A portable Raspberry Pi-based camera set-up to record behaviours of frogs and other small animals under artificial or natural shelters in remote locations

We describe a Raspberry Pi-based camera system that is portable, robust and weatherproof, with a close-up focus (2.5 cm). We show that this camera system can be used in remote locations with high rainfall and humidity. The camera has an Infrared LED light to film in dark places and can continuously record up to 21 days (504 h). We also describe how to make concrete artificial shelters to mount the camera in. One of the great strengths of this shelter/camera set-up is that the animals choose to take up residence and can then be filmed for extended periods with no disturbance. Furthermore, we give examples of how shelters and cameras could be used to film a range of behaviours in not only many small cryptic amphibian species but also other small vertebrates and invertebrates globally.

An invasive pathogen drives directional niche contractions in amphibians

Global change is causing an unprecedented restructuring of ecosystems, with the spread of invasive species being a key driver. While population declines of native species due to invasives are well documented, much less is known about whether new biotic interactions reshape niches of native species. Here we quantify geographic range and realized-niche contractions in Australian frog species following the introduction of amphibian chytrid fungus Batrachochytrium dendrobatidis, a pathogen responsible for catastrophic amphibian declines worldwide. We show that chytrid-impacted species experienced proportionately greater contractions in niche breadth than geographic distribution following chytrid emergence. Furthermore, niche contractions were directional, with contemporary distributions of chytrid-impacted species characterized by higher temperatures, lower diurnal temperature range, higher precipitation and lower elevations. Areas with these conditions may enable host persistence with chytrid through lower pathogenicity of the fungus and/or greater demographic resilience. Nevertheless, contraction to a narrower subset of environmental conditions could increase host vulnerability to other threatening processes and should be considered in assessments of extinction risk and during conservation planning. More broadly, our results emphasize that biotic interactions can strongly shape species realized niches and that large-scale niche contractions due to new species interactions-particularly emerging pathogens-could be widespread.

Ongoing declines for the world's amphibians in the face of emerging threats

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

Linking physiology and climate to infer species distributions in Australian skinks

Climate has a key impact on animal physiology, which in turn can have a profound influence on geographic distributions. Yet, the mechanisms linking climate, physiology and distribution are not fully resolved. Using an integrative framework, we tested the predictions of the climatic variability hypothesis (CVH), which states that species with broader distributions have broader physiological tolerance than range-restricted species, in a group of Lampropholis skinks (8 species, 196 individuals) along a latitudinal gradient in eastern Australia. We investigated several physiological aspects including metabolism, water balance, thermal physiology, thermoregulatory behaviour and ecological performance. Additionally, to test whether organismal information (e.g. behaviour and physiology) can enhance distribution models, hence providing evidence that physiology and climate interact to shape range sizes, we tested whether species distribution models incorporating physiology better predict the range sizes than models using solely climatic layers. In agreement with the CVH, our results confirm that widespread species can tolerate and perform better at broader temperature ranges than range-restricted species. We also found differences in field body temperatures, but not thermal preference, between widespread and range-restricted species. However, metabolism and water balance did not correlate with range size. Biophysical modelling revealed that the incorporation of physiological and behavioural data improves predictions of Lampropholis distributions compared with models based solely on macroclimatic inputs, but mainly for range-restricted species. By integrating several aspects of the physiology and niche modelling of a group of ectothermic animals, our study provides evidence that physiology correlates with species distributions. Physiological responses to climate are central in establishing geographic ranges of skinks, and the incorporation of processes occurring at local scales (e.g. behaviour) can improve species distribution models.

The first linkage map for Australo-Papuan Treefrogs (family: Pelodryadidae) reveals the sex-determination system of the Green-eyed Treefrog (Litoria serrata)

Amphibians represent a useful taxon to study the evolution of sex determination because of their highly variable sex-determination systems. However, the sex-determination system for many amphibian families remains unknown, in part because of a lack of genomic resources. Here, using an F1 family of Green-eyed Treefrogs (Litoria serrata), we produce the first genetic linkage map for any Australo-Papuan Treefrogs (family: Pelodryadidae). The resulting linkage map contains 8662 SNPs across 13 linkage groups. Using an independent set of sexed adults, we identify a small region in linkage group 6 matching an XY sex-determination system. These results suggest Litoria serrata possesses a male heterogametic system, with a candidate sex-determination locus on linkage group 6. Furthermore, this linkage map represents the first genomic resource for Australo-Papuan Treefrogs, an ecologically diverse family of over 220 species.

Revision of zigzag geckos (Diplodactylidae: Amalosia) in eastern Australia, with description of five new species

Geckos of the genus Amalosia Wells & Wellington, 1984 occur across eastern and northern Australia. Only five species are described but additional diversity has been recognised for some time. Here we assess species diversity in eastern Australia, using morphological and genetic (ND4 mtDNA) data. We describe five new species, all morphologically distinct and highly genetically distinct (>25% divergence). Amalosia hinesi sp. nov. is found in woodlands on the western side of the Great Dividing Range in south-east Queensland and north-east New South Wales. Amalosia saxicola sp. nov. is a large species found on rocks in the MackayTownsville areas of mid-east Queensland, including on many offshore islands. Amalosia nebula sp. nov. is restricted to rocky areas in upland sclerophyll forest of the Wet Tropics region of north-east Queensland. Amalosia capensis sp. nov. is a small species found in the northern half of Cape York Peninsula. Amalosia queenslandia sp. nov. is a small species that is widespread through woodlands over much of eastern and central Queensland. These species are diagnosed from other Amalosia species in eastern Australia, including A. cf. rhombifer which occurs in north-western Queensland. Amalosia cf. rhombifer is part of the clades comprising the remainder of the A. rhombifer complex across the Northern Territory and Western Australia, which will be dealt with separately. Herein, we also we also synonymise the monotypic genus Nebulifera with Amalosia. This revision brings the number of Amalosia species to ten.

Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification

The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups which vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of⁠, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas.

Initiation of speciation across multiple dimensions in a rock-restricted, tropical lizard

Population isolation and concomitant genetic divergence, resulting in strong phylogeographical structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology and mating traits. Here we explored these multiple dimensions in two young (Plio-Pleistocene) species complexes of gekkonid lizards (Heteronotia) from the Kimberley-Victoria River regions of tropical Australia. Using mitochondrial DNA screening and exon capture phylogenomics, we show that the rock-restricted Heteronotia planiceps exhibits exceptional fine-scale phylogeographical structure compared to the codistributed habitat generalist Heteronotia binoei. This indicates pervasive population isolation and persistence in the rock-specialist, and thus a high rate of speciation initiation across this geographically complex region, with levels of genomic divergence spanning the "grey zone" of speciation. Proximal lineages of H. planiceps were often separated by different rock substrates, suggesting a potential role for ecological isolation; however, phylogenetic incongruence and historical introgression were inferred between one such pair. Ecomorphological divergence among lineages within both H. planiceps and H. binoei was limited, except that limestone-restricted lineages of H. planiceps tended to be larger than rock-generalists. By contrast, among-lineage divergence in the chemical composition of epidermal pore secretions (putative mating trait) exceeded ecomorphology in both complexes, but with less trait overlap among lineages in H. planiceps. This system-particularly the rock-specialist H. planiceps-highlights the role of multidimensional divergence during incipient speciation, with divergence in genomes, ecomorphology and chemical signals all at play at very fine spatial scales.

<i>Corrigendum to</i>: White-footed dunnarts (<i>Sminthopsis leucopus</i>) in Queensland&#x2019;s Wet Tropics, with the description of a new subspecies

A population of white-footed dunnarts (<i>Sminthopsis leucopus</i>) occurs in the Wet Tropics bioregion of tropical north Queensland, Australia separated by about 1800&#x2009;km from conspecifics in temperate New South Wales, Victoria and Tasmania. We conducted targeted surveys for <i>S. leucopus</i> in north-east Queensland and obtained new records, including the first reported capture of the species in Queensland in 18&#x2009;years. We assessed the genetic and morphological divergence of the north Queensland population against New South Wales, Victorian and Tasmanian <i>S. leucopus</i>, in conjunction with distribution and habitat differences, to assess whether this isolate should be described as a distinct taxon. Sequencing of the mitochondrial Cytochrome <i>b</i> gene revealed genetic divergence estimates of 2.3&#x2013;2.8% and 4.3&#x2013;4.8% between the north Queensland population and <i>S. l. ferruginifrons</i> (Victoria) and <i>S. l. leucopus</i> (Tasmania) respectively. Based on genetic divergence, cranial morphology, differences in habitat, and geographical isolation, we describe the north Queensland population as a new subspecies of <i>Sminthopsis leucopus</i>. We suggest a conservation classification of Endangered given its small distribution, apparent low density, tropical upland location and potential threats, especially related to climate change.

Historical biogeography highlights the role of Miocene landscape changes on the diversification of a clade of Amazonian tree frogs

The diversification processes underlying why Amazonia hosts the most species-rich vertebrate fauna on earth remain poorly understood. We studied the spatio-temporal diversification of a tree frog clade distributed throughout Amazonia (Anura: Hylidae: Osteocephalus, Tepuihyla, and Dryaderces) and tested the hypothesis that Miocene mega wetlands located in western and central Amazonia impacted connectivity among major biogeographic areas during extensive periods. We assessed the group’s diversity through DNA-based (16S rRNA) species delimitation to identify Operational Taxonomic Units (OTUs) from 557 individuals. We then selected one terminal for each OTU (n = 50) and assembled a mitogenomic matrix (~14,100 bp; complete for 17 terminals) to reconstruct a Bayesian, time-calibrated phylogeny encompassing nearly all described species. Ancestral area reconstruction indicates that each genus was restricted to one of the major Amazonian biogeographic areas (western Amazonia, Guiana Shield and Brazilian Shield, respectively) between ~10 and 20 Mya, suggesting that they diverged and diversified in isolation during this period around the Pebas mega wetland. After 10 Mya and the transition to the modern configuration of the Amazon River watershed, most speciation within each genus continued to occur within each area. In Osteocephalus, only three species expanded widely across Amazonia (< 6 Mya), and all were pond-breeders. Species with other breeding modes remained mostly restricted to narrow ranges. The spectacular radiation of Osteocephalus was probably driven by climatic stability, habitat diversity and the acquisition of new reproductive modes along the Andean foothills and western Amazonia. Our findings add evidence to the importance of major hydrological changes during the Miocene on biotic diversification in Amazonia.

Composition of a chemical signalling trait varies with phylogeny and precipitation across an Australian lizard radiation

The environment presents challenges to the transmission and detection of animal signalling systems, resulting in selective pressures that can drive signal divergence amongst populations in disparate environments. For chemical signals, climate is a potentially important selective force because factors such as temperature and moisture influence the persistence and detection of chemicals. We investigated an Australian lizard radiation (Heteronotia) to explore relationships between a sexually dimorphic chemical signalling trait (epidermal pore secretions) and two key climate variables: temperature and precipitation. We reconstructed the phylogeny of Heteronotia with exon capture phylogenomics, estimated phylogenetic signal in amongst-lineage chemical variation and assessed how chemical composition relates to temperature and precipitation using multivariate phylogenetic regressions. High estimates of phylogenetic signal indicate that the composition of epidermal pore secretions varies amongst lineages in a manner consistent with Brownian motion, although there are deviations to this, with stark divergences coinciding with two phylogenetic splits. Accounting for phylogenetic non-independence, we found that amongst-lineage chemical variation is associated with geographic variation in precipitation but not temperature. This contrasts somewhat with previous lizard studies, which have generally found an association between temperature and chemical composition. Our results suggest that geographic variation in precipitation can affect the evolution of chemical signalling traits, possibly influencing patterns of divergence amongst lineages and species.

Long distance (>20 km) downstream detection of endangered stream frogs suggests an important role for eDNA in surveying for remnant amphibian populations

Background

Globally, amphibian species have suffered drastic population declines over the past 40 years. Hundreds of species are now listed as Critically Endangered, with many of these considered "possibly extinct". Most of these species are stream-dwelling frogs inhabiting remote, montane areas, where remnant populations are hard to find using traditional surveys. Environmental DNA (eDNA) could revolutionize surveys for 'missing' and endangered amphibian populations by screening water samples from downstream sections to assess presence in the upstream catchments. However, the utility of this survey technique is dependent on quantifying downstream detection probability and distances.

Methods

Here we tested downstream detection distances in two endangered stream frogs (Litoria lorica and L. nannotis) that co-occur in a remote stream catchment in north-east Australia, and for which we know precise downstream distributional limits from traditional surveys. Importantly, the two last populations of L. lorica persist in this catchment: one small (~1,000 frogs) and one very small (~100 frogs). We conducted eDNA screening at a series of sites kilometers downstream from the populations using precipitation from two fixed water volumes (15 and 100 mL) and via water filtering (mean 1,480 L).

Results

We detected L. nannotis and the small L. lorica population (~1,000 frogs) at most sampling sites, including 22.8 km downstream. The filtration method was highly effective for far-downstream detection, as was precipitation from 100 mL water samples, which also resulted in consistent detections at the far-downstream sites (including to 22.8 km). In contrast, we had limited downstream detection success for the very small L. lorica population (~100 frogs).

Discussion

The ecological aspects of our study system, coupled with thorough traditional surveys, enabled us to measure downstream eDNA detection distances with accuracy. We demonstrate that eDNA from a small population of approximately 1,000 frogs can be detected as far as 22.8 km downstream from the population. Water filtration is considered best for eDNA detection of rare aquatic species-indeed it was effective in this study-but we also achieved far-downstream detections when precipitating eDNA from 100 mL water samples. Collecting small water volumes for subsequent precipitation in the lab is more practical than filtration when surveying remote areas. Our downstream detection distances (>20 km) suggest eDNA is a valuable tool for detecting rare stream amphibians. We provide recommendations on optimal survey methods.

A national-scale dataset for threats impacting Australia's imperiled flora and fauna

Australia is in the midst of an extinction crisis, having already lost 10% of terrestrial mammal fauna since European settlement and with hundreds of other species at high risk of extinction. The decline of the nation's biota is a result of an array of threatening processes; however, a comprehensive taxon-specific understanding of threats and their relative impacts remains undocumented nationally. Using expert consultation, we compile the first complete, validated, and consistent taxon-specific threat and impact dataset for all nationally listed threatened taxa in Australia. We confined our analysis to 1,795 terrestrial and aquatic taxa listed as threatened (Vulnerable, Endangered, or Critically Endangered) under Australian Commonwealth law. We engaged taxonomic experts to generate taxon-specific threat and threat impact information to consistently apply the IUCN Threat Classification Scheme and Threat Impact Scoring System, as well as eight broad-level threats and 51 subcategory threats, for all 1,795 threatened terrestrial and aquatic threatened taxa. This compilation produced 4,877 unique taxon-threat-impact combinations with the most frequently listed threats being Habitat loss, fragmentation, and degradation (n = 1,210 taxa), and Invasive species and disease (n = 966 taxa). Yet when only high-impact threats or medium-impact threats are considered, Invasive species and disease become the most prevalent threats. This dataset provides critical information for conservation action planning, national legislation and policy, and prioritizing investments in threatened species management and recovery.

A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis

Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse vertebrate group-Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost.

Parallel evolution of toepads in rock-dwelling lineages of a terrestrial gecko (Gekkota: Gekkonidae: Heteronotia binoei)

Selection for effective locomotion can lead to specialized morphological structures. Adhesive toepads, which have arisen independently in different lizard clades, facilitate the use of vertical and inverted substrates. Their evolution is poorly understood because functionally intermediate morphological configurations between padless and pad-bearing forms are rare. To shed light on toepad evolution, we assessed the subdigital morphology of phylogenetically distinct lineages of the Bynoe’s gecko species complex (Heteronotia binoei). Most populations of H. binoei are terrestrial, but two relatively distantly related saxicoline (rock-dwelling) lineages have enlarged terminal subdigital scales resembling toepads. We reconstructed the ancestral terminal subdigital scale size of nine lineages of H. binoei in eastern Australia, including these two saxicoline lineages. Additionally, we compared the subdigital microstructures of four lineages: the two saxicoline lineages and their respective terrestrial sister-lineages. Surprisingly, all four lineages had fully developed setae, but the setae of the two saxicoline lineages were significantly longer, branched more often and were more widely spaced than the terrestrial sister-lineages. We conclude that the saxicoline lineages represent examples of parallel evolution of enlarged adhesive structures in response to vertical substrate use, and their morphology represents a useful model as an intermediate state in toepad evolution.

Calling behaviour in the invasive Asian house gecko (Hemidactylus frenatus) and implications for early detection

Abstract ContextAcoustic communication is common in some animal groups, with an underlying function typically associated with mating or territoriality. Resolving the function of calls is valuable both in terms of understanding the fundamental biology of the species and, potentially, for applied reasons such as detection. Early detection is a key step in exclusion and eradication of invasive species, and calling behaviour can be used in this regard. The Asian house gecko (Hemidactylus frenatus) is one of a minority of lizards that uses acoustic communication. However, despite how conspicuous the call is, its function remains poorly resolved. It is also one of the world’s most invasive species, with exclusion via early detection being the key form of control. AimsThe aim was to resolve calling patterns and underlying function of the loud, multiple-chirp call (‘chik, chik, chik…’) in H. frenatus, in the context of using the results for developing effective methods for detection of new and establishing populations. MethodsThe calls of wild H. frenatus were recorded to assess peaks in calling activity. Also, laboratory experiments were performed to determine which individuals call, what causes them to call and the degree of call variation among individuals. Key resultsAssessment of calling behaviour in the wild revealed greater calling activity in warmer months, and five- to 10-fold peaks in calling activity at sunset and 30min before sunrise. Laboratory experiments revealed that calls were uttered exclusively by males and primarily by adults (although juveniles can call). Males called more when they were paired with females as opposed to other males. Calls differed among geckos, including the expected negative correlation between dominant frequency and body size. ConclusionsThe results suggest that the multiple-chirp call functions as a territory or sexual broadcast by males, perhaps containing information such as body size. ImplicationsDetection success can be maximised by performing acoustic surveys (by human or machine) during the calling peaks at 30min before sunrise and at sunset, particularly during warm nights. However, these surveys will only be effective for detecting adult males. The results also suggest that good quality recordings could potentially be used to identify individual geckos.

Beauty in the eye of the beholder: a new species of gecko (Diplodactylidae: Lucasium) from inland north Queensland, Australia

The Einasleigh Uplands bioregion of central north Queensland, Australia, harbours a unique suite of reptiles that have begun to receive significant attention in the last 20 years. This has resulted in a number of new reptile species being described, and recognition that others await description. We describe a new species of Lucasium Wermuth, 1965 from the western Einasleigh Uplands. Lucasium iris sp. nov. is genetically distinct and morphologically diagnosable from all congeners by its large size, long and narrow tail, nares in contact with rostral scale, homogeneous body scales, distinct vertebral stripe, and paired, enlarged, apical subdigital lamellae. It is known from low rocky hills in a localised area of the Gregory Range, has the most restricted known distribution of any Lucasium, and is the only Lucasium endemic to Queensland. The new species appears most closely related to L. steindachneri (Boulenger, 1885), based on mitochondrial DNA sequences, but has a colour-pattern more similar to L. immaculatum Storr, 1988. All three of these species occur in the Einasleigh Uplands, but only L. steindachneri is known to occur in sympatry with L. iris sp. nov. In addition to the description of the new species, we present records of Lucasium immaculatum from the Einasleigh Uplands, which represent a significant known range extension.

Quantifying range decline and remaining populations of the large marsupial carnivore of Australia’s tropical rainforest

Large predators are particularly susceptible to population declines due to large area requirements, low population density, and conflict with humans. Their low density and secretive habits also make it difficult to know the spatial extent, size, and connectivity of populations; declines hence can go unnoticed. Here, we quantified decline in a large marsupial carnivore, the spotted-tailed quoll (Dasyurus maculatus gracilis), endemic to the Wet Tropics rainforest of northeast Australia. We compiled a large database of occurrence records and used species distributional modeling to estimate the distribution in four time periods (Pre-1956, 1956–1975, 1976–1995, 1996–2016) using climate layers and three human-use variables. The most supported variables in the distribution models were climatic, with highly suitable quoll habitat having relatively high precipitation, low temperatures, and a narrow annual range in temperature. Land-use type and road density also influenced quoll distribution in some time periods. The modeling revealed a significant decline in the distribution of D. m. gracilis over the last century, with contraction away from peripheral areas and from large areas of the Atherton Tablelands in the center of the distribution. Tests of the change in patch availability for populations of 20, 50, and 100 individuals revealed a substantial (17–32%) decline in available habitat for all population sizes, with a particular decline (31–40%) in core habitat (i.e., excluding edges). Six remaining populations were defined. Extrapolating capture–recapture density estimates derived from two populations in 2017 suggests these populations are small and range from about 10 to 160 individuals. Our total population estimate sums to 424 individuals, but we outline why this estimate is positively skewed and that the actual population size may be &lt; 300 individuals. Continued decline and apparent absence in areas of highly suitable habitat suggests some threats are not being captured in our models. From our results, we provide management and research recommendations for this enigmatic predator.

Australian lizards are outstanding models for reproductive biology research

Australian lizards are a diverse group distributed across the continent and inhabiting a wide range of environments. Together, they exhibit a remarkable diversity of reproductive morphologies, physiologies, and behaviours that is broadly representative of vertebrates in general. Many reproductive traits exhibited by Australian lizards have evolved independently in multiple lizard lineages, including sociality, complex signalling and mating systems, viviparity, and temperature-dependent sex determination. Australian lizards are thus outstanding model organisms for testing hypotheses about how reproductive traits function and evolve, and they provide an important basis of comparison with other animals that exhibit similar traits. We review how research on Australian lizard reproduction has contributed to answering broader evolutionary and ecological questions that apply to animals in general. We focus on reproductive traits, processes, and strategies that are important areas of current research, including behaviours and signalling involved in courtship; mechanisms involved in mating, egg production, and sperm competition; nesting and gestation; sex determination; and finally, birth in viviparous species. We use our review to identify important questions that emerge from an understanding of this body of research when considered holistically. Finally, we identify additional research questions within each topic that Australian lizards are well suited for reproductive biologists to address.

Distribution and diet of feral cats (Felis catus) in the Wet Tropics of north-eastern Australia, with a focus on the upland rainforest

Abstract ContextFeral cats have been identified as a key threat to Australia’s biodiversity, particularly in arid areas and tropical woodlands. Their presence, abundance and potential impacts in rainforest have received less attention. AimsTo investigate the distribution and diet of feral cats (Felis catus) in upland rainforest of the Wet Tropics. MethodsWe collated available occurrence records from the Wet Tropics, and data from upland camera-trapping surveys over an 8-year period, to assess geographic and elevational distribution of feral cats in the bioregion. We also assessed the diet of feral cats from scats collected at upland sites. Key resultsFeral cats are widespread through the Wet Tropics bioregion, from the lowlands to the peaks of the highest mountains (&gt;1600m), and in all vegetation types. Abundance appears to vary greatly across the region. Cats were readily detected during camera-trap surveys in some upland rainforest areas (particularly in the southern Atherton Tablelands and Bellenden Ker Range), but were never recorded in some areas (Thornton Peak, the upland rainforest of Windsor Tableland and Danbulla National Park) despite numerous repeated camera-trap surveys over the past 8 years at some of these sites. Scat analysis suggested that small mammals comprise ~70% of the diet of feral cats at an upland rainforest site. Multivariate analysis could not detect a difference in mammal community at sites where cats were detected or not. ConclusionsFeral cats are widespread in the Wet Tropics and appear to be common in some upland areas. However, their presence and abundance are variable across the region, and the drivers of this variability are not resolved. Small mammals appear to be the primary prey in the rainforest, although the impacts of cats on the endemic and threatened fauna of the Wet Tropics is unknown. ImplicationsGiven their documented impact in some ecosystems, research is required to examine the potential impact of cats on Wet Tropics fauna, particularly the many upland endemic vertebrates. Studies are needed on (1) habitat and prey selection, (2) population dynamics, and (3) landscape source–sink dynamics of feral cats in the Wet Tropics.

Camera traps are an effective method for identifying individuals and determining the sex of spotted-tailed quolls (Dasyurus maculatus gracilis)

We compared two bait station techniques for determining the sex and identifying individual spotted-tailed quolls (Dasyurus maculatus gracilis) using images taken by camera traps. One method used bait in a plastic mesh bag and the other was a new method using a raised bait canister to entice the quolls to stand on their hind legs and present their ventral surface to the camera. Individuals were identified from multiple images of their unique spot pattern, and sex was determined from ventral images. The bait bag method was better for detecting quolls and both methods performed similarly in allowing observers to identify individuals from images. However, the bait canister method was superior for determining sex of individuals. Using this new bait canister method, individual identification was possible in 202 out of 206 detection events and the sex of 81% (47 of 58) of identified individuals was confidently assigned from multiple detections. This bait station design can therefore provide additional data on individual quolls and reduces the need for more invasive live-trapping techniques. This methodology could be adapted for other mammals in Australia and worldwide.

Description of three new velvet geckos (Diplodactylidae: Oedura) from inland eastern Australia, and redescription of Oedura monilis De Vis

Inland eastern Australia has a complex array of habitats, driven by variation in topography, geology and moisture. This broad region is relatively poorly surveyed compared to coastal eastern Australia and likely contains significant numbers of undescribed reptiles. Oedura monilis is found through much of this region but has been shrouded in taxonomic uncertainty since its original description. Here I assess variation across the range of 'O. monilis' and show that it consists of two species: a widespread species in the northern half of the range and a widespread species in the southern half of the range. These two species are readily diagnosed by colour pattern and aspects of shape and scalation. I show that the name O. monilis applies to the northern species. I also show that the name O. attenboroughi Wells Wellington applies to the northern populations, making it a junior synonym of O. monilis. I describe the southern widespread species as Oedura elegans sp. nov.. I also describe two new, highly localised species from inland eastern Queensland that are allied to O. monilis: Oedura picta sp. nov. from a rocky range in the Moranbah-Dysart region, and Oedura lineata sp. nov. from brigalow forest remnants in the Arcadia Valley. These two species are distinct for colour pattern and aspects of size, shape and scalation. Oedura lineata sp. nov. has a very small and fragmented range, and is restricted to a highly threatened habitat type. It therefore warrants conservation attention. I also provide more detailed diagnoses for O. coggeri Bustard and O. tryoni De Vis, and demonstrate that the name O. ocellata Boulenger is a junior synonym of O. tryoni.

A new species of Phyllurus leaf-tailed gecko (Lacertilia: Carphodactylidae) from The Pinnacles, north-east Australia

Recent surveys of rocky rainforest in the Townsville region have found additional populations of Phyllurus geckos. One of these populations was discovered at The Pinnacles, an isolated area of habitat in between the distributions of P. gulbaru and P. amnicola. Genetic and morphological data shows that this population is most similar to P. gulbaru Hoskin, Couper Schneider, 2003 but divergent in a number of traits. Here we describe this population as a new species, P. pinnaclensis sp. nov., based on genetic divergence and differences in a number of morphometric and scalation traits from other populations of Phyllurus. Phyllurus pinnaclensis sp. nov. appears to be restricted to a few small areas of deeply layered rock with associated dry rainforest. This habitat is fire-sensitive and increased frequency and intensity of fires (due to late season burns and high fuel loads of invasive grasses) threatens to reduce and fragment these dry rainforest patches. Other threats include potential future invasion of the habitat by introduced Asian House Geckos (Hemidactylus frenatus Duméril Bibron, 1836) and illegal collecting. Given the very small and fragmented distribution and potential reduction in habitat area due to fire, P. pinnaclensis sp. nov. warrants a Critically Endangered listing. Resolving the distributional change of dry rainforest in the Townsville region in recent decades, particularly in regards to fire, is key to resolving the status of this and other locally threatened taxa that depend on this habitat.

Beyond the model: expert knowledge improves predictions of species' fates under climate change

The need to proactively manage landscapes and species to aid their adaptation to climate change is widely acknowledged. Current approaches to prioritizing investment in species conservation generally rely on correlative models, which predict the likely fate of species under different climate change scenarios. Yet, while model statistics can be improved by refining modeling techniques, gaps remain in understanding the relationship between model performance and ecological reality. To investigate this, we compared standard correlative species distribution models to highly accurate, fine-scale, distribution models. We critically assessed the ecological realism of each species' model, using expert knowledge of the geography and habitat in the study area and the biology of the study species. Using interactive software and an iterative vetting with experts, we identified seven general principles that explain why the distribution modeling under- or overestimated habitat suitability, under both current and predicted future climates. Importantly, we found that, while temperature estimates can be dramatically improved through better climate downscaling, many models still inaccurately reflected moisture availability. Furthermore, the correlative models did not account for biotic factors, such as disease or competitor species, and were unable to account for the likely presence of micro refugia. Under-performing current models resulted in widely divergent future projections of species' distributions. Expert vetting identified regions that were likely to contain micro refugia, even where the fine-scale future projections of species distributions predicted population losses. Based on the results, we identify four priority conservation actions required for more effective climate change adaptation responses. This approach to improving the ecological realism of correlative models to understand climate change impacts on species can be applied broadly to improve the evidence base underpinning management responses.

A new species of velvet gecko (Diplodactylidae: Oedura) from sandstone habitats of inland north Queensland, Australia

We describe a new species of velvet gecko (Diplodactylidae: Oedura) from the sandstone ranges of central-north Queensland, Australia. Oedura argentea sp. nov. is a medium-sized (SVL 61-80 mm) gecko that is distinguished from its congeners by a combination of its relatively small size, a pattern of 5-6 dark-edged pale transverse bands from neck to pelvis, a silvery iris, a slender tail, a single cloacal spur, and in possessing 14-22 pre-cloacal pores in males. Oedura argentea sp. nov. is a sandstone specialist currently known only from the Gregory Range and nearby sandstone outcropping at Bulleringa National Park. Further surveys are required to determine the limits of distribution through this region. Oedura argentea sp. nov. is the fifth described species of Oedura in north-eastern Queensland. We also assess the name O. fracticolor De Vis, 1884 because it is an unresolved name pertaining to this general region. Based on colour-pattern and locality in the original description, we conclude that O. fracticolor is a senior synonym of O. castelnaui (Thominot, 1889); however, we propose that priority be overturned under Articles 23.9.1.1 and 23.9.1.2 of the ICZN (1999) and that the name O. fracticolor be regarded as nomen oblitum and O. castelnaui a nomen protectum.

Phylogenomics of a rapid radiation: the Australian rainbow skinks

Background

The application of target capture with next-generation sequencing now enables phylogenomic analyses of rapidly radiating clades of species. But such analyses are complicated by extensive incomplete lineage sorting, demanding the use of methods that consider this process explicitly, such as the multispecies coalescent (MSC) model. However, the MSC makes strong assumptions about divergence history and population structure, and when using the full Bayesian implementation, current computational limits mean that relatively few loci and samples can be analysed for even modest sized radiations. We explore these issues through analyses of an extensive (> 1000 loci) dataset for the Australian rainbow skinks. This group consists of 3 genera and 41 described species, which likely diversified rapidly in Australia during the mid-late Miocene to occupy rainforest, woodland, and rocky habitats with corresponding diversity of morphology and breeding colouration. Previous phylogenetic analyses of this group have revealed short inter-nodes and high discordance among loci, limiting the resolution of inferred trees. A further complication is that many species have deep phylogeographic structure – this poses the question of how to sample individuals within species for analyses using the MSC.

Results

Phylogenies obtained using concatenation and summary coalescent species tree approaches to the full dataset are well resolved with generally consistent topology, including for previously intractable relationships near the base of the clade. As expected, branch lengths at the tips are substantially overestimated using concatenation. Comparisons of different strategies for sampling haplotypes for full Bayesian MSC analyses (for one clade and using smaller sets of loci) revealed, unexpectedly, that combining haplotypes across divergent phylogeographic lineages yielded consistent species trees.

Conclusions

This study of more than 1000 loci provides a strongly-supported estimate of the phylogeny of the Australian rainbow skinks, which will inform future research on the evolution and taxonomy of this group. Our analyses suggest that species tree estimation with the MSC can be quite robust to violation of the assumption that the individuals representing a taxon are sampled from a panmictic population.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1130-4) contains supplementary material, which is available to authorized users.

Naïve rainforest frogs on Cape York, Australia, are at risk of the introduction of amphibian chytridiomycosis disease

Amphibian chytridiomycosis disease has caused widespread declines and extinctions of frogs in cool, wet habitats in eastern Australia. Screening suggests that the disease does not yet occupy all areas modelled to be environmentally suitable, including rainforests on Cape York Peninsula. Cape Melville is an area of rainforest with several endemic frogs, including the stream-associated Melville Range treefrog (Litoria andiirrmalin), which is deemed at particular risk of disease impacts. We tested 40 L. andiirrmalin for chytrid infection by PCR and found them all to be negative. In conjunction with previous testing at another high-risk location, McIlwraith Range, this suggests that endemic rainforest frogs on Cape York have been spared the introduction of chytridiomycosis. We discuss how the disease could get to these areas, what can be done to reduce the risk, and suggest an emergency procedure should it be introduced.

Resolving distribution and population fragmentation in two leaf-tailed gecko species of north-east Australia: key steps in the conservation of microendemic species

North Queensland harbours many microendemic species. These species are of conservation concern due to their small and fragmented populations, coupled with threats such as fire and climate change. We aimed to resolve the distribution and population genetic structure in two localised Phyllurus leaf-tailed geckos: P. gulbaru and P. amnicola. We conducted field surveys to better resolve distributions, used Species Distribution Models (SDMs) to assess the potential distribution, and then used the SDMs to target further surveys. We also sequenced all populations for a mitochondrial gene to assess population genetic structure. Our surveys found additional small, isolated populations of both species, including significant range extensions. SDMs revealed the climatic and non-climatic variables that best predict the distribution of these species. Targeted surveys based on the SDMs found P. gulbaru at an additional two sites but failed to find either species at other sites, suggesting that we have broadly resolved their distributions. Genetic analysis revealed population genetic structuring in both species, including deeply divergent mitochondrial lineages. Current and potential threats are overlain on these results to determine conservation listings and identify management actions. More broadly, this study highlights how targeted surveys, SDMs, and genetic data can rapidly increase our knowledge of microendemic species, and direct management.

Extinction debt from climate change for frogs in the wet tropics

The effect of twenty-first-century climate change on biodiversity is commonly forecast based on modelled shifts in species ranges, linked to habitat suitability. These projections have been coupled with species-area relationships (SAR) to infer extinction rates indirectly as a result of the loss of climatically suitable areas and associated habitat. This approach does not model population dynamics explicitly, and so accepts that extinctions might occur after substantial (but unknown) delays-an extinction debt. Here we explicitly couple bioclimatic envelope models of climate and habitat suitability with generic life-history models for 24 species of frogs found in the Australian Wet Tropics (AWT). We show that (i) as many as four species of frogs face imminent extinction by 2080, due primarily to climate change; (ii) three frogs face delayed extinctions; and (iii) this extinction debt will take at least a century to be realized in full. Furthermore, we find congruence between forecast rates of extinction using SARs, and demographic models with an extinction lag of 120 years. We conclude that SAR approaches can provide useful advice to conservation on climate change impacts, provided there is a good understanding of the time lags over which delayed extinctions are likely to occur.

A new skink (Scincidae: Liburnascincus) from rocky habitat on Cape York, northeast Australia

The genus Liburnascincus is composed of saxicoline skinks restricted to northeast Australia. This small radiation consists of one widespread species, L. mundivensis, found in a variety of rocky habitats in eastern Queensland, and two localized species, L. coensis and L. scirtetis, restricted to granite boulder habitats on Cape York Peninsula, in north Queensland. Here we describe a fourth species, L. artemis sp. nov., from the Bamboo Range, a low rocky range on Cape York. As for other Liburnascincus, the new species is a saxicoline skink that is active on boulder surfaces primarily early and late in the day. Liburnascincus artemis sp. nov. is most similar to L. mundivensis but can be diagnosed based on longer limbs, higher toe and finger lamellae counts, lower midbody scale count, and other aspects of morphology, scalation and colour pattern. Liburnascincus artemis sp. nov. is currently known from a very small area but further surveys will likely extend the range. It is geographically separated from L. mundivensis to the south by unsuitable habitat in the Laura region, but it may abut the range of L. coensis to the north. Despite a small distribution, L. artemis sp. nov. occurs at high density at the known sites and appears to be currently secure. In this paper we also discuss the distributions and biogeography of Liburnascincus more broadly.

Two new skinks (Scincidae: Glaphyromorphus) from rainforest habitats in north-eastern Australia

Tropical rainforest is largely restricted in Australia to the fairly continuous Wet Tropics region and disconnected patches to the north on Cape York. The Wet Tropics is relatively well explored and studied, whereas the rainforests of Cape York have received less attention due to their remoteness. Here we describe two new species of Glaphyromorphus skinks from rainforest areas on Cape York. The two new species are most similar to each other and to G. fuscicaudis and G. nigricaudis, but both are readily diagnosed on numerous traits. Glaphyromorphus othelarrni sp. nov. is diagnosed from all similar species by its supralabial count (typically 8 vs 7), high number of subdigital lamellae beneath the 4th finger (14-15 vs < 14), and its relatively longer limbs. Glaphyromorphus nyanchupinta sp. nov. is diagnosed from all similar species by its small body size (max SVL = ~ 54 mm vs > 85 mm) and slender body shape, low number of subdigital lamellae beneath the 4th toe (17-20 vs generally 20 or more), and head and body pattern. Both species also differ from each other and similar congeners in other aspects of body shape, scalation and colour pattern. Glaphyromorphus othelarrni sp. nov. is restricted to boulder-strewn rainforest of the Melville Range, whilst Glaphyromorphus nyanchupinta sp. nov. is known only from upland rainforest in the McIlwraith Range. We discuss patterns of rainforest vertebrate endemism on Cape York, and the importance of lithorefugia in generating these.

Two new subspecies of the leaf-tailed gecko Phyllurus ossa (Lacertilia: Carphodactylidae) from mid-eastern Queensland, Australia

Following the discovery of a new population of Phyllurus ossa on Whitsunday Island in the Cumberland Island Group, eastern Queensland, we conducted both genetic and morphological analyses to assess differences between all known populations. The analyses revealed three genetically distinct, morphologically diagnosable, geographical units. The differences are such that we recognise these as subspecies: Phyllurus ossa ossa restricted to the Mt Ossa/Mt Pelion/ Mt Charlton/ St Helens Gap area; P. ossa hobsoni subsp. nov. on Mt Dryander and in the Conway Range and P. ossa tamoya subsp. nov. currently only known from Whitsunday Island. There are now 11 recognised taxa in Phyllurus. The three P. ossa subspecies are narrowly distributed and closely associated with exposed rock in low to mid-elevation vine forests. Their current distributions are shaped by past climate change that progressively contracted and fragmented the distribution of rainforests in eastern Australia. The recognition of these subspecies has land management/conservation implications.

Environmental refuge from disease-driven amphibian extinction

Species that are tolerant of broad environmental gradients may be less vulnerable to epizootic outbreaks of disease. Chytridriomycosis, caused by the fungus Batrachochytrium dendrobatidis, has been linked to extirpations and extinctions of amphibian species in many regions. The pathogen thrives in cool, moist environments, and high amphibian mortality rates have commonly occurred during chytridiomycosis outbreaks in amphibian populations in high-elevation tropical rainforests. In Australia several high-elevation species, including the armored mist frog (Litoria lorica), which is designated as critically endangered by the International Union for the Conservation of Nature (IUCN), were believed to have gone extinct during chytridiomycosis outbreaks in the 1980s and early 1990s. Species with greater elevational ranges disappeared from higher elevations, but remained common in the lowlands. In June 2008, we surveyed a stream in a high-elevation dry sclerophyll forest and discovered a previously unknown population of L. lorica and a population of the waterfall frog (Litoria nannotis). We conducted 6 additional surveys in June 2008, September 2008, March 2009, and August 2009. Prevalences of B. dendrobatidis infection (number infected per total sampled) were consistently high in frogs (mean 82.5%, minimum 69%) of both species and in tadpoles (100%) during both winter (starting July) and summer (starting February). However, no individuals of either species showed clinical signs of disease, and they remained abundant (3.25 - 8.75 individuals of L. lorica and 6.5-12.5 individuals of L. nannotis found/person/100 m over 13 months). The high-elevation dry sclerophyll site had little canopy cover, low annual precipitation, and a more defined dry season than a nearby rainforest site, where L. nannotis was more negatively affected by chytridiomycosis. We hypothesize this lack of canopy cover allowed the rocks on which frogs perched to warm up, thereby slowing growth and reproduction of the pathogen on the hosts. In addition, we suggest surveys for apparently extinct or rare species should not be limited to core environments.

Phylogeographic divergence in the widespread delicate skink (Lampropholis delicata) corresponds to dry habitat barriers in eastern Australia

BACKGROUND

The mesic habitats of eastern Australia harbour a highly diverse fauna. We examined the impact of climatic oscillations and recognised biogeographic barriers on the evolutionary history of the delicate skink (Lampropholis delicata), a species that occurs in moist habitats throughout eastern Australia. The delicate skink is a common and widespread species whose distribution spans 26° of latitude and nine major biogeographic barriers in eastern Australia. Sequence data were obtained from four mitochondrial genes (ND2, ND4, 12SrRNA, 16SrRNA) for 238 individuals from 120 populations across the entire native distribution of the species. The evolutionary history and diversification of the delicate skink was investigated using a range of phylogenetic (Maximum Likelihood, Bayesian) and phylogeographic analyses (genetic diversity, ΦST, AMOVA, Tajima's D, Fu's F statistic).

RESULTS

Nine geographically structured, genetically divergent clades were identified within the delicate skink. The main clades diverged during the late Miocene-Pliocene, coinciding with the decline and fragmentation of rainforest and other wet forest habitats in eastern Australia. Most of the phylogeographic breaks within the delicate skink were concordant with dry habitat or high elevation barriers, including several recognised biogeographic barriers in eastern Australia (Burdekin Gap, St Lawrence Gap, McPherson Range, Hunter Valley, southern New South Wales). Genetically divergent populations were also located in high elevation topographic isolates inland from the main range of L. delicata (Kroombit Tops, Blackdown Tablelands, Coolah Tops). The species colonised South Australia from southern New South Wales via an inland route, possibly along the Murray River system. There is evidence for recent expansion of the species range across eastern Victoria and into Tasmania, via the Bassian Isthmus, during the late Pleistocene.

CONCLUSIONS

The delicate skink is a single widespread, but genetically variable, species. This study provides the first detailed phylogeographic investigation of a widespread species whose distribution spans virtually all of the major biogeographic barriers in eastern Australia.

Patterns of persistence and isolation indicate resilience to climate change in montane rainforest lizards

Globally, montane tropical diversity is characterized by extraordinary local endemism that is not readily explained by current environmental variables indicating a strong imprint of history. Montane species often exist as isolated populations under current climatic conditions and may have remained isolated throughout recent climatic cycles, leading to substantial genetic and phenotypic divergence. Alternatively, populations may have become contiguous during colder climates resulting in less divergence. Here we compare responses to historical climate fluctuation in a montane specialist skink, Lampropholis robertsi, and its more broadly distributed congener, L. coggeri, both endemic to rainforests of northeast Australia. To do so, we combine spatial modelling of potential distributions under representative palaeoclimates, multi-locus phylogeography and analyses of phenotypic variation. Spatial modelling of L. robertsi predicts strong isolation among disjunct montane refugia during warm climates, but with potential for localized exchange during the most recent glacial period. In contrast, predicted stable areas are more widespread and connected in L. coggeri. Both species exhibit pronounced phylogeographic structuring for mitochondrial and nuclear genes, attesting to low dispersal and high persistence across multiple isolated regions. This is most prominent in L. robertsi, for which coalescent analyses indicate that most populations persisted in isolation throughout the climate cycles of the Pleistocene. Morphological divergence, principally in body size, is more evident among isolated populations of L. robertsi than L. coggeri. These results highlight the biodiversity value of isolated montane populations and support the general hypothesis that tropical montane regions harbour high levels of narrow-range taxa because of their resilience to past climate change.

Distribution and population genetic structure of the critically endangered skink Nangura spinosa, and the implications for management

Many threatened species occur as small, isolated populations. Understanding the extent and genetic distinctiveness of these populations is essential for management. Nangura spinosa is a critically endangered skink known from two small populations in dry rainforest in south-east Queensland. We conducted targeted surveys between 2001 and 2010 at the two known N. spinosa sites (Nangur National Park, Oakview National Park area) and in 22 nearby forest blocks with potentially suitable habitat. N. spinosa was found only at the two previously known sites, which are ~36 km apart. The skink appears to be declining at Nangur NP, to an estimated extent of occurrence of 7.4 ha and potentially no more than 35 adults. In contrast, we increase the extent of occurrence at Oakview to 360 ha, where the population is at least in the hundreds. Sequencing of two mtDNA genes revealed considerable genetic divergence between the two populations (3.8% for ND4; 1.2% for 16S), suggesting an extended period of separation. Population fragmentation is therefore not the result of recent land clearing, but of long-term isolation by unsuitable habitat. Each population should be considered a distinct management unit. More data are required on population size and trends, recruitment and threats, particularly for the Nangur population.