Jarod Lyon

Observations on the distribution and abundance of carp and native fish, and their responses to a habitat restoration trial in the Murray River, Australia

Abstract A native fish strategy has been initiated to rehabilitate native fish populations in the Murray‐Darling Basin, Australia. The reintroduction of large woody debris (LWD) into the Basins large lowland rivers is one of the restoration activities in the strategy. The results from three separate studies undertaken on the Murray River between Yarrawonga and Tocumwal are presented on the relationship between carp (Cyprinus carpio), native species, and LWD to examine whether native species and carp compete for LWD habitat. The first study reports on the relative abundance of carp and native fish in a river reach. Since 1995 carp abundance has declined, whereas the abundance of native fish populations has remained relatively constant providing little support for the hypothesis that competition for LWD habitat is having effects at the population level effects. The second study reports on the relationship between LWD, river channel position, and its use as habitat by carp and native species. A statistically significant relationship was observed between native fish, LWD, the location within a meander, and curvature of the meander. There was no statistically significant relation between carp and any of these parameters indicating that carp utilise a variety of riverine habitats, whereas native species were strongly associated with LWD. The third study reports on an experiment that tested the response of carp to the placement of new LWD habitat. The response from carp was statistically inconclusive. The combination of these studies suggest that it is unlikely that carp and native species are directly competing for LWD habitat and it is unlikely that carp will inundate restored LWD habitats and preclude native species.

Recovery of the endangered trout cod, Maccullochella macquariensis: what have we achieved in more than 25 years?

Recovery of threatened species is often necessarily a long-term process. The present paper details the progress towards the recovery of trout cod, Maccullochella macquariensis, an iconic, long-lived fish species first listed as threatened in the 1980s. The objectives, actions and progress over three successive national recovery plans (spanning 18 years) are assessed, documenting changes to population distribution and abundance and updating ecological knowledge. Increased knowledge (especially breeding biology and hatchery techniques, movements, habitats and genetics) has greatly influenced recovery actions and the use of a population model was developed to assist with management options and stocking regimes. Key recovery actions include stocking of hatchery-produced fish to establish new populations, regulations on angling (including closures), education (particularly identification from the closely related Murray cod, M. peelii) and habitat rehabilitation (especially re-instatement of structural woody habitats). In particular, the establishment of new populations using hatchery stocking has been a successful action. The importance of a coordinated long-term approach is emphasised and, although there is uncertainty in ongoing resourcing of the recovery program, much has been achieved and there is cautious optimism for the future of this species.

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.

Estimating population size in the presence of temporary migration using a joint analysis of telemetry and capture-recapture data

Summary 1. Temporary migration – where individuals can leave and re-enter a sampled population – is a feature of many capture–mark–recapture (CMR) studies of mobile populations which, if unaccounted for, can lead to biased estimates of population capture probabilities and consequently biased estimates of population abundance. 2. We present a method for incorporating radiotelemetry data within a CMR study to eliminate bias due to temporary migration using a Bayesian state-space model. 3. Our results indicate that using a relatively small number of telemetry tags, it is possible to greatly reduce bias in estimates of capture probabilities using telemetry data to model transition probabilities in and out of the sampling area. In a capture–recapture data set for trout Cod in the Murray river, Australia, accounting for temporary migration led to overall higher estimates of capture probabilities than models assuming permanent or zero migration. Also, individual heterogeneity in detectability can be managed through explicit modelling. We show how accounting for temporary migration when estimating capture probabilities can be used to estimate the abundance and size distribution of a population as though it were closed. 4. Our model provides a basis for more complex models that might integrate telemetry data into other CMR scenarios, thus allowing for greater precision in estimates of vital rates that might otherwise be biased by temporary migration. Our results highlight the importance of accounting for migration in survey design and parameter estimation, and the potential scope for supplementing large-scale CMR data sets with a subset of auxiliary data that provide information on processes that are hidden to primary sampling processes.

Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity

Adaptive differences across species’ ranges can have important implications for population persistence and conservation management decisions. Despite advances in genomic technologies, detecting adaptive variation in natural populations remains challenging. Key challenges in gene–environment association studies involve distinguishing the effects of drift from those of selection and identifying subtle signatures of polygenic adaptation. We used paired‐end restriction site‐associated DNA sequencing data (6,605 biallelic single nucleotide polymorphisms; SNPs) to examine population structure and test for signatures of adaptation across the geographic range of an iconic Australian endemic freshwater fish species, the Murray cod Maccullochella peelii. Two univariate gene–association methods identified 61 genomic regions associated with climate variation. We also tested for subtle signatures of polygenic adaptation using a multivariate method (redundancy analysis; RDA). The RDA analysis suggested that climate (temperature‐ and precipitation‐related variables) and geography had similar magnitudes of effect in shaping the distribution of SNP genotypes across the sampled range of Murray cod. Although there was poor agreement among the candidate SNPs identified by the univariate methods, the top 5% of SNPs contributing to significant RDA axes included 67% of the SNPs identified by univariate methods. We discuss the potential implications of our findings for the management of Murray cod and other species generally, particularly in relation to informing conservation actions such as translocations to improve evolutionary resilience of natural populations. Our results highlight the value of using a combination of different approaches, including polygenic methods, when testing for signatures of adaptation in landscape genomic studies.

Identifying environmental correlates of intraspecific genetic variation.

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species’ range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

Does wood type influence the colonisation of this habitat by macroinvertebrates in large lowland rivers

Submerged woody habitat provides the major structure around which ecological processes operate in many lowland rivers. Colonisation by macroinvertebrates was measured in a south-eastern Australian river over a 32-day period in an experiment testing the hypothesis that wood type influences the invertebrate assemblage structure. The wood types were green wood, dry wood, and dry but previously waterlogged wood. All wood used was river red gum (Eucalyptus camaldulensis). Macroinvertebrates colonised previously waterlogged wood more rapidly than green or dry wood. The assemblage structure varied significantly over the sampling period, with copepods and cladocerans numerically dominating the assemblage during the first few days after the introduction of the wood. The assemblage became more diverse through time and was numerically dominated by dipterans, ephemeropterans and trichopterans. The results indicate that there was little difference in the time taken for macroinvertebrate colonisation after wood introduction when using either green or dry wood. This has implications for large-scale restoration projects, where green wood is likely to be a more readily available option for reintroduction than dry wood.

Predicting natural instream woody-habitat loads across large river networks

Past waterway management practices worldwide involved extensive removal of instream woody habitat (IWH) and riparian vegetation. The importance of instream woody habitat for healthy aquatic ecosystems has now been recognised, with management approaches reversed to reintroduce instream woody habitat and replant riverbanks. Knowledge of natural or pre-disturbance IWH loads is useful to guide such restoration programs; however, such datasets are often unavailable. In this study, natural IWH loads were mapped along 105km of undisturbed rivers in south-eastern Australia. This field dataset was modelled, using boosted regression trees, against geomorphic, environmental and climatic variables to predict natural IWH loads in rivers across Victoria. Mapped natural IWH loads averaged 0.029m3m–2 (±0.005), ranging from 0.083 to 0.002m3m–2. Natural IWH volumes were predicted to range from 0 to 0.102m3m–2. Distinct IWH loading trends were noticeable over larger spatial scales. Eastern Victoria showed relatively lower natural IWH loads than did western Victoria. Because many stream restoration efforts do not have a quantifiable knowledge of natural IWH load, the results of the present study provide some guidance. The predicted IWH loadings are a useful first step in identifying broad areas for further investigation and a natural condition base for current IWH condition modelling.

Is climate change driving recruitment failure in Australian bass Macquaria novemaculeata in southern latitudes of the species range

Flow regimes have been fundamentally altered in many of the world’s river systems. There is a need to restore components of natural flow variability to protect freshwater biodiversity. The Australian bass is a long-lived, catadromous percichthyid endemic to coastal drainages of south-eastern Australia. Little is known of the timing and magnitude of flows considered important for recruitment and growth of individuals in southern latitudes of the species range. Herein we generate nearly 50 years of otolith-derived recruitment and growth histories for Australian bass and relate these to hydrologic, climatic and demographic variables. We found that younger Australian bass grew fastest in years following a cooler spring, whereas the growth of older fish exhibited little response to temperature. Australian bass year class strength was positively related to high flows in spring and in a negative curvilinear way to spring temperature. A lack of suitable natural flows in spring may be responsible for little to no recruitment of Australian bass in the Genoa River over the past two decades. Based on our findings, the continuing trend of lower rainfall and higher temperatures, coupled with river regulation in some systems in the region, will likely result in depressed juvenile growth and prolonged periods of recruitment failure over the medium to longer term, with significant implications for the viability of populations.

Flow magnitude and variability influence growth of two freshwater fish species in a large regulated floodplain river

Fish are often targets for environmental watering outcomes under the premise that aspects of the flow regime are linked to key components of their life-history. This study examined the conceptual link between variability in river discharge and fish productivity by measuring annual growth patterns (generated using sclerochronology over a 22-year period) of two native freshwater cod Maccullochella spp. species over a range of flow conditions in a regulated Australian floodplain River. We found a positive relationship between fish growth, flow variability and river discharge. Flow variability during spring and summer-autumn, as well as their antecedent values, was particularly important in explaining annual growth of the nationally endangered Maccullochella macquariensis. Growth of Maccullochella peelii displayed similar patterns, though were more closely aligned with spring discharge. These results are consistent with the general view that increased river regulation, due to its suppression of flow magnitude and variability, has been a major contributing factor in the decline of native fish populations throughout the world. Our results provide support and guidance for the use of environmental water delivery, and have broad application to rivers worldwide for which any quantification of ecological impacts of regulation, and responses to water management remain scarce.