of Glossogobius giuris. Extant types and difficulties assigning the types of known species are also discussed. A key is provided to aid identification of Australian species of Glossogobius.

Tropical sardines (Family Clupeidae) are an important component of many marine fisheries in the Indo-West Pacific region. In Timor-Leste, a small, less-developed country within this region,‘sardiña’are some of the more commonly caught and consumed fish. Yet there is little published information from Timor-Leste about the species composition of these fisheries, nor their biology or ecology. We document the knowledge of Timorese fishers on nine locally distinguished sardine types that contribute to fisheries, and relate these to at least nine species: four species of ‘Flat-bodied Sardinellas’ (Sardinellasubg.Clupeoniaspp.), one species of ‘Round-bodied Sardinella’ (Sardinellasubg.Sardinella lemuru), two species of ‘Tropical Pilchards’ (Amblygasterspp.) and a ‘Tropical Herring’ species (Herklotsichthys quadrimaculatus), all from the Clupeidae family; and oneDussumieriaspecies from the Dussumieriidae family. We record variations in local sardine names across the country and document aspects of fishers’ knowledge relevant to understanding and managing the fisheries, including local sardine species’ seasonality, habitat, movements, interannual variation, as well as post-harvest characteristics in relation to perishability. In general, local names relate more closely with groups of species than individual species, although some names also distinguish fish size within species-groups. The local knowledge identified in this study has immediate application to inform fisheries monitoring and management, and to identify areas for future research. Notably, Timorese fishers recognize and make use of the strong association between some sardine species-groups and seasonally turbid river plumes. While further research is required to understand the underlying mechanisms of this association, this emphasizes the need to consider coastal fisheries and fisher livelihood impacts when assessing any plans or proposals that may alter river flow or water quality. Fishers also recognize migratory behavior of some sardine species, in particular the Flat bodied Sardinellas (S. gibbosaand others) along the north-west coast of Timor-Leste and across the border into Indonesian West Timor. Such insights complicate and need to be accounted for in initiatives for co-management or community-based management of Timor-Leste’s coastal waters and their fisheries.

A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here, we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (1) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles and to hold aside individuals involved in contemporary admixture for independent consideration; (2) apply phylogenetic techniques to identify lineages; (3) assess diagnosability of those lineages as potential candidate species; (4) interpret the diagnosable lineages in a geographical context (sympatry, parapatry, allopatry); (5) assess significance of difference or trends in the context of sampling intensity; and (6) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We adopt this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not discussed explicitly in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.

Snubnose gobies (genus Pseudogobius: Gobionellinae) are ubiquitous to, and important components of, estuarine ecosystems of the Indo-west Pacific. These small benthic fishes occur in freshwater, brackish and marine habitats such as mangroves, sheltered tide pools and lowland streams, and represent a model group for understanding the biodiversity and biogeography of estuarine fauna. To develop the species-level framework required for a concurrent morphological taxonomic appraisal, we undertook thorough sampling around the extensive Australian coastline, referenced to international locations, as part of a molecular systematic review using both nuclear and mitochondrial markers. The results indicate that while there are currently eight recognised species, the true diversity is close to double this, with a hotspot of endemism located in Australia. Complicated patterns were observed in southern Australia owing to two differing zones of introgression/admixture. Key drivers of diversity in the group appear to include plate tectonics, latitude, and historic barriers under glacial maxima, where an interplay between ready dispersal and habitat specialisation has led to regional panmixia but frequent geographic compartmentalisation within past and present landscapes. The findings have significant implications for biodiversity conservation, coastal and estuarine development, the basic foundations of field ecology, and for applied use such as in biomonitoring.

The prevalence of unrecognised cryptic species impairs biodiversity estimates, clouds biological research and hinders conservation planning. As the rate of cryptic species detection increases globally, research is needed to determine how frequent cryptic species are, whether they are more common in given management regions, and whether these patterns are consistent across taxonomic groups. The Kimberley region in remote northwestern Australia harbours some of the most speciose, and morphologically and functionally diverse, endemic animal and plant communities on the continent. The rugged and changeable landscape also appears to contain a large proportion of cryptic terrestrial species, raising the question of whether similar patterns are also found among aquatic taxa, which have yet to be studied using integrative systematic approaches. If true, then the actual levels of aquatic biodiversity are yet to be fully realised. Here we conducted a molecular assessment of where species boundaries may exist in the Kimberley regions' most speciose freshwater fish family, the Terapontidae (grunters), with a combined morphological assessment of the regions' most speciose terapontid genus, Syncomistes. Assessment of nuclear markers (54 allozyme loci), sequence data (mitochondrial cytochrome b (cytb); nuclear recombination activation gene one (RAG1)) and 31 meristic and 36 morphometric characters provides evidence for 13 new candidate species across three different genera. Many of these candidate species are narrow range endemics. Our findings raise several questions about the evolutionary origin of the Kimberley's endemic fish fauna and highlight the likelihood that freshwater fish species diversity in the Kimberley is severely under-represented by current systematic frameworks, with significant implications for ecological research, conservation and management.

Biotic and abiotic forces govern the evolution of trophic niches, which profoundly impact ecological and evolutionary processes and aspects of species biology. Herbivory is a particularly interesting trophic niche because there are theorized trade-offs associated with diets comprised of low quality food that might prevent the evolution of herbivory in certain environments. Herbivory has also been identified as a potential evolutionary "dead-end" that hinders subsequent trophic diversification. For this study we investigated trophic niche evolution in Clupeoidei (anchovies, sardines, herrings, and their relatives) and tested the hypotheses that herbivory is negatively correlated with salinity and latitude using a novel, time-calibrated molecular phylogeny, trophic guilds delimited using diet data and cluster analysis, and standard and phylogenetically-informed statistical methods. We identified eight clupeoid trophic guilds: molluscivore, terrestrial invertivore, phytoplanktivore, macroalgivore, detritivore, piscivore, crustacivore, and zooplanktivore. Standard statistical methods found a significant negative correlation between latitude and the proportion of herbivorous clupeoids (herbivorous clupeoid species/total clupeoid species), but no significant difference in the proportion of herbivorous clupeoids between freshwater and marine environments. Phylogenetic least squares regression did not identify significant negative correlations between latitude and herbivory or salinity and herbivory. In clupeoids there were five evolutionary transitions from non-herbivore to herbivore guilds and no transitions from herbivore to non-herbivore guilds. There were no transitions to zooplanktivore, the most common guild, but it gave rise to all trophic guilds, except algivore, at least once. Transitions to herbivory comprised a significantly greater proportion of diet transitions in tropical and subtropical (35°) relative to temperate areas (35°). Our findings suggest cold temperatures may constrain the evolution of herbivory and that herbivory might act as an evolutionary "dead-end" that hinders subsequent trophic diversification, while zooplanktivory acts as an evolutionary "cradle" that facilitates trophic diversification.

Aim Changing preferences regarding which species humans have transported to new regions can have major consequences for the potential distribution of alien taxa, but the mechanisms shaping these patterns are poorly understood. We assessed the extent to which changes in human preferences for transporting and introducing alien freshwater fishes have altered their biogeography. Location Australia. Methods We compiled an up‐to‐date database of alien freshwater fishes established in drainages in Australia before and after the number of established alien fish species doubled (pre‐1970 and post‐1970, respectively). Using metacommunity models, we analysed the influence of species traits and drainage features on the distribution of alien fishes that established pre‐ and post‐1970. Results Alien fishes in Australia were introduced via four main transport pathways: acclimatization, aquaculture, biocontrol and ornamental trade. The relative importance of each pathway changed substantially between the two periods, accompanied by changes in the distribution of alien fishes and the variables predicting their distribution. Pre‐1970, most species (64%) were introduced by acclimatization societies for purposes such as angling and biocontrol, and these fish have established in inland drainages more heavily impacted by human activities. In contrast, most of the post‐1970 introductions (69%) were ornamental fishes, with most species established in small, north‐eastern, tropical and subtropical coastal drainages. Main conclusions Substantial changes in introduction preferences and transport pathways over time have altered both the patterns and underlying processes shaping the biogeography of alien fishes in Australia. Our findings highlight the need for caution when using historical data to infer potential future distributions of alien species. The continuing spread of alien species means traditional biogeographical units may no longer be identifiable in the foreseeable future.

The bacterium Edwardsiella ictaluri is considered to be one of the most significant pathogens of farmed catfish in the United States of America and has also caused mortalities in farmed and wild fishes in many other parts of the world. E. ictaluri is not believed to be present in wild fish populations in Australia, although it has previously been detected in imported ornamental fishes held in quarantine facilities. In an attempt to confirm freedom from the bacterium in Australian native fishes, we undertook a risk-based survey of wild catfishes from 15 sites across northern Australia. E. ictaluri was detected by selective culturing, followed by DNA testing, in Wet Tropics tandan (Tandanus tropicanus) from the Tully River, at a prevalence of 0.40 (95% CI 0.21-0.61). The bacterium was not found in fishes sampled from any of the other 14 sites. This is the first report of E. ictaluri in wild fishes in Australia.

Regulation has profoundly altered the ecological character of many rivers in the world, with pronounced effects in dryland systems subject to competing demand for water between the environment and ...

The diets and trophic guilds of small fishes were examined along marine sandy beaches and in estuaries at depths

The ‘maccullochi species group’ of rainbowfishes are small and distinctly patterned freshwater fishes of streams and swamps, comprising around eight species. The species from which the group bears its name, Melanotaenia maccullochi Ogilby, 1915, has been thought to comprise three forms occurring in distinct geographic areas, and recent mitochondrial genetic data provides matching patterns of likely inter-specific divergence. Here we undertake a detailed investigation of the taxonomic status of M. maccullochi using a combined lines of evidence approach incorporating multiple nuclear genetic markers (55 allozyme loci), mitochondrial DNA sequence data (1141 bp cytochrome b) and morphology (examination of a suite of 38 morphometric and meristic characters). As all three datasets provide support for a three-way split, we accordingly describe two new species and redescribe M. maccullochi sensu stricto. McCulloch’s Rainbowfish M. maccullochi, a species with brown body stripes and red fins occurs in northeast Queensland and is redescribed based on 338 specimens, 13.1–53.0 mm SL. This species was one of the first rainbowfishes to become known in the aquarium hobby. A second form with darker stripes on a contrasting light white-grey body and with distinct sub-marginal black bands in the dorsal and anal fins, distributed across northern and eastern Cape York Peninsula, Torres Strait and southern central New Guinea, is described as Sahul Rainbowfish M. sahulensis sp. nov. based on 267 specimens, 13.4–48.4 mm SL. A diminutive and well geographically isolated form occurring below the escarpment of the Tabletop Range in Litchfield National Park, Northern Territory possessing a more prominent and purplish mid-lateral stripe, is described as the Little Rainbowfish Melanotaenia wilsoni sp. nov. based on 50 specimens, 19.3–33.3 mm SL. A combination of morphological characters is useful for separating the respective taxa with M. wilsoni sp. nov. the most distinctive, typically having fewer vertebrae, lateral scales, cheek scales, procurrent caudal rays and anal rays and proportionally a shorter maxilla and snout than either of the other two species. Useful characters for further separating M. sahulensis sp. nov. from M. maccullochi include slightly higher counts of vertebrae, lateral scales and anal rays and proportionally greater body depth, body width and pre-dorsal distance. Information on the known distribution, habitats and conservation status of the three species is summarised, with the Northern Territory species being a narrow-range endemic with specific environmental requirements.

Although hybridization between non-sibling species rarely results in viable or fertile offspring, it occasionally produces self-perpetuating or sexually-parasitic lineages in which ancestral genomes are inherited clonally and thus may persist as ‘ghost species’ after ancestor extinction. Ghost species have been detected in animals and plants, for polyploid and diploid organisms, and across clonal, semi-clonal, and even sexual reproductive modes. Here we use a detailed investigation of the evolutionary and taxonomic status of a newly-discovered, putative ghost lineage (HX) in the fish genus Hypseleotris to provide perspectives on several important issues not previously explored by other studies on ghost species, but relevant to ongoing discussions about their detection, conservation, and artificial re-creation. Our comprehensive genetic (allozymes, mtDNA) and genomic (SNPs) datasets successfully identified a threatened sexual population of HX in one tiny portion of the extensive distribution displayed by two hemi-clonal HX-containing lineages. We also discuss what confidence should be placed on any assertion that an ancestral species is actually extinct, and how to assess whether any putative sexual ancestor represents a pure remnant, as shown here, or a naturally-occurring resurrection via the crossing of compatible clones or hemi-clones.

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.

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.

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.

Genetic variation plays a pivotal role in species viability and the maintenance of population genetic variation is a main focus of conservation biology. Threatened species often show reduced genetic variation compared to non-threatened species, and this is considered indicative of lowered evolutionary potential, compromised reproductive fitness, and elevated extinction risk. The southern purple-spotted gudgeon, Mogurnda adspersa, is a small freshwater fish with poor dispersal potential that was once common throughout the Murray–Darling Basin (MDB) and along the central east coast of Australia. Its numbers and distribution have shrunk dramatically in the MDB due to flow alteration, degradation of habitat, decreasing water quality, and introduction of alien species. We used microsatellite DNA markers to assess population structure and genetic variation at both large (i.e. across basin) and fine (i.e. within river catchments) spatial scales using a substantial sampling effort across the species range (n = 579 individuals; 35 localities). The results consistently indicated very low levels of genetic variation throughout, including along the east coast where the species is relatively common. At the broader scale, three highly differentiated groups of populations were found, concordant with previously reported genealogical distinctiveness. Hence we propose each group as a distinct Evolutionarily Significant Unit. We also inferred a minimum of 12 management units in M. adspersa, with no appreciable gene flow between them. Our study discloses findings relevant for both long- and short-term management, as it informs on the geographic context in which conservation priorities should be defined and specifies biological units for population monitoring and translocations.

The complete mitochondrial genomes of four fish species of the commercially important family Latidae were sequenced using the Illumina MiSeq, thereby significantly increasing the mitogenomic resources for the family. Whole mitogenome-based phylogenetic analysis supports the monophyly of the genus Lates and more generally the family Latidae. The mitogenome sequences from this study will be useful for future assessments of the diversity within and between Lates species and studies of phylogenetic relationships within the diverse and taxonomically challenging perciform fishes.

Globally, freshwater fishes are declining at an alarming rate. Despite much evidence of catastrophic declines, few Australian species are listed as threatened under national legislation. We aim to help redress this by identifying the Australian freshwater fishes that are in the most immediate risk of extinction. For 22 freshwater fishes (identified as highly threatened by experts), we used structured expert elicitation to estimate the probability of extinction in the next ~20 years, and to identify key threats and priority management needs. All but one of the 22 species are small (50% probability of extinction in the next ~20 years. Collectively, the biggest factor contributing to the likelihood of extinction of the freshwater fishes considered is that they occur in small (distributions ≤44km2), geographically isolated populations, and are threatened by a mix of processes (particularly alien fishes and climate change). Nineteen of these species are unlisted on national legislation, so legislative drivers for recovery actions are largely absent. Research has provided strong direction on how to manage ~35% of known threats to the species considered, and, of these, ~36% of threats have some management underway (although virtually none are at the stage where intervention is no longer required). Increased resourcing, management intervention and social attitudinal change is urgently needed to avert the impending extinction of Australia’s most imperilled freshwater fishes.

The freshwater melanotaeniid genus Cairnsichthys is endemic to a relatively small area of specialised habitat within the Wet Tropics bioregion of north-eastern Queensland, Australia. It was previously considered as monotypic, including only a single species, C. rhombosomoides (Nichols & Raven, 1928). The recent discovery of an apparently-isolated population in the Daintree rainforest, approximately 120 km north of the known range extent, prompted a detailed investigation of its taxonomic status using a combined lines of evidence approach. We provide compelling evidence from multiple nuclear genetic markers (52 allozyme loci), mitochondrial DNA sequence data (1141 bp cytochrome b) and morphology (examination of a suite of 38 morphometric and meristic characters) that supports north-south splitting of C. rhombosomoides. Accordingly, we describe the northern population as a distinct species, C. bitaeniatus sp. nov., on the basis of 25 specimens, 34.7–65.6 mm SL. The new species differs morphologically primarily by having a more slender and narrow shape, featuring a flatter, straighter predorsal profile and shorter second dorsal fin base; possession of slightly smaller scales, reflected in higher counts of lateral scales and predorsal scales; typically more vertebrae; and colour differences including a more robust, short black stripe across the upper operculum, a pronounced yellow patch on the anteroventral body and usually a more conspicuous second dark stripe on the lower body, with adult males generally having yellowish compared to reddish fins. We also provide a generic diagnosis for Cairnsichthys and a redescription of C. rhombosomoides. Information on the known distribution, habitats and conservation status of species in the genus is summarised, the new species being of particular concern as a narrow range endemic with specific environmental requirements.

Background Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes that warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics. Results We generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads, representing approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 and 967 Mbp. The final assembled genome is contained in 6404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared with the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with an 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27 240 high-quality protein-coding genes were predicted from the clown anemonefish, 26 211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches. Conclusions We present the first genome of any anemonefish and demonstrate the value of low coverage (∼11×) long Nanopore read sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic, and phylogenetic studies specifically for clownfish and more generally for other related fish species of the family Pomacentridae.

There are high rates of regional and global extinctions among freshwater species and few chances for recovery. We report here on the rediscovery after 30. years of a small fish, the southern-purple spotted gudgeon (Mogurnda adspersa), once widespread in the southern Murray-Darling Basin of south-eastern Australia. The rediscovery was in a region, the Lower Murray, where temperate riverine and wetland habitats are modified by a broad spectrum of changes including intensive flow regulation and diversions. There was some doubt whether the rediscovered population was a true remnant or a recent introduction, particularly as there was a translocated population in a nearby artificial habitat. Fortunately, a non-government organisation acted to rescue into captivity about 50 specimens as the remaining wetland habitat dried completely, soon after rediscovery, as a consequence of a decade-long drought and water diversions. We describe the habitat and ecology of fish in the rediscovery site, and provide genetic data, both nuclear (50 allozyme loci) and mtDNA (1141 base pairs; two genes), to show that they were true remnants of the regional native population. This information allows clear planning for future recovery including reintroductions, and is a case study that provides strategies, and hope, for conservation and management concerning other modified habitats. Specifically, it highlights the need for a rapid response to conserve threatened species, the recognition of remnant natural values in altered environments, and the treatment of new finds as native until there is alternate evidence.

The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is presented consisting of 42,110 scaffolds with a total size of 708 Mb (2.85% gaps) representing 93.95% of core eukaryotic genes. Using a k-mer-based method, a genome size of 900 Mb was also estimated. We present an update on the phylogenomics of fishes based on a total of 27 species (23 fish species and 4 tetrapods) using 177 orthologous proteins (71,360 amino acid sites), which supports established relationships except that arowana is placed as the sister lineage to all teleost clades (Bayesian posterior probability 1.00, bootstrap replicate 93%), that evolved after the teleost genome duplication event rather than the eels (Elopomorpha). Evolutionary rates are highly heterogeneous across the tree with fishes represented by both slowly and rapidly evolving lineages. A total of 94 putative pigment genes were identified, providing the impetus for development of molecular markers associated with the spectacular colored phenotypes found within this species.

Northern Australia is biologically diverse and of national and global conservation signicance. Its ancient landscape contains the world’s largest area of savannah ecosystem in good ecological condition and its rivers are largely free-flowing. Agriculture, previously confined largely to open range-land grazing, is set to expand in extent and to focus much more on irrigated cropping and horticulture. Demands on the water resources of the region are thus, inevitably increasing. Reliable information is required to guide and inform development and help plan for a sustainable future for the region which includes healthy rivers that contain diverse fish assemblages. Based on a range of information sources, including the outcomes of recent and extensive new field surveys, this study maps the distribution of the 111 freshwater fishes (excluding elasmobranches) and 42 estuarine vagrants recorded from freshwater habitats of the region. We classify the habitat use and migratory biology of each species. This study provides a comprehensive assessment of the diversity and distribution of fishes of the region within a standardised nomenclatural framework. In addition, we summarise the outcomes of recent phylogeographic and phylogenetic research using molecular technologies to identify where issues of taxonomy may need further scrutiny. The study provides an informed basis for further research on the spatial arrangement of biodiversity and its relationship to environmental factors (e.g. hydrology), conservation planning and phylogentic variation within individual taxa.

The threatened Yarra pygmy perch (Nannoperca obscura) is an obligate freshwater fish endemic to the south-eastern coast of mainland Australia, where a majority of river systems have been heavily modified since European settlement. The purpose of this garden study was to explore any relationship between the growth rate of juvenile N. obscura with respect to salinity. Trials were conducted encompassing perceived and potential ranges within the species’ environment, through five salinity treatments and recorded growth after 8 weeks. Two brood-groups were trialed simultaneously to observe any intrapopulation variance in phenotypic response potentially linked to genetic variance. The salinity trials found a clear model indicating increasing growth for moderate salinities (i.e. 2.5–7.5 ppt), therefore identifying the ideal salinity range for N. obscura juveniles. Phenotypic response between brood-groups was varied and inconsistent, potentially reflecting low genetic variability. With a limited genetic variance restricting adaptability, tolerance to a changing environment would be reduced. Therefore increased salinization and subsequent flushing events within habitats may be key threats to the species’ survival.

Many species of freshwater crayfish of the endemic Australian genus Euastacus are threatened with extinction. Routine monitoring of most Euastacus species is minimal, and a subsequent lack of information has hampered prioritization of conservation and management efforts. The present study investigated population parameters and temporal changes in abundance in a disjunct population of Euastacus bispinosus. This occurs at the western extent of the range of the species in the state of South Australia (SA) and inhabits a groundwater-dependent karst habitat distinct from the larger population in the Victorian Glenelg basin. Euastacus bispinosus was recorded at sites within seven karst rising-springs as well as two isolated locations (sinkhole and cave), which expanded the extent of occurrence of the species in SA, but the area of occupancy remains limited. Most subpopulations contained low numbers, had little or no signs of recruitment, were dominated by large crayfish, and demonstrated a high incidence of gonopore aberrations. Declines in abundance were observed across these subpopulations between 2006 and 2011, although these declines were not statistically significant. Of critical importance to the conservation of the species in SA is ensuring that groundwater discharge is maintained in karst rising-springs, hydrological connectivity is enhanced between subpopulations and degradation within habitats is reversed. Further monitoring and research is necessary to gain a clear understanding of the status of subpopulations of the species over time. Copyright © 2014 John Wiley & Sons, Ltd.

Summary The Native Fish Strategy (NFS) for Australia’s Murray-Darling Basin was specifically targeted at managing and rehabilitating an entire fish community. Over half of the native fishes (24 of 44 known species) and four fish communities of the Murray-Darling Basin (MDB) are listed as threatened at either national or state level. One of six ‘Driving Actions’ under the NFS focused on protecting threatened native fish species, and this study reviews a series of NFS case studies during and immediately after the Millennium Drought (1997–2010) which was south-eastern Australia’s worst drought on record. Fish rescues, breeding programmes, the creation of an emergency response contingency fund, and expert panels and workshops were all projects that contributed significantly to conserving threatened fishes. The diversity of approaches taken and lessons learned are highlighted, to formulate future directions for threatened fish recovery.

Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species-level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south-eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range-wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 521–540.

Next generation sequencing was used to develop 15 new polymorphic microsatellite markers for the commercially and recreationally important fish mulloway (Argyrosomus japonicus). Improved knowledge of the genetic structure of the species is necessary for fisheries and environmental management. In a population of mulloway, we found that genetic variation and heterozygosity were high in most of our loci (mean number of alleles per locus = 9.46; mean heterozygosity = 0.660). To test the usefulness of our new markers for genetic research on other sciaenids, we cross amplified samples from eight other related sciaenid species, including three that form important fisheries and others that have significant conservation issues. We found that most of our new primers pairs produced scorable profiles in each of the other important sciaenids.

Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South-eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of river coalescence during low sea levels. Our specific hypothesis is that the degree of phylogeographic divergence between coastal river basins should correspond to the continental shelf width of each region. This predicts that genetic divergences between river basins should be lowest in regions with a wider continental shelf and that regions with similar continental shelf width should have similar genetic divergences. Pygmy perches (Nannoperca australis and Nannoperca 'flindersi') in south-eastern Australia provide an ideal opportunity to test these biogeographic hypotheses. Phylogeographic patterns were examined based on range-wide sampling of 82 populations for cytochrome b and 23 polymorphic allozyme loci. Our results recovered only limited support for our continental shelf width hypothesis, although patterns within Bass clade were largely congruent with reconstructed low sea-level drainage patterns. In addition, we identified several instances of drainage divide crossings, typically associated with low elevational differences. Our results demonstrate high levels of genetic heterogeneity with important conservation implications, especially for declining populations in the Murray-Darling Basin and a highly restricted disjunct population in Ansons River, Tasmania.

Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray-Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity-a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.