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Cryptic mortality in fisheries relates to the unobserved or unrecorded mortality in a target ecosystem and is an important aspect of harvest management for fishery managers. Depredation is a key, observable form of cryptic mortality that relates to predators consuming a targeted species being caught within a fishing industry. This is of particular interest to the Queensland spanner crab fishing industry, where additional unobserved or unrecorded mortality through depredation of catch could be restricting current efforts to rebuild the population. High-resolution cameras were deployed on 178 baited tangle-nets (dillies) to investigate cryptic mortality, species interactions, and depredation within the spanner crab Ranina ranina fishery in Queensland, Australia. Physical parameters including current speed, temperature, depth, and time of soak were recorded. Depredation events were observed in the fishery by two species of endangered batoid species, the bowmouth guitarfish Rhina ancylostoma and wedgefish Rhynchobatus spp. However, rates of depredation in the fishery were low, with only 3.82% of crabs depredated. Fishing losses were calculated by comparing the total crabs on retrieval of a dilly, against total crabs observed while still soaking (MaxN) and at the beginning of retrieval. Overall, there was a loss of 37% in potentially harvested crabs through a combination of cryptic mortality and inefficient fishing practices. However, 27% of the losses could be reduced through shorter deployment times. We identified a significant correlation between the rate of depredation and current speed (∼0.6–0.8 knots), soak time and depth (<35 m). We also report spanner crab shell damage caused by mantis shrimp interactions, that likely contribute to an increase in spanner crabs discards due to unmarketable product. By identifying the species and drivers involved in spanner crab depredation, this study provides insights into ways that depredation events can be mitigated and managed

Shark depredation is a complex social-ecological issue that affects a range of fisheries worldwide. Increasing concern about the impacts of shark depredation, and how it intersects with the broader context of fisheries management, has driven recent research in this area, especially in Australia and the United States. This review synthesises these recent advances and provides strategic guidance for researchers aiming to characterise the occurrence of depredation, identify the shark species responsible, and test deterrent and management approaches to reduce its impacts. Specifically, the review covers the application of social science approaches, as well as advances in video camera and genetic methods for identifying depredating species. The practicalities and considerations for testing magnetic, electrical, and acoustic deterrent devices are discussed in light of recent research. Key concepts for the management of shark depredation are reviewed, with recommendations made to guide future research and policy development. Specific management responses to address shark depredation are lacking, and this review emphasizes that a “silver bullet” approach for mitigating depredation does not yet exist. Rather, future efforts to manage shark depredation must rely on a diverse range of integrated approaches involving those in the fishery (fishers, scientists and fishery managers), social scientists, educators, and other stakeholders.

Context: In Australia, the health of our marine, estuarine and freshwater fishes are of critical importance. The aquatic and marine ecosystems, and the fishes that occupy them each have an important role in our country’s ecological, economic, cultural and social wealth. Climate change, resource over-exploitation, invasive animals and diseases, and habitat degradation are just a few of the burgeoning threats that researchers and managers must address to ensure the prosperity of Australia’s natural fisheries resources. In addition, differences in legislative frameworks among jurisdictions hinder our ability to coherently manage fish resources at scales that are relevant biologically, ecologically and socially.Aims: Here, we identify the key research priorities for fish and fisheries research in Australia, across seven thematic fields of study.Methods: Research priorities were evaluated using a horizon scanning approach which identified research questions related to the field of fish and fisheries research in Australia.Key results: A total of 284 unique research questions were categorised and prioritised, resulting in the formation of the top 10 highest priority research questions across each of the seven themes.Conclusions: The outcomes from this work can be used to directly complement ongoing work from research providers working in the field of fish and fisheries as well as the development of new areas of research.Implications: The priorities identified will enable researchers and policy makers to identify critical knowledge gaps, develop collaborative research programs, investigate novel approaches, and to improve transparency around decision-making processes.

Solutions occurring within complex systems such as recovery of species are urgently needed. One path forward involves action agendas that extend across the full range of stakeholder groups. Approaches that can foster cooperative behavior across a range of vested interests can create environments supporting species recovery. This paper reports the stakeholder identification process used to gather divergent opinions. A total of 923 priorities from 239 stakeholders were identified. Consensus approaches were utilized, resulting in 25 top priorities, selected by 61 stakeholders. This study demonstrates how consensus areas for action can be illuminated and supported by diverse stakeholder groups whose relationships have previously been indicated as antagonistic. Results indicate support for a range of actions that can be implemented to protect iconic fish species such as pearl perch and snapper in Southeast Queensland. Stakeholders supported actions that; change fishing practices for groups (recreational, commercial and charter); extended monitoring and reporting; improved compliance; changes to fishing management practices; extended fishing control measures and the construction of additional artificial reef habitats.

Swordfish (Xiphias gladius) are a widely distributed (45°N–45°S) large pelagic fish targeted by fisheries worldwide. Swordfish that occur at high latitudes tend to disproportionately be large adults, so their movements have implications for population dynamics and fisheries management. In the southwest Pacific, little is known about this subset of the stock and existing evidence suggests limited movement from the subtropics into cooler high latitude waters. Here, we capitalize on the recent emergence of a recreational swordfish fishery off temperate southeast Australia to characterize movements of swordfish caught in the fishery with pop-up satellite archival transmitting tags. Data were recovered from tags deployed for 56–250 days on 11 swordfish (50–350 kg) tagged between 38 and 43°S in the western Tasman Sea. Five swordfish entered the Coral Sea (< 30°S), with four reaching north to 11–24°S, up to 3275 km away from location of capture. Behavior modelling suggests these four individuals rapidly transited north until encountering 23–27 °C water, at which point they lingered in the area for several months, consistent with spawning-related partial migration. One migrating swordfish still carrying a tag after the spawning season returned to ~ 120 km of its release location, suggesting site fidelity. Movements toward the central south Pacific were confined to two individuals crossing 165°E. Swordfish predominantly underwent normal diel vertical migration, descending into the mesopelagic zone at dawn (median daytime depth 494.9 m, 95% CI 460.4–529.5 m). Light attenuation predicted daytime depth, with swordfish rising by up to 195 m in turbid water. At night, swordfish were deeper during the full moon, median night-time depth 45.8 m (37.8–55.5) m versus 18.0 m (14.9–21.8) m at new moon. Modelling fine-scale (10 min−1) swordfish depth revealed dynamic effects of moon phase varying predictably across time of night with implications for fisheries interactions. Studying high

Permeable phylogeographic barriers characterize the vast open ocean, boosting gene flow and counteracting population differentiation and speciation of widely distributed and migratory species. However, many widely distributed species consists of distinct populations throughout their distribution, evidencing that our understanding of how the marine environment triggers population and species divergence are insufficient. The sailfish is a circumtropical and highly migratory billfish that inhabits warm and productive areas. Despite its ecological and socioeconomic importance as a predator and fishery resource, the species is threatened by overfishing, requiring innovative approaches to improve their management and conservation status. Thus, we presented a novel high-quality reference genome for the species and applied a seascape genomics approach to understand how marine environmental features may promote local adaptation and how it affects gene flow between populations. We delimit two populations between the Atlantic and Indo-Western Pacific oceans and detect outlier loci correlated with sea surface temperature, salinity, oxygen, and chlorophyll concentrations. However, the most significant explanatory factor that explains the differences between populations was isolation by distance. Despite recent population drops, the sailfish populations are not inbred. For billfishes in general, genome-wide heterozygosity was found to be relatively low compared to other marine fishes, evidencing the need to counteract overfishing effects. In addition, in a climate change scenario, management agencies must implement state-of-the-art sequencing methods, consider our findings in their management plans, and monitor genome-wide heterozygosity over time to improve sustainable fisheries and the long-term viability of its populations.

Researchers from Queensland’s Department of Agriculture and Fisheries evaluated the population biology and stock structure of the Black Jewfish (Protonibea diacanthus) in Queensland waters. The project was focused around high catch areas in central Queensland which account for the majority of harvest from the Queensland East Coast fishery. Whole specimens were collected during 2020 and 2021, through a complimentary approach of sampling commercial fishery catches during the open fishing season (January and February), and through representative fishery independent sampling (March to December). The collection of additional samples for genetics was undertaken across the species’ distribution in Queensland and part of the Northern Territory, and was heavily supported by assistance from the commercial, recreational, charter and Indigenous fishing communities. The research was able to characterise key aspects of the species’ population biology and population structure which have been used to directly inform the stock assessment and fishery management in Queensland waters.

Background and aim Billfish are epipelagic marine predators facing increasing pressures such as overfishing and rising global temperatures. Overfishing is a major concern, as they are caught by industrial longline fishers targeting tuna. Billfish are targeted by multiple fishing sectors, which provides food, socio-economic and cultural benefits. To support effective billfish management and conservation, it is essential to understand their spatial distribution and the environmental factors that may influence it. Location The focus of this study is the Indian Ocean (IO), where there are gaps in understanding the interactions between fisheries and billfish distribution. Three of six billfish species are at risk from overfishing. Therefore, determining their distribution is crucial to their management and conservation. Methods Using Ocean Biogeographic Information System (OBIS) occurrence data, Indian Ocean Tuna Commission (IOTC) catch data, and environmental covariates, we applied species distribution models to investigate the spatial extent of the realized niches of six billfish species in the IO. We also determined the role and relative importance of environmental drivers. Moreover, we evaluated the association between species’ spatial distribution and the fishing effort distribution. Results We found niche partitioning and overlap among the six species identified spatial distribution, with higher species richness in the northern region of the IO and off the East coast of Africa. Temperature, mixed layer depth and salinity were identified as the most important predictors of species distribution, with moderately warm and stable environments preferred by most billfish species. Areas with high species richness and high fishing effort overlap were primarily found in the Areas Beyond National Jurisdiction (ABNJ). In contrast, areas with high species diversity richness and low fishing effort were found mainly in the Exclusive Economic Zone (EEZ). Main conclusion S

Researchers from Queensland’s Department of Agriculture and Fisheries, James Cook University, and the University of Western Australia tested a range of otolith-based and genetic methods to identify hatchery-born from wild-born Barramundi. The project took place in the Dry Tropics region, where extensive historical and ongoing impoundment stocking (release of hatchery-born Barramundi into freshwater bodies) may be contributing to the downstream wild-capture marine and estuarine fishery. Fish samples were collected from the commercial and recreational wild-capture marine and estuarine fishery in 2019 and 2020, following the major Townsville floods in February 2019. The team identified a cost-effective means of using trace elements in fish otoliths to reliably distinguish hatchery-origin from wild-origin fish, measure the contribution of stocked fish to the wild population, and assess the sustainability of the wild-capture fishery.

Context: In Australia, the health of our marine, estuarine and freshwater fishes are of critical importance. The aquatic and marine ecosystems, and the fishes that occupy them each have an important role in our country’s ecological, economic, cultural and social wealth. Climate change, resource over-exploitation, invasive animals and diseases, and habitat degradation are just a few of the burgeoning threats that researchers and managers must address to ensure the prosperity of Australia’s natural fisheries resources. In addition, differences in legislative frameworks among jurisdictions hinder our ability to coherently manage fish resources at scales that are relevant biologically, ecologically and socially.Aims: Here, we identify the key research priorities for fish and fisheries research in Australia, across seven thematic fields of study.Methods: Research priorities were evaluated using a horizon scanning approach, which identified research questions related to the field of fish and fisheries research in Australia.Key results: A total of 284 questions unique research questions were categorised and prioritised, resulting in the formation of the top 10 highest priority research questions across each of the seven themes.Conclusions: The outcomes from this work can be used to directly complement ongoing work from research providers working in the field of fish and fisheries as well as the development of new areas of research.Implications: The priorities identified will enable researchers and policy makers to identify critical knowledge gaps, develop collaborative research programs, investigate novel approaches, and to improve transparency around decision-making processes.

Context: Alien freshwater snails pose a substantial risk to Australian native aquatic biota.Aims: This study aims to determine the thermal and salinity ranges of two introduced species within Australia, Pomacea sp. and Anentome sp., to facilitate predictions of their potential geographic range should they become widely established.Methods: Laboratory tests were conducted to assess behavioural responses of snails to altered temperature or salinity after different acclimation regimes.Key results: After acclimation at 25°C, Pomacea sp. had a median activity range of 13.5–38°C and Anentome sp. of 12–38.5°C. Higher acclimation temperatures produced observable effects, whereas lower acclimation temperatures did not. Salinity tolerances differed, with Pomacea sp. remaining active at up to 8 parts per thousand (ppt) (after acclimation at 25°C), with acclimation at 20°C resulting in a lower salinity tolerance. By contrast, Anentome sp. snails were active at up to 5 ppt after low salinity acclimation, demonstrating enhanced salinity tolerance compared with non-salinity acclimations.Conclusions: These results showed that both snails are capable of surviving temperatures and salinities that would allow invasion into subtropical and warm-temperate Australian aquatic systems.Implications: Free from the constraints of natural predators, competitors, and parasites, these snails should be of great concern to biosecurity agencies in Australia.

Shark depredation is a complex social-ecological issue that affects a range of fisheries worldwide. Increasing concern about the impacts of shark depredation, and how it intersects with the broader context of fisheries management, has driven recent research in this area, especially in Australia and the United States. This review synthesises these recent advances and provides strategic guidance for researchers aiming to characterise the occurrence of depredation, identify the shark species responsible, and test deterrent and management approaches to reduce its impacts. Specifically, the review covers the application of social science approaches, as well as advances in video camera and genetic methods for identifying depredating species. The practicalities and considerations for testing magnetic, electrical, and acoustic deterrent devices are discussed in light of recent research. Key concepts for the management of shark depredation are reviewed, with recommendations made to guide future research and policy development. Specific management responses to address shark depredation are lacking, and this review emphasizes that a “silver bullet” approach for mitigating depredation does not yet exist. Rather, future efforts to manage shark depredation must rely on a diverse range of integrated approaches involving those in the fishery (fishers, scientists and fishery managers), social scientists, educators, and other stakeholders.

Black jewfish (Protonibea diacanthus) are caught on the east coast of Queensland by commercial, recreational, charter and Indigenous fishers. The fishery is focused around Central Queensland, and has recently experienced a large shift in commercial effort and gear types. The species was historically considered a byproduct species within the inshore net fishery, but has now become a targeted line caught species. In Australia, black jewfish are found from Exmouth Gulf in Western Australia, north and east across Northern Australia, to the east coast of Queensland. Research suggests that stocks cover hundreds of kilometres. This is the first stock assessment of the Queensland East Coast stock. The stock assessment was conducted on calendar years and included input data through to December 2021. Eight model scenarios were run, covering different combinations of recreational dead catch and population steepness (productivity parameter). Base case (preferred) scenario results suggested that biomass declined gradually from the 1940s to the 1980s and has increased slightly since then. The spawning stock level at the beginning of 2022 for base-case scenarios was estimated to be between 56% and 99% with a median estimate of 79%. The estimates from other scenarios ranged from 80% to 92%. Despite high uncertainty around the exact level of biomass, the model outputs indicate that the biomass is probably at or above the target reference point of 60% unfished biomass.

We report on the findings of a collaborative research project that was designed to identify and measure the effects of environmental drivers on the abundance and population dynamics of key Queensland fishery species. The project was co-funded by the Commonwealth Government’s Fisheries Research and Development Corporation (FRDC) and carried out by a multi-disciplinary team of scientists from the University of Queensland (UQ), the Queensland Department of Agriculture and Fisheries (DAF) and the Australian Institute of Marine Science (AIMS). The research team applied modern statistical, data science and modelling techniques in combination with biological insights into the life cycles of the three target species. Background With increasing evidence that environmental conditions in the marine environment are changing rapidly, it is becoming ever more important to understand how these changes may impact on the population dynamics and abundance of important fish stocks. Understanding the influence of environmental conditions can provide greater certainty that the risk of overfishing (under adverse environmental conditions) or under harvesting (under favourable conditions) are accounted for by resource managers. This project aimed to identify the environmental factors which may be influencing the recruitment, catchability or productivity of Snapper, Pearl Perch, and Spanner Crab stocks in Queensland. Results from this work will support sustainable management of Queensland’s fisheries by directly informing the assessment and management of these key species within Queensland waters.

Since the Miocene profound climatic changes have influenced the biology and ecology of species worldwide, such as their connectivity, genetic population structure, and biogeography. The goal herein is to evaluate the phylogeography of sailfish Istiophorus platypterus between the Atlantic, Indian, and Pacific oceans. Our results evidenced a high genetic diversity and three distinct populations among the ocean basins with limited gene flow among them. In addition, the species is characterized by two deep evolutionary lineages that diverged during the Miocene/Pliocene transition, one of them is circumtropical while the other is restricted to the Atlantic Ocean. These lineages evolved along the successive glacial-interglacial cycles from the Pleistocene and remained isolated from each other in glacial refugium until deglaciation. Assessments of sailfish suggest it may be subject to overfishing and the results herein imply the need to re-evaluate the current stock delimitations and management measures adopted by the Regional Fisheries Management Organizations, especially in the Atlantic and the Indo-Western Pacific oceans to effectively manage the species. In addition, this work highlights that both lineages should at least be treated as two distinct management units in the Atlantic Ocean until their taxonomic status is fully resolved, given their high genetic divergence.

The introduction and spread of non-native species poses a significant threat to the health of freshwater ecosystems, and has recently been identified as the single biggest danger to threatened species survival in Australia. Notwithstanding, the importation, trade and keeping of exotic and potentially invasive freshwater fishes in Australia is significant, resulting in greater propagule pressure and higher risk for deliberate or incidental release into native waterways. The jaguar cichlid (Parachromis managuensis) is an invasive cichlid that has established non-native populations in many countries throughout the world. In December 2014, the Department of Agriculture and Fisheries in Queensland was notified of an incursion of jaguar cichlids in a stormwater retention dam in the Pioneer River Catchment, Mackay, Queensland. Rotenone was applied to the dam in January 2015, and around 200 jaguar cichlid specimens at various life history stages were destroyed. Follow up surveys into mid-2015 did not detect the presence of any jaguar cichlid in the dam or in nearby creeks. In September 2017, the Department was notified of a wild capture of a mature jaguar cichlid in Fursden Creek, 1.5 km from the original incursion site. Follow up surveys in 2018/19 have also detected jaguar cichlid juveniles in surrounding tributaries, indicating successful establishment and naturalisation of the species in Australia for the first time. © Holmes et al.

We evaluated the population structure of M. nigricans within the Pacific Ocean using 17 microsatellite loci and 6204 single nucleotide polymorphisms. Evidence from both types of genetic markers supported the null hypothesis of a single genetic population throughout the Pacific Ocean. This study provides insight into the current stock structure of M. nigricans and discusses the implications for fisheries management.

The introduction and spread of non-native species poses a significant threat to the health of freshwater ecosystems, and has recently been identified as the single biggest danger to threatened species survival in Australia. Notwithstanding, the importation, trade and keeping of exotic and potentially invasive freshwater fishes in Australia is significant, resulting in greater propagule pressure and higher risk for deliberate or incidental release into native waterways. The jaguar cichlid (Parachromis managuensis) is an invasive cichlid that has established non-native populations in many countries throughout the world. In December 2014, the Department of Agriculture and Fisheries in Queensland was notified of an incursion of jaguar cichlids in a stormwater retention dam in the Pioneer River Catchment, Mackay, Queensland. Rotenone was applied to the dam in January 2015, and around 200 jaguar cichlid specimens at various life history stages were destroyed. Follow up surveys into mid-2015 did not detect the presence of any jaguar cichlid in the dam or in nearby creeks. In September 2017, the Department was notified of a wild capture of a mature jaguar cichlid in Fursden Creek, 1.5 km from the original incursion site. Follow up surveys in 2018/19 have also detected jaguar cichlid juveniles in surrounding tributaries, indicating successful establishment and naturalisation of the species in Australia for the first time. © Holmes et al.

Marine infrastructure development throughout southeast Queensland is fast-paced, with the ongoing expansion of our major ports and harbours, airports and road infrastructure. Our cities and regional centres continue to expand along the Queensland coastline and into the marine environment through dredging and land reclamation. These activities are managed from an environmental protection perspective at the local, State and Commonwealth government levels. Here we examine the maintenance and capital dredging works undertaken by the Port of Brisbane Pty Ltd (PBPL), Department of Transport and Main Roads (DTMR) and Brisbane Airport Corporation (BAC), which are necessary for maintaining ports and marina infrastructure, roads and runways. A variety of methods has been adopted over the past few decades for managing potential marine environmental impacts from these dredging activities. This chapter explores the different monitoring tools implemented by the PBPL, DTMR and BAC for managing potential impacts from port and harbour maintenance, capital works programs and operational activities. We consider the regulatory environment and how this influences port and harbour works, road and airport infrastructure development within the Bay. We also explore new technology and approaches to monitoring and the areas of future research and investigation to help contribute towards a sustainable future for Moreton Bay.

We investigated whether commercially landed black marlin Istiompax indica were being misidentified by fisheries observers operating throughout the Pacific Ocean. Of 83 samples reported by observers as I. indica, 77% were genetically identified to be blue marlin Makaira nigricans and 2% to be striped marlin Kajikia audax. The high rate of misidentification by observers places considerable uncertainty over historic catch ratios of Indo-Pacific marlin and stock assessments relying on the validity of these data.

Multiple paternity has been documented as a reproductive strategy in both viviparous and ovoviviparous elasmobranchs, leading to the assumption that multiple mating may be ubiquitous in these fishes. However, with the majority of studies conducted on coastal and nearshore elasmobranchs that often form mating aggregations, parallel studies on pelagic, semi-solitary species are lacking. The tiger shark (Galeocerdo cuvier) is a large pelagic shark that has an aplacental viviparous reproductive mode which is unique among the carcharhinids. A total of 112 pups from four pregnant sharks were genotyped at nine microsatellite loci to assess the possibility of multiple paternity or polyandrous behaviour by female tiger sharks. Only a single pup provided evidence of possible multiple paternity, but with only seven of the nine loci amplifying for this individual, results were inconclusive. In summary, it appears that the tiger sharks sampled in this study were genetically monogamous. These findings may have implications for the genetic diversity and future sustainability of this population.

The billfishes are a group of highly migratory fishes comprising two extant families. The family Xiphiidae is monotypic and contains only the broadbill swordfish (Xiphias gladius Linnaeus, 1758), while the nine-other species of billfishes constitute the family Istiophoridae. The outcomes of past phylogenetic investigations using partial nuclear and mitochondrial (mtDNA) sequences recommended a restructuring of Istiophoridae, by expanding the three existing genera into five: Makaira, Istiophorus, Kajikia, Istiompax, and Tetrapturus. However, several aspects of the Istiophoridae phylogeny remain unresolved, including the position of the genus Istiompax. In this investigation, we sequenced the whole mitogenomes for all istiophorid billfish species. Phylogenetic analyses supported the presence of five genera within Istiophoridae and resolved the placement of Istiompax as the sister taxon to Kajikia + Tetrapturus. Genetic identity between the striped marlin [Kajikia audax (Philippi, 1887)] and the white marlin [Kajikia albida (Poey, 1860)] was found to be higher than between Indo-Pacific and Atlantic clades of both the blue marlin (Makaira nigricans Lacépède, 1802) and sailfish [Istiophorus platypterus (Shaw, 1792)], suggesting recent isolation or ongoing genetic connectivity between K. audax and K. albida. An assessment of mtDNA gene regions identified NADH dehydrogenase subunit 4 (ND4) as best reflecting the phylogenetic reconstruction using the whole mitogenomes, while cytochrome b (Cytb) was the only gene region able to separate all species of billfishes in the present study. Our investigation increased the phylogenetic resolution of istiophorid billfishes and underscores the need for further investigations to fully resolve the complex genetic relationships within Tetrapturus and Kajikia.