Who do you move? A stochastic population model to guide translocation strategies for an endangered freshwater fish in south-eastern Australia

Immediate Genetic Augmentation and Enhanced Habitat Connectivity Are Required to Secure the Future of an Iconic Endangered Freshwater Fish Population

Genetic diversity is rapidly lost from small, isolated populations by genetic drift. Measuring the level of genetic drift using effective population size (N e) is highly useful for management. Single-cohort genetic N e estimators approximate the number of breeders in one season (N b): a value < 100 signals likely inbreeding depression. Per-generation N e < 1000 estimated from multiple cohort signals reduced adaptive potential. Natural populations rarely meet assumptions of N e-estimation, so interpreting estimates is challenging. Macquarie perch is an endangered Australian freshwater fish threatened by severely reduced range, habitat loss, and fragmentation. To counteract low N e, augmented gene flow is being implemented in several populations. In the Murrumbidgee River, unknown effects of water management on among-site connectivity impede the design of effective interventions. Using DArT SNPs for 328 Murrumbidgee individuals sampled across several sites and years with different flow conditions, we assessed population structure, site isolation, heterozygosity, inbreeding, and N e. We tested for inbreeding depression, assessed genetic diversity and dispersal, and evaluated whether individuals translocated from Cataract Reservoir to the Murrumbidgee River bred, and interbred with local fish. We found strong genetic structure, indicating complete or partial isolation of river fragments. This structure violates assumptions of N e estimation, resulting in strongly downwardly biased N b estimates unless assessed per-site, highlighting the necessity to account for population structure while estimating N e. Inbreeding depression was not detected, but with low N b at each site, inbreeding and inbreeding depression are likely. These results flagged the necessity to address within-river population connectivity through flow management and genetic mixing through translocations among sites and from other populations. Three detected genetically diverse offspring of a translocated Cataract fish and a local parent indicated that genetic mixing is in progress. Including admixed individuals in estimates yielded lower N e but higher heterozygosity, suggesting heterozygosity is a preferable indicator of genetic augmentation.

Planning and implementing genetic rescue of an endangered freshwater fish population in a regulated river, where low flow reduces breeding opportunities and may trigger inbreeding depression

Augmenting depleted genetic diversity can improve the fitness and evolutionary potential of wildlife populations, but developing effective management approaches requires genetically monitored test cases. One such case is the small, isolated and inbred Cotter River population of an endangered Australian freshwater fish, the Macquarie perch Macquaria australasica, which over 3 years (2017-2019) received 71 translocated migrants from a closely related, genetically more diverse population. We used genetic monitoring to test whether immigrants bred, interbred with local fish and augmented population genetic diversity. We also investigated whether levels of river flow affected recruitment, inbreeding depression and juvenile dispersal. Fish length was used to estimate the age, birth year cohort and growth of 524 individuals born between 2016 and 2020 under variable flow conditions. DArT genome-wide genotypes were used to assess individual ancestry, heterozygosity, short-term effective population size and identify parent-offspring and full-sibling families. Of 442 individuals born after translocations commenced, only two (0.45%) were of mixed ancestry; these were half-sibs with one translocated parent in common. Numbers of breeders and genetic diversity for five birth year cohorts of the Cotter River fish were low, especially in low-flow years. Additionally, individuals born in the year of lowest flow evidently suffered from inbreeding depression for juvenile growth. The year of highest flow was associated with the largest number of breeders, lowest inbreeding in the offspring and greatest juvenile dispersal distances. Genetic diversity decreased in the upstream direction, flagging restricted access of breeders to the most upstream breeding sites, exacerbated by low river flow. Our results suggest that the effectiveness of translocations could be increased by focussing on upstream sites and moving more individuals per year; using riverine sources should be considered. Our results indicate that river flow sufficient to facilitate fish movement through the system would increase the number of breeders, promote individuals' growth, reduce inbreeding depression and promote genetic rescue.

Management strategy of the naked carp (Gymnocypris przewalskii) in the Qinghai lake using matrix population modeling

Naked carp (Gymnocypris przewalskii) is the only fish species commercially harvested in Qinghai Lake, which is the largest inland saltwater lake in China. Multiple ecological stresses such as long-term overfishing, drying-up of riverine inflows, and decreases in spawning habitat caused the naked carp population to decrease from 320,000 tons before the 1950s to only 3000 tons by the early 2000s. We used matrix projection population modeling to quantitatively simulate the dynamics of the naked carp population from the 1950s to the 2020s. Five versions of the matrix model were developed from the field and laboratory information that represented different population states (high but declining, low abundance, very low abundance, initial recovery, pristine). Equilibrium analysis was applied to density-independent versions of the matrices and population growth rate, age composition, and elasticities were compared among versions. Stochastic, density-dependent version of the most recent decade (recovering) version was used to simulate the time-dependent responses to a range of levels of artificial reproduction (addition of age-1 from hatchery) and of the pristine version to simulate combinations of fishing rate and minimum age of harvest. Results showed the major role of overfishing in the population decline and that the population growth rate was most sensitive to the survival of juveniles and the spawning success of early-age adults. Dynamic simulations showed a rapid population response to artificial reproduction when population abundance was low and that if artificial reproduction continues at its current level, then population biomass would reach 75% of its pristine biomass after 50 years. Simulations with the pristine version identified sustainable fishing levels and the importance of protecting the first few ages of maturity. Overall, modeling results showed that artificial reproduction under conditions of no fishing is an effective approach to restoring the naked carp population. Further effectiveness should consider maximizing survival in the months just after release and maintaining genetic and phenotypic diversity. More information on density-dependent growth, survival, and reproduction, as well as on the genetic diversity and growth and migratory behavior (phenotypic variation) of released and native-spawned fish, would help inform management and conservation strategies and practices going forward.

Direct and Molecular Observation of Movement and Reproduction by Candy Darter, Etheostoma osburni, an Endangered Benthic Stream Fish in Virginia, USA

Direct and indirect measures of individual movement provide valuable knowledge regarding a species’ resiliency to environmental change. Information on patterns of movement can inform species management and conservation but is lacking for many imperiled fishes. The Candy Darter, Etheostoma osburni, is an endangered stream fish with a dramatically reduced distribution in Virginia in the eastern United States, now known from only four isolated populations. We used visual implant elastomer tags and microsatellite DNA markers to directly describe movement patterns in two populations. Parentage analysis based on parent-offspring pairs was used to infer movement patterns of young-of-year and age-1 individuals, as well as the reproductive contribution of certain adults. Direct measurements of movement distances were generally similar between methods, but microsatellite markers revealed greater distances moved, commensurate with greater spatial frames sampled. Parent-offspring pairs were found throughout the species’ 18.8-km distribution in Stony Creek, while most parent-offspring pairs were in 2 km of the 4.25-km distribution in Laurel Creek. Sibship reconstruction allowed us to characterize the mating system and number of spawning years for adults. Our results provide the first measures of movement patterns of Candy Darter as well as the spatial distribution of parent-offspring pairs, which may be useful for selecting collection sites in source populations to be used for translocation or reintroductions. Our results highlight the importance of documenting species movement patterns and spatial distributions of related individuals as steps toward understanding population dynamics and informing translocation strategies. We also demonstrate that the reproductive longevity of this species is greater than previously described, which may be the case for other small stream fishes.

Reproductive ecology of a critically endangered alpine galaxiid

Stocky galaxias Galaxias tantangara is a newly described freshwater fish restricted to a single population, occupying a 3 km reach of a small headwater stream in the upper Murrumbidgee River catchment of south-eastern Australia. This species is listed as critically endangered under IUCN Red List criteria, and knowledge of the species' ecology is critical for future conservation efforts to establish additional populations by translocation and captive breeding. This study details the first account of spawning and reproductive ecology of G. tantangara, including reproductive development, timing of spawning and a description of one spawning site. Peak gonadosomatic index was observed in March/April in males and in October in females. Absolute fecundity ranged from 211 oocytes for a 76 mm length to caudal fork (LCF) fish to 810 oocytes for a 100 mm LCF fish. The observation of spent females in mid-November 2017 and discovery of an egg mass 8 days later suggest that spawning had occurred, and over a relatively short period. Larvae were subsequently detected in monthly electrofishing surveys in December 2017. Findings from this study provide new understanding of existing and future threats to G. tantangara and have important implications for conservation management of not only this species but also other closely related threatened Galaxias species.

Testing the adaptive advantage of a threatened species over an invasive species using a stochastic population model

Introduced species are a major threat to freshwater biodiversity. Often eradication is not feasible, and management must focus on reducing impacts on native wildlife. This requires an understanding of how native species are affected but also how environmental characteristics influence population dynamics of both invasive and native species. Such insights can inform how to manipulate systems in order to take advantage of life-history traits native species possesses that invaders do not. The highly invasive fish, Gambusia holbrooki, has been implicated in the decline of many freshwater fish and amphibians. In south-eastern Australia, one of these is the threatened native fish, Galaxiella pusilla. As G. pusilla can survive periods without surface water, this presents an opportunity for adaptive management, given G. holbrooki lack these adaptations. We develop a stochastic population model to explore the impact of G. holbrooki on G. pusilla and test the feasibility of both natural and management-induced drying to protect this species. Our results support recent empirical studies showing G. holbrooki are a serious threat to G. pusilla persistence, especially through impacts on larval survival. While persistence is more likely in water bodies that frequently dry out, even optimal natural drying regimes may be insufficient when impacts from G. holbrooki are high. However, management-induced drying may allow persistence of G. pusilla in sites inhabited by both species. Given our model outcomes, the biology of these species and the habitats they occupy, we recommend maintaining or restoring aquatic and riparian vegetation and natural drying regimes to protect G. pusilla from G. holbrooki, in addition to undertaking management-induced drying of invaded water bodies. Our results provide insights into how the effects of G. holbrooki may be mitigated for other native species, which is important given this species is perhaps the most pervasive invader of freshwater ecosystems. We conclude with a discussion of the potential for using disturbance processes in the management of invasive species more broadly in freshwater and terrestrial systems.

Adjusting the Prerelease Gut Microbial Community by Diet Training to Improve the Postrelease Fitness of Captive-Bred Acipenser dabryanus

As one of the most important tool for biodiversity restoration and endangered species conservation, reintroduction has been implemented worldwide. In reintroduction projects, prerelease conditioning could effectively increase postrelease fitness and survival by improving animals’ adaptation to transformation from artificial to natural environments. However, how early-life diet training affects individuals’ adaptation, fitness, and survival after release remains largely unknown. We hypothesized that early-life diet training would adjust the host’s gut microbial community, the gut microbial community would influence the host’s diet preference, and the host’s diet preference would impact its adaptation to diet provision transformation and then determine postrelease fitness and survival. To verify this hypothesis, we investigated the growth characteristics and gut microbes of Yangtze sturgeon (Acipenser dabryanus) trained with natural and formula diets at both the prerelease and postrelease stages. The results showed that (1) the gut microbial communities of the individuals trained with a natural diet (i.e., natural diet group) and formula diet (i.e., formula diet group) evolved to the optimal status for their corresponding diet provisions, (2) the individuals in the natural diet group paid a lower cost (i.e., changed their gut microbial communities less) during diet transformation and release into the natural environment than did the individuals in the formula diet group, and (3) the gut microbes in the natural diet group better supported postrelease fitness and survival than did the gut microbes in the formula diet group. The results indicated that better prerelease diet training with more appropriate training diets and times could improve the reintroduction of Yangtze sturgeon by adjusting the prerelease gut microbial community. Because a relationship between diet (preference) and gut microbes is common in animals from insects (such as Drosophila melanogaster) to mammals (such as Homo sapiens), our hypothesis verified by the case study on Yangtze sturgeon applies to other animals. We therefore encourage future studies to identify optimal training diets and times for each species to best adjust its prerelease gut microbial community and then improve its postrelease fitness and survival in reintroduction projects.

Limited contributions of released animals from zoos to North American conservation translocations

With the loss of biodiversity accelerating, conservation translocations such as reintroductions are becoming an increasingly common conservation tool. Conservation translocations must source individuals for release from either wild or captive-bred populations. We asked what proportion of North American conservation translocations rely on captive breeding and to what extent zoos and aquaria (hereafter zoos) fulfill captive breeding needs. We searched for mention of captive breeding and zoo involvement in all 1863 articles included in the North American Conservation Translocations database, which comprises journal articles and grey literature published before 2014 on conservation translocations in Canada, the United States, Mexico, the Caribbean, and Central America before 2014 as identified by a comprehensive literature review. Conservation translocations involved captive breeding for 162 (58%) of the 279 animal species translocated. Fifty-four zoos contributed animals for release. The 40 species of animals bred for release by zoos represented only 14% of all animal species for which conservation translocations were published and only 25% of all animal species that were bred for releases occurring in North America. Zoo contributions varied by taxon, ranging from zoo-bred animals released in 42% of amphibian conservation translocations to zero contributions for marine invertebrates. Proportional involvement of zoos in captive-breeding programs for release has increased from 1974 to 2014 (r = 0.325, p = 0.0313) as has the proportion of translocation-focused scientific papers coauthored by zoo professionals (from 0% in 1974 to 42% in 2013). Although zoos also contribute to conservation translocations through education, funding, and professional expertise, increasing the contribution of animals for release in responsible conservation translocation programs presents a future conservation need and opportunity. We especially encourage increased dialogue and planning between the zoo community, academic institutions, and governments to optimize the direct contribution zoos can make to wildlife conservation through conservation translocations.

Spawning-stock characteristics and migration of a lake-bound population of the endangered Macquarie perch Macquaria australasica

The intrapopulation variability in the size and age structure of the spawning stock and migration of the threatened Macquarie perch Macquaria australasica in Lake Dartmouth was investigated between 2008 and 2016. Sampling centred on the core reproductive period (October-December) when mature fish migrate from the lake into riverine habitat to spawn. Spawning fish were predominantly large, spanning a broad age structure, with a high proportion of fish (25%) aged 15-30 years. The overall median size of spawning fish did not change for males or females during the 9 year study period. The size of the smaller mature male fish did change in some years suggesting a small proportion of male M. australasica matured at age 1+ and 2+. Acoustic telemetry employed over 3 years showed that M. australasica were most likely to be in the spawning reach from October to mid-December, migrated to this reach annually and moved large distances throughout the lake all year, with no evidence for any spatial structuring. Mature fish sometimes occupied the spawning reach for several months after the core reproductive period, which increased their vulnerability to recreational fishing. Males tagged in the lake were seldom recorded in the spawning reach, presumably because a high proportion had not yet entered the spawning stock despite their size suggesting maturity. Maintaining a broad age and size-structure of the spawning stock of long-lived iteroparous fish species is crucial for recruitment stability and population persistence. Overexploitation of the spawning stock has probably contributed to previous population declines in the lake as well as the collapse of other M. australasica populations in south-eastern Australia.

Using a Population Model to Inform the Management of River Flows and Invasive Carp (Cyprinus carpio)

Carp are a highly successful invasive fish species, now widespread, abundant and considered a pest in south-eastern Australia. To date, most management effort has been directed at reducing abundances of adult fish, with little consideration of population growth through reproduction. Environmental water allocations are now an important option for the rehabilitation of aquatic ecosystems, particularly in the Murray-Darling Basin. As carp respond to flows, there is concern that environmental watering may cause floodplain inundation and provide access to spawning habitats subsequently causing unwanted population increase. This is a management conundrum that needs to be carefully considered within the context of contemporary river flow management (natural, environmental, irrigation). This paper uses a population model to investigate flow-related carp population dynamics for three case studies in the Murray-Darling Basin: (1) river and terminal lakes; (2) wetlands and floodplain lakes; and (3) complex river channel and floodplain system. Results highlight distinctive outcomes depending on site characteristics. In particular, the terminal lakes maintain a significant source carp population regardless of river flow; hence any additional within-channel environmental flows are likely to have little impact on carp populations. In contrast, large-scale removal of carp from the lakes may be beneficial, especially in times of extended low river flows. Case studies 2 and 3 show how wetlands, floodplain lakes and the floodplain itself can now often be inundated for several months over the carp spawning season by high volume flows provided for irrigation or water transfers. Such inundations can be a major driver of carp populations, compared to within channel flows that have relatively little effecton recruitment. The use of a population model that incorporates river flows and different habitats for this flow-responsive species, allows for the comparison of likely population outcomes for differing hydrological scenarios to improve the management of risks relating to carp reproduction and flows.

Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow

Genetic diversity underpins the ability of populations to persist and adapt to environmental changes. Substantial empirical data show that genetic diversity rapidly deteriorates in small and isolated populations due to genetic drift, leading to reduction in adaptive potential and fitness and increase in inbreeding. Assisted gene flow (e.g. via translocations) can reverse these trends, but lack of data on fitness loss and fear of impairing population "uniqueness" often prevents managers from acting. Here, we use population genetic and riverscape genetic analyses and simulations to explore the consequences of extensive habitat loss and fragmentation on population genetic diversity and future population trajectories of an endangered Australian freshwater fish, Macquarie perch Macquaria australasica. Using guidelines to assess the risk of outbreeding depression under admixture, we develop recommendations for population management, identify populations requiring genetic rescue and/or genetic restoration and potential donor sources. We found that most remaining populations of Macquarie perch have low genetic diversity, and effective population sizes below the threshold required to retain adaptive potential. Our simulations showed that under management inaction, smaller populations of Macquarie perch will face inbreeding depression within a few decades, but regular small-scale translocations will rapidly rescue populations from inbreeding depression and increase adaptive potential through genetic restoration. Despite the lack of data on fitness loss, based on our genetic data for Macquarie perch populations, simulations and empirical results from other systems, we recommend regular and frequent translocations among remnant populations within catchments. These translocations will emulate the effect of historical gene flow and improve population persistence through decrease in demographic and genetic stochasticity. Increasing population genetic connectivity within each catchment will help to maintain large effective population sizes and maximize species adaptive potential. The approach proposed here could be readily applicable to genetic management of other threatened species to improve their adaptive potential.