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Species 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

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

The biogeography of islands is often strongly influenced by prior geological events. Corucia zebrata (Squamata: Scincidae) is endemic to the geologically complex Solomon Archipelago in Northern Melanesia. We examined the level of divergence for different island populations of C. zebrata and discussed these patterns in light of Pleistocene land bridges, island isolation, and island age. Corucia zebrata was sampled from 14 locations across the Solomon Archipelago and sequenced at two mitochondrial genes (ND2 and ND4; 1697 bp in total) and four nuclear loci (rhodopsin, an unknown intron, AKAP9, and PTPN12). Measures of genetic divergence, analyses of genetic variation, and Bayesian phylogenetic inference were used and the data assessed in light of geological information. Populations of C. zebrata on separate islands were found to be genetically different from each other, with reciprocal monophyly on mitochondrial DNA. Populations on islands previously connected by Pleistocene land bridges were marginally less divergent from each other than from populations on other nearby but isolated islands. There are indications that C. zebrata has radiated across the eastern islands of the archipelago within the last 1–4 million years. Nuclear loci were not sufficiently informative to yield further information about the phylogeography of C. zebrata on the Solomon Archipelago. Analyses of the mitochondrial data suggest that dispersal between islands has been very limited and that there are barriers to gene flow within the major islands. Islands that have been isolated during the Pleistocene glacial cycles are somewhat divergent in their mitochondrial genotypes, however, isolation by distance (IBD) and recent colonization of isolated but geologically younger islands appear to have had stronger effects on the phylogeography of C. zebrata than the Pleistocene glacial cycles. This contrasts with patterns reported for avian taxa, and highlights the fact that biogeographic regions for island species cannot be directly extrapolated among taxa of differing dispersal ability.

Relationships between the three classes of Neodermata (parasitic Platyhelminthes) are much debated and restrict our understanding of the evolution of parasitism and contingent adaptations. The historic view of a sister relationship between Cestoda and Monogenea (Cercomeromorphae; larvae bearing posterior hooks) has been dismissed and the weight of evidence against monogenean monophyly has mounted. We present the nucleotide sequence of the complete mitochondrial (mt) genome of Benedenia seriolae (Monogenea: Monopisthocotylea: Capsalidae), the first complete non-gyrodactylid monopisthocotylean mt genome to be reported. We also include nucleotide sequence data for some mt protein coding genes for a second capsalid, Neobenedenia sp. Analyses of the new mt genomes with all available platyhelminth mt genomes provide new phylogenetic hypotheses, which strongly influence perspectives on the evolution of diet in the Neodermata. Our analyses do not support monogenean monophyly but confirm that the Digenea and Cestoda are each monophyletic and sister groups. Epithelial feeding monopisthocotyleans on fish hosts are basal in the Neodermata and represent the first shift to parasitism from free-living ancestors. The next evolutionary step in parasitism was a dietary change from epithelium to blood. The common ancestor of Digenea + Cestoda was monogenean-like and most likely sanguinivorous. From this ancestral condition, adult digeneans and cestodes independently evolved dietary specialisations to suit their diverse microhabitats in their final vertebrate hosts. These improved perspectives on relationships fundamentally enhance our understanding of the evolution of parasitism in the Neodermata and in particular, the evolution of diet.

Eucalypt woodlands have been extensively cleared in southern Australia for agricultural production and the scattered trees that remain ("paddock trees") are at risk of extinction without conservation action to lift recruitment rates. Here we assessed the reproductive, demographic, and genetic structure of trees from two vegetation types (paddock vs. intact vegetation fragments) for each of two species of eucalypts to characterize post-clearance population structure and to evaluate paddock trees as seed sources for revegetation. Paddock trees of both species were structurally larger than trees in vegetation fragments, but seedlings and saplings were completely absent in paddocks due to ongoing agricultural land use. Eucalyptus leucoxylon paddock trees had high mortality, but overall paddock trees were not in poorer condition than fragment trees. E. leucoxylon paddock trees had lower reproductive output than trees in fragments, and Eucalyptus camaldulensis paddock trees had higher. Levels of genetic diversity of adult trees were very similar in the two vegetation types, and there was no genetic differentiation between paddock trees and remnant vegetation across our survey sites. These results suggest that paddock trees represent a potential source of seed to contribute to genetically diverse woodland restoration plantings, though further trials will be required to evaluate seedling survival on agriculturally modified land and under predicted future climate conditions.

The morphological based taxonomy of highly derived parasite groups is likely to poorly reflect their evolutionary relationships. The taxonomy of the monogenean family Capsalidae, which comprises approximately 180 species of flatworm parasites that predominantly attach to external surfaces of chondrichthyan and teleost fishes, is based mainly on six morphological characters. The phylogenetic history of the family is largely unknown. We reconstructed the phylogenetic relationships of 47 species in 20 genera from eight of the nine subfamilies, from nucleotide sequences of three unlinked nuclear genes, 28S ribosomal RNA, Histone 3 and Elongation Factor 1 alpha. Our phylogeny was well corroborated, with 75% of branches receiving strong support from both Bayesian posterior probabilities and maximum likelihood bootstrap proportions and all nodes showed positive partitioned likelihood support for each of the three genes. We found that the family was monophyletic, with the Gyrodactylidae and Udonellidae forming the sister group. The Capsalinae was monophyletic, however, our data do not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Entobdella, Listrocephalos, Neobenedenia and Tristoma, but Benedenia and Neoentobdella were polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on the molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification shows little correspondence with the phylogenetic relationships within the family.

Scattered trees are set to be lost from agricultural landscapes within the next century without sustained effort to increase recruitment. Thus, understanding the reproductive dynamics of scattered tree populations will be critical in determining how they can contribute to population restoration. The distance between conspecifics should be a key predictor of reproductive success, as more isolated trees are expected to receive fewer pollinator visits and experience increased transfer of self-pollen during longer pollinator foraging bouts. Further, isolation effects should be greater in species with less mobile pollinators. Here we contrast the effects of plant isolation on reproductive success of two species of eucalypt "paddock trees", Eucalyptus camaldulensis and Eucalyptus leucoxylon, with insect- and bird-pollination, respectively. Seed production was not affected by tree isolation in either the insect- or bird-pollinated species and once outliers were removed, neither was there an effect on germination rate. As somatic mutations may bias outcrossing rate estimates, we initially screened our microsatellite markers for mutations but found no variation in microsatellite profiles throughout the canopy of trees. Individual outcrossing rates did not decline with increasing tree isolation in either the insect- or bird-pollinated species, though there was considerable variation in these rates at large distances, suggesting that pollination becomes unreliable with increasing tree isolation. We found that pollination distances have likely increased in tree species in agricultural landscapes, and that this may be facilitated by introduced honeybees in the case of E. camaldulensis. We therefore suggest that even isolated trees of these species produce seed of sufficient quantity and quality to contribute to population restoration.

Complete nucleotide sequences of the cytochrome b and 12S rRNA genes and partial sequences of the mitochondrial 16S rRNA gene and the nuclear ɛ-globin gene were obtained from multiple exemplars of the New Guinean dasyurid, Myoictis. Allozyme data were also obtained from most of the same animals. The molecular data show that the genus comprises a number of genetically distinct lineages which correspond with groups proposed by Woolley (2005) on the basis of a number of morphological traits, including the form of the tail i.e. Myoictis leucura (sp. nov.), M. melas, M. wallacei and M. wavicus (new status). Divergence dates estimated from the weighted-average distances for the combined cytochrome b and 12S rRNA data, calibrated with a dasyurid-thylacine divergence 25 million years ago, suggest that the early cladogenic events separating Myoictis took place in the late Miocene. Subsequent separation of M. wavicus and M. leucura from a common ancestor as well as some genetic differentiation within M. melas, took place in the medial Pliocene.

The Cotesia flavipes species complex of parasitic wasps are economically important worldwide for the biological control of lepidopteran stem borers. The complex currently comprises three species: Cotesia flavipes Cameron, C. sesamiae (Cameron) and C. chilonis (Matsumura) (Hymenoptera: Braconidae), which appear morphologically similar. Despite their economic importance, little is known about the genetic diversity and phylogeography of these parasitoids. Differences in the biology of geographic populations have generally been interpreted as genetic divergence among strains, but direct genetic evidence is lacking. In Australia, several stem borer pests in neighbouring countries have been identified as significant threats to the sugar industry. However, the status of C. flavipes in Australia is unknown. To examine the genetic variation among worldwide populations of the C. flavipes complex and investigate the status of the Australian C. flavipes-like species, partial sequence data were generated for ...

Monitor lizards are emblematic reptiles that are widely distributed in the Old World. Although relatively well studied in vertebrate research, their biogeographic history is still controversial. We constructed a molecular dataset for 54 anguimorph species, including representatives of all families with detailed sampling of the Varanidae (38 species). Our results are consistent with an Asian origin of the Varanidae followed by a dispersal to Africa 41 (49–33) Ma, possibly via an Iranian route. Another major event was the dispersal of monitors to Australia in the Late Eocene–Oligocene 32 (39–26) Ma. This divergence estimate adds to the suggestion that Australia was colonized by several squamate lineages prior to the collision of the Australian plate with the Asian plate starting 25 Ma.

There have been no molecular genetic examinations of mating systems in the Australian varanid lizards (genus Varanus) despite their high species diversity, the abundance of some species and difficulties with direct observation of behaviourally cryptic species in the field. We developed 10 polymorphic microsatellite loci and assessed their utility in a range of varanid species. Observed heterozygosities in the three species assessed ranged from 30% to 100%. These loci should be useful for investigation of population structure, gene flow and mating systems in Varanus acanthurus, V. baritji and V. tristis and may also be of use in other varanid species.

The semi-fossorial scincid lizard, Lerista bougainvillii, is oviparous throughout its extensive range in south-eastern mainland Australia. However, two widely separated (by approximately 1000 km) island populations are viviparous; in these populations the eggshell is lost and females retain their offspring in utero until embryogenesis complete. One mainland population in south-eastern Victoria shows an intermediate condition, in which the eggshells are incomplete and uterine embryogenesis is prolonged. Morphological and electrophoretic analyses confirm a high degree of morphological and genetic similarity between populations (i.e. there is no evidence for the presence of more than one species), and phenetic analyses of these data show that each of the two disjunct viviparous populations more closely resembles adjacent oviparous populations than the other viviparous group. Hence, we infer that viviparity may have arisen twice within L. bougainvillii, in both cases on offshore islands with a cold climate.

Recent conceptual and methodological advances have increased the ability to apply multifaceted approaches to species delimitation, which is particularly useful in delimiting recently diversified species where single lines of evidence lead to incorrect species delimitation or assignment of individuals to species (e.g. cryptic, morphological species and paraphyletic, hybridizing species). Species of the Australian Gehyra gecko radiation have historically proven difficult to delimit due the group’s uniform, almost continent-wide geographic distribution and conservative morphology, contrasting high chromosomal and genetic diversity. Using an integrated approach to species delimitation taking advantage of morphological, geographic distributional and multi-locus genetic data, we investigate the diversity within three Gehyra species from the Australian arid zone. Our results show that these species represent eight distinct phylogenetic lineages, which display different patterns of morphological distinction and reproductive isolation. Using a recently developed Bayesian species delimitation method, we also find different levels of support for putative species dependent on priors for population size and timing of diversification assumed. Our results show that the current taxonomy does not adequately account for the diversity of the group. Discrepancies between lines of evidence indicate that diversification of the group is recent and ongoing, thus posing challenges for both species concepts and delimitation.

Background Understanding the dispersal and genetic structure of invasive insects across islands is important for designing management plans that are appropriate at spatial and temporal scales. For invasive parasites, population dynamics are largely determined by the distribution and density of their host species. The introduced parasitic fly, Philornis downsi, parasitises nestlings of endemic birds on all major islands of the Galápagos archipelago. The fly's high mortality and fitness impacts are of conservation concern for vulnerable and declining species of Darwin's finches. Using microsatellite data in Bayesian clustering and landscape genetic analyses, we examine gene flow and dispersal in P. downsi between three islands and across habitats (highlands, lowlands) and examine for the presence of population bottlenecks. We also examine variation at the mitochondrial gene CO1 across islands to establish if cryptic species were present. Results Both the mitochondrial and microsatellite data were consistent with there being a single species across islands. We found low genetic differentiation between islands and strong evidence for inter-island gene flow, or shared recent ancestry among individuals. Landscape genetic analysis identified two genetic clusters: one encompassing Santa Cruz and Isabela, and one on Floreana Island. There was no evidence of genetic differentiation between habitats and molecular variance was mainly attributable to within individuals. The combined P. downsi population was found to have undergone a population bottleneck. Conclusion Philornis downsi populations have high connectivity within and between islands, with low levels of genetic differentiation between Floreana and the other two islands examined. The genetic bottleneck found across islands suggests there was a small founding population or few introduction events of P. downsi. The high dispersal capacity and wide habitat use of P. downsi highlights the significant threat that this parasite poses to the Galápagos avifauna. Our findings are relevant for assessing the viability of methods to control P. downsi on Galápagos, such as the sterile insect technique.

Five healthy adult female first-generation hybrid tree frogs were produced by interspecific breeding of closely related tree frogs Litoria splendida and L. caerulea in a cage containing large numbers of males and females of both species. Phylogenetic analysis of mitochondrial DNA sequences established the female parent to be L. splendida. The peptide profile of the hybrid frogs included the neuropeptide caerulein, four antibiotics of the caerin 1 family and several neuronal nitric oxide synthase inhibitors of the caerin 1 and 2 classes of peptides. The skin secretions of the hybrids contained some peptides common to only one parent, some produced by both parental species, and four peptides expressed by the hybrids but not the parental species.

Molecular data derived from allozymes and mitochondrial nucleotide sequences, in combination with karyotypes, sex ratios, and inheritance data, have revealed the widespread Australian lizard Menetia greyii to be a complex of sexual and triploid unisexual taxa. Three sexual species, three presumed parthenogenetic lineages, and one animal of uncertain status were detected amongst 145 animals examined from south-central Australia, an area representing less than one-seventh of the total distribution of the complex. Parthenogenesis appears to have originated via interspecific hybridization, although presumed sexual ancestors could only be identified in two cases. The allozyme and mtDNA data reveal the presence of many distinct clones within the presumed parthenogenetic lineages. This new instance of vertebrate parthenogenesis is a first for the Scincidae and only the second definitive case of unisexuality in an indigenous Australian vertebrate.

Phylogenetic relationships among the venomous Australo-Papuan elapid snake radiation remain poorly resolved, despite the application of diverse data sets. To examine phylogenetic relationships among this enigmatic group, portions of the cytochrome b and 16S rRNA mitochondrial DNA genes were sequenced from 19 of the 20 terrestrial Australian genera and 6 of the 7 terrestrial Melanesian genera, plus a sea krait (Laticauda) and a true sea snake (Hydrelaps). These data clarify several significant issues in elapid phylogeny. First, Melanesian elapids form sister groups to Australian species, indicating that the ancestors of the Australian radiation came via Asia, rather than representing a relict Gondwanan radiation. Second, the two major groups of sea snakes (sea kraits and true sea snakes) represent independent invasions of the marine environment. Third, the radiation of viviparous Australian elapids is much older than has been suggested from immunological data. Parsimony analyses were unable to resolve relationships among the Australian radiation, a problem previously encountered with analyses of other (morphological, electrophoretic, karyotypic, immunological) data sets on these species. These data suggest that the reason for this continued difficulty lies in the timing of speciation events: the elapids apparently underwent a spectacular adaptive radiation soon after reaching Australia, such that divergences are ancient even within genera. Indeed, intrageneric divergences are almost as large as intergeneric divergences. Although this timing means that our sequence data cannot fully resolve phylogenetic relationships among the Australian elapids, the data suggest a close relationship of the following clades: Pseudonaja with Oxyuranus; Ogmodon with Toxicocalamus; Demansia with Aspidomorphus; Echiopsis with Denisonia; the "Notechis" lineage with Drysdalia coronoides; and Rhinoplocephalus and Suta with Drysdalia coronata. At least two of the Australian genera (Drysdalia and Simoselaps) appear to be paraphyletic. These sequence data support many of the conclusions reached by earlier studies using other types of data, but additional information will be needed before the phylogeny of the Australian elapids can be fully resolved.

Of the three species of taipan, Oxyuranus temporalis is the least known, being described only recently from a single juvenile specimen. We redescribe the species based on additional adult specimens from the Great Victoria Desert. Molecular genetic variation between the three localities from which the species is known was low, suggesting a single widespread population or recent radiation. Limited analysis of faecal material and gut contents suggested solely mammalian prey. The additional specimens suggest the possibility of a considerable distribution across sandy deserts of the central and western interior of Australia. Further studies and fieldwork are required to more accurately determine its geographic range, quantify the toxicity of the venom and assess the suitability of available antivenoms.

The currently recorded Fame Island herpetofauna comprises 24 species of reptile. This is a strict subset of the more diverse herpetofauna recorded from adjacent Peron Peninsula. Wc describe the broader geographic distributions and habitat associations of each species, and discuss the biogeography of the island herpelofauna in the context of the Carnarvon Basin biogeographic region. The reduced island diversity is presumably due to a combination of lesser sampling effort and'drop out' extinctions following drowning of the continental shelf and severance of the island around 6S00 years ago.

Variation in chromosomes and allozymes was assayed among bisexual populations of the genus Heteronotia. Three major cytotypes of H. binoei, A6, A6-2, and SM6, are recognized on the basis of variation in the morphology of chromosome 6. The A6 and A6-2 cytotypes can be further subdivided into a series of karyomorphs by polytypic variation in the distribution of C-band heterochromatin. Allozyme comparisons revealed little differentiation, with few fixed differences and many shared polymorphisms among the chromosome groups. In a phenetic analysis, geographically widespread samples from the SM6 cytotype clustered together, as did CA6 karyomorph samples. Karyotypes and allozymes were also assayed from representatives of H. spelea and an undescribed form of Heteronotia. Phylogenetic analysis of chromosome data supported monophyly of the SM6 cytotype, but suggested that the A6-2 cytotype, and thus H. binoei as currently defined, is paraphyletic. At least five groups, most of which should be considered as species, can be delineated within Heteronotia: H. spelea, an undescribed form, SM6 H. binoei, A6-2 H. binoei, and other H. binoei. The genetic data are consistent with Heteronotia being a relatively recent member of the Australian herpetofauna, but indicate greater diversity than has been recognized previously.

Variation at 18 allozyme loci was assayed among representatives of the geographically widespread, triploid parthenogenetic form of Heteronotia binoei. A minimum of 52 different genotypes were observed among 143 individuals. Virtually all localities sampled had multiple genotypes among the unisexuals. This represents unusually high genotypic diversity for a unisexual vertebrate. Heterozygosity in the triploids was higher than in diploid bisexual populations of H. binoei. Comparison with the alleles present in the diploid bisexuals confirms that the parthenogens are hybrids and indicates that most of the genotypic diversity stems from repetitive hybrid origins. However, the presence of some alleles unique to the parthenogens suggests that mutation adds to their genetic diversity. The genetic structure of this geographically widespread parthenogen suggests the hypothesis that the persistence and spread of the unisexual lineages is facilitated by genotypic diversity.