Dispersal patterns and population structuring among platypuses, Ornithorhynchus anatinus, throughout south-eastern Australia

Applying a modified streamlined disease risk analysis framework to a platypus conservation translocation, with special consideration for the conservation of ecto- and endoparasites

Platypuses are the world's most evolutionarily distinct mammal and have several host-specific ecto- and endoparasites. With platypus populations declining, consideration should also be given to preserving these high conservation priority parasites alongside their charismatic host. A disease risk analysis (DRA) was performed for a platypus conservation translocation, using a modified streamlined methodology that incorporated a parasite conservation framework. DRA frameworks rarely consider parasite conservation. Rather, parasites are typically considered myopically in terms of the potential harm they may cause their host. To address this, a previously proposed parasite conservation framework was incorporated into an existing streamlined DRA methodology. Incorporation of the two frameworks was achieved readily, although there is opportunity for further refinement of this process. This DRA is significant as it is the first performed for any monotreme species, and implements the emerging approach of balancing the health and disease risk of the host with parasite conservation.

Fragmentation by major dams and implications for the future viability of platypus populations

The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (F_ST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; F_ST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, F_ST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.

Synergistic effects of a severe drought and fire on platypuses

The strong inter-dependence between terrestrial and freshwater ecosystems, mediated by the character of vegetation and landscapes, can have significant impacts to freshwater species. A changing climate towards hotter and drier climates is already increasing fire frequencies and severity around the world. The platypus (Ornithorhynchus anatinus) is an iconic freshwater Australia species, facing increasing threats since European colonisation and with a distribution which coincides with fire prone areas. While some evidence suggest platypuses are resilience to fires, the combination of severe wildfires and reduced water availability may significantly impact platypus populations. In this short communication we investigated the effects of fire on platypus populations in two rivers, following an extreme drought, comparing burnt and unburnt in adjacent river catchments, with similar habitat and geomorphology. Findings suggests significantly low platypus numbers in burned sites compared to those on the unburnt river, as well as to known densities across the species' range. Whether the fires directly impacted platypuses remains undetermined but the timing of the fires as well as an extreme drought likely impacted recruitment as we did not record any juveniles on both rivers. Platypuses are increasingly under threat from direct and indirect human developments across much of their range and increased frequency and severity of fires and droughts will further strain the viability of platypus populations, particularly in small streams more likely to dry out. Improving the resilience of platypus populations and their freshwater environments to both droughts and fires needs to become a priority.

Long-term movements and activity patterns of platypus on regulated rivers

The platypus is a semi-aquatic mammal, endemic to freshwater habitats of eastern Australia. There are gaps in the understanding of platypus movement behaviour within river systems, including spatial and temporal organization of individuals. We tracked movements of 12 platypuses on the regulated Snowy and Mitta Mitta Rivers for up to 12-months, the longest continuous tracking of platypus using acoustic telemetry. Platypuses remained relatively localized, occupying 0.73-8.45 km of river over 12 months, consistent with previous tracking studies over shorter periods. Males moved further than females, and larger males had higher cumulative movements, suggesting a possible relationship to metabolic requirements. Platypuses moved greater distances on the Mitta Mitta River, possibly associated with impacts of altered flow regimes to their macroinvertebrate diet. Increased movements and diurnal activity during winter were primarily driven by males, possibly attributable to breeding behaviours, rather than increased costs of winter foraging. Evidence for relatively small movements has implications for declining populations, given areas of localised declines are unlikely to be supplemented by migrating platypuses, especially when dispersal is restricted by dam walls. Understanding platypus movement behaviour is pertinent for their conservation, as water resource development and habitat modification continue to reduce connectivity between populations across their distribution.

Where are the platypuses (Ornithorhynchus anatinus) now? A snapshot in time of their distribution in the Greater Brisbane region

Distribution data on platypus populations within the Greater Brisbane region is currently lacking, limiting our understanding of their population status. We report 4 years of platypus environmental DNA data from waterways in this region and compare them to historical observational records from 1990 to 2016 to determine any changes to their distribution. Twenty-one of the 54 eDNA sampled waterways were sampled multiple times and had records of previous platypus presence. Five of these 21 repeatedly sampled waterways (24%) did not have evidence of platypus presence, based on eDNA. This raises the concern that platypuses may no longer inhabit these waterways. We hope this study encourages further investigations on platypus to identify the extent of their decline within the region, along with possible broader state-wide review of their conservation status for future protection.

The platypus: evolutionary history, biology, and an uncertain future

The platypus (Ornithorhynchus anatinus) is one of the world's most evolutionarily distinct mammals, one of five extant species of egg-laying mammals, and the only living species within the family Ornithorhynchidae. Modern platypuses are endemic to eastern mainland Australia, Tasmania, and adjacent King Island, with a small introduced population on Kangaroo Island, South Australia, and are widely distributed in permanent river systems from tropical to alpine environments. Accumulating knowledge and technological advancements have provided insights into many aspects of its evolutionary history and biology but have also raised concern about significant knowledge gaps surrounding distribution, population sizes, and trends. The platypus' distribution coincides with many of Australia's major threatening processes, including highly regulated and disrupted rivers, intensive habitat destruction, and fragmentation, and they were extensively hunted for their fur until the early 20th century. Emerging evidence of local population declines and extinctions identifies that ecological thresholds have been crossed in some populations and, if threats are not addressed, the species will continue to decline. In 2016, the IUCN Red Listing for the platypus was elevated to "Near Threatened," but the platypus remains unlisted on threatened species schedules of any Australian state, apart from South Australia, or nationally. In this synthesis, we review the evolutionary history, genetics, biology, and ecology of this extraordinary mammal and highlight prevailing threats. We also outline future research directions and challenges that need to be met to help conserve the species.

Insights into Platypus Population Structure and History from Whole-Genome Sequencing

The platypus is an egg-laying mammal which, alongside the echidna, occupies a unique place in the mammalian phylogenetic tree. Despite widespread interest in its unusual biology, little is known about its population structure or recent evolutionary history. To provide new insights into the dispersal and demographic history of this iconic species, we sequenced the genomes of 57 platypuses from across the whole species range in eastern mainland Australia and Tasmania. Using a highly improved reference genome, we called over 6.7 M SNPs, providing an informative genetic data set for population analyses. Our results show very strong population structure in the platypus, with our sampling locations corresponding to discrete groupings between which there is no evidence for recent gene flow. Genome-wide data allowed us to establish that 28 of the 57 sampled individuals had at least a third-degree relative among other samples from the same river, often taken at different times. Taking advantage of a sampled family quartet, we estimated the de novo mutation rate in the platypus at 7.0 × 10-9/bp/generation (95% CI 4.1 × 10-9-1.2 × 10-8/bp/generation). We estimated effective population sizes of ancestral populations and haplotype sharing between current groupings, and found evidence for bottlenecks and long-term population decline in multiple regions, and early divergence between populations in different regions. This study demonstrates the power of whole-genome sequencing for studying natural populations of an evolutionarily important species.

Postglacial dispersal patterns and mitochondrial genetic structure of the Pyrenean desman (Galemys pyrenaicus) in the northwestern region of the Iberian Peninsula

The genetic structure of small semiaquatic animals may be influenced by dispersal across both rivers and land. The relative importance of these two modes of dispersal may vary across different species and with ecological conditions and evolutionary periods. The Pyrenean desman (Galemys pyrenaicus) is an endemic mammal of the Iberian Peninsula with a strong phylogeographic structure and semiaquatic habits, thus making it an ideal model to study the effects of river and overland dispersal on its genetic structure. Thanks to different types of noninvasive samples, we obtained an extensive sampling of the Pyrenean desman from the northwestern region of the Iberian Peninsula and sequenced two mitochondrial DNA fragments. We then analyzed, using an isolation‐by‐distance approach, the correlation between phylogenetic distances and geographical distances measured along both river networks and land to infer the relative importance of river and overland dispersal. We found that the correlations in the whole area and in a large basin were consistent with an effect of overland dispersal, which may be due to the postglacial colonization of new territories using terrestrial corridors and, possibly, a more extensive fluvial network that may have been present during the Holocene. However, in a small basin, likely to be less influenced by the impact of ancient postglacial dispersal, the correlations suggested significant overall effects of both overland and river dispersal, as expected for a semiaquatic mammal. Therefore, different scales and geographical regions reflect different aspects of the evolutionary history and ecology of this semiaquatic species using this isolation‐by‐distance method. The results we obtained may have crucial implications for the conservation of the Pyrenean desman because they reinforce the importance of interbasin dispersal for this species in the studied area and the need to protect the whole riverine ecosystem, including rivers, upland streams and terrestrial corridors between basins.

Diversity and phylogeny of south-east Queensland Bathynellacea

The crustacean order Bathynellacea is amongst the most diverse and widespread groups of subterranean aquatic fauna (stygofauna) in Australia. Interest in the diversity and biogeography of Australian Bathynellacea has grown markedly in recent years. However, relatively little information relating to this group has emerged from Queensland. The aim of this study was to investigate bathynellacean diversity and phylogeny in south-east Queensland. Relationships between the south-east Queensland fauna and their continental relatives were evaluated through the analysis of combined mitochondrial and nuclear DNA sequence data. Bathynellaceans were collected from alluvial groundwater systems in three catchments in south-east Queensland. This study revealed a diverse bathynellacean fauna with complex evolutionary relationships to related fauna elsewhere in Queensland, and on the wider Australian continent. The multifamily assemblage revealed here is likely to represent several new species, and at least one new genus within the Parabathynellidae. These taxa likely have relatively restricted geographic distributions. Interestingly, the south-east Queensland Bathynellacea appeared to be distantly related to their north-east Queensland counterparts. Although it was not possible to determine the generic identities of their closest relatives, the south-east Queensland Parabathynellidae appear to be most closely affiliated with southern and eastern Australian lineages. Together with previous survey data, the findings here suggest that there is likely to be considerable bathynellacean diversity in alluvial groundwater systems across the wider Queensland region. Further assessment of stygofauna distributions in south-east Queensland is necessary to understand the biological implications of significant groundwater use and development in the region.

Life history and dynamics of a platypus (Ornithorhynchus anatinus) population: four decades of mark-recapture surveys

Knowledge of the life-history and population dynamics of Australia's iconic and evolutionarily distinct platypus (Ornithorhynchus anatinus) remains poor. We marked-recaptured 812 unique platypuses (total 1,622 captures), over four decades (1973-2014) in the Shoalhaven River, Australia. Strong sex-age differences were observed in life-history, including morphology and longevity. Apparent survival of adult females (Φ = 0.76) were higher than adult males (Φ = 0.57), as in juveniles: females Φ = 0.27, males Φ = 0.13. Females were highly likely to remain in the same pool (adult: P = 0.85, juvenile: P = 0.88), while residency rates were lower for males (adult: P = 0.74, juvenile: P = 0.46). We combined survival, movement and life-histories to develop population viability models and test the impact of a range of life-history parameters. While using estimated apparent survival produced unviable populations (mean population growth rate r = -0.23, extinction within 20 years), considering residency rates to adjust survival estimates, indicated more stable populations (r = 0.004, p = 0.04 of 100-year extinction). Further sensitivity analyses highlighted adult female survival and overall success of dispersal as most affecting viability. Findings provide robust life-history and viability estimates for a difficult study species. These could support developing large-scale population dynamics models required to underpin a much needed national risk assessment for the platypus, already declining in parts of its current distribution.

landgenreport: a new r function to simplify landscape genetic analysis using resistance surface layers

We describe functions recently added to the r package popgenreport that can be used to perform a landscape genetic analysis (LGA) based on landscape resistance surfaces, which aims to detect the effect of landscape features on gene flow. These functions for the first time implement a LGA in a single framework. Although the approach has been shown to be a valuable tool to study gene flow in landscapes, it has not been widely used to date, despite the type of data being widely available. In part, this is likely due to the necessity to use several software packages to perform landscape genetic analyses. To apply LGA functions, two types of data sets are required: a data set with spatially referenced and genotyped individuals, and a resistance layer representing the effect of the landscape. The function outputs three pairwise distance matrices from these data: a genetic distance matrix, a cost distance matrix and a Euclidean distance matrix. Statistical tests are performed to test whether the cost matrix contributes to the understanding of the observed population structure. A full report on the analysis and outputs in the form of plots and tables of all intermediate steps of the LGA is produced. It is possible to customize the LGA to allow for different cost path approaches and measures of genetic distances. The package is written in the r language and is available through the Comprehensive r Archive. Comprehensive tutorials and information on how to install and use the package are provided at the authors' website (www.popgenreport.org).

Variation in platypus (Ornithorhynchus anatinus) life-history attributes and population trajectories in urban streams

An understanding of animal population dynamics relies on identifying life-history attributes associated with population growth and determining how these are affected by environmental variables. We analysed platypus population processes over a 10-year period through mark–recapture studies conducted in three spatially independent stream systems located in the suburbs of Melbourne, Australia. The three populations were collectively characterised by a slightly male-biased adult sex ratio (1.15 : 1) and relatively low reproductive success (<0.5 juvenile captured annually per adult female). An estimated 16% of core residents disappeared annually and 18% of marked juveniles were recaptured as adults. However, some demographic parameters (reproductive success, frequency of non-core adult captures) varied significantly among populations. Estimates of annual core population size in the three systems varied asynchronously, with different trajectories in population size potentially reflecting habitat differences (amount of urban development, reliability of surface flow) as well as variation in spatial isolation and catchment history (implementation of stream rehabilitation programs, occurrence of severe floods). Across all three populations, significant variability in annual reproductive success was explained by linear relationships with the amount of rainfall recorded in the five months before breeding (positive) and after juveniles emerge from nesting burrows (negative).