Search

Genomic diversity is a fundamental component of Earth’s total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species’ range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.

Urbanisation changes landscapes, often simplifying and homogenising natural ecosystems while introducing novel environments. Although this transformation often adversely impacts native wildlife, generalist species that exhibit broad dietary and habitat requirements can persist and take advantage of urban environments. To understand which life history traits most influence the occurrence of a diverse snake assemblage in an urban environment, we leveraged a dataset of 5102 detection records for 12 snake species in the tropical city of Darwin, Australia. By building ecological niche models, calculating urban niche hypervolume, and compiling life history data, we analysed the diversity of environments occupied by each species and determined which landscape components were most associated with occurrence data. In keeping with our hypothesis that generalist species would be more successful, we found that species with broader habitat and dietary preferences, as well as a penchant for arboreality, were associated with larger urban niche hypervolumes and more frequent human–snake interactions. Additionally, we found that colubrid snakes had significantly larger urban niche hypervolumes than elapid species. These findings contribute to understanding how life history traits aid wildlife persistence in, and adaptation to, urban ecosystems, and have implications for landscape design and conservation management.

Context Increases in fire frequency, intensity and extent are occurring globally. Relative to historical, Indigenous managed conditions, contemporary landscapes are often characterised by younger age classes of vegetation and a much smaller representation of long-unburnt habitat. Objectives We argue that, to conserve many threatened vertebrate species in Australia, landscape management should emphasise the protection of existing long-unburnt patches from fire, as well as facilitate the recruitment of additional long-unburnt habitat, while maintaining historically relevant age distributions of more recently burned patches. Methods We use a range of case studies and ecosystem types to illustrate three lines of evidence: (1) that many threatened vertebrate species depend on mid- to late-successional ecosystem attributes; (2) disturbance to long-unburnt habitat tends to increase risk of future disturbance and ecosystem collapse; and (3) contemporary landscapes exhibit a range of characteristics that differ to historical conditions and require context-specific management. Conclusions It is crucial that we adequately consider the implications of altered contemporary landscapes for management activities that aim to conserve threatened vertebrates. Contemporary landscapes often lack a range of critical structural and compositional components typical of late-successional habitat that are required for the persistence of threatened vertebrates. We need to shift towards strategic, objective-driven approaches that identify and protect long-unburnt habitats and promote their recruitment to enable recovery of many declining and threatened species.

Invasive plants are a threat to natural ecosystems worldwide with urban wetlands being some of the most susceptible and highly modified environments of all. The tiger snake (Notechis scutatus) is a top predator that persists in urban wetlands in south-western Australia, many of which have been degraded by introduced kikuyu grass (Cenchrus clandestinus). To evaluate the potential impact of kikuyu grass on habitat quality for western tiger snakes we quantified the structural features of habitats within wetlands degraded by kikuyu grass and compared them to wetlands with native vegetation, examined tiger snake prey availability, assessed predation risk for juvenile snakes using clay models, and measured the thermal quality of the vegetation. Proliferation of kikuyu grass reduced habitat structural heterogeneity by reducing available bare ground and increasing vegetation density. This homogenisation of habitat structure had little effect on the predation risk for juveniles or the thermal properties of tiger snake shelter sites; however, one key snake prey species, the motorbike frog, had significantly lower abundance in the most impacted habitat. Habitat types with more structural complexity also offered tiger snakes more stable thermal regimes and lower predation risk. These findings indicate that the current extent of kikuyu grass invasion offers overall similar habitat quality for tiger snakes and may contribute to their persistence in urban wetlands, but they, along with their anuran prey, may befit from some increased habitat structural complexity in open areas.

Tree hollows are a critical resource for many arboreal vertebrates, including many threatened species. In northern Australia’s vast tropical savannas, arboreal mammals are of particular conservation concern, as many have exhibited rapid population declines in recent decades. To understand the extent to which arboreal vertebrates compete for tree hollows in these savannas, we used motion-activated cameras to estimate rates of hollow visitation (i.e. individuals seen at the hollow entrance) and hollow use (i.e. individuals seen entering or exiting a hollow) by all vertebrate species at 29 hollows over a nine-month wet season period in the tropical savanna of Melville Island, Australia. We assessed the frequency of interactions between vertebrate species at the tree hollows. We recorded 21 vertebrate species visiting hollows, with larger hollows most frequently visited: 84% with entrance diameter > 10 cm. Larger-bodied mammal species were more likely to use larger hollows, in larger trees, at greater heights. However, smaller-bodies species also visited and used large hollows. The brush-tailed rabbit-rat (Conilurus penicillatus) used relatively shallow hollows close to the ground, and these hollows were most frequently visited by monitors (Varanus spp.) and snakes. This arboreal rodent has declined severely in recent decades, most likely due to predation by feral cats, and it is noteworthy that their hollow selection behaviour may be associated with increased predation risk. Our study highlights the importance of large tree hollows for a range of taxa in the tropical savannas of northern Australia and the potential impact of reductions in the density of large hollows on hollow-dependent species. Frequent, intense fires are a threat to large hollow-bearing trees, with appropriate fire management needed to conserve this resource and help to stem mammal declines.

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.

Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype-environment associations may show different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptus regnans) at two spatial scales: A species-wide data set and a topographically-complex subregional data set. We genotyped 367 individual trees at over 3700 single-nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range-wide scale. A total of 39 genic or near-genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation.

Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world’s most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (FST = 0.21–0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.

Global wildlife trade is a multibillion-dollar industry and a significant driver of vertebrate extinction risk. Yet, few studies have quantified the impact of wild harvesting for the illicit pet trade on populations. Long-lived species, by virtue of their slow life history characteristics, may be unable to sustain even low levels of collecting. Here, we assessed the impact of illegal collecting on populations of endangered broad-headed snakes (Hoplocephalus bungaroides) at gated (protected) and ungated (unprotected) sites. Because broad-headed snakes are long-lived, grow slowly and reproduce infrequently, populations are likely vulnerable to increases in adult mortality. Long-term data revealed that annual survival rates of snakes were significantly lower in the ungated population than the gated population, consistent with the hypothesis of human removal of snakes for the pet trade. Population viability analysis showed that the ungated population has a strongly negative population growth rate and is only prevented from ultimate extinction by dispersal of small numbers of individuals from the gated population. Sensitivity analyses showed that the removal of a small number of adult females was sufficient to impose negative population growth and suggests that threatened species with slow life histories are likely to be especially vulnerable to illegal collecting.

Natural disturbance regimes in forest ecosystems are being rapidly modified by anthropogenic pressures, including silvicultural practices and climate change. Australian forests dominated by mountain ash (Eucalyptus regnans) are critically endangered, with wildfires and clearfell logging predicted to cause ecosystem collapse within the next 50 years. To investigate the influence of disturbance on patterns and extent of genetic diversity in mountain ash, we compare replicated sites with three different disturbance histories (undisturbed, burnt, and logged). We employ genetic analysis at five chloroplast microsatellite loci and 2866 nuclear single-nucleotide polymorphisms (SNPs) to estimate within- and among- population genetic diversity, and assess the extent of fine-scale spatial genetic structure among individuals, for the three disturbance treatments. Consistent with the expectation of extensive pollen dispersal but limited seed dispersal, we detected low levels of genetic differentiation at nuclear SNPs (FST = 0.067), and very high levels of differentiation at cpDNA microsatellites (FST = 0.751). While differences among treatments at nuclear SNPs were small, we found stronger spatial genetic structure in the undisturbed treatment, higher levels of genetic differentiation in the logged treatment and greater partitioning of genetic diversity among logged sites. Analysis of cpDNA revealed significantly higher levels of total and within-site genetic diversity in the logged treatment than the burnt or undisturbed treatments, with haplotypes entering the system via the use of non-local seed in the regeneration process. We suggest that artificial regeneration activities should utilise a greater number of maternal parents, which could be achieved via variable retention harvesting or utilising a regional admixture provenancing approach.

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.

Conservation management often uses information on genetic population structure to assess the importance of local provenancing for ecological restoration and reintroduction programs. For species that do not exhibit complete reproductive isolation, the estimation of population genetic parameters may be influenced by the extent of admixture. Therefore, to avoid perverse outcomes for conservation, genetically informed management strategies must determine whether hybridization between species is relevant, and the extent to which observed population genetic patterns are shaped by interspecific versus intraspecific gene flow. We used genotyping by sequencing to identify over 2,400 informative single nucleotide polymorphisms across 18 populations of Eucalyptus regnans F. Muell., a foundation tree species of montane forests in south‐eastern Australia. We used these data to determine the extent of hybridization with another species, Eucalyptus obliqua L'Hér., and investigate how admixture influences genetic diversity parameters, by estimating metrics of genetic diversity and examining population genetic structure in datasets with and without admixed individuals. We found hybrid individuals at all sites and two highly introgressed populations. Hybrid individuals were not distributed evenly across environmental gradients, with logistic regression identifying hybrids as being associated with temperature. Removal of hybrids resulted in increases in genetic differentiation (F ST), expected heterozygosity, observed heterozygosity and the inbreeding coefficient, and different patterns of isolation by distance. After removal of hybrids and introgressed populations, mountain ash showed very little population genetic structure, with a small effect of isolation by distance, and very low global F ST(0.03). Our study shows that, in plants, decisions around provenancing of individuals for restoration depend on knowledge of whether hybridization is influencing population genetic structure. For species in which most genetic variation is held within populations, there may be little benefit in planning conservation strategies around environmental adaptation of seed sources. The possibility for adaptive introgression may also be relevant when species regularly hybridize.

Global wildlife trade is a multibillion-dollar industry and a significant driver of vertebrate extinction risk. Yet, few studies have quantified the impact of wild harvesting for the illicit pet trade on populations. Long-lived species, by virtue of their slow life history characteristics, may be unable to sustain even low levels of harvesting. Here, we assessed the impact of illegal poaching on a metapopulation of endangered broad-headed snakes (Hoplocephalus bungaroides) at gated (protected) and ungated (unprotected) populations. Because broad-headed snakes are long-lived, grow slowly and reproduce infrequently, populations are likely vulnerable to increases in adult mortality. Long-term data revealed that annual survival rates of snakes were significantly lower in the ungated population than the gated population, consistent with the hypothesis of human removal of snakes for the pet trade. Population viability analysis showed that the ungated population has a strongly negative population growth rate and is only prevented from ultimate extinction by dispersal of small numbers of individuals from the gated population. Sensitivity analyses showed that the removal of a small number of adult females was sufficient to impose negative population growth and suggests that threatened species with slow life histories are likely to be especially vulnerable to illegal poaching.

Anthropogenic modifications to climate and natural fire regimes are occurring globally, leading to the production of environments that may be unsuitable for some species. Fire-intolerant plant species that rely on specific fire regimes for reproduction are at risk of population decline when successive fires occur in less than the time taken to produce seed. Quantifying key fire-related life history traits in such species is therefore critical for developing models of population viability, species distributions and ecosystem persistence. We studied the Australian mountain ash (Eucalyptus regnans), the world’s tallest angiosperm and an ecologically and economically important keystone species. We tested whether mountain ash populations exhibit variation in susceptibility to increasing fire frequency by characterising the response of key vital rates to stand age (time since fire) under different environmental conditions. We found that the time taken to produce seed varied geographically. Mean growth rates were greater in areas receiving higher levels of solar radiation, a trend that became stronger with tree age. Tree size and age had the strongest influence on the production of fruit capsules. Mature fruit capsules were found in trees as young as 11 years old, but stands may not contain reproductively viable seed crops until they are more than 21 years old. Our results show that environmental factors influence the primary juvenile period of a keystone obligate seeder, in turn affecting the time taken for a population to develop a reproductively viable seed amount of seed. Reduced fire return intervals may therefore constrain the species’ realised niche (and geographic distribution) to areas where it can tolerate shorter fire return intervals due to faster growth and maturation. We suggest that populations of obligate seeders that reach reproductive viability faster are thus more likely to persist when exposed to multiple fires in short succession. Intra-stand variation in seed crops suggests that selection could also act on rapidly-maturing individuals, resulting in some populations exhibiting high levels of precocious reproductive activity.

Tiger snakes (Notechis scutatus) in wetlands of South-West Western Australia (SW WA) are commonly parasitised by the nematode Ophidascaris pyrrhus. Host-parasite interactions are complex and can potentially be impacted by factors such as urbanisation or climate. We assessed whether urbanisation, distance to wetland sites, and climatic factors have influenced parasitism in tiger snakes from specimens collected over the last century. We dissected 91 museum specimens of tiger snakes across SW WA and counted gastrointestinal nematodes. Binomial generalised linear modelling, with presence/absence of nematodes as a response variable, was used to determine which factors were driving infection. Model selection using AICc values showed that proximity to wetlands, rainfall and topographic wetness were most strongly associated with the probability of infection of snakes by nematodes. We also found a slight positive correlation between nematode abundance and annual mean maximum temperature. We found no significant influence of distance to urban centre on nematode burdens; however, our results suggest that water-related variables are a key driver of nematode parasitism in tiger snakes in SW WA. We also suggest that urbanisation is still of interest as its role in wetland and climate modification may increase parasitism in wetland snakes., Graphical abstract Image 1, Highlights • Nematode prevalence increases closer to wetlands, and in drier climates. • Nematode abundance possibly increases with annual mean maximum temperature. • Proximity to urbanisation has not influenced parasitism.

Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879-1960), 102 'recent' (1989-2012) and 52 'current' (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980's. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater's high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.