Strong philopatry in an estuarine-dependent fish.

Understanding fish movement is critical in determining the spatial scales in which to appropriately manage wild populations. Genetic markers provide a natural tagging approach to assess the degree of gene flow and population connectivity across a species distribution. We investigated the genetic structure of black bream Acanthopagrus butcheri across its entire distribution range in Australia, as well as regional scale gene flow across south-eastern Australia by undertaking a comprehensive analysis of the populations in estuaries across the region. We applied genome-wide sampling of single-nucleotide polymorphism (SNP) markers generated from restriction site-associated DNA sequencing. Genetic structure and potential gene flow was assessed using principal component analyses and admixture analyses (STRUCTURE). Using 33,493 SNPs, we detected broad scale genetic structuring, with limited gene flow among regional clusters (i.e. Western Australia, South Australia and western Victoria; and eastern Victoria, Tasmania and New South Wales). This is likely the result of unsuitable habitats, strong ocean currents (e.g. the Leeuwin Current and the East Australian Current), large water bodies (e.g. Bass Strait) and known biogeographical provinces across the continent. Local-scale genetic structuring was also identified across the south-eastern Australian estuaries sampled, reflecting that the coexistence of both migratory and resident individuals within populations (i.e. partial migration), and the movement of fish into coastal waters, still results in strong philopatry across the region. Instances of movement among estuaries at this spatial scale were primarily found between adjacent estuaries and were likely attributed to lone migrants utilising inshore coastal currents for movement beyond nearby habitats. Targeting SNP markers in A. butcheri at this continental scale highlighted how neither spatial proximity of estuaries nor black bream's ability to move into coastal waters reflects increased gene flow. Overall, our findings highlight the importance of location-specific management.

Systematic assessment of the brown tree frog (Anura: Pelodryadidae: Litoria ewingii) reveals two endemic species in South Australia.

The brown tree frog (Litoria ewingii) is a relatively widespread, commonly encountered pelodryadid frog from south-eastern Australia, known for its characteristic whistling call. The distribution of Litoria ewingii spans over more than 350,000 km2, encompassing a range of moist temperate habitats, and is fragmented by well-known biogeographic barriers. A preliminary analysis of mitochondrial DNA sequences revealed evidence for deep phylogenetic structure between some of these fragmented populations. In this study, we sought to re-evaluate the systematics and taxonomy of Litoria ewingii sensu lato by analysing variation in nuclear and mitochondrial DNA, adult morphology and male advertisement calls throughout the species range. Our analyses reveal two additional, deeply divergent and allopatric lineages in South Australia. We herein re-describe Litoria ewingii from Tasmania, southern New South Wales, Victoria and south-eastern South Australia, resurrect the name Litoria calliscelis for a species occurring in the Mount Lofty Ranges and Fleurieu Peninsula in South Australia, and describe a new species, Litoria sibilus sp. nov., endemic to Kangaroo Island.

The macroevolutionary singularity of snakes.

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.

A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea.

Germline colonization by retroviruses results in the formation of endogenous retroviruses (ERVs). Most colonization's occurred millions of years ago. However, in the Australo-Papuan region (Australia and New Guinea), several recent germline colonization events have been discovered. The Wallace Line separates much of Southeast Asia from the Australo-Papuan region restricting faunal and pathogen dispersion. West of the Wallace Line, gibbon ape leukemia viruses (GALVs) have been isolated from captive gibbons. Two microbat species from China appear to have been infected naturally. East of Wallace's Line, the woolly monkey virus (a GALV) and the closely related koala retrovirus (KoRV) have been detected in eutherians and marsupials in the Australo-Papuan region, often vertically transmitted. The detected vertically transmitted GALV-like viruses in Australo-Papuan fauna compared to sporadic horizontal transmission in Southeast Asia and China suggest the GALV-KoRV clade originates in the former region and further models of early-stage genome colonization may be found. We screened 278 samples, seven bat and one rodent family endemic to the Australo-Papuan region and bat and rodent species found on both sides of the Wallace Line. We identified two rodents (Melomys) from Australia and Papua New Guinea and no bat species harboring GALV-like retroviruses. Melomys leucogaster from New Guinea harbored a genomically complete replication-competent retrovirus with a shared integration site among individuals. The integration was only present in some individuals of the species indicating this retrovirus is at the earliest stages of germline colonization of the Melomys genome, providing a new small wild mammal model of early-stage genome colonization.

Phylogeography, hybrid zones and contemporary species boundaries in the south-eastern Australian smooth frogs (Anura: Myobatrachidae: Geocrinia).

Paleo-climatic fluctuations have driven episodic changes in species distributions, providing opportunities for populations to diverge in isolation and hybridise following secondary contact. Studies of phylogeographic diversity and patterns of gene flow across hybrid zones can provide insight into contemporary species boundaries and help to inform taxonomic and conservation inferences. Here we explore geographic diversity within the acoustically divergent yet morphologically conserved south-eastern Australian smooth frog complex and assess gene flow across a narrow hybrid zone using mitochondrial nucleotide sequences and nuclear genome-wide single nucleotide polymorphisms. Our analyses reveal the presence of an evolutionarily distinct taxon restricted to the Otway Plains and Ranges, Victoria, which forms a narrow (9-30 km wide), spatiotemporally stable (>50 years) hybrid zone with Geocrinia laevis, which we describe herein as a new species.

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.

Two new species of green treefrogs (Pelodryadidae: Litoria) from the northern slopes of Papua New Guinea's Central Cordillera.

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.

A new species of barred frog, Mixophyes (Anura: Myobatrachidae) from south-eastern Australia identified by molecular genetic analyses.

Mixophyes are large ground-dwelling myobatrachid frogs from eastern Australia and New Guinea. Several of the species found in mid-eastern and south-eastern Australia are listed as threatened, due largely to declines presumably caused by the amphibian disease chytridiomycosis. Given the wide distribution of several of these species and that their distributions cross well-known biogeographic boundaries that often correspond to deep genetic breaks or species boundaries among closely related vertebrates, we undertook a molecular genetic assessment of population structure across the range of each species to determine the presence of undescribed species. Of the four species of Mixophyes subject to molecular population genetic analyses, one, the Stuttering Frog (Mixophyes balbus), showed a level of diversity consistent with the presence of two species. Morphometric, meristic and bioacoustic analyses corroborate these distinctions, and a new species is described for the populations south of the Macleay River valley in mid-eastern New South Wales to east Gippsland in Victoria. Applying the IUCN Red List threat criteria the new species meets the conservation status assessment criteria for Endangered 2B1a,b because its extent of occupancy and area of occupancy are below the threshold value and it has declined and disappeared from the southern two thirds of its distribution over the past 30 years.

Five new species of the pelodryadid genus Litoria Tschudi from the southern versant of Papua New Guinea's Central Cordillera, with observations on the diversification of reproductive strategies in Melanesian treefrogs.

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.

Avian surfactant protein (SP)-A2 first arose in an early tetrapod before the divergence of amphibians and gradually lost the collagen domain.

The air-liquid interface of the mammalian lung is lined with pulmonary surfactants, a mixture of specific proteins and lipids that serve a dual purpose-enabling air-breathing and protection against pathogens. In mammals, surfactant proteins A (SP-A) and D (SP -D) are involved in innate defence of the lung. Birds seem to lack the SP-D gene, but possess SP-A2, an additional SP-A-like gene. Here we investigated the evolution of the SP-A and SP-D genes using computational gene prediction, homology, simulation modelling and phylogeny with published avian and other vertebrate genomes. PCR was used to confirm the identity and expression of SP-A analogues in various tissue homogenates of zebra finch and turkey. In silico analysis confirmed the absence of SP-D-like genes in all 47 published avian genomes. Zebra finch and turkey SP-A1 and SP-A2 sequences, confirmed by PCR of lung homogenates, were compared with sequenced and in silico predicted vertebrate homologs to construct a phylogenetic tree. The collagen domain of avian SP-A1, especially that of zebra finch, was dramatically shorter than that of mammalian SP-A. Amphibian and reptilian genomes also contain avian-like SP-A2 protein sequences with a collagen domain. NCBI Gnomon-predicted avian and alligator SP-A2 proteins all lacked the collagen domain completely. Both avian SP-A1 and SP-A2 sequences form separate clades, which are most closely related to their closest relatives, the alligators. The C-terminal carbohydrate recognition domain (CRD) of zebra finch SP-A1 was structurally almost identical to that of rat SP-A. In fact, the CRD of SP-A is highly conserved among all the vertebrates. Birds retained a truncated version of mammalian type SP-A1 as well as a non-collagenous C-type lectin, designated SP-A2, while losing the large collagenous SP-D lectin, reflecting their evolutionary trajectory towards a unidirectional respiratory system. In the context of zoonotic infections, how these evolutionary changes affect avian pulmonary surface protection is not clear.

Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex).

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.

Geography-Dependent Horizontal Gene Transfer from Vertebrate Predators to Their Prey.

Horizontal transfer (HT) of genes between multicellular animals, once thought to be extremely rare, is being more commonly detected, but its global geographic trend and transfer mechanism have not been investigated. We discovered a unique HT pattern of Bovine-B (BovB) LINE retrotransposons in vertebrates, with a bizarre transfer direction from predators (snakes) to their prey (frogs). At least 54 instances of BovB HT were detected, which we estimate to have occurred across time between 85 and 1.3 Ma. Using comprehensive transcontinental sampling, our study demonstrates that BovB HT is highly prevalent in one geographical region, Madagascar, suggesting important regional differences in the occurrence of HTs. We discovered parasite vectors that may plausibly transmit BovB and found that the proportion of BovB-positive parasites is also high in Madagascar where BovB thus might be physically transported by parasites to diverse vertebrates, potentially including humans. Remarkably, in two frog lineages, BovB HT occurred after migration from a non-HT area (Africa) to the HT hotspot (Madagascar). These results provide a novel perspective on how the prevalence of parasites influences the occurrence of HT in a region, similar to pathogens and their vectors in some endemic diseases.

A new species of Philoria (Anura: Limnodynastidae) from the uplands of the Gondwana Rainforests World Heritage Area of eastern Australia.

The six species of mountain frogs (Philoria: Limnodynastidae: Anura) are endemic to south-eastern Australia. Five species occur in headwater systems in mountainous north-eastern New South Wales (NSW) and south-eastern Queensland (Qld), centred on the Gondwana Rainforests of Australia World Heritage Area. A previous molecular genetic analysis identified divergent genetic lineages in the central and western McPherson Ranges region of Qld and NSW, but sampling was inadequate to test the species status of these lineages. With more comprehensive geographic sampling and examination of the nuclear genome using SNP analysis, we show that an undescribed species, P. knowlesi sp. nov., occurs in the central and western McPherson Ranges (Levers Plateau and Mount Barney complex). The new species is not phylogenetically closely related to P. loveridgei in the nuclear data but is related to one of two divergent lineages within P. loveridgei in the mtDNA data. We postulate that the discordance between the nuclear and mtDNA outcomes is due to ancient introgression of the mtDNA genome from P. loveridgei into the new species. Male advertisement calls and multivariate morphological analyses do not reliably distinguish P. knowlesi sp. nov. from any of the Philoria species in northeast NSW and southeast Qld. The genetic comparisons also enable us to define further the distributions of P. loveridgei and P. kundagungan. Samples from the Lamington Plateau, Springbrook Plateau, Wollumbin (Mt Warning National Park), and the Nightcap Range, are all P. loveridgei, and its distribution is now defined as the eastern McPherson Ranges and Tweed caldera. Philoria kundagungan is distributed from the Mistake Mountains in south-eastern Qld to the Tooloom Scrub on the Koreelah Range, southwest of Woodenbong, in NSW, with two subpopulations identified by SNP analysis. We therefore assessed the IUCN threat category of P. loveridgei and P. kundagungan and undertook new assessments for each of its two subpopulations and for the new taxon P. knowlesi sp. nov., using IUCN Red List criteria. Philoria loveridgei, P. kundagungan (entire range and northern subpopulation separately) and P. knowlesi sp. nov. each meet criteria for Endangered (EN B2(a)(b)[i, iii]). The southern subpopulation of P. kundagungan, in the Koreelah Range, meets criteria for Critically Endangered (CE B2(a)(b)[i, iii]). These taxa are all highly threatened due to the small number of known locations, the restricted nature of their breeding habitat, and direct and indirect threats from climate change, and the potential impact of the amphibian disease chytridiomycosis. Feral pigs are an emerging threat, with significant impacts now observed in Philoria breeding habitat in the Mistake Mountains.

Genetic and Ecogeographic Controls on Species Cohesion in Australia's Most Diverse Lizard Radiation.

AbstractSpecies vary extensively in geographic range size and climatic niche breadth. If range limits are primarily determined by climatic factors, species with broad climatic tolerances and those that track geographically widespread climates should have large ranges. However, large ranges might increase the probability of population fragmentation and adaptive divergence, potentially decoupling climatic niche breadth and range size. Conversely, ecological generalism in large-ranged species might lead to higher gene flow across climatic transitions, increasing species' cohesion and thus decreasing genetic isolation by distance (IBD). Focusing on Australia's iconic Ctenotus lizard radiation, we ask whether species range size scales with climatic niche breadth and the degree of population isolation. To this end, we infer independently evolving operational taxonomic units (OTUs), their geographic and climatic ranges, and the strength of IBD within OTUs based on genome-wide loci from 722 individuals spanning 75 taxa. Large-ranged OTUs were common and had broader climatic niches than small-ranged OTUs; thus, large ranges do not appear to simply result from passive tracking of widespread climatic zones. OTUs with larger ranges and broader climatic niches showed relatively weaker IBD, suggesting that large-ranged species might possess intrinsic attributes that facilitate genetic cohesion across large distances and varied climates. By influencing population divergence and persistence, traits that affect species cohesion may play a central role in large-scale patterns of diversification and species richness.

Taxonomic revision of south-eastern Australian giant burrowing frogs (Anura: Limnodynastidae: Heleioporus Gray).

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)).

A new hip-pocket frog from mid-eastern Australia (Anura: Myobatrachidae: Assa).

The hip-pocket frog (Assa darlingtoni), a small terrestrial myobatrachid frog found in mid-eastern Australia, has a highly derived, unusual, reproductive mode involving a unique form of male parental care. Males have subcutaneous pouches that open near the hip, and the developing tadpoles are carried in these pouches to post metamorphosis. It is found on several isolated mountain ranges in closed forest habitats, associated with high rainfall and temperate or sub-tropical climates. We established genetic relationships among specimens sampled across the range using phylogenetic analyses of thousands of single nucleotide polymorphisms (SNPs) from the nuclear genome and mitochondrial ND2 gene nucleotide sequences. These analyses uncovered two lineages that are genetically distinct in both nDNA and mtDNA analyses and that have low levels of divergence in male advertisement calls and are morphologically cryptic. Our data support separate species status for each lineage, based on the molecular genetic data. The first, which we name as a new species, Assa wollumbin sp. nov., is restricted to a single mountain, Wollumbin (= Mount Warning), the eroded cone of an ancient shield volcanothe Tweed Volcano. The second, the nominal species A. darlingtoni, has a wider distribution in five geographically disjunct subpopulations along 430 km of the Great Dividing Range in south-eastern Queensland and north-eastern New South Wales. The distributions of the two species closely approach within 15 km of each other on the central plug and rim of the caldera of the Tweed Volcano. Assa wollumbin sp. nov. meets the conservation criteria for Critically Endangered [A3(e), B2(a,b)]. When all subpopulations of A. darlingtoni are combined the conservation assessment is Endangered [A3(e), B2(a,b)]. Because of the fragmented nature of the distribution of A. darlingtoni, combined with the genetic evidence of concordant sub-structuring, we also conducted a conservation assessment on the five subpopulations. Two were assessed as Critically Endangered (DAguilar Range and Conondale/Blackall Ranges), and the remainder as Endangered (Dorrigo Plateau, McPherson Ranges, and Gibraltar Ranges/Washpool).

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.

Phylogeography, historical demography and systematics of the world's smallest pythons (Pythonidae, Antaresia).

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.

Revision of the Litoria watjulumensis (Anura: Pelodryadidae) group from the Australian monsoonal tropics, including the resurrection of L. spaldingi.

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.

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life.

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.].