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Ectotherms are considered vulnerable to climate change as many operate at close to their thermal maxima. Exposure to higher temperatures could reduce activity by forcing animals to shelter in thermal refugia to avoid exceeding lethal limits. While rising temperatures should reduce activity in tropical species, the situation is less clear for temperate-zone species where activity can be constrained by both low and high temperatures. Here, we measure the effects of natural variation in environmental temperatures on activity in a temperate grassland lizard and show that it is operating at its upper thermal limit in summer even when sheltering in thermal refuges. As air temperatures increased above 32°C, lizard activity declined markedly as individuals sought refuge in cool microhabitats while still incurring substantial metabolic costs. We estimate that warming over the last two decades has required these lizards to increase their energy intake by over 20% to offset metabolic losses caused by rising temperatures. Our results show that recent increases in temperature are sufficient to exceed the thermal and metabolic limits of temperate-zone lizards. Extended periods of high temperatures could place natural populations of ectotherms under significantly increased environmental stress and contribute to population declines and extinction.

The introduction of species into new environments provides the opportunity for the evolution of new forms through admixture and novel selection pressures. The common brushtail possum, Trichosurus vulpecula vulpecula from the Australian mainland and T.v.fuliginosus from Tasmania, were introduced multiple times to New Zealand from Australia to become one of New Zealand’s most significant pests. Although derived from two subspecies, possums in New Zealand are generally considered to be a single entity. In a previous analysis, we showed that possums in the Hawkes Bay region of New Zealand appeared to consist of at least two overlapping populations. Here, we extend that analysis using a genotype-by-sequencing approach to examine the origins and population structure of those possums and compare their genetic diversity to animals sampled from Australia. We identify two populations of each subspecies in Hawkes Bay and provide clear evidence of a contact zone between them in which a hybrid form is evident. Our analysis of private alleles shows higher rates of dispersal into the contact zone than away from it, suggesting that the contact zone functions as a sink (and hence as a barrier) between the two subspecies. Given the widespread and overlapping distribution of the two subspecies across both large islands in New Zealand, it is possible that many such contact zones exist. These results suggest an opportunity for a more targeted approach to controlling this pest by recognising sub-specific differences and identifying the contact zones that may form between them.

Reptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about mechanisms of sex chromosome turnover. Recent studies have made significant progress in better understanding diversity and conservation of reptile sex chromosomes, with however no reptile master sex determination genes identified. Here we describe an integrated genomics and cytogenetics pipeline, combining probes generated from the microdissected sex chromosomes with transcriptome and genome sequencing to explore the sex chromosome diversity in non-model Australian reptiles. We tested our pipeline on a turtle, two species of geckos, and a monitor lizard. Genes identified on sex chromosomes were compared to the chicken genome to identify homologous regions among the four species. We identified candidate sex determining genes within these regions, including conserved vertebrate sex-determining genes爬行动物的性别决定一直备受关注，其性别决定和剂量补偿机制的多样性是我们理解复杂的性染色体转换机制的绝佳材料。近年来，关于爬行动物性染色体多样性和保护的研究取得了一系列重要进展，但目前爬行动物的主效性别决定基因被报道和研究地极少。该文发展了一套将基因组学和细胞遗传学结合起来的研究性染色体的方法。我们首先通过显微解剖获得性染色体特异的探针，再与转录组和基因组测序相结合，从而探索研究了多个澳大利亚非模式爬行动物的性染色体多样性。我们在一种龟、两种壁虎和一种巨蜥中测试了我们的流程。通过将性染色体上的基因与鸡的基因组相比较，我们推断了这四个物种与鸡的同源的候选性别决定区域。我们在这些区域中发现了候选的性别决定基因，包括在脊椎动物中比较保守的性别决定基因

Aspects of within-population spatial structure are often neglected in the modeling of population viability. To analyze the relevance of the spatial structure of single populations to population persistence, we compared the results of three models developed for the territorial, arboreal gecko Oedura reticulata: (1) a spatially structured model in which both low and high densities incur mortality costs due to increased movement, (2) a spatially structured model in which the Allee effect is removed, and (3) a spatially unstructured model in which there are no effects of density on mortality. Compared with nonspatial model populations, spatially structured populations exhibited reduced persistence. The Allee effect contributed only a small amount to the reduction in persistence. Increased mortality at high densities caused by difficulties in finding territories markedly reduced persistence in the spatially structured models compared with the density-independent nonspatial model. We argue that the inclusion of elements of spatial structure may considerably influence the estimation of extinction risk in population viability analyses.Los aspectos de la estructura espacial dentro de una población son frecuentemente ignorados en el modelado de viabilidad poblacional. Para analizar la importancia de la estructura espacial de poblaciones individuales en la persistencia de una población, comparamos los resultados de tres modelos desarrollados para un gecko arbóreo territorial, Oedura reticulata: (1) un modelo estructurado espacialmente en el cual tanto las densidades bajas como altas incurren en costos de mortalidad debido a un incremento en el movimiento, (2) un modelo estructurado espacialmente en el cual el efecto Allee es removido y (3) un modelo estructurado espacialmente en el cual no hay efectos de la densidad sobre la mortalidad. Comparados con modelos de poblaciones no espaciales, las poblaciones estructuradas espacialmente exhibieron una persistencia reducida. El efecto Allee contribuyóúnicamente con una pequeña proporción de la reducción en la persistencia. El incremento en mortalidad a elevadas densidades debido a la dificultad en encontrar territorios, disminuyó marcadamente la persistencia en los modelos estructurados espacialmente en comparación con los modelos no espaciales, denso-independientes. Argumentamos que la inclusión de los elementos de la estructura espacial puede influenciar considerablemente la estimación de los riesgos de extinción en los análisis de viabilidad poblaciones.

Agricultural modification is one of the main drivers of global biodiversity decline. Vegetation clearance, tillage, grazing, and the application of fertilisers and pesticides have significantly affected native plants and animals. Reptiles can be vulnerable to agricultural practices, and localised declines in reptile biodiversity have been detected. However, the causes of these declines are likely to be many and will vary among reptiles with different life histories. Fossorial reptiles (those that mainly live below ground) are likely to be particularly vulnerable to soil and ground cover disturbance and yet are little studied in the context of agricultural practices. Here, we test the proposition that habitat disturbance caused by agricultural modification is a good predictor of decline or absence of a fossorial lizard. Specifically, we used boosted regression trees to model the relationship between five habitat factors and site abundance of the threatened Pink‐tailed Worm‐lizard (Aprasia parapulchella; Pygopodidae). We found that vegetation characteristics were the best predictors of A. parapulchella abundance. In particular, the relative contributions to our model of percentage cover of native large tussock‐forming grasses and site floristic score were 46% and 33%, respectively. Other variables that contributed to the explanation of abundance were percentage cover of rocks (10%), number of turnable rocks (5%) and relative density of rocks occupied by ants of the size class known to occur with A. parapulchella (5%). Our findings suggest that agricultural management or restoration strategies that promote ground‐layer vegetation characteristic of low levels of modification are likely to be most beneficial for the conservation of this species. Our findings and methods may be applicable to understand and study the presence and abundance of other fossorial or semi‐fossorial reptiles with specialised habitat preferences. Further research is required to establish the generality of our findings with respect to other such species around the world.

Sex reversal at high temperatures during embryonic development (e.g., ZZ females) provides the opportunity for new genotypic crosses (e.g., ZZ male × ZZ female). This raises the alarming possibility that climatic warming could lead to the loss of an entire chromosome-one member of the sex chromosome pair (the Y or W)-and the transition of populations to environmental sex determination (ESD). Here we examine the evolutionary dynamics of sex-determining systems exposed to climatic warming using theoretical models. We found that the loss of sex chromosomes is not an inevitable consequence of sex reversal. A large frequency of ZZ sex reversal (50% reversal from male to female) typically divides the outcome between loss of the ZW genotype and the stable persistence of ZZ males, ZW females and ZZ females. The amount of warming associated with sex chromosome loss depended on several features of wild populations-environmental fluctuation, immigration, heritable variation in temperature sensitivity and differential fecundity of sex-reversed individuals. Chromosome loss was partially or completely buffered when sex-reversed individuals suffered a reproductive fitness cost, when immigration occurred or when heritable variation for temperature sensitivity existed. Thus, under certain circumstances, sex chromosomes may persist cryptically in systems where the environment is the predominant influence on sex.

Habitat loss and fragmentation are likely to seriously impact parasites, a less studied but critical component of ecosystems, yet we lack long-term experimental evidence. Parasites structure communities, increase connectivity in food webs, and account for a large proportion of an ecosystem's total biomass. Food web models predict that parasites with multiple obligate hosts are at greater risk of extinction because the local extinction, or reduction in abundance, of any host will result in a life-cycle bottleneck for the parasite. We examine the response of a parasite and its multiple hosts to forest fragmentation over 26 years in the Wog Wog Habitat Fragmentation Experiment in southeastern Australia. The parasite is the nematode Hedruris wogwogensis, its intermediate host is the amphipod, Arcitalitrus sylvaticus, and its definitive host is the skink, Lampropholis guichenoti. In the first decade after fragmentation, nematodes completely disappeared from the matrix (plantation forestry) and all but disappeared from their definitive host (skinks) in fragments, and by the third decade after fragmentation had not appreciably recovered anywhere in the fragmented landscape compared to continuous forest. The low prevalence of the nematode in the fragmented landscape was associated with the low abundance of one or the other host in different decades: low abundance of the intermediate host (amphipod) in the first decade and low abundance of the definitive host (skink) in the third decade. In turn, the low abundance of each host was associated with changes to the abiotic environment over time due largely to the dynamically changing matrix as the plantation trees grew. Our study provides rare long-term experimental evidence of how disturbance can cause local extinction in parasites with life cycles dependent on more than one host species through population bottlenecks at any life stage. Mismatches in the abundance of multiple hosts over time are likely to be common following disturbance, thus causing parasites with complex life cycles to be particularly susceptible to habitat fragmentation and other disturbances. The integrity of food webs, communities, and ecosystems in fragmented landscapes may be more compromised than presently appreciated due to the sensitivity of parasites to habitat fragmentation.

Reptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about sex chromosome turnover and evolution. However, reptile sex chromosome variation remains largely uncharacterized and no reptile master sex determination genes have yet been identified. Here we describe a powerful and cost-effective “chromosomics” approach, combining probes generated from the microdissected sex chromosomes with transcriptome sequencing to explore this diversity in non-model Australian reptiles with heteromorphic or cryptic sex chromosomes. We tested the pipeline on a turtle, a gecko, and a worm-lizard, and we also identified sequences located on sex chromosomes in a monitor lizard using linked-read sequencing. Genes identified on sex chromosomes were compared to the chicken genome to identify homologous regions among the four species. We identified candidate sex determining genes within these regions, including conserved vertebrate sex-determining genes pdgfa, pdgfra amh and wt1, and demonstrated their testis or ovary-specific expression. All four species showed gene-by-gene rather than chromosome-wide dosage compensation. Our results imply that reptile sex chromosomes originated by independent acquisition of sex-determining genes on different autosomes, as well as translocations between different ancestral macro- and micro-chromosomes. We discuss the evolutionary drivers of the slow differentiation, but rapid turnover, of reptile sex chromosomes.

Sex-determination mechanisms and sex chromosomes are known to vary among reptile species and, in a few celebrated examples, within populations of the same species. The oriental garden lizard, Calotes versicolor, is one of the most intriguing species in this regard, exhibiting evidence of multiple sex-determination modes within a single species. One possible explanation for this unusual distribution is that in C. versicolor, different modes of sex determination are confined to a particular population or a species within a cryptic species complex. Here, we report on a population genetic analysis using SNP data from a methylation-sensitive DArT sequencing analysis and mitochondrial DNA data obtained from samples collected from six locations: three from Bangladesh and three from Thailand. Our aim was to determine whether C. versicolor is best described as a single species with multiple lineages or as multiple species, as well as if its sex-determination mechanisms vary within or between species. We present evidence that the latter possibility is the case and that C. versicolor comprises a complex of cryptic species. We also identify sex-linked markers within these species and use them to identify modes of sex determination. Overall, our results suggest that different sex-determination modes have evolved among closely related species and within populations of Agamid lizards.

O_LISoftware for realistically simulating complex population genomic processes is revolutionizing our understanding of evolutionary processes, and providing novel opportunities for integrating empirical data with simulations. However, the integration between simulation software and software designed for working with empirical data is currently not well developed. In particular, SLiM 3.0, which is one of the most powerful population genomic simulation frameworks for linking evolutionary dynamics with ecological patterns and processes is a standalone scripting language with limited data manipulation abilities. Here we present slimr, an R package designed to create a seamless link between SLiM 3.0 and the R development environment, with its powerful data manipulation and analysis tools. C_LIO_LIWe show how slimr, in combination with SliM, facilitates smooth integration between genetic data, ecological data and simulation in a single environment. The package enables pipelines that begin with data reading, cleaning, and manipulation, proceed to constructing empirically-based parameters and initial conditions for simulations, then to running numerical simulations, and finally to retrieving simulation results in a format suitable for comparisons with empirical data - aided by advanced analysis and visualization tools provided by R (such as ABC and deep learning). C_LIO_LIWe demonstrate the use of slimr with an example from our own work on the landscape population genomics of desert mammals, highlighting the advantage of having a single integrated tool for both data analysis and simulation. C_LIO_LIslimr makes the powerful simulation ability of SliM 3.0 directly accessible to R users, allowing integrated simulation projects that incorporate empirical data without the need to switch between software environments. This should provide more opportunities for evolutionary biologists and ecologists to use realistic simulations to better understand the interplay between ecological and evolutionary processes. slimr is available at https://rdinnager.github.io/slimr/. C_LI

Increasing rates of habitat fragmentation globally underscore the importance of understanding the full spectrum of fragmentation’s ecological consequences. Fragmentation alters the thermal environment of fragments, which may alter the body size of ectothermic organisms and in turn impact survival and reproduction. To determine whether experimental habitat fragmentation alters body size in the heliothermic, ground-dwelling common garden skink (Lampropholis guichenoti). We use body size data spanning 29 years to experimentally test the prediction that lizards will experience morphological changes in forest fragments but not in non-fragmented controls. Lizards were smaller in forest fragments relative to those in the non-fragmented controls after the fragmentation treatment was applied. For lizards within forest fragments, the greater the exposure to deforested areas, the greater the decline in body size. This pattern was strongest in the first 5 years following fragmentation and weakened or reversed over time as the pine plantation matrix surrounding the fragments matured. Using sampling site-scale temperature data for the most recent 5 years of the experiment, we show that temperature predicts lizard body size. Our findings are consistent with predictions made under the temperature-size rule that ectotherms will be smaller in fragmented landscapes because of temperature increases at newly created edges. Our results raise new concerns about the effects of fragmentation on organisms in remnant patches and offer new research priorities, as more evidence is needed to determine the generality of body size declines in fragmented landscapes. Our results also highlight that body size declines, often attributed to climate change, may be amplified by habitat fragmentation, which has been global in its impact.

Dragon lizards (Squamata: Agamidae) comprise about 520 species in six subfamilies distributed across Asia, Australasia and Africa. Only five species are known to have sex chromosomes. All of them possess ZZ/ZW sex chromosomes, which are microchromosomes in four species from the subfamily Amphibolurinae, but much larger in Phrynocephalus vlangalii from the subfamily Agaminae. In most previous studies of these sex chromosomes, the focus has been on Australian species from the subfamily Amphibolurinae, but only the sex chromosomes of the Australian central bearded dragon (Pogona vitticeps) are well-characterized cytogenetically. To determine the level of synteny of the sex chromosomes of P. vitticeps across agamid subfamilies, we performed cross-species two-colour FISH using two bacterial artificial chromosome (BAC) clones from the pseudo-autosomal regions of P. vitticeps. We mapped these two BACs across representative species from all six subfamilies as well as two species of chameleons, the sister group to agamids. We found that one of these BAC sequences is conserved in macrochromosomes and the other in microchromosomes across the agamid lineages. However, within the Amphibolurinae, there is evidence of multiple chromosomal rearrangements with one of the BACs mapping to the second-largest chromosome pair and to the microchromosomes in multiple species including the sex chromosomes of P. vitticeps. Intriguingly, no hybridization signal was observed in chameleons for either of these BACs, suggesting a likely agamid origin of these sequences. Our study shows lineage-specific evolution of sequences/syntenic blocks and successive rearrangements and reveals a complex history of sequences leading to their association with important biological processes such as the evolution of sex chromosomes and sex determination.

Agamid lizards (Squamata: Agamidae) are karyotypically heterogeneous. Among the 101 species currently described from Australia, all are from the subfamily Amphibolurinae. This group is, with some exceptions, karyotypically conserved, and all species involving heterogametic sex show female heterogamety. Here, we describe the chromosomes of 2 additional Australian agamid lizards, Tympanocryptis lineata and Rankinia diemensis. These species are phylogenetically and cytogenetically sisters to the well-characterised Pogona vitticeps, but their sex chromosomes and other chromosomal characteristics are unknown. In this study, we applied advanced molecular cytogenetic techniques, such as fluorescence in situ hybridisation (FISH) and cross-species gene mapping, to characterise chromosomes and to identify sex chromosomes in these species. Our data suggest that both species have a conserved karyotype with P. vitticeps but with subtle rearrangements in the chromosomal landscapes. We could identify that T. lineata possesses a female heterogametic system (ZZ/ZW) with a pair of sex microchromosomes, while R. diemensis may have heterogametic sex chromosomes, but this requires further investigations. Our study shows the pattern of chromosomal rearrangements between closely related species, explaining the speciation within Australian agamid lizards of similar karyotypes.

The DNA detection of wildlife from environmental samples has the potential to contribute significantly to wildlife management and ecological research. In terrestrial ecosystems, much work has focused on the identification of mammal predators from faecal (scat) samples. However, the relatively high time and financial costs of collecting and analysing scat DNA remain barriers to more widespread implementation of such DNA detection methods, especially for high-throughput surveys. Here, we evaluate methods used for DNA extraction from scats, as applied to detection of the Australian red fox, an introduced predator. We compare the relative costs of two approaches: the method previously used to screen thousands of scat samples in surveys over several years, and a modified version which involves swabbing scats at the time of collection and using a mechanised liquid handling platform to extract DNA from the swabs. We demonstrate that mechanised DNA extraction from swabs is more efficient than manual DNA extraction from whole scats, in terms of both time and resources. This provides a means for rapid, high-throughput screening of scats for the presence of mammal predators, enabling time-effective management responses to non-invasive surveys.

Aim Range expansions facilitated by humans or in response to local biotic or abiotic stressors provide the opportunity for species to occupy novel environments. Classifying the status of newly expanded populations can be difficult, particularly when the timing and nature of the range expansion are unclear. Should native species in new habitats be considered invasive pests or actively conserved? Here, we present an analytical framework applied to an Australian marsupial, the sugar glider (Petaurus breviceps), a species that preys upon on an endangered parrot in Tasmania, and whose provenance was uncertain. Location Tasmania, Australia. Methods We conducted an extensive search of historical records for sugar glider occurrences in Tasmania. Source material included museum collection data, early European expedition logs, community observation records, and peer‐reviewed and grey literature. To determine the provenance of the Tasmanian population, we sequenced two mitochondrial genes and one nuclear gene in Tasmanian animals (n = 27) and in individuals across the species' native range. We then estimated divergence times between Tasmania and southern Australian populations using phylogenetic and Bayesian analyses. Results We found no historical evidence of sugar gliders occurring in Tasmania prior to 1835. All Tasmanian individuals (n = 27) were genetically identical at the three genes surveyed here with those individuals being 0.125% divergent from individuals from a population in Victoria. Bayesian analysis of divergence between Tasmanian individuals and southern Australian individuals suggested a recent introduction of sugar gliders into Tasmania from southern Australia. Main conclusions Molecular and historical data demonstrate that Tasmanian sugar gliders are a recent, post‐European, anthropogenic introduction from mainland Victoria. This result has implications for the management of the species in relation to their impact on an endangered parrot. The analytical framework outlined here can assist environmental managers with the complex task of assessing the status of recently expanded or introduced native species.

The geographical distribution of a species is limited by factors such as climate, resources, disturbances and species interactions. Environmental niche models attempt to encapsulate these limits and represent them spatially but do not always incorporate disturbance factors. We constructed MaxEnt models derived from a remotely sensed vegetation classification with, and without, an agricultural modification variable. Including agricultural modification improved model performance and led to more sites with native vegetation and fewer sites with exotic or degraded native vegetation being predicted suitable for A. parapulchella. Analysis of a relatively well-surveyed sub-area indicated that including agricultural modification led to slightly higher omission rates but markedly fewer likely false positives. Expert assessment of the model based on mapped habitat also suggested that including agricultural modification improved predictions. We estimate that agricultural modification has led to the destructi...

The ability to detect the incursion of an invasive species or destroy the last individuals during an eradication program are some of the most difficult aspects of invasive species management. The presence of foxes in Tasmania is a contentious issue with recent structured monitoring efforts, involving collection of carnivore scats and testing for fox DNA, failing to detect any evidence of foxes. Understanding the likelihood that monitoring efforts would detect fox presence, given at least one is present, is therefore critical for understanding the role of scat monitoring for informing the response to an incursion. We undertook trials to estimate the probability of fox scat detection through monitoring by scat‐detector dogs and person searches and used this information to critically evaluate the power of scat monitoring efforts for detecting foxes in the Tasmanian landscape. The probability of detecting a single scat present in a 1‐km2 survey unit was highest for scat‐detector dogs searches (0.053) compared with person searches (x¯≅0.015) for each 10 km of search effort. Simulation of the power of recent scat monitoring efforts undertaken in Tasmania from 2011 to 2015 suggested that single foxes would have to be present in at least 20 different locations or fox breeding groups present in at least six different locations, in order to be detected with a high level of confidence (>0.80). We have shown that highly structured detection trials can provide managers with the quantitative tools needed to make judgments about the power of large‐scale scat monitoring programs. Results suggest that a fox population, if present in Tasmania, could remain undetected by a large‐scale, structured scat monitoring program. Therefore, it is likely that other forms of surveillance, in conjunction with scat monitoring, will be necessary to demonstrate that foxes are absent from Tasmania with high confidence.

Environmental governance aims to support positive ecological outcomes by establishing effective joint decision-making processes. Yet, complex environmental problems, such as invasive species management, often require urgent action under conditions of uncertainty. Establishing clear and workable environmental governance arrangements in these circumstances can be challenging, or even overlooked completely, in the rush to take action. We undertook an exploratory study, involving semi-structured interviews with 15 policy-makers and scientists, to examine the proposition that some aspects of environmental governance can be more important than others when urgent action is required under conditions of uncertainty. We analysed qualitative data regarding the major decisions points of a case study of invasive species management in Tasmania, Australia. We identified specific elements of governance that, when used under conditions of urgency and uncertainty, can: (a) undermine the ability to establish effective governance arrangements over the longer-term; or alternatively (b) lay the foundation for inclusive and adaptable governance arrangements. Aspects of environmental governance that can be more important than others when responding to urgent and uncertain problems relate to: assessing context; establishing a temporary task-force and setting goals; co-producing knowledge with stakeholders; engaging early; and clarifying and communicating responsibilities and governance arrangements. From our findings, we pose questions for policy-makers and practitioners to ask when responding to urgent problems, creating an opportunity to establish basic governance arrangements even when immediate action is required. These basic arrangements can have the capacity to evolve and respond to increasing levels of certainty, complexity and inclusion.

Sex chromosomes in some reptiles share synteny with distantly related amniotes in regions orthologous to squamate chromosome 2. The latter finding suggests that chromosome 2 was formerly part of a larger ancestral (amniote) super-sex chromosome and raises questions about how sex chromosomes are formed and modified in reptiles. Australian dragon lizards (Agamidae) are emerging as an excellent model for studying these processes. In particular, they exhibit both genotypic (GSD) and temperature-dependent (TSD) sex determination, show evidence of transitions between the two modes and have evolved non-homologous ZW sex microchromosomes even within the same evolutionary lineage. They therefore represent an excellent group to probe further the idea of a shared ancestral super-sex chromosome and to investigate mechanisms for transition between different sex chromosome forms. Here, we compare sex chromosome homology among eight dragon lizard species from five genera to identify key cytological differences and the mechanisms that may be driving sex chromosome evolution in this group. We performed fluorescence in situ hybridisation to physically map bacterial artificial chromosome (BAC) clones from the bearded dragon, Pogona vitticeps&rsquo, ZW sex chromosomes and a nucleolar organising region (NOR) probe in males and females of eight Agamid species exhibiting either GSD or TSD. We show that the sex chromosome derived BAC clone hybridises near the telomere of chromosome 2q in all eight species examined. This clone also hybridises to the sex microchromosomes of three species (P vitticeps, P. barbata and Diporiphora nobbi) and a pair of microchromosomes in three others (Ctenophorus pictus, Amphibolurus norrisi and Amphibolurus muricatus). No other chromosomes are marked by the probe in two species from the closely related genus Physignathus. A probe bearing nucleolar organising region (NOR) sequences maps close to the telomere of chromosome 2q in all eight species, and to the ZW pair in P. vitticeps and P. barbata, the W microchromosome in D. nobbi, and several microchromosomes in P. cocincinus. Our findings provide evidence of sequence homology between chromosome 2 and the sex chromosomes of multiple agamids. These data support the hypothesis that there was an ancestral sex chromosome in amniotes that gave rise to squamate chromosome 2 and raises the prospect that some particular property of this chromosome has favoured its role as a sex chromosome in amniotes. It is likely that the amplification of repetitive sequences associated with this region has driven the high level of heterochromatinisation of the sex-specific chromosomes in three species of agamid. Our data suggest a possible mechanism for chromosome rearrangement, including inversion and duplication near the telomeric regions of the ancestral chromosome 2 and subsequent translocation to the ZW sex microchromosomes in three agamid species. It is plausible that these chromosome rearrangements involving sex chromosomes also drove speciation in this group.

Taxonomic research is of fundamental importance in conservation management of threatened species, providing an understanding of species diversity on which management plans are based. The grassland earless dragon lizards (Agamidae: Tympanocryptis ) of southeastern Australia have long been of conservation concern but there have been ongoing taxonomic uncertainties. We provide a comprehensive taxonomic review of this group, integrating multiple lines of evidence, including phylogeography (mtDNA), phylogenomics (SNPs), external morphology and micro X-ray CT scans. Based on these data we assign the lectotype of T. lineata to the Canberra region, restrict the distribution of T. pinguicolla to Victoria and name two new species: T. osbornei sp. nov. (Cooma) and T. mccartneyi sp. nov. (Bathurst). Our results have significant conservation implications. Of particular concern is T. pinguicolla , with the last confident sighting in 1969, raising the possibility of the first extinction of a reptile on mainland Australia. However, our results are equivocal as to whether T. pinguicolla is extant or extinct, emphasizing the immediate imperative for continued surveys to locate any remaining populations of T. pinguicolla . We also highlight the need for a full revision of conservation management plans for all the grassland earless dragons.

Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates non-invasive ecological studies, but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity, and utility. Our framework makes possible a rigorous evaluation of likely sources of error. The first five steps can be conducted relatively rapidly and (where reference DNA sequences are available) require minimal laboratory resources, enabling assessment of primer suitability before investing in further work. Steps six to eight require more costly laboratory analyses, but are essential to evaluate risks of false positive and false negative results, while step 9 relates to field implementation. As an example, we have developed and evaluated primers to specifically amplify part of the mitochondrial ND2 gene from Australian bandicoots. If adopted during the early stages of primer development, our framework will facilitate large-scale implementation of well-designed DNA tests to detect specific wildlife from eDNA samples. This will provide researchers and managers with an understanding of the strengths and limitations of their data and the conclusions that can be drawn from them. This article is protected by copyright. All rights reserved.

Species are the most commonly recognised unit for conservation management, yet significant variation can exist below the level of taxonomic recognition and there is a lack of consensus around how a species might be defined. This definition has particular relevance when species designations are used to apportion conservation effort and when definitions might be made through legislation. Here, we use microsatellite DNA analyses to test the proposition that the last remaining populations of the endangered grassland earless dragon (Tympanocryptis pinguicolla) harbour substantial cryptic genetic variation. Our study provides strong evidence that long historical isolation and the recent impacts of urbanization, have led to genetic differentiation in microsatellite DNA allele frequencies and high numbers of private alleles among three genetic clusters. This differentiation is partially concordant with previous mitochondrial DNA analyses, which show the two regions (Canberra and Monaro) where this species exists, to be reciprocally monophyletic, but differs through the identification of a third genetic cluster that splits a northern Canberra cluster from that of southern Canberra. Our data also identify a stark contrast in population genetic structure between clusters such that high levels of genetic structure are evident in the highly urbanised Canberra region but not in the largely rural Monaro region. We conclude that this species, like many reptiles, harbours considerable cryptic variation and currently comprises three distinct and discrete units. These units could be classified as separate species for the purpose of conservation under the relevant Australian and international Acts drawing management appropriate to that status.

Sex biases in bird populations, particularly an excess of males, can threaten small, isolated populations by reducing reproductive rates. A skew in sex-ratio can be caused by (i) differential mortality at conception or hatching, (ii) differential survival to adulthood, or (iii) stochastic population processes. However, an observed sex-ratio bias can also result from a bias in census methods rather than a realised bias. Distinguishing between the two possibilities is critical to identifying the underlying causes. An excess of males has long been observed in the Kangaroo Island population of the endangered South Australian Glossy Black-Cockatoo (Calyptorhynchus lathami halmaturinus) (Psittaciformes: Cacatuidae), and our census data confirm this. Here, we use DNA-based sexing to test the accuracy of morphologically based nestling sex assignments in C. l. halmaturinus. We find that in all but one case, the DNA-based sexing was concordant with the sex assigned as nestlings, thus confirming the validity of nestling plumage-based sexing in a larger sample from this population. Our analysis of nestling sex data suggests that the adult sex-ratio is a function of a skew at fledging and not caused by higher rates of female mortality post fledging.

Cryptic lineages, comprising species complexes with deep genetic structuring across the landscape but without distinct morphological differences, impose substantial difficulties for systematists and taxonomists in determining true species diversity. Here, we present an integrative approach that combines data from phylogeography and geometric morphometric analyses of three-dimensional cranial models to revisit the uncertain taxonomy of earless dragons from southern and central Australia that at one time or another have been included under the name Tympanocryptis lineata . Our approach finds strong support for seven previously described species, and more importantly, five undescribed Tympanocryptis taxa for which we provide a taxonomic treatment. We also find evidence of introgression and hybridization in three discrete contact zones between lineages, supported by mitochondrial and nuclear genes, as well as morphological analyses. With a sampling design that includes at least five individuals for each genetic lineage with corresponding X-ray microcomputed tomography scans, we perform comparative evolutionary analyses to show that there is a significant phylogenetic signal in Tympanocryptis cranial shape. Our results demonstrate the importance of using multiple specimens in each genetic lineage, particularly in cases of potential hybridization, and that geometric morphometrics, when used in an integrative framework, is a powerful tool in species delimitation across cryptic lineages. Our results lay the groundwork for future evolutionary studies in this widespread group across multiple environmental types and identify several species of immediate conservation concern with a focus on T. petersi sp. nov. We suggest that this species has undergone significant population declines and warrants a full conservation assessment.

The microscopic characteristics of downy barbules of feathers can assist with species identification in forensic investigations, particularly when only minute fragments remain. Using light microscopy (LM) and scanning electron microscopy (SEM), we characterised the feather morphology of 62 species of birds from 18 Orders including representatives of all Orders found in Australia, except Sphenisciformes (penguins). We demonstrate that with a few notable exceptions, Australian birds display similar feather characteristics to their well-studied Northern hemisphere relatives. We also show that the microscopic characteristics of downy barbules can be used to differentiate these Orders. A more detailed investigation of 39 parrot species revealed substantial similarities among the species, indicating that microscopic characteristics could not differentiate among parrot species. However, there were some features (barbule length and macroscopic features, i.e. colour), that may provide clues as to the species of or...

Summary Diagnostic DNA tests have become important for species detection from environmental samples and are increasingly applied to the analysis of ecological systems and in wildlife management. The availability of reference DNA sequences from many taxa enables the development of diagnostic PCR primers. Where there is a high risk of false-positive PCR amplification, or where even a low rate of false positives has serious management implications, DNA sequencing is crucial for accurate specimen identification. The ability of DNA sequencing to discriminate among target and non-target species must be explored for each system. The red fox Vulpes vulpes is an invasive pest in Australia. A fox-specific PCR and sequencing test has been applied to a systematic survey of scats collected in Tasmania, where the management of a recent fox incursion remains controversial. We investigated the risk that DNA sequences obtained using this test might be mistakenly assigned to fox in cases of non-specific amplification, or mistakenly assigned to another species when fox DNA was correctly amplified. We conducted an analysis of barcoding efficacy using cytochrome b sequences from 74 vertebrates. In our analysis, no non-fox sequences were identified as fox (false positives) and no genuine fox sequences were misidentified (false negatives). This two-stage DNA test, including PCR screening and sequencing steps, can reliably discriminate fox DNA from that of other Australian species. Synthesis and applications. DNA tests are attractive to wildlife managers interested in detecting species that are cryptic or difficult to identify. When DNA data directly influence management decisions, it is important to understand the limitations of the genetic markers and the likely causes of failed identifications or erroneous species assignments. We show that short cytochrome b sequences can provide high specificity for vertebrate species assignment. We highlight the importance of developing appropriate reference sequence data bases for each study system, and of evaluating the potential for misidentification of different taxa.

The sex chromosomes in Sauropsida (reptiles and birds) have evolved independently many times. They show astonishing diversity in morphology ranging from cryptic to highly differentiated sex chromosomes with male (XX/XY) and female heterogamety (ZZ/ZW). Comparing such diverse sex chromosome systems thus provides unparalleled opportunities to capture evolution of morphologically differentiated sex chromosomes in action. Here, we describe chromosomal mapping of 18 microsatellite repeat motifs in eight species of Sauropsida. More than two microsatellite repeat motifs were amplified on the sex-specific chromosome, W or Y, in five species (Bassiana duperreyi, Aprasia parapulchella, Notechis scutatus, Chelodina longicollis, and Gallus gallus) of which the sex-specific chromosomes were heteromorphic and heterochromatic. Motifs (AAGG)n and (ATCC)n were amplified on the W chromosome of Pogona vitticeps and the Y chromosome of Emydura macquarii, respectively. By contrast, no motifs were amplified on the W chromosome of Christinus marmoratus, which is not much differentiated from the Z chromosome. Taken together with previously published studies, our results suggest that the amplification of microsatellite repeats is tightly associated with the differentiation and heterochromatinization of sex-specific chromosomes in sauropsids as well as in other taxa. Although some motifs were common between the sex-specific chromosomes of multiple species, no correlation was observed between this commonality and the species phylogeny. Furthermore, comparative analysis of sex chromosome homology and chromosomal distribution of microsatellite repeats between two closely related chelid turtles, C. longicollis and E. macquarii, identified different ancestry and differentiation history. These suggest multiple evolutions of sex chromosomes in the Sauropsida.

The first report of reptile sex reversal in the wild and rapid transition between genetic and environmental sex determination in the Australian bearded dragon (Pogona vitticeps) There have been repeated evolutionary transitions in reptiles between genetic and temperature-dependent sex determination, the regulatory process that initiates differentiation of the gonads in the early embryo to form either testes or ovaries. Various mechanisms have been proposed to explain the transition, including a role for sex reversal. Clare Holleley et al. present the first report of reptile sex reversal in the wild, associated with rapid transition between genetic and environmental sex determination. In a study of the Australian bearded dragon (Pogona vitticeps), they observe sex reversal at the warmer end of the animals geographic range. When sex-reversed females mate with normal males, the chromosomal sex determination system is lost and temperature-dependent sex determination is established. It is not known whether climate-induced changes in sex determination are advantageous or detrimental to the process of evolutionary adaptation. Sex determination in animals is amazingly plastic. Vertebrates display contrasting strategies ranging from complete genetic control of sex (genotypic sex determination) to environmentally determined sex (for example, temperature-dependent sex determination)1. Phylogenetic analyses suggest frequent evolutionary transitions between genotypic and temperature-dependent sex determination in environmentally sensitive lineages, including reptiles2. These transitions are thought to involve a genotypic system becoming sensitive to temperature, with sex determined by gene–environment interactions3. Most mechanistic models of transitions invoke a role for sex reversal3,4,5. Sex reversal has not yet been demonstrated in nature for any amniote, although it occurs in fish6 and rarely in amphibians7,8. Here we make the first report of reptile sex reversal in the wild, in the Australian bearded dragon (Pogona vitticeps), and use sex-reversed animals to experimentally induce a rapid transition from genotypic to temperature-dependent sex determination. Controlled mating of normal males to sex-reversed females produces viable and fertile offspring whose phenotypic sex is determined solely by temperature (temperature-dependent sex determination). The W sex chromosome is eliminated from this lineage in the first generation. The instantaneous creation of a lineage of ZZ temperature-sensitive animals reveals a novel, climate-induced pathway for the rapid transition between genetic and temperature-dependent sex determination, and adds to concern about adaptation to rapid global climate change.

Summary Polymerase chain reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identified – test sensitivity and specificity, respectively), particularly in combination with sequencing, is uncommon. This is important because PCR-based tests are prone to contamination in sampling and the laboratory. Here, we use an experimental case–control approach to estimate the sensitivity and specificity of a sequential PCR-based wildlife detection test used to identify incursions of red foxes into Tasmania from predator faeces (scats). Our results show that the sensitivity of the fox test is high (∼94%) for the PCR-based test on its own, but this decreases to ∼84% when combined with the DNA sequencing step. In contrast, the specificity increases from ∼96% in the PCR-only test to ˜99·6% after inclusion of the DNA sequencing step. The intense public scrutiny of the fox eradication programme in Tasmania has undoubtedly influenced the application of a sequential PCR test that maximizes specificity at the expense of sensitivity and so increases the risk that scats containing fox DNA would not be detected. This could lead to the establishment of foxes in Tasmania as a consequence. Synthesis and applications. Importantly, the estimation of the sensitivity and specificity of sequential tests enables decisions about the risk associated with mistaken identification (i.e. false negatives vs. false positives) to be quantified for decision-makers. The cost of false-negative errors should be balanced against the costs of false-positive errors, which could include the expenditure incurred in the application of unnecessary management actions were foxes not in fact present. Understanding the risks and costs associated with both false-negative and false-positive errors is therefore a key component to the decision-making process for the management of the Tasmanian fox incursion.

Reptiles are in global decline with nearly 20% of species currently threatened with extinction. Despite these alarming trends, data documenting detailed changes in reptile populations remain sparse and the methods for detecting those changes are largely unevaluated. Rock turning is one commonly used method for detecting the presence or absence of reptiles. Here, we use data from four years of rock turning surveys for the endangered Tympanocryptis pinguicolla to estimate the probability of species occurrence while accounting for detectability. Our data set was zero-inflated with only 36 detections despite some 69,146 detection attempts (rocks turned) across 60 sites. Our analysis revealed the species probability of detection per detection attempt is extremely low (0.00098 (95% CI: 0.00064–0.00142)) and suggested that the species remained undetected at some sampling sites where it was present. Indeed, our estimate of actual site occupancy was nearly double the naive estimate obtained when not accounting for detectability, suggesting the species is more widespread than previously thought. Our results highlight some important considerations for landscape conservation planning for T. pinguicolla and rupicoline (rock inhabiting) reptiles more generally. In particular, the application of rock turning as a sampling technique must be questioned given the low confidence of detecting a presence in the study reported here and the likely destructive nature of the approach. We recommend that the effectiveness of detection surveys by rock turning be fully evaluated for any species before it is applied widely as a detection technique and suggest that other approaches such as camera traps may prove equally or more effective while being less destructive.

In this chapter we explore the potential role of knowledge management in the development of environmental policy. we apply the seven c’s knowledge management model in the context of a very complex policymaking scenario, namely the potential eradication of the red fox in tasmania. this endeavour needed to integrate science, community, government and other stakeholders to design and implement effective policy and we shall argue that adopting a knowledge management approach might have helped to integrate the stakeholders and improve outcomes. first, we outline the case study, identifying some of the critical challenges to policy development and implementation. second, we identify why knowledge management needs to be more overtly considered in the role of policy making and the value of the seven c’s model in revealing where integration could usefully be used to improve outcomes. third, we present a framework for analysing context that enables a systematic analysis of our case study. fourth, we link the knowledge management model and the contextual framework together and apply them to the policymaking example. lastly, we consider the lessons learned and how knowledge management and systematic contextual analysis can add value to the policymaking process.

We developed a mini-barcode based on the 12S rRNA gene to identify predator from scats in Tasmania. To test the sensitivity of our primers to detect low template DNA samples, we set up serial dilutions of six DNA extracts originating from museum samples, representing each of the six mammal predators that might be detected in Tasmania (Tasmanian devil, eastern quoll, spotted tail quoll, cat, dog and fox).

Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover. Instead, targeted short diagnostic markers are required to serve as diagnostic mini-barcodes. The mitochondrial genome is a useful source of such trace DNA markers because it provides good resolution at the species level and occurs in high copy numbers per cell. We developed a mini-barcode based on a short (178 bp) fragment of the conserved 12S ribosomal ribonucleic acid mitochondrial gene sequence, with the goal of discriminating amongst the scats of large mammalian predators of Australia. We tested the sensitivity and specificity of our primers and can accurately detect and discriminate amongst quolls, cats, dogs, foxes, and devils from trace DNA samples. Our approach provides a cost-effective, time-efficient, and non-invasive tool that enables identification of all 8 medium-large mammal predators in Australia, including native and introduced species, using a single test. With modification, this approach is likely to be of broad applicability elsewhere.

Evaluating homology between the sex chromosomes of different species is an important first step in deducing the origins and evolution of sex-determining mechanisms in a clade. Here, we describe the preparation of Z and W chromosome paints via chromosome microdissection from the Australian marbled gecko (Christinus marmoratus) and their subsequent use in evaluating sex chromosome homology with the ZW chromosomes of the Kwangsi gecko (Gekko hokouensis) from eastern Asia. We show that the ZW sex chromosomes of C. marmoratus and G. hokouensis are not homologous and represent independent origins of female heterogamety within the Gekkonidae. We also show that the C. marmoratus Z and W chromosomes are genetically similar to each other as revealed by C-banding, comparative genomic hybridization, and the reciprocal painting of Z and W chromosome probes. This implies that sex chromosomes in C. marmoratus are at an early stage of differentiation, suggesting a recent origin.

The emerging availability of microsatellite markers from mammalian sex chromosomes provides opportunities to investigate both male- and female-mediated gene flow in wild populations, identifying patterns not apparent from the analysis of autosomal markers alone. Tammar wallabies (Macropus eugenii), once spread over the southern mainland, have been isolated on several islands off the Western Australian and South Australian coastlines for between 10 000 and 13 000 years. Here, we combine analyses of autosomal, Y-linked and X-linked microsatellite loci to investigate genetic variation in populations of this species on two islands (Kangaroo Island, South Australia and Garden Island, Western Australia). All measures of diversity were higher for the larger Kangaroo Island population, in which genetic variation was lowest at Y-linked markers and highest at autosomal markers (θ=3.291, 1.208 and 0.627 for autosomal, X-linked and Y-linked data, respectively). Greater relatedness among females than males provides evidence for male-biased dispersal in this population, while sex-linked markers identified genetic lineages not apparent from autosomal data alone. Overall genetic diversity in the Garden Island population was low, especially on the Y chromosome where most males shared a common haplotype, and we observed high levels of inbreeding and relatedness among individuals. Our findings highlight the utility of this approach for management actions, such as the selection of animals for translocation or captive breeding, and the ecological insights that may be gained by combining analyses of microsatellite markers on sex chromosomes with those derived from autosomes.

Australia’s natural temperate grasslands have diminished to 0.5 % of their former area since European settlement and, as a consequence, are highly fragmented and modified. Many vertebrate species that live in temperate grasslands are habitat specialists and therefore are at risk of decline through habitat loss and fragmentation. The grassland earless dragon (Tympanocryptis pinguicolla) is one such species. Once widespread, T. pinguicolla is now restricted to two general locations; the first is near Canberra in the Australian Capital Territory (including some adjacent land near Queanbeyan), and the second is the Monaro Tablelands in New South Wales. Here, we use microsatellite DNA data collected from the largest remaining populations near Canberra to examine genetic structure in this species in the context of the rapidly expanding urban landscape in this region. Our study revealed that, despite separation by only relatively small distances (largest distance ~13 km), the T. pinguicolla populations are highly genetically structured with little admixture. Our analyses also revealed that the population with the largest census size, but which has recently crashed in population size, exhibited little detectable gene flow to other populations and is essentially isolated. Our data indicate that significant barriers to dispersal exist among the remaining T. pinguicolla populations and that management of this species cannot rely on natural dispersal to bolster declining populations. Many different agencies and landholders are responsible for the protection of these remnant populations and a co-ordinated effort is required to provide reasonable confidence that the species will persist.

Habitat fragmentation can cause high levels of inbreeding within populations by creating small isolated populations and therefore can affect population survival. While most genetic studies of fragmented systems focus on the impact of habitat fragmentation on interpatch patterns or processes, here we focus on inbreeding (avoidance) processes within patches. We used both genetic and mark-recapture data to study within-patch processes in fragmented and continuous populations of the gecko Oedura reticulata in the Western Australian Wheatbelt. Our results revealed that O. reticulata in fragments and continuous populations alike share a promiscuous mating system (involving both polygyny and polyandry) and exhibit no detectable difference in mean levels of relatedness. However, we also found that proportions of full- and half-sib matings were higher in the habitat fragments, subadults disperse further, and all demographic classes move further and more frequently. We contend that the net result of this combination of promiscuity and greater movement is that small isolated populations have been able to retain mean levels of relatedness similar to those in nearby continuous habitat despite fragmentation and close to complete isolation over generations. It is likely that these behavioral changes have ameliorated some of the genetic effects caused by habitat fragmentation, potentially delaying reductions in the fitness effects expected from fragmentation into small populations.

Reptiles, as the sister group to birds and mammals, are particularly valuable for comparative genomic studies among amniotes. The Australian central bearded dragon (Pogona vitticeps) is being developed as a reptilian model for such comparisons, with whole-genome sequencing near completion. The karyotype consists of 6 pairs of macrochromosomes and 10 pairs microchromosomes (2n = 32), including a female heterogametic ZW sex microchromosome pair. Here, we present a molecular cytogenetic map for P. vitticeps comprising 87 anchor bacterial artificial chromosome clones that together span each macro- and microchromosome. It is the first comprehensive cytogenetic map for any non-avian reptile. We identified an active nucleolus organizer region (NOR) on the sub-telomeric region of 2q by mapping 18S rDNA and Ag-NOR staining. We identified interstitial telomeric sequences in two microchromosome pairs and the W chromosome, indicating that microchromosome fusion has been a mechanism of karyotypic evolution in Australian agamids within the last 21 to 19 million years. Orthology searches against the chicken genome revealed an intrachromosomal rearrangement of P. vitticeps 1q, identified regions orthologous to chicken Z on P. vitticeps 2q, snake Z on P. vitticeps 6q and the autosomal microchromosome pair in P. vitticeps orthologous to turtle Pelodiscus sinensis ZW and lizard Anolis carolinensis XY. This cytogenetic map will be a valuable reference tool for future gene mapping studies and will provide the framework for the work currently underway to physically anchor genome sequences to chromosomes for this model Australian squamate.

Although wild pig populations are known to sometimes be infected by Salmonella, the situation in Australia has received little attention and few population-based, planned studies have been conducted. Understanding the distribution of Salmonella infections within wild pig populations allows the potential hazard posed to co-grazing livestock to be assessed. We sampled a remote and isolated wild pig population in northwestern Australia. Faecal and mesenteric lymph node samples were collected from 651 wild pigs at 93 locations and cultured for Salmonella. The population sampled was typical of wild pig populations in tropical areas of Australia, and sampling occurred approximately halfway through the population's breeding season (38% of the 229 adult females were pregnant and 35% were lactating). Overall, the prevalence of Salmonella infection based on culture of 546 freshly collected faecal samples was 36.3% (95% CI 32.1-40.7%), and based on culture of mesenteric lymph nodes was 11.9% (95% CI, 9.4-15.0%). A total of 39 serovars (139 isolates) were identified--29 in faecal samples and 24 in lymph node samples--however neither Salmonella enterica serovar Typhimurium nor Salmonella Cholerasuis were isolated. There was a significant (p0.0001) disagreement between faecal and lymph node samples with respect to Salmonella isolation, with isolation more likely from faecal samples. Prevalence differed between age classes, with piglets being less likely to be faecal-positive but more likely to be lymph node positive than adults. The distribution of faecal-positive pigs was spatially structured, with spatial clusters being identified. Study results suggest that this population of wild pigs is highly endemic for Salmonella, and that Salmonella is transmitted from older to younger pigs, perhaps associated with landscape features such as water features. This might have implications for infection of co-grazing livestock within this environment.

Summary 1. Invasive vertebrate species are a world-wide threat to biodiversity and agricultural production. The presence of foxes, one of the most damaging invasive vertebrates introduced to Australia, has now been confirmed in the island state of Tasmania, placing at risk many species of native vertebrates and substantial agricultural industry. 2. Effective eradication of such a rare but elusive carnivore requires robust strategies informed by novel but systematic detection. 3. We combine DNA detection approaches for trace samples with systematic stratified and opportunistic surveys of carnivore scats to estimate the current distribution of foxes in Tasmania. We use that DNA evidence and other hard evidence provided by carcasses and other material to build a predictive model of fox habitat suitability for all of Tasmania. 4. We demonstrate that this destructive species is widespread in northern and eastern Tasmania but has not yet reached the limits of its range. The widespread nature of this distribution reveals that targeting fox activity hotspots only for eradication is unlikely to be successful and that a strategic and statewide approach is required. Our habitat suitability model can provide a basis for prioritizing areas for fox management. 5. Synthesis and applications. Our approach highlights the importance of early and preemptive surveys of recently established, and therefore rare, invasive species and the necessity of providing a sound and defensible approach to determining the distribution of the invasive species. This approach provides a template for the systematic detection of rare cryptic carnivores.

Interleukins are a group of cytokines with complex immunomodulatory functions that are important for regulating immunity in vertebrate species. Reptiles and mammals last shared a common ancestor more than 350 million years ago, so it is not surprising that low sequence identity has prevented divergent interleukin genes from being identified in the central bearded dragon lizard, Pogona vitticeps, in its genome assembly. To determine the complete nucleotide sequences of key interleukin genes, we constructed full-length transcripts, using the Trinity platform, from short paired-end read RNA sequences from stimulated spleen cells. De novo transcript reconstruction and analysis allowed us to identify interleukin genes that are missing from the published P. vitticeps assembly. Identification of key cytokines in P. vitticeps will provide insight into the essential molecular mechanisms and evolution of interleukin gene families and allow for characterization of the immune response in a lizard for comparison with mammals.