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We describe two new species of moderate-sized (male body length 26.5–29.8 mm and 41.0 mm), predominantly green treefrogs in the genus Litoria from hill forest on the northern slopes of Papua New Guinea’s Central Cordillera. Phylogenetic analysis of mitochondrial ND4 nucleotide sequences shows that the first species is related to Litoria iris (Tyler) and its allies. It is morphologically most similar to Litoria mystax, a small green treefrog known only from the holotype that was described more than 100 years ago from the north coast of western New Guinea but differs from that species in having longer legs and a broader head. The second species is closest to Litoria gasconi, a species known only from the foothills of the Foja Mountains in Papua Province, Indonesian New Guinea, and the Prince Alexander Mountains in northern Papua New Guinea. It has a net average sequence divergence of 10% from L. gasconi and can be distinguished morphologically from it and from other pelodryadids by the presence of a striking pattern of spots and blotches on the ventral surfaces and on the hidden surfaces of the limbs. These descriptions add to the rapidly increasing known diversity of frogs in hill and lower montane forest, habitats that support the most diverse frog communities on mainland New Guinea.

New Guinea has the most diverse insular frog fauna in the world, and rates of species discovery and description have increased rapidly in the last two decades. Pelodryadid treefrogs are the second most diverse family of anurans on the island but their taxonomy, relationships, and especially ecology remain poorly documented. Based on differences in morphology, advertisement calls (where available) and phylogenetic analyses of a 787 base pair alignment from the mitochondrial ND4 gene and flanking tRNA, we describe five new species of small treefrogs from hill and lower montane forests in the high rainfall belt that straddles the southern versant of Papua New Guinea’s Central Cordillera. Three of these species are known only from forest growing on karst substrates, adding to the growing number of herpetofauna species currently known only from the extensive karst habitats of Papua New Guinea’s South-fold Mountains. We also describe the arboreal breeding strategies of two of the new species, and report obligate treehole (phytotelm) breeding in New Guinean frogs for the first time. The new phytotelm–breeding species has juveniles with colour and patterning that closely resemble bird droppings, suggesting defensive mimicry or masquerade. A preliminary phylogeny suggests that arboreal-breeding frogs do not form a monophyletic group and that arboreal breeding has evolved multiple times within the New Guinean pelodryadid radiation. A further striking feature of the phylogeny is poor support for most basal nodes in the most diverse radiation of Melanesian Pelodryadidae, suggesting rapid ecological diversification and speciation, potentially following colonisation from Australia and/or mountain uplift. These new taxa and observations highlight previously unrecognised ecological and reproductive diversity in the Melanesian Pelodryadidae.

Across Australia’s monsoon tropics and vast arid zone isolated regions or ‘islands’ of upland or rocky habitat are home to disjunct populations of many taxa of plants and animals. Comparative analyses of lineages that occur across these habitat islands provide opportunities to understand when and how environmental change drove isolation and diversification across arid Australia. Here we present an analysis of mitochondrial genetic diversity across disjunct populations of geckos in the Nephrurus asper group. Dating analyses suggest that disjunct and genetically divergent populations spanning the northern half of Australia diverged through the Plio–Pleistocene. Based on the timing of divergence and current habitat associations we hypothesise that species in this lineage were isolated by the expansion of unsuitable arid-zone habitats from the late Pliocene onwards. Across most areas, these barriers appear to be sandy or stony deserts. However, in eastern Australia genetically divergent populations are separated by grassland on flat vertisol-dominated soils (‘blacksoils’), suggesting that these habitats also expanded during the late Pliocene aridification. Finally, we show that western Queensland populations formerly referred to N. asper are genetically divergent and diagnosable on the basis of colour pattern and, herein, recognise these populations as a distinct species. https://zoobank.org/urn:lsid:zoobank.org:pub:9508CAAA-D014-452D-A3DA-325851615FA7

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.

The bleating tree frog (Litoria dentata) is one of the more prominent pelodryadid frogs of eastern Australia by virtue of its extremely loud, piercing, male advertisement call. A member of the Litoria rubella species group, L. dentata has a broad latitudinal distribution and is widespread from coastal and subcoastal lowlands through to montane areas. A recent mitochondrial DNA analysis showed a deep phylogeographic break between populations of L. dentata on the mid-north coast of New South Wales. Here we extended the mitochondrial survey with more geographically comprehensive sampling and tested the systematic implications of our findings with nuclear genome wide single-nucleotide polymorphism, morphological and male advertisement call datasets. While similar in appearance and in male advertisement call, our integrative analysis demonstrates the presence of three species which replace each other in a north-south series. We redescribe Litoria dentata, which is restricted to coastal north-eastern New South Wales, and formally describe Litoria balatus sp. nov., from south-eastern Queensland, and Litoria quiritatus sp. nov., from the mid-coast of New South Wales to north-eastern Victoria.

Background A 7 question non-validated swallow screen (Any reported swallowing difficulties? Any coughing with food or fluids? Any choking? Does food get stuck when eating? Any recurrent chest infections? Any pain when swallowing? Any difficulty swallowing tablets?) is used by an integrated care team for older persons to prioritise referrals to the Speech and Language Therapy (SLT) service. This study identified the proportion of patients screened who appropriately required a clinical dysphagia assessment and intervention. Methods This was a retrospective study from September 2020 to June 2021. Patients were assessed by the Clinical Specialist SLT who determined if swallow impairment was present and whether intervention was required. Age, gender and clinical frailty score were documented. Patients who resided out of the catchment area or who had already received an SLT service were excluded. Results The average age was 80 years, range 67–103. The male to female ratio was 2:1 and the average clinical frailty score (CFS) was 5. N = 42(32%) screened positive. N = 29(69%) attended for SLT assessment. N = 27(93.1%) had a swallow impairment identified. N = 20 were discharged following a single intervention and 9 required further SLT intervention. Conclusion Presbyphagia is generally asymptomatic and results from age related anatomical and physiological changes, reduced functional reserve and sarcopenia. Older adults compensate for these difficulties and do not seek assistance. Presbyphagia may progress to dysphagia, resulting in adverse outcomes. The high rate of SLT confirmed swallow impairment and need for SLT intervention highlights a need to prospectively refine and validate this 7 question swallow screen.

Background Dysphagia is common in older adults living in Residential Long-Term Care (RLTC) settings, requiring timely diagnosis and appropriate management to avoid potential complications and improve quality of life. Current dysphagia prevalence rates, screening and management practices in RLTC settings in the Republic of Ireland are not known. Methods An online survey was developed, consisting of 40 questions to determine dysphagia prevalence rates and associated nursing practices in screening and managing dysphagia in RLTC settings. An expert panel was formed with individuals having clinical experience in swallow screening and dysphagia management in older adults. We calculated Item-level Content Validity Index (I-CVI) and modified Kappa statistic (k), to adjust for chance agreement, for all 40 items in terms of representativeness and clarity. A survey item is considered relevant where I-CVI≥0.78, between 0.70 and 0.77 requires revision, and below 0.70, is eliminated. For k values, agreement levels are considered as low (k=< 0.40), fair (k=0.40–0.59), good (k=0.60–0.74) and high (k=≥ 0.75). Results The expert panel consisted of three nurse managers, two nurse specialists and three senior speech and language therapists with postgraduate qualifications, up to three years of experience in dysphagia related research and three to thirty-six years of clinical practice. For clarity, all items scored I-CVI≥0.78 and k=≥0.75 except four items, for which I-CVI=0.75 and k=0.72. For representativeness, only one item had an I-CVI=0.75 and k=0.72, with all other scoring I-CVI≥0.78 and k=≥ 0.75. Conclusion Findings suggest that the DPP-RLTCS has high content validity in terms of clarity and representativeness even after adjusting for chance agreement.

Background Standardised identification of patients for medication review using nurse-delivered, frailty-specific pharmacy prioritisation toolkits should maximise effective use of limited pharmacy resources. A frailty-specific pharmacy prioritisation toolkit was introduced in a 21 bed older persons’ rehabilitation unit to standardise pharmacy referrals and categorise the interventions made. Methods The frailty-specific pharmacy prioritisation toolkit was applied to consecutive patients by upskilled rehabilitation nurses to identify patients for weekly senior pharmacist review over a 5-month period from 18th Jan 2022 to 24th May 2022. Regular use of high-risk medication, greater than 10 medications, patients with specific pharmaceutical concerns such as a desire to reduce their medication burden, acute or chronic kidney injury and admission potentially related to medications or admission with non-mechanical falls are included in this toolkit. Pharmacist interventions included recommendations on medications to be weaned or stopped, dose-adjusted, started or restarted and identification of prescribing errors. Age, gender and interventions were recorded onto Excel and data was analysed using descriptive statistics. Results The total number of patients screened was 82. Eighty five percent (n=70) fulfilled criteria for a medication review. Mean age (SD) was 77(10.9) years. Female:male ratio was 1.5:1. Review was completed in 50% (n=35) of these cases. In total there were 228 interventions, with a mean (SD) of 6.5 (2.4) per patient. Eighty-four recommendations were made to wean or stop medication and thirty to dose adjust, of which 60% (n=18) were proton pump inhibitor dose reduction. Thirty-eight were to start or restart a medication, 34% (n=13) of which were for bone protection. Eleven prescribing errors were identified. Conclusion The pharmacy prioritisation toolkit applied by existing rehabilitation nurses successfully identified patients for medication review. The review rate reflects a need for a twice-weekly senior pharmacy resource.

Background Cognitive outcomes for frail older adult inpatients with a first episode of Delirium are unknown. Aim: To determine cognitive outcomes of frail older inpatients after a first episode of Delirium. Methods Consecutive frail older inpatients with a 4AT score >/= 4, without a previous history of cognitive impairment, over a 12-month period (January to December 2021) were invited for formal cognitive assessment 8-12 weeks after their delirium occurred. Collateral history, medication review, Addenbrookes (ACE III), bloods and CT brain were undertaken. Data was prospectively entered onto Excel and analysed using descriptive statistics. Results Fifty-one patients with a mean age of 82 years (SD=6) were referred to the Advanced Nurse Practitioner (ANP) Delirium Clinic. Median Clinical Frailty Score (CFS) was 6 with a male: female ratio of 1:2. Forty- seven percent (n=24) attended; 35 % (n-18) did not attend; 18 % (n=9) died prior to assessment. The ratio of male to female attendees was 1: 2.4. There was no difference in CFS or age between attenders and non-attenders. Thirty-three percent (n=8) of patients who attended had potentially reversible causes (high anti-cholinergic burden, folate deficiency, sleep disorder) of cognitive impairment requiring intervention. Sixty-seven percent (n=16) were diagnosed with dementia at the Delirium Clinic; 16.6% (n=4) were diagnosed with Mild Cognitive Impairment; 4% (n=1) had a resolved delirium; 8% (n=2) were referred to consultant Memory Clinic and one patient remained too unwell to assess. The median ACE III score of patients diagnosed with dementia was 54/100 (SD = 18). Conclusion Pro-active follow up of patients with a first episode of Delirium led to early diagnosis of dementia and mild cognitive impairment with supportive interventions. Earlier ANP intervention, during the acute phase of delirium, has been introduced in order to improve clinic attendance.

Background Vestibular dysfunction accounts for 25% of dizziness complaints. In 30-50% of these cases, dizziness is attributed to Benign Paroxysmal Positional Vertigo (BPPV). Thirty percent of people will experience vestibular dysfunction in their lifetime, with likelihood increasing with age. Individuals with vestibular dysfunction are eight times more likely to experience a fall. Vestibular assessment and rehabilitation services can be difficult to access. Methods A Plan, Do, Study, Act (PDSA) cycle was undertaken. All referrals to the Older Persons’ Services Clinics from November 2021 to May 2022 were triaged by an Integrated Care Team for the Older Person and scheduled for Comprehensive Geriatric Assessment (CGA). In the course of CGA, patients who reported symptoms suggestive of vestibular dysfunction received assessment by a Physiotherapist with vestibular expertise. Results were entered on an Excel spreadsheet and analysed using descriptive statistics. Results Six patients (4 female, 2 male) received vestibular assessment and treatment. Mean age was 75 years (SD: 11) with median Clinical Frailty Score of 4 (vulnerable). Reported symptoms were dizziness (n=3) and spinning (n=3). Sixteen percent (n=1) reported a fall and 66% (n=4) reported fear of falling. All patients had symptom duration of >2 years. Following vestibular assessment, the following diagnoses were made; right posterior canal BPPV, (n=2), vestibular migraine (n=2), right horizontal canal canalithiasis BPPV, with secondary diagnosis of persistent postural-perceptual dizziness (n=1) and left peripheral vestibular hypofunction due to vestibular neuronitis (n=1). The mean number of Physiotherapy visits per person was 4. Three patients reported full resolution of symptoms. The remaining 3 reported an improvement in symptoms and confidence to self-manage. Conclusion This small cohort of older persons with chronic vestibular dysfunction benefited from vestibular diagnosis and intervention. The next step of the process is to include specific vestibular screening questions into CGA. This will enable Integrated Care Team members to screen more specifically for vestibular dysfunction.

Background Opportunistic screening of older adults results in early detection of frailty. The Variable Indicative of Placement (VIP) is validated to identify those being admitted to hospital who may benefit from specialist geriatric assessment. VIP screening was gradually introduced throughout hospital-based outpatient clinics in April 2021. The aim of this study was to quantify patient benefit following VIP screening. Methods A positive VIP triggered referral for Comprehensive Geriatric Assessment (CGA). Exclusion criteria included prior CGA within a year, nursing home resident or patient declined assessment. Data was prospectively entered onto Excel by a trained administrator. Demographics, Clinical Frailty Score (CFS), modified Barthel Index (mBI) and patient interventions post CGA, between July 2021 and April 2022, were analysed using descriptive statistics. Results Of 168 referrals received, 52 were excluded, 53 completed and 63 await review. Thirty-five of those excluded had a prior CGA. Mean (SD) age of patients receiving CGA was 79 (7.6) years. Male:female ratio was 1:1.4. Median (SD) CFS was 6 (0.8) and median (SD) mBI was 16(3.9). There was a mean (SD) of 2.8 (1.6) targeted interventions per patient. Eighty three percent (n=43) required medication changes, 47% (n=25) bone health management, 28% (n=15) dietician, 26% (n=14) occupational therapy, 17% (n=9) public health nursing, 17% (n=9) speech and language therapy, 17% (n=9) memory assessment and 15% (n=8) physiotherapy. Conclusion Outpatient clinic VIP screening resulted in identification of frail older adults who benefited from CGA. The VIP should be validated in various outpatient settings.

Background The aetiology of malnutrition is multifactorial, with age a facilitating factor. It is associated with poorer physical and mental health and functional ability in frail older persons. Nutritional screening is a key domain in Comprehensive Geriatric Assessment (CGA). This study assessed the relationship between malnutrition risk and other drivers of frailty in the older person by CGA. Methods All patients who had a CGA completed by an Integrated Care Team for Older Persons from March 2020 to July 2021 inclusive were studied. Data was entered onto an Excel database by a trained administrator. The variables included were: age, gender, swallow screen, living alone, cognition, loneliness, Clinical Frailty Scale (CFS) score, falls history and risk of malnutrition using the Malnutrition-Screening Tool (MST). Odds ratio (OR), 95% Confidence Intervals (CI) was used to determine if there was an association between malnutrition risk and each variable in the total group. Results In total, 567 patients (325 female, 242 male), mean age 82yrs (SD =19), with median CFS of 6 were studied. Sixty-eight percent (n=384) reported a fall, 37.2% (n=211) had a positive swallow screen, 44% (n=251) lived alone, 35% (n=198) had positive cognitive screening, 14% (n=80) reported loneliness and 31.6% (n=179) were identified as at risk of malnutrition. A positive association was identified between risk of malnutrition and cognitive impairment (OR 1.9, 95%CI 1.2-3.1) and a reported fall (OR 2.2, 95%CI 1.4-3.5). In the population who had a fall and risk of malnutrition, the association remained in those aged ≥80yrs (OR 2.6, 95% CI 1.46 – 4.5) and female (OR 3.6, 95%CI 1.7 – 7.4). Conclusion The risk of malnutrition is associated with falls risk and cognitive impairment in frail older persons. Frail older persons identified by integrated care team for older persons with falls risk & cognitive impairment will be targeted for specialist dietetic intervention.

Australia and New Guinea (together referred to as Sahul) were linked by land for much of the late Tertiary and share many biotic elements. However, New Guinea is dominated by rainforest, and northern Australia by savannah. Resolving patterns of biotic interchange between these two regions is critical to understanding the expansion and contraction of both habitat types. The green tree frog (Litoria caerulea) has a vast range across northern and eastern Australia and New Guinea. An assessment of mitochondrial and morphological diversity in this nominal taxon in New Guinea reveals two taxa. True Litoria caerulea occurs in disjunct savannahs of the Trans-Fly, Central Province and across northern Australia, with very low genetic divergence, implying late Pleistocene connectivity. A previously unrecognised taxon is endemic to New Guinea and widespread in lowland swampy rainforest. Date estimates for the divergence of the new species suggest Pliocene connectivity across lowland tropical habitats of northern Australia and New Guinea. In contrast, the new species shows shallow phylogeographic structuring across the central mountains of New Guinea, implying recent dispersal between the northern and southern lowlands. These results emphasise that the extent and connectivity of lowland rainforest and savannah environments across northern Australia and southern New Guinea have undergone profound shifts since the late Pliocene. http://zoobank.org/urn:lsid:zoobank.org:pub:A577A415-0B71-4663-B4C1-7271B97298CD

Background: The direct effect of the COVID‐19 pandemic on patients with intestinal failure (IF) has not been described. Methods: We conducted a nationwide study of U.K. IF centres to evaluate the infection rates, presentations and outcomes in patients with types 2 and 3 IF. Results: A total of 45 patients with IF contracted COVID‐19 between March and August 2020; this included 26 of 2191 (1.2%) Home Parenteral Nutrition (HPN)‐dependent adults and 19 of 298 (6.4%) adults hospitalized with type 2 IF. The proportion of patients receiving nursing care for HPN administration was higher in those with community‐acquired COVID‐19 (66.7%) than the proportion in the entire HPN cohort (26.1%; p

The Nusa Tenggara island chain consists of an archipelago that runs roughly east-west in eastern Indonesia. As part of Wallacea, it has never been connected to any continental landmass, and has been subject to a variety of biological invasions that have populated the islands. Here, we examine the craniometric and molecular genetic records of several species of Rattus sensu lato in the island chain. We use the predictions of expanding population edge phenotypic selection in an effort to understand the movement of Rattus rattus and Rattus exulans through the archipelago. We also examine the mitochondrial haplotype networks of R. argentiventer, R. exulans, and the R. rattus Complex (RrC) and microsatellite allele frequency clustering patterns for the RrC, to examine relationships within and between Nusa Tenggara populations, and those of Asia and the Pacific where relevant for each taxon. In the RrC LIV and RrC LII haplotype networks, 20 haplotypes with seven from Nusa Tenggara were observed for RrC LIV, and 100 haplotypes with seven from Nusa Tenggara observed for RrC LII. The top performing RrC craniometric model had a negative association between size and distance from the easternmost point of the samples from Nusa Tenggara, consistent with increasing size moving west to east. The cytochrome b network for the R. exulans sequences comprised 14 haplotypes, with three observed from mainland Southeast Asia, one shared with Nusa Tenggara and regions further east, and another haplotype observed in Nusa Tenggara and in the Pacific. The R. exulans craniometric model selection produced four equally well performing models, with no migration scenario preferred. Finally, the haplotype network of R. argentiventer comprised 10 haplotypes, with six observed in Nusa Tenggara, including a relatively early cluster from the east of the archipelago. Our results are compatible with a polyphasic and polydirectional invasion of Nusa Tenggara by Rattus, likely beginning with RrC from the west to the east, an expansion of R. exulans from Flores, seemingly in no preferred overall direction, and finally the invasion of R. argentiventer from the east to the west. We find some support for the Dong Son drum maritime exchange network contributing to the distribution of the latter species.

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]

Genomic data are a powerful tool for the elucidation of evolutionary patterns at the population level and above. The combined analysis of genomic and morphological data can result in species delimitation hypotheses that reflect evolutionary history better than traditional taxonomy or any individual source of evidence. Here, we used thousands of single nucleotide polymorphisms, mitochondrial sequences, and comprehensive morphological data to characterize the evolutionary history of the ridge-tailed monitors in the Varanus acanthurus complex (V. acanthurus, V. baritji, and V. storri), a group of saxicolous lizards with a wide distribution in Australia, the driest vegetated continent. We found substantial genetic structure in the group and identify nine geographically clustered populations. Based on admixture patterns and species delimitation analyses we propose a taxonomic scheme that differs from current taxonomy. We consider V. acanthurus as monotypic, synonymize V. baritji with V. a. insulanicus (as a redefined V. insulanicus), elevate the subspecies of V. storri to full species (V. storri and V. ocreatus), and describe a new species from a previously identified center of endemism. The relationships among the species remain unresolved, likely as a result of fast speciation. Our study highlights the capability of large datasets to illuminate admixture patterns, biogeographic history, and species limits, even when phylogeny is not completely resolved. Furthermore, our results highlight the impact that the Cenozoic aridification of Australia had on saxicolous taxa and the role of mesic rocky escarpments as refugia. These habitats apparently allowed the persistence of lineages that became sources of colonization for arid environments.

The rarely encountered giant burrowing frog, Heleioporus australiacus, is distributed widely in a variety of sclerophyll forest habitats east of the Great Dividing Range in south-eastern Australia. Analyses of variation in nucleotide sequences of the mitochondrial ND4 gene and thousands of nuclear gene SNPs revealed the presence of two deeply divergent lineages. Multivariate morphological comparisons show the two lineages differ in body proportions with > 91% of individuals being correctly classified in DFA. The two lineages differ in the number and size of spots on the lateral surfaces and the degree by which the cloaca is surrounded by colour patches. The mating calls are significantly different in number of pulses in the note. The presence of a F2 hybrid in the area where the distribution of the two taxa come into closest proximity leads us to assign subspecies status to the lineages, as we have not been able to assess the extent of potential genetic introgression. In our sampling, the F2 hybrid sample sits within an otherwise unsampled gap of ~90km between the distributions of the two lineages. The nominate northern sub-species is restricted to the Sydney Basin bioregion, while the newly recognised southern subspecies occurs from south of the Kangaroo Valley in the mid-southern coast of New South Wales to near Walhalla in central Gippsland in Victoria. The habitat of the two subspecies is remarkably similar. Adults spend large portions of their lives on the forest floor where they forage and burrow in a variety of vegetation communities. The southern subspecies occurs most commonly in dry sclerophyll forests with an open understory in the south and in open forest and heath communities with a dense understory in the north of its distribution. The northern subspecies is also found in dry open forests and heaths in association with eroded sandstone landscapes in the Sydney Basin bioregion. Males of both taxa call from both constructed burrows and open positions on small streams, differing from the five Western Australian species of Heleioporus where males call only from constructed burrows. Using the IUCN Red List process, we found that the extent of occupancy and area of occupancy along with evidence of decline for both subspecies are consistent with the criteria for Endangered (A2(c)B2(a)(b)).

New Guinea has been considered both as a refuge for mesic rainforest-associated lineages that contracted in response to the late Cenozoic aridification of Australia and as a centre of biotic diversification and radiation since the mid-Miocene or earlier. Here, we estimate the diversity and a phylogeny for the Australo-Papuan forest dragons (Sauria: Agamidae; ~20 species) in order to examine the following: (1) whether New Guinea and/or proto-Papuan Islands may have been a biogeographical refuge or a source for diversity in Australia; (2) whether mesic rainforest environments are ancestral to the entire radiation, as may be predicted by the New Guinea refuge hypothesis; and (3) more broadly, how agamid ecological diversity varies across the contrasting environments of Australia and New Guinea. Patterns of lineage distribution and diversity suggest that extinction in Australia, and colonization and radiation on proto-Papuan islands, have both shaped the extant diversity and distribution of forest dragons since the mid-Miocene. The ancestral biome for all Australo-Papuan agamids is ambiguous. Both rainforest and arid-adapted radiations probably started in the early Miocene. However, despite deep-lineage diversity in New Guinea rainforest habitats, overall species and ecological diversity is low when compared with more arid areas, with terrestrial taxa being strikingly absent.

Sally Potter, Ana C. Afonso Silva, Jason G. Bragg, Sarah R. Catalano, Stephen Donnellan, Paul Doughty, Mitchell L. Scott, Craig Moritz

© 2018 Elsevier Inc. This manuscript version is made available under the CC-BY-NC-ND 4.0 license: http://creativecommons.org/licenses/by-nc-nd/4.0/ This author accepted manuscript is made available following 12 month embargo from date of publication (December 2018) in accordance with the publisher’s archiving policy, Palaeoclimatic events and biogeographical processes since the mid-Tertiary have played an important role in shaping the evolution and distribution of Australian fauna. However, their impacts on fauna in southern and arid zone regions of Australia are not well understood. Here we investigate the phylogeography of an Australian scincid lizard, Tiliqua rugosa, across southern Australia using mitochondrial DNA (mtDNA) and 11 nuclear DNA markers (nuDNA), including nine anonymous nuclear loci. Phylogenetic analyses revealed three major mtDNA lineages within T. rugosa, geographically localised north and south of the Murray River in southern Australia, and west of the Nullarbor Plain. Molecular variance and population analyses of both mtDNA and nuDNA haplotypes revealed significant variation among the three populations, although potential introgression of nuDNA markers was also detected for the Northern and Southern population. Coalescent times for major mtDNA lineages coincide with an aridification phase, which commenced after the early Pliocene and increased in intensity during the Late Pliocene-Pleistocene. Species distribution modelling and a phylogeographic diffusion model suggest that the range of T. rugosa may have contracted during the Last Glacial Maximum and the locations of optimal habitat appear to coincide with the geographic origin of several distinct mtDNA lineages. Overall, our analyses suggest that Plio-Pleistocene climatic changes and biogeographic barriers associated with the Nullarbor Plain and Murray River have played a key role in shaping the present-day distribution of genetic diversity in T. rugosa and many additional ground-dwelling animals distributed across southern Australia.

We show that the Wotjulum frog, Litoria watjulumensis (Copland, 1957), comprises two deeply divergent mitochondrial DNA lineages that are also reciprocally monophyletic for a nuclear gene locus and have discrete distributions. The taxa are differentiated in multivariate analysis of shape but show no appreciable differences in colour and pattern. The two taxa differ substantially in the degree of female biased sexual size dimorphism, with the western taxon showing considerably more pronounced dimorphism. We subsequently resurrect Litoria (Hyla) spaldingi (Hosmer, 1964) for populations from east of the Daly River system in the Northern Territory through to western Queensland and restrict L. watjulumensis to populations from the Kimberley region of north-western Australia and the Victoria River system of the western Northern Territory. The complex advertisement call of L. spaldingi is described for the first time.

Population declines and range contractions among Australian frogs that commenced in the early 1980s continue in some species that were once widespread. The generality of this pattern has been difficult to discern, especially for those species that are encountered rarely because they have restricted periods of calling activity with poorly defined habitat preferences, and are not common. Several lines of evidence indicate that Litoria littlejohni is such a species. This frog was once known from mid-eastern New South Wales to eastern Victoria, and evidence from wildlife atlas databases and targeted searches indicate that it has declined in large portions of its former range, leaving several populations that are isolated, in some cases restricted in distribution, and of small size. We investigated the relationships among populations using mitochondrial ND4 nucleotide sequences and single nucleotide polymorphisms (SNPs) from the nuclear genome. We found that northern and southern populations form two highly divergent genetic groups whose distributions abut at the southern margin of the Sydney Basin Bioregion and these genetic groups also show divergence in morphology and male advertisement calls. Here we describe the populations to the south of the Sydney Basin Bioregion as a new species and provide information on its distribution and ecology. In light of the apparent isolation and small size of known populations of the new species and the consequent restriction of the range of L. littlejohni, we assessed the conservation status of both species.

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals., Author summary Polyploidy or whole genome duplication is rare in animals and usually polyploid animals reproduce asexually. The Australian burrowing frogs of the genus Neobatrachus form an interesting exception amongst vertebrates with multiple independently originated autotetraploid sexual species. We generated population genomic data from 87 animals representing all six diploid and three tetraploid species of Neobatrachus. We show that, while diploid Neobatrachus species seem to be isolated from each other, their sister tetraploid species experience substantial levels of gene flow, and have wider distributions. Furthermore, we observe asymmetric gene flow from diploids to tetraploids. Based on our genomic and climate analyses we suggest that such inter-specific hybridization mediated by whole genome duplication rescues species diversity and allows tetraploids to more easily avoid impacts of climate-induced habitat loss.

Amphibian genomes are usually challenging to assemble due to large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.

Ecological opportunities can be provided to organisms that cross stringent biogeographic barriers towards environments with new ecological niches. Wallace’s and Lyddeker’s lines are arguably the most famous biogeographic barriers, separating the Asian and Australo-Papuan biotas. One of the most ecomorphologically diverse groups of reptiles, the pythons, is distributed across these lines, and are remarkably more diverse in phenotype and ecology east of Lydekker’s line in Australo-Papua. We used an anchored hybrid enrichment approach, with near complete taxon sampling, to extract mitochondrial genomes and 376 nuclear loci to resolve and date their phylogenetic history. Biogeographic reconstruction demonstrates that they originated in Asia around 38-45 Ma and then invaded Australo-Papua around 23 Ma. Australo-Papuan pythons display a sizeable expansion in morphological space, with shifts towards numerous new adaptive optima in head and body shape, coupled with the evolution of new micro-habitat preferences. We provide an updated taxonomy of pythons and our study also demonstrates how ecological opportunity following colonization of novel environments can promote morphological diversification in a formerly ecomorphologically conservative group. [Adaptive radiation; anchored hybrid enrichment; biogeography; morphometrics; snakes.]

Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragonVaranus komodoensisand the smallest Australian dwarf goannas,Varanuslength and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. We use a phylogenomic approach to estimate the relationships among living and extinct varaniform lizards, incorporating both exon-capture molecular and morphological datasets. Our results suggest that communities of AustralianVaranusshow high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.

Translocation is an increasingly common component of species conservation efforts. However, translocated populations often suffer from loss of genetic diversity and increased inbreeding, and thus may require active management to establish gene flow across isolated populations. Assisted gene flow can be laborious and costly, so recipient and source populations should be carefully chosen to maximise genetic diversity outcomes. The greater stick-nest rat (GSNR, Leporillus conditor), a threatened Australian rodent, has been the focus of a translocation program since 1985, resulting in five extant translocated populations (St Peter Island, Reevesby Island, Arid Recovery, Salutation Island and Mt Gibson), all derived from a remnant wild population on the East and West Franklin Islands. We evaluated the genetic diversity in all extant GSNR populations using a large single nucleotide polymorphism dataset with the explicit purpose of informing future translocation planning. Our results show varying levels of genetic divergence, inbreeding and loss of genetic diversity in all translocated populations relative to the remnant source on the Franklin Islands. All translocated populations would benefit from supplementation to increase genetic diversity, but two—Salutation Island and Mt Gibson—are of highest priority. We recommend a targeted admixture approach, in which animals for supplementation are sourced from populations that have low relatedness to the recipient population. Subject to assessment of contemporary genetic diversity, St Peter Island and Arid Recovery are the most appropriate source populations for genetic supplementation. Our study demonstrates an effective use of genetic surveys for data-driven management of threatened species.

Refereed/Peer-reviewed Effective land management and biodiversity conservation policy relies on good records of native species occurrence and habitat association, but for many animal groups these data are inadequate. In the Murray–Darling Basin (MDB), the most environmentally and economically important catchment in Australia, knowledge gaps exist on the occurrence and habitat associations of insectivorous bat species. We relied on the interest and effort of citizen scientists to assist with the most intensive insectivorous bat survey ever undertaken in the MDB region of South Australia. We used an existing network of Natural Resource Management groups to connect interested citizens and build on historical observations of bat species using a fleet of 30 Anabat Swift bat detectors. The survey effort more than doubled the number of bat occurrence records for the area in two years (3000 records; cf. 2693 records between 1890 and 2018; freely available through the Atlas of Living Australia). We used multinomial logistic regression to look at the relationship between three types of environmental covariates: flight space, nearest open water source and vegetation type. There were no differences in species richness among the environmental covariates. The records have been, and will continue to be, used to inform government land management policy, more accurately predict the impact of development proposals on bat populations, and update conservation assessments for microbat species. A social survey tool also showed that participation in the project led to positive behaviours, and planned positive behaviours, for improving bat habitat on private land.

Effective fisheries management generally requires reliable data describing the target species’ life-history characteristics, the size of its harvested populations, and overall catch estimates, to set sustainable quotas and management regulations. However, stock assessments are often not available for long-lived marine species such as sharks, making predictions of the long-term population impacts of variable catch rates difficult. Fortunately, stage- or age-structured population models can assist if sufficient information exists to estimate survival and fertility rates. Using data collected from the bronze whaler (Carcharhinus brachyurus) fishery in South Australia as a case study, we estimated survival probabilities from life tables of harvested individuals, as well as calculated natural mortalities based on allometric predictions. Fertility data (litter size, proportion mature) from previous studies allowed us to build a fertility vector. Deterministic matrices built using estimates of life-table data or natural mortality (i.e. harvested-augmented and natural mortality) produced instantaneous rates of change of 0.006 and 0.025, respectively. Assuming an incrementing total catch at multiples of current rates, stochastic simulations suggest the relative rate of population decline starts to become precipitous around 25% beyond current harvest rates. This is supported by a sharp increase in weighted mean age of the population around 25% increase on current catches. If the catch is assumed to be proportional (i.e. a constant proportion of the previous year’s population size), the relative r declines approximately linearly with incrementing harvest beyond the current rate. A global sensitivity analysis based on a Latin-hypercube sampling design of seven parameters revealed that variation in the survival estimates derived from the life tables was by far the dominant (boosted-regression tree relative influence score = 91.14%) determinant of model performance (measured as variation in the long-term average rate of population change r). While current harvest rates therefore appear to be sustainable, we recommend that fisheries-management authorities attempt to sample a broader size range of individuals (especially older animals) and pursue stock assessments. Our models provide a framework for assessing the relative susceptibility of long-lived fishes to harvest pressure when detailed stock data are missing.

Reintroduction programs aim to restore self-sustaining populations of threatened species to their historic range. However, demographic restoration may not reflect genetic restoration, which is necessary for the long-term persistence of populations. Four threatened Australian mammals, the greater stick-nest rat (Leporillus conditor), greater bilby (Macrotis lagotis), burrowing bettong (Bettongia lesueur) and western barred bandicoot (Perameles bougainville), were reintroduced at Arid Recovery Reserve in northern South Australia over the last 18 years. These reintroductions have been deemed successful based on population growth and persistence, however the genetic consequences of the reintroductions are not known. We generated large single nucleotide polymorphism (SNP) datasets for each species currently at Arid Recovery and compared them to samples collected from founders. We found that average genetic diversity in all populations at the Arid Recovery Reserve are close to, or exceeding, the levels measured in the founders. Increased genetic diversity in two species was achieved by admixing slightly diverged and inbred source populations. Our results suggest that genetic diversity in translocated populations can be improved or maintained over relatively long time frames, even in small conservation reserves, and highlight the power of admixture as a tool for conservation management.

The endangered subspecies of Southern Emu-Wren (Stipiturus malachurus intermedius) in the Mount Lofty Ranges (MLR), South Australia has a fragmented distribution and poor dispersal capabili...

Background Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes. Results Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri – songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. Conclusions We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines. Electronic supplementary material The online version of this article (10.1186/s13100-017-0104-1) contains supplementary material, which is available to authorized users.

Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric morphometrics on Antaresia, a clade of four currently recognised dwarf pythons from Australia and New Guinea (Antaresia childreni, A. stimsoni, A. maculosa and A. perthensis). Our integrative analyses of phylogenetics, population structure, species delimitation, historical demography and morphometrics revealed that the true evolutionary diversity is not well reflected in the current appraisal of the diversity of the group. We find that Antaresia childreni and A. stimsoni comprise a widespread network of populations connected by gene flow and without evidence of species-level divergence among them. However, A. maculosa shows considerable genetic structuring which leads us to recognise two subspecies in northeastern Australia and a new species in Torres Strait and New Guinea. These two contrasting cases of over and under estimation of diversity, respectively, illustrate the power of thorough integrative approaches into understanding evolution of biodiversity. Furthermore, our analyses of historical demographic patterns highlight the importance of the Kimberley, Pilbara and Cape York as origins of biodiversity in Australia.

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., In order to inform conservation effort, there is urgent need for rigorous taxonomic research to describe species under threat of extinction. Implementation of a new prioritization method identified 282 Australian reptile species needing taxonomic research, of which 17.6% represent undescribed species of conservation concern; this approach could be readily implemented across many faunal groups.

Summary The intestinal trematode Gastrodiscus aegyptiacus (G. aegyptiacus) has been recognised in equids around the world for many years, but its pathogenicity is yet to be confirmed. This report describes seven cases of severe G. aegyptiacus infestation, including six cases of caecal intussusception.

Australia's lizard fauna is among the most diverse in the world. Yet for the continent's vast northern Monsoonal Tropics, recent genomic and morphological evidence indicate that current taxonomy significantly underestimates actual biological diversity. Apparently widespread species typically contain ancient phylogenetic divisions or confounded taxonomic boundaries. Resolving the distributions and relationships across tropical species complexes reveals higher diversity than is recognised taxonomically and may warrant substantial taxonomic changes. For conservation assessments however, we need not wait for revised taxonomy, because phylogenetically informed analyses can use the best available data to inform conservation priorities now, independent of taxonomy. We present results of a large-scale conservation analysis based on comparative phylogeography of ten genera of lizards in two families (Gekkonidae and Scincidae) across the “Top End” of northern Australia, an ecologically and topographically diverse landscape recognised for its high biodiversity and indigenous cultural values. We combine the distributions and phylogeny of evolutionary lineages across multiple species complexes to estimate phylogenetic endemism, a measure of the extent to which evolutionary diversity is geographically concentrated. We demonstrate new methods for conservation assessment to incorporate phylogenetic diversity both within and across species, and for cases where taxonomy is uncertain or incomplete. We identify five hotspots of endemism, some previously known such as the Arnhem Plateau but others that are newly identified such as the Wessel & English Company Islands and the Darwin-Litchfield area. We find that, weighted by range size, the 28% of the region within protected areas holds 44% of the region's sampled phylogenetic diversity.

New Guinea is home to the world’s most diverse insular frog biota, but only a small number of taxa have been included in genetically informed assessments of species diversity. Here we describe two new species of New Guinea treefrog in the genus Litoria that were first flagged during assessments of genetic diversity (DNA barcoding) and are currently only known from the holotypes. Litoria pterodactyla sp. nov. is a large green species in the Litoria graminea species complex from hill forests in Western Province, Papua New Guinea and is the third member of this group known from south of the Central Cordillera. Litoria vivissimia sp. nov. is a small, spike-nosed species from mid-montane forests on the Central Cordillera. It is morphologically very similar to Litoria pronimia, but occurs nearly 1000 m higher than any known locality for that species. More extensive genetically informed assessment of diversity in New Guinea frogs seems certain to reveal many more as-yet-unrecognised taxa in complexes of morphologically similar species.

Polyploidy plays an important role in evolution because it can lead to increased genetic complexity and speciation. It also provides an extra copy buffer and increases genetic novelty. While both common and well-studied in plants, polyploidy is rare in animals, and most polyploid animals reproduce asexually. Amphibians represent a dramatic vertebrate exception, with multiple independent sexually reproducing polyploid lineages, but very few cases have been studied in any detail. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful model animal polyploid system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent origins. We document higher genetic diversity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on evolution of adaptation in animals.

The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of this genus. Our molecular genetic data support two major clades, corresponding to L. albertisii and L. fredparkeri, but offer no support for the other four species. Our morphological data also only support two species. We therefore recognize L. albertisii and L. fredparkeri as valid species and place L. biakensis, L. meridionalis, L. huonensis and L. montanus into synonymy. We found that L. albertisii and L. fredparkeri are sympatric in western New Guinea; an atypical pattern compared to other Papuan species complexes in which the distributions of sister taxa are partitioned to the north and south of the island's central mountain range. For the purpose of conservation management, overestimation of species diversity within Leiopython has resulted in the unnecessary allocation of resources that could have been expended elsewhere. We strongly caution against revising the taxonomy of geographically widespread species groups when little or no molecular genetic data and only small morphological samples are available.

High-throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci, and we now know that many lineages also exhibit substantial cryptic diversity. Here, we present a set of phylogenetically diverse transcriptome resources to enable exon-based sequence capture studies of Australian vertebrates, including transcriptome sequences for four species of birds, four frogs, seven lizards and seven mammals. We also use exon data from the marsupial transcriptomes we generated to examine an approach for choosing a moderate number (dozens or hundreds) of phylogenetically informative exons based on a single transcriptome sequence, and a relatively distant reference genome.