Phylogenetics and evolution of bell frogs (Litoria aurea species-group, Anura: Hylidae) based on mitochondrial ND4 sequences

Climate variability impacts on diversification processes in a biodiversity hotspot: a phylogeography of ancient pseudoscorpions in south-western Australia

The south-western division of Australia is the only biodiversity hotspot in Australia and is well-known for extreme levels of local endemism. Climate change has been identified as a key threat for flora and fauna, but very few data are presently available to evaluate its impact on invertebrate fauna. Here, we derive a molecular phylogeography for pseudoscorpions of the genus Pseudotyrannochthonius that in the south-west are restricted to regions with the highest rainfall. A dated molecular phylogeny derived from six gene fragments is used for biogeographic reconstruction analyses, spatial mapping, environmental niche-modelling, and to infer putative species. Phylogenetic analyses uncover nine clades with mostly allopatric distributions and often small linear ranges between 0.5 and 130 km. Molecular dating suggests that the origins of contemporary diversity fall into a period of warm/humid Palaeogene climates, but splits in the phylogeny coincide with major environmental shifts, such as significant global cooling during the Middle Miocene. By testing several models of historical biogeography available for the south-west, we determine that Pseudotyrannochthonius is an ancient relict lineage that principally follows a model of allopatric speciation in mesic zone refugia, although there are derivations from this model in that some species are older and distribution patterns more complex than expected. Ecological niche models indicate that drier and warmer future climates will lead to range contraction towards refugia of highest rainfall, probably mimicking past variations that have generated high diversity in these areas. Their conservation management will be crucial for preserving the unique biodiversity heritage of the south-west.

Indiscriminate feeding by an alien population of the spotted-thighed frog (Litoria cyclorhyncha) in southern Australia and potential impacts on native biodiversity

Litoria cyclorhyncha (Hylidae) is native to southern Western Australia, but a naturalised population has established on the Eyre Peninsula, South Australia. We investigated the diet of this exotic population to assess potential impacts on biodiversity and ecosystems. Seventy-six frogs were collected from three different habitats and their diet items assigned to parataxonomic units (PU) within orders. Stomach contents were diverse, containing 467 prey items from 19 orders and 135 PU, with extrapolation suggesting a diet of ~200 PU. Shannon diversity estimates of prey items consumed produced different rankings for the three habitats at the PU and order level. Therefore, estimates at the order level may not be representative of the actual diversity of prey items. L. cyclorhyncha consumed mainly arthropods and low numbers of conspecific young frogs, geckos and a juvenile house mouse. This generalist, indiscriminate predatory diet is similar to that of other hylids and implies that the species poses a risk to native biodiversity and ecosystem processes by predation and competition. Therefore, further spread of this species needs to be prevented. Our findings can inform effective policies and management actions to mitigate future impacts of L. cyclorhyncha.

Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog (Litoria raniformis) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis. However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

Human-assisted invasions of pacific islands by litoria frogs: a case study of the bleating tree frog on Lord Howe Island

There are substantial differences among taxonomic groups in their capacity to reach remote oceanic islands via long-distance overwater dispersal from mainland regions. Due to their permeable skin and intolerance of saltwater, amphibians generally require human-assisted dispersal to reach oceanic islands. Several Litoria frog species have been introduced to remote islands throughout the Pacific Ocean region. Lord Howe Island (LHI) is an oceanic island that lies approximately 600 km east of the Australian mainland and has a diverse, endemic biota. The bleating tree frog (Litoria dentata) is native to mainland eastern Australia, but was accidentally introduced to LHI in the 1990s, yet its ecology and potential impact on LHI has remained unstudied. We used a mitochondrial phylogeographical approach to determine that L. dentata was introduced from the Ballina region in northeastern New South Wales. The founding population was likely accidentally introduced with cargo shipped from the mainland. We also completed the first detailed investigation of the distribution, ecology and habitat use of L. dentata on LHI. The species is widespread on LHI and is prevalent in human habitat, cattle pasture and undisturbed forest. We discuss the potential impact of introduced Litoria species on Pacific islands and outline what biosecurity protocols could be implemented to prevent the introduction of further amphibian species to the ecologically sensitive oceanic area.

Biogeography and speciation of terrestrial fauna in the south-western Australian biodiversity hotspot

The south-western land division of Western Australia (SWWA), bordering the temperate Southern and Indian Oceans, is the only global biodiversity hotspot recognised in Australia. Renowned for its extraordinary diversity of endemic plants, and for some of the largest and most botanically significant temperate heathlands and woodlands on Earth, SWWA has long fascinated biogeographers. Its flat, highly weathered topography and the apparent absence of major geographic factors usually implicated in biotic diversification have challenged attempts to explain patterns of biogeography and mechanisms of speciation in the region. Botanical studies have always been central to understanding the biodiversity values of SWWA, although surprisingly few quantitative botanical analyses have allowed for an understanding of historical biogeographic processes in both space and time. Faunistic studies, by contrast, have played little or no role in defining hotspot concepts, despite several decades of accumulating quantitative research on the phylogeny and phylogeography of multiple lineages. In this review we critically analyse datasets with explicit supporting phylogenetic data and estimates of the time since divergence for all available elements of the terrestrial fauna, and compare these datasets to those available for plants. In situ speciation has played more of a role in shaping the south-western Australian fauna than has long been supposed, and has occurred in numerous endemic lineages of freshwater fish, frogs, reptiles, snails and less-vagile arthropods. By contrast, relatively low levels of endemism are found in birds, mammals and highly dispersive insects, and in situ speciation has played a negligible role in generating local endemism in birds and mammals. Quantitative studies provide evidence for at least four mechanisms driving patterns of endemism in south-western Australian animals, including: (i) relictualism of ancient Gondwanan or Pangaean taxa in the High Rainfall Province; (ii) vicariant isolation of lineages west of the Nullarbor divide; (iii) in situ speciation; and (iv) recent population subdivision. From dated quantitative studies we derive four testable models of historical biogeography for animal taxa in SWWA, each explicit in providing a spatial, temporal and topological perspective on patterns of speciation or divergence. For each model we also propose candidate lineages that may be worthy of further study, given what we know of their taxonomy, distributions or relationships. These models formalise four of the strongest patterns seen in many animal taxa from SWWA, although other models are clearly required to explain particular, idiosyncratic patterns. Generating numerous new datasets for suites of co-occurring lineages in SWWA will help refine our understanding of the historical biogeography of the region, highlight gaps in our knowledge, and allow us to derive general postulates from quantitative (rather than qualitative) results. For animals, this process has now begun in earnest, as has the process of taxonomically documenting many of the more diverse invertebrate lineages. The latter remains central to any attempt to appreciate holistically biogeographic patterns and processes in SWWA, and molecular phylogenetic studies should - where possible - also lead to tangible taxonomic outcomes.

Molecular systematics and biogeography of Logania R.Br. (Loganiaceae)

The angiosperm genus Logania R.Br. (Loganiaceae) is endemic to the mainland of Australia. A recent genetic study challenged the monophyly of Logania, suggesting that its two sections, Logania sect. Logania and Logania sect. Stomandra, do not group together. Additionally, the genus has a disjunct distribution, with a gap at the Nullarbor Plain in southern Australia. Therefore, Logania is a favourable candidate to gain insight into phylogenetic relationships and how these might intersect with Earth-history events. Our phylogenetic analyses of DNA sequences of two chloroplast markers (petD and rps16) showed that Logania sect. Logania and L. sect. Stomandra were each resolved as monophyletic, but the genus (as currently circumscribed) was not. Based on our Bayesian estimates of divergence times, the disjunct distributions within Logania sect. Stomandra could have been caused by flooding of the Eucla Basin. However, this biogeographical process cannot account for the distribution of Logania sect. Logania, with long-distance dispersal and establishment seeming more likely.

Three divergent lineages within an Australian marsupial (Petrogale penicillata) suggest multiple major refugia for mesic taxa in southeast Australia

Mesic southeastern Australia represents the continent's ancestral biome and is highly biodiverse, yet its phylogeographic history remains poorly understood. Here, we examine mitochondrial DNA (mtDNA) control region and microsatellite diversity in the brush-tailed rock-wallaby (Petrogale penicillata;n = 279 from 31 sites), to assess historic evolutionary and biogeographic processes in southeastern Australia. Our results (mtDNA, microsatellites) confirmed three geographically discrete and genetically divergent lineages within brush-tailed rock-wallabies, whose divergence appears to date to the mid-Pleistocene. These three lineages had been hypothesized previously but data were limited. While the Northern and Central lineages were separated by a known biogeographic barrier (Hunter Valley), the boundary between the Central and Southern lineages was not. We propose that during particularly cool glacial cycles, the high peaks of the Great Dividing Range and the narrow adjacent coastal plain resulted in a more significant north-south barrier for mesic taxa in southeastern Australia than has been previously appreciated. Similarly, located phylogeographic breaks in codistributed species highlight the importance of these regions in shaping the distribution of biodiversity in southeastern Australia and suggest the existence of three major refuge areas during the Pleistocene. Substructuring within the northern lineage also suggests the occurrence of multiple local refugia during some glacial cycles. Within the three major lineages, most brush-tailed rock-wallaby populations were locally highly structured, indicating limited dispersal by both sexes. The three identified lineages represent evolutionarily significant units and should be managed to maximize the retention of genetic diversity within this threatened species.

Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf galaxias (G. pusilla)

The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.

Elucidation of cryptic diversity in a widespread nearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamic landscape

We investigate the evolutionary history of the wide-ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range-wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well-supported clades, five of which correspond to well-defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate-driven range shifts, have all played a role in the historical diversification of H. arenicolor.

High levels of population subdivision in a morphologically conserved Mediterranean toad (Alytes cisternasii) result from recent, multiple refugia: evidence from mtDNA, microsatellites and nuclear genealogies

Pleistocene glaciations often resulted in differentiation of taxa in southern European peninsulas, producing the high levels of endemism characteristic of these regions (e.g. the Iberian Peninsula). Despite their small ranges, endemic species often exhibit high levels of intraspecific differentiation as a result of a complex evolutionary history dominated by successive cycles of fragmentation, expansion and subsequent admixture of populations. Most evidence so far has come from the study of species with an Atlantic distribution in northwestern Iberia, and taxa restricted to Mediterranean-type habitats remain poorly studied. The Iberian Midwife toad (Alytes cisternasii) is a morphologically conserved species endemic to southwestern and central Iberia and a typical inhabitant of Mediterranean habitats. Applying highly variable genetic markers from both mitochondrial and nuclear genomes to samples collected across the species' range, we found evidence of high population subdivision within A. cisternasii. Mitochondrial haplotypes and microsatellites show geographically concordant patterns of genetic diversity, suggesting population fragmentation into several refugia during Pleistocene glaciations followed by subsequent events of geographical and demographic expansions with secondary contact. In addition, the absence of variation at the nuclear beta-fibint7 and Ppp3caint4 gene fragments suggests that populations of A. cisternasii have been recurrently affected by episodes of extinction and recolonization, and that documented patterns of population subdivision are the outcome of recent and multiple refugia. We discuss the evolutionary history of the species with particular interest in the increasing relevance of Mediterranean refugia for the survival of genetically differentiated populations during the Pleistocene glaciations as revealed by studies in co-distributed taxa.

Impact of Plio-Pleistocene arid cycling on the population history of a southwestern Australian frog

Southwestern Australia is regarded as a global biodiversity hotspot. The region contains a high number of endemic species, ranging from Gondwanan relicts to much more recently evolved plant and animal species. Myobatrachid frogs are diverse in southwestern Australia, and while we know they have speciated in situ in the southwest, we know little about the temporal and geographical patterning of speciation events. Crinia georgiana is an ideal subject to test hypotheses concerning the effect of climatic history on southwestern Australian anurans, as it is an old lineage with a broad distribution covering the entire region. We compiled an extensive phylogeographical data set based on 1085 bp of the mitochondrial gene ND2 for 68 individuals from 18 sites across the species' range. Two major genetic clades were identified which were largely confined to the high rainfall and southeast coastal biogeographical zones, respectively. The clades appear to have diverged around the Plio-Pleistocene border (1.26-1.72 million years ago), concordant with increasing intensity and frequency of arid climate cycles. Subsequent phylogeographical structure appears to have developed primarily during the Pleistocene climatic fluctuations that also have been integral in generating species diversity in the endemic southwestern Australian flora. Phylogeographical analyses identified several dispersal routes, possible refugial areas within the range of the species and also regions of secondary contact. Dispersal routes identified may now be closed to the species because of habitat destruction and salinity problems in inland regions, posing concerns about the evolutionary potential of the species in light of predicted climate change.

A congruent molecular signature of vicariance across multiple plant lineages

Explaining disjunct distributions, or why closely related organisms are often separated by apparently severe barriers such as oceans or deserts, is a great challenge for historical biogeography. Competing explanations are long-distance dispersal across a barrier, and vicariance, in which disjunct taxa are descended from an ancestral population that was split by formation of the barrier. Vicariance explanations are testable by their prediction that near-simultaneous speciation should have occurred across multiple lineages of organisms between the disjunct areas because the origin of a barrier would potentially disrupt gene flow within multiple species. To date, there have been few studies providing evidence for multiple synchronous ancient divergences across a barrier whose origin coincides with the timing of the speciation events. Here, we use relaxed molecular-clock dating to investigate the timing of south-western (SW) versus south-eastern (SE) divergences in 23 pairs of plant lineages in southern Australia. Sixteen of the divergences correlate with the origin, 13-14 million years (Myr) ago, of the arid treeless Nullarbor Plain. The Nullarbor Plain currently forms a substantial barrier to SW-SE migration but during the last 45Myr this region has experienced multiple episodes of marine inundation and subaerial exposure. Thus, there have been multiple events that could have caused either isolation and speciation, or secondary contact, among the taxa of southern Australia. The strong molecular signal of coincident speciation in many diverse lineages during a short period provides the best evidence to date linking synchronous speciation to an ancient vicariance event.