Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota

Protecting the innocent: studying short-range endemic taxa enhances conservation outcomes

A major challenge confronting many contemporary systematists is how to integrate standard taxonomic research with conservation outcomes. With a biodiversity crisis looming and ongoing impediments to taxonomy, how can systematic research continue to document species and infer the ‘Tree of Life’, and still maintain its significance to conservation science and to protecting the very species it strives to understand? Here we advocate a systematic research program dedicated to documenting short-range endemic taxa, which are species with naturally small distributions and, by their very nature, most likely to be threatened by habitat loss, habitat degradation and climate change. This research can dovetail with the needs of industry and government to obtain high-quality data to inform the assessment of impacts of major development projects that affect landscapes and their biological heritage. We highlight how these projects are assessed using criteria mandated by Western Australian legislation and informed by guidance statements issued by the Environmental Protection Authority (Western Australia). To illustrate slightly different biological scenarios, we also provide three case studies from the Pilbara region of Western Australia, which include examples demonstrating a rapid rise in the collection and documentation of diverse and previously unknown subterranean and surface faunas, as well as how biological surveys can clarify the status of species thought to be rare or potentially threatened. We argue that ‘whole of biota’ surveys (that include all invertebrates) are rarely fundable and are logistically impossible, and that concentrated research on some of the most vulnerable elements in the landscape – short-range endemics, including troglofauna and stygofauna – can help to enhance conservation and research outcomes.

Genetic diversity and biogeographic history inform future conservation management strategies for the rare sunset frog (Spicospina flammocaerulea)

Outlining the distribution of genetic variation, patterns of gene flow and clarifying the biogeographic processes underlying population history are critical components of a comprehensive conservation strategy for endangered or vulnerable species. We provide this information for the vulnerable sunset frog (Spicospina flammocaerulea) using a comprehensive genetic dataset (ND2) with samples from 17 of 22 geographic localities where this species has been found. From genetic, biogeographic and coalescent-based analyses, we document the existing genetic variation, likely movement patterns and explore the biogeographic history of S. flammocaerulea. While catchment-based genetic variation is well documented in other high-rainfall taxa in south-western Australia, a much more complex scenario including dispersal across ridge lines between catchments better explains the distribution of genetic variation and observed patterns of gene flow in S. flammocaerulea. The population history of S. flammocaerulea is strongly indicative of recent population contraction and expansion, which may be related to late Pleistocene climate fluctuations. This suggests that this species can adapt or move in response to fluctuating climates provided suitable habitats or expansion areas are available. However, like many other endemic taxa with limited geographic ranges in south-western Australia, the potential to shift distributions is hampered by being land-locked within an agricultural landscape, limiting management options in the face of climate change.

Redescription of the western desert taipan, Oxyuranus temporalis (Serpentes:Elapidae), with notes on its distribution, diet and genetic variation

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.

Molecular evidence for ten species and Oligo-Miocene vicariance within a nominal Australian gecko species (Crenadactylus ocellatus, Diplodactylidae)

BACKGROUND

Molecular studies have revealed that many putative 'species' are actually complexes of multiple morphologically conservative, but genetically divergent 'cryptic species'. In extreme cases processes such as non-adaptive diversification (speciation without divergent selection) could mask the existence of ancient lineages as divergent as ecologically and morphologically diverse radiations recognised as genera or even families in related groups. The identification of such ancient, but cryptic, lineages has important ramifications for conservation, biogeography and evolutionary biology. Herein, we use an integrated multilocus genetic dataset (allozymes, mtDNA and nuclear DNA) to test whether disjunct populations of the widespread nominal Australian gecko species Crenadactylus ocellatus include distinct evolutionary lineages (species), and to examine the timing of diversification among these populations.

RESULTS

We identify at least 10 deeply divergent lineages within the single recognised species Crenadactylus ocellatus, including a radiation of five endemic to the Kimberley region of north-west Australia, and at least four known from areas of less than 100 km2. Lineages restricted to geographically isolated ranges and semi-arid areas across central and western Australia are estimated to have began to diversify in the late Oligocene/early Miocence (~20-30 mya), concurrent with, or even pre-dating, radiations of many iconic, broadly sympatric and much more species-rich Australian vertebrate families (e.g. venomous snakes, dragon lizards and kangaroos).

CONCLUSIONS

Instead of a single species, Crenadactylus is a surprisingly speciose and ancient vertebrate radiation. Based on their deep divergence and no evidence of recent gene flow, we recognise each of the 10 main lineages as candidate species. Molecular dating indicates that the genus includes some of the oldest vertebrate lineages confounded within a single species yet identified by molecular assessments of diversity. Highly divergent allopatric lineages are restricted to putative refugia across arid and semi-arid Australia, and provide important evidence towards understanding the history and spread of the Australian arid zone, suggesting at a minimum that semi-arid conditions were present by the early Miocene, and that severe aridity was widespread by the mid to late Miocene. In addition to documenting a remarkable instance of underestimation of vertebrate species diversity in a developed country, these results suggest that increasing integration of molecular dating techniques into cryptic species delimitation will reveal further instances where taxonomic conservatism has led to profound underestimation of not only species numbers, but also highly significant phylogenetic diversity and evolutionary history.

Evolutionary origins and diversification of dragon lizards in Australia's tropical savannas

Australia's monsoonal tropics are dominated by the largest and least modified savanna woodlands in the world, and they are globally significant for their high biodiversity and regional endemism. Despite this, there have been very few molecular studies of the evolutionary origins and diversification of vertebrates in this region. The semi-arboreal dragon lizards of Lophognathus and Amphibolurus are widely distributed in the savanna and dry sclerophyll woodlands of Australasia, including the monsoon tropics. We sequenced a ~1400 bp region of mitochondrial DNA and a ~1400 bp nuclear gene (RAG1) to investigate the phylogenetic relationships and phylogeographic structuring of all seven species of Lophognathus and Amphibolurus. Our analyses show that there is a higher level of species and generic diversity in the monsoon tropics than previously thought, and a full morphological review and taxonomic revision of these genera is required. Relaxed molecular clock analyses indicate that species across both genera originated in the late Miocene and early Pliocene, with significant phylogeographic structure within species. We did not find any evidence that the monsoon tropics species were a monophyletic group that had diversified within the region; instead Amphibolurus and Lophognathus represent at least three independent evolutionary colonizations of the monsoon tropics. It is probable that the origins and phylogeographic patterns of the northern Lophognathus species have evolved under the climatic influence of the Australian monsoon, rather than being either an ancient Gondwanan lineage that pre-dates the monsoon or the result of a more recent dispersal event across Wallace's Line.

Island species radiation and karyotypic stasis in Pachycladon allopolyploids

Background

Pachycladon (Brassicaceae, tribe Camelineae) is a monophyletic genus of ten morphologically and ecogeographically differentiated, and presumably allopolyploid species occurring in the South Island of New Zealand and in Tasmania. All Pachycladon species possess ten chromosome pairs (2n = 20). The feasibility of comparative chromosome painting (CCP) in crucifer species allows the origin and genome evolution in this genus to be elucidated. We focus on the origin and genome evolution of Pachycladon as well as on its genomic relationship to other crucifer species, particularly to the allopolyploid Australian Camelineae taxa. As species radiation on islands is usually characterized by chromosomal stasis, i.e. uniformity of chromosome numbers/ploidy levels, the role of major karyotypic reshuffling during the island adaptive and species radiation in Pachycladon is investigated through whole-genome CCP analysis.

Results

The four analyzed Pachycladon species possess an identical karyotype structure. The consensual ancestral karyotype is most likely common to all Pachycladon species and corroborates the monophyletic origin of the genus evidenced by previous phylogenetic analyses. The ancestral Pachycladon karyotype (n = 10) originated through an allopolyploidization event between two genomes structurally resembling the Ancestral Crucifer Karyotype (ACK, n = 8). The primary allopolyploid (apparently with n = 16) has undergone genome reshuffling by descending dysploidy toward n = 10. Chromosome "fusions" were mediated by inversions, translocations and centromere inactivation/loss. Pachycladon chromosome 3 (PC3) resulted from insertional fusion, described in grasses. The allopolyploid ancestor originated in Australia, from the same or closely related ACK-like parental species as the Australian Camelineae allopolyploids. However, the two whole-genome duplication (WGD) events were independent, with the Pachycladon WGD being significantly younger. The long-distance dispersal of the diploidized Pachycladon ancestor to New Zealand was followed by the Pleistocene species radiation in alpine habitats and characterized by karyotypic stasis.

Conclusions

Karyotypic stasis in Pachycladon suggests that the insular species radiation in this genus proceeded through homoploid divergence rather than through species-specific gross chromosomal repatterning. The ancestral Pachycladon genome originated in Australia through an allopolyploidization event involving two closely related parental genomes, and spread to New Zealand by a long-distance dispersal. We argue that the chromosome number decrease mediated by inter-genomic reshuffling (diploidization) could provide the Pachycladon allopolyploid founder with an adaptive advantage to colonize montane/alpine habitats. The ancestral Pachycladon karyotype remained stable during the Pleistocene adaptive radiation into ten different species.

History of Australian aridity: chronology in the evolution of arid landscapes

Australian climate and vegetation, known from marine and lacustrine sediments and fossils, varied dramatically throughout the Cenozoic Era, with several warm reversals superimposed on overall drying and cooling. A suite of landforms, including stony deserts, dunefields and playa lakes, formed in response to the advancing aridity but their age generally remained uncertain until fairly recently, owing to a lack of suitable dating methods. Within the last 5 years, the chronology of Late Quaternary fluctuations of lakes, dunes and dust-mantles has been established by luminescence dating methods, and mid-Pleistocene onset of playa conditions in a few closed basins has been estimated using palaeomagnetic reversal chronology. Only recently has it been shown, by cosmogenic isotope dating, that major tracts of arid landforms including the Simpson Desert dunefield, and stony deserts of the Lake Eyre Basin, were formed in early Pleistocene and late Pliocene times, respectively. These landscapes represent a stepwise response to progressive climatic drying and, speculatively, were accompanied by biological adaptations. Recent molecular DNA studies indicate that Australia's arid-adapted species evolved from mesic-adapted ancestors during the Pliocene or earlier, but whether speciation rapidly accompanied the development of stony deserts and other arid geomorphological provinces awaits further studies of arid landscape chronology.

Birth of a hotspot of intraspecific genetic diversity: notes from the underground

Hotspots of intraspecific diversity have been observed in most species, often within areas of putative Pleistocene refugia. They have thus mostly been viewed as the outcome of prolonged stability of large populations within the refugia. However, recent evidence has suggested that several other microevolutionary processes could also be involved in their formation. Here, we investigate the contribution of these processes to current range-wide patterns of genetic diversity in the Italian endemic mole Talpa romana, using both nuclear (30 allozyme loci) and mitochondrial markers (cytochrome b sequences). Southern populations of this species showed an allozyme variation that is amongst the highest observed in small mammals (most populations had an expected heterozygosity of 0.10 or above), which was particularly unexpected for a subterranean species. Population genetic, phylogeographic and historical demographic analyses indicated that T. romana populations repeatedly underwent allopatric differentiations followed by secondary admixture within the refugial range in southern Italy. A prolonged demographic stability was reliably inferred from the mitochondrial DNA data only for a population group located north and east of the Calabrian peninsula, showing comparatively lower levels of allozyme variability, and lacking evidence of secondary admixture with other groups. Thus, our results point to the admixture between differentiated lineages as the main cause of the higher levels of diversity of refugial populations. When compared with the Pleistocene evolutionary history recently inferred for species from both the same and other geographic regions, these results suggest the need for a reappraisal of the role of gene exchange in the formation of intraspecific hotspots of genetic diversity.

Does incubation temperature fluctuation influence hatchling phenotypes in reptiles? A test using parthenogenetic geckos

Many lineages of parthenogenetic organisms have persisted through significant environmental change despite the constraints imposed by their fixed genotype and limited evolutionary potential. The ability of parthenogens to occur sympatrically with sexual relatives may in part be due to phenotypic plasticity in their responses to their environment, especially with respect to incubation temperature--a maternally selected trait. Here we measured the incubation temperatures selected by two lineages of triploid parthenogenic geckos in the Heteronotia binoei complex by allowing them to deposit clutches along a thermal gradient. The average nest temperature selected was 28.4 degrees C, with no significant differences between parthenogenic races or individual clones. To investigate the effect of nest-temperature variability on physiological and morphological traits, we incubated eggs from different races at one of four incubation regimes (32 degrees +/- 0 degrees, +/- 3 degrees , +/- 5 degrees , or +/- 9 degrees C). Embryos incubated at constant 32 degrees C developed faster than embryos reared under increasing extremes of diel temperature fluctuation (+/- 3 degrees , +/- 5 degrees C), and incubation at 32 degrees +/- 9 degrees C was unsuccessful. Incubation regime had no effect on the body size, preferred substrate temperature, or mass-specific .V(O2) of hatchlings. However, parthenogenic race had a significant effect on egg mass, tail length, snout-to-vent length, total length, and .V(O2) . We conclude that developmental traits are strongly influenced by clonal genotypes in this parthenogenic complex but are well buffered against fluctuations in incubation temperature.

Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia's arid zone, the golden perch (Macquaria ambigua)

Rivers provide an excellent system to study interactions between patterns of biodiversity structure and ecological processes. In these environments, gene flow is restricted by the spatial hierarchy and temporal variation of connectivity within the drainage network. In the Australian arid zone, this variability is high and rivers often exist as isolated waterholes connected during unpredictable floods. These conditions cause boom/bust cycles in the population dynamics of taxa, but their influence on spatial genetic diversity is largely unknown. We used a landscape genetics approach to assess the effect of hydrological variability on gene flow, spatial population structure and genetic diversity in an Australian freshwater fish, Macquaria ambigua. Our analysis is based on microsatellite data of 590 samples from 26 locations across the species range. Despite temporal isolation of populations, the species showed surprisingly high rates of dispersal, with population genetic structure only evident among major drainage basins. Within drainages, hydrological variability was a strong predictor of genetic diversity, being positively correlated with spring-time flow volume. We propose that increases in flow volume during spring stimulate recruitment booms and dispersal, boosting population size and genetic diversity. Although it is uncertain how the hydrological regime in arid Australia may change under future climate scenarios, management strategies for arid-zone fishes should mitigate barriers to dispersal and alterations to the natural flow regime to maintain connectivity and the species' evolutionary potential. This study contributes to our understanding of the influence of spatial and temporal heterogeneity on population and landscape processes.

Evolutionary diversification of the lizard genus Bassiana (Scincidae) across Southern Australia

Background

Relatively recent (Plio-Pleistocene) climatic variations had strong impacts on the fauna and flora of temperate-zone North America and Europe; genetic analyses suggest that many lineages were restricted to unglaciated refuges during this time, and have expanded their ranges since then. Temperate-zone Australia experienced less severe glaciation, suggesting that patterns of genetic structure among species may reflect older (aridity-driven) divergence events rather than Plio-Pleistocene (thermally-mediated) divergences. The lizard genus Bassiana (Squamata, Scincidae) contains three species that occur across a wide area of southern Australia (including Tasmania), rendering them ideally-suited to studies on the impact of past climatic fluctuations.

Methodology/Principal Findings

We performed molecular phylogenetic and dating analyses using two partial mitochondrial genes (ND2 and ND4) of 97 samples of Bassiana spp. Our results reveal a pattern of diversification beginning in the Middle Miocene, with intraspecific diversification arising from 5.7 to 1.7 million years ago in the Upper Miocene-Lower Pleistocene.

Conclusions/Significance

In contrast to the temperate-zone Northern Hemisphere biota, patterns of evolutionary diversification within southern Australian taxa appear to reflect geologically ancient events, mostly relating to east-west discontinuities imposed by aridity rather than (as is the case in Europe and North America) relatively recent recolonisation of northern regions from unglaciated refugia to the south.

The maintenance of disparate levels of clonality, genetic diversity and genetic differentiation in disjunct subspecies of the rare Banksia ionthocarpa

The evolutionary potential of plant species that reproduce via predominantly clonal means and the conditions under which clonality is favoured are not well known. Long-term clonal reproduction is expected to result in a number of readily detectable genetic signals not present in populations that reproduce by sexual means. We use a hierarchical sampling strategy to assess genotype probabilities and confirm that two rare sister taxa of Banksia ionthocarpa have contrasting modes of reproduction. Banksia ionthocarpa subsp. chrysophoenix reproduces clonally. Populations had low levels of genotypic diversity and were comprised of large clonal patches consisting of many ramets that covered hundreds of square metres and showed little intermixing. The taxon was genetically depauperate (mean Na = 1.97, mean P = 0.66, mean He = 0.282), had high levels of genetic differentiation between populations (θ = 0.481), and populations exhibited excess heterozygosity and linkage disequilibrium (LD) among loci, suggesting historically high levels of clonality. In contrast, the sister taxon B. ionthocarpa subsp. ionthocarpa, which occurs in an area with more than twice the annual rainfall and less extreme minimum and maximum temperatures, showed no evidence of clonality, high levels of genotypic diversity, greater genetic diversity (mean Na = 3.31, mean P = 0.81, mean He = 0.405), lower levels of genetic differentiation between populations (θ = 0.253) and no evidence of excess heterozygosity or LD among loci. We suggest that the development of clonality in subsp. chrysophoenix is associated with its more marginal environment and enhanced by response to recurrent fires.

Plumage patterns are good indicators of taxonomic diversity, but not of phylogenetic affinities, in Australian grasswrens Amytornis (Aves: Maluridae)

The grasswrens (Maluridae: Amytornis) are elusive songbirds from the arid zones of Australia. Although some other Australian bird genera are also largely restricted to arid regions, none show the level of localized taxonomic diversity seen in Amytornis. Furthermore, their cryptic plumage patterns provide excellent camouflage but make it difficult to determine whether shared patterns reflect phylogenetic relationships or adaptations to similar terrain. To resolve the systematics and patterns of ecological diversification within Amytornis, we here present the results of a phylogenetic analysis of mitochondrial and nuclear multi-locus data for all recognized species and most subspecies, using traditional concatenation-based methods as well as a coalescent-based species-tree approach. Phylogenetic patterns retrieved by the species-tree approach were highly congruent with traditional methods, although branch support was generally higher in concatenation-based analysis, suggesting that species-tree methods may furnish more conservative results. In terms of identifying taxonomic diversity there was good concordance between plumage-based assessments and DNA distances. The same concordance was not found when comparing plumage-based and DNA-based predictions of phylogenetic relationships. Four primary lineages were identified: (a) barbatus; (b) merrotsyi; (c) the textilis complex, purnelli, ballarae, goyderi and housei; and (d) woodwardi, dorotheae, and the striatus complex. There was no robust resolution of relationships between lineages. It appears that in Amytornis, plumage differentiation between discrete populations is taxonomically significant, and not greatly influenced by ecophenotypic variation. However, at the deeper phylogenetic level, similar suites of plumage characters may be phylogenetically uninformative because of homoplasy. The study reveals higher levels of taxonomic diversity in Amytornis than previously recognized, with many taxa being highly localized. Such extensive short range endemism is mainly encountered in poorly-dispersing invertebrates and is unique in Australian birds. The identification here of the additional restricted range taxa has important conservation implications.

Geographic variation in the age of temperate-zone reptile and amphibian species: Southern Hemisphere species are older

Despite controversy over alternative definitions, the species is the fundamental operational unit of biodiversity, and species are the building-blocks of conservation. But is a 'species' from one part of the world the same as a 'species' from elsewhere? Our meta-analysis of molecular phylogenetic data reveals that reptile and amphibian species distributed in temperate-zone areas of the Northern Hemisphere are younger than taxa from the Southern Hemisphere, probably reflecting the greater impact of past climatic variation on Northern Hemisphere habitats. Because a species' age may influence its vulnerability to anthropogenic threats, geographical variation in species ages should be incorporated into conservation planning.

Multilocus analysis of honeyeaters (Aves: Meliphagidae) highlights spatio-temporal heterogeneity in the influence of biogeographic barriers in the Australian monsoonal zone

Multilocus studies in phylogenetics and comparative phylogeography have the power to explore a broader spectrum of evolutionary questions than either discipline has alone. To examine the origins of sympatry in a group of closely related birds of mostly mesic eucalypt woodlands in Australia, we reconstructed the relationships among species of Entomyzon and Melithreptus honeyeaters (Aves: Passeriformes: Meliphagidae) using a mitochondrial marker, ND2, and six non-coding nuclear loci (total 4719 base pairs). By sampling across the geographical range of each species, we studied not only their phylogenetic relationships to each other but also the spatial distribution of their genetic diversity. We tested several biogeographic hypotheses concerning the role of Pleistocene environmental change in Australia. Phylogenetic gene trees support the current understanding of E. cyanotis as the sister to Melithreptus. Non-monophyly of M. lunatus in Australia's southern temperate woodlands highlights the need for a revision of systematics within Melithreptus. Phylogeographic analysis of the three northern species in Australia's monsoon tropics, M. gularis, M. albogularis and E. cyanotis, suggests that the roles of the Carpentarian and Torresian Barriers in shaping geographic structure in each of the species have been more complex and temporally dynamic than earlier morphology-based arguments of vicariance had suggested. We discuss their roles as ecological filters as well as barriers.

A Phylogeny and Timescale for the Evolution of Pseudocheiridae (Marsupialia: Diprotodontia) in Australia and New Guinea

PSEUDOCHEIRIDAE (MARSUPIALIA: Diprotodontia) is a family of endemic Australasian arboreal folivores, more commonly known as ringtail possums. Seventeen extant species are grouped into six genera (Pseudocheirus, Pseudochirulus, Hemibelideus, Petauroides, Pseudochirops, Petropseudes). Pseudochirops and Pseudochirulus are the only genera with representatives on New Guinea and surrounding western islands. Here, we examine phylogenetic relationships among 13 of the 17 extant pseudocheirid species based on protein-coding portions of the ApoB, BRCA1, ENAM, IRBP, Rag1, and vWF genes. Maximum parsimony, maximum likelihood, and Bayesian methods were used to estimate phylogenetic relationships. Two different relaxed molecular clock methods were used to estimate divergence times. Bayesian and maximum parsimony methods were used to reconstruct ancestral character states for geographic provenance and maximum elevation occupied. We find robust support for the monophyly of Pseudocheirinae (Pseudochirulus + Pseudocheirus), Hemibelidinae (Hemibelideus + Petauroides), and Pseudochiropsinae (Pseudochirops + Petropseudes), respectively, and for an association of Pseudocheirinae and Hemibelidinae to the exclusion of Pseudochiropsinae. Within Pseudochiropsinae, Petropseudes grouped more closely with the New Guinean Pseudochirops spp. than with the Australian Pseudochirops archeri, rendering Pseudochirops paraphyletic. New Guinean species belonging to Pseudochirops are monophyletic, as are New Guinean species belonging to Pseudochirulus. Molecular dates and ancestral reconstructions of geographic provenance combine to suggest that the ancestors of extant New Guinean Pseudochirops spp. and Pseudochirulus spp. dispersed from Australia to New Guinea ∼12.1-6.5 Ma (Pseudochirops) and ∼6.0-2.4 Ma (Pseudochirulus). Ancestral state reconstructions support the hypothesis that occupation of high elevations (>3000 m) is a derived feature that evolved on the terminal branch leading to Pseudochirops cupreus, and either evolved in the ancestor of Pseudochirulus forbesi, Pseudochirulus mayeri, and Pseudochirulus caroli, with subsequent loss in P. caroli, or evolved independently in P. mayeri and P. forbesi. Divergence times within the New Guinean Pseudochirops clade are generally coincident with the uplift of the central cordillera and other highlands. Diversification within New Guinean Pseudochirulus occurred in the Plio-Pleistocene after the establishment of the Central Range and other highlands. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10914-010-9129-7) contains supplementary material, which is available to authorized users.

Plio-pleistocene diversification and connectivity between mainland and Tasmanian populations of Australian snakes (Drysdalia, Elapidae, Serpentes)

The genus Drysdalia contains three recognised species of elapid (front-fanged) snakes, distributed across south-eastern Australia (including Tasmania). Here we aim to clarify the biogeography and phylogeographical relationships of this poorly documented region. We conducted molecular phylogenetic and dating analyses, using mitochondrial genes (ND4 and cyt-b). Our analyses suggest that divergence events among the three extant species, and among major lineages within those species, are congruent with Plio-pleistocene climatic variations. Two highly divergent genetic lineages within Drysdalia coronoides occur in Tasmania. Molecular dating suggests that these lineages were isolated from the mainland in the Pleistocene.

Evolutionary speed limited by water in arid Australia

The covariation of biodiversity with climate is a fundamental pattern in nature. However, despite the ubiquity of this relationship, a consensus on the ultimate cause remains elusive. The evolutionary speed hypothesis posits direct mechanistic links between ambient temperature, the tempo of micro-evolution and, ultimately, species richness. Previous research has demonstrated faster rates of molecular evolution in warmer climates for a broad range of poikilothermic and homeothermic organisms, in both terrestrial and aquatic environments. In terrestrial systems, species richness increases with both temperature and water availability and the interaction of those terms: productivity. However, the influence of water availability as an independent variable on micro-evolutionary processes has not been examined previously. Here, using methodology that limits the potentially confounding role of cladogenetic and demographic processes, we report, to our knowledge, the first evidence that woody plants living in the arid Australian Outback are evolving more slowly than related species growing at similar latitudes in moist habitats on the mesic continental margins. These results support a modified evolutionary speed explanation for the relationship between the water-energy balance and plant diversity patterns.

Diversification and persistence at the arid-monsoonal interface: australia-wide biogeography of the Bynoe's gecko (Heteronotia binoei; Gekkonidae)

Late Neogene aridification in the Southern Hemisphere caused contractions of mesic biota to refugia, similar to the patterns established by glaciation in the Northern Hemisphere, but these episodes also opened up new adaptive zones that spurred range expansion and diversification in arid-adapted lineages. To understand these dynamics, we present a multilocus (nine nuclear introns, one mitochondrial gene) phylogeographic analysis of the Bynoe's gecko (Heteronotia binoei), a widely distributed complex spanning the tropical monsoon, coastal woodland, and arid zone biomes in Australia. Bayesian phylogenetic analyses, estimates of divergence times, and demographic inferences revealed episodes of diversification in the Pliocene, especially in the tropical monsoon biome, and range expansions in the Pleistocene. Ancestral habitat reconstructions strongly support recent and independent invasions into the arid zone. Our study demonstrates the varied responses to aridification in Australia, including localized persistence of lineages in the tropical monsoonal biome, and repeated invasion of and expansion through newly available arid-zone habitats. These patterns are consistent with those found in other arid environments in the Southern Hemisphere, including the South African succulent karoo and the Chilean lowlands, and highlight the diverse modes of diversification and persistence of Earth's biota during the glacial cycles of the Pliocene and Pleistocene.

VIEWPOINT. Is the Australian subterranean fauna uniquely diverse?

Australia was historically considered a poor prospect for subterranean fauna but, in reality, the continent holds a great variety of subterranean habitats, with associated faunas, found both in karst and non-karst environments. This paper critically examines the diversity of subterranean fauna in several key regions for the mostly arid western half of Australia. We aimed to document levels of species richness for major taxon groups and examine the degree of uniqueness of the fauna. We also wanted to compare the composition of these ecosystems, and their origins, with other regions of subterranean diversity world-wide. Using information on the number of ‘described’ and ‘known’ invertebrate species (recognised based on morphological and/or molecular data), we predict that the total subterranean fauna for the western half of the continent is 4140 species, of which ~10% is described and 9% is ‘known’ but not yet described. The stygofauna, water beetles, ostracods and copepods have the largest number of described species, while arachnids dominate the described troglofauna. Conversely, copepods, water beetles and isopods are the poorest known groups with less than 20% described species, while hexapods (comprising mostly Collembola, Coleoptera, Blattodea and Hemiptera) are the least known of the troglofauna. Compared with other regions of the world, we consider the Australian subterranean fauna to be unique in its diversity compared with the northern hemisphere for three key reasons: the range and diversity of subterranean habitats is both extensive and novel; direct faunal links to ancient Pangaea and Gondwana are evident, emphasising their early biogeographic history; and Miocene aridification, rather than Pleistocene post-ice age driven diversification events (as is predicted in the northern hemisphere), are likely to have dominated Australia’s subterranean speciation explosion. Finally, we predict that the geologically younger, although more poorly studied, eastern half of the Australian continent is unlikely to be as diverse as the western half, except for stygofauna in porous media. Furthermore, based on similar geology, palaeogeography and tectonic history to that seen in the western parts of Australia, southern Africa, parts of South America and India may also yield similar subterranean biodiversity to that described here.

Phylogeography of the Australian sugar glider (Petaurus breviceps): evidence for a new divergent lineage in eastern Australia

The sugar glider (Petaurus breviceps) shows considerable variation in external morphology and mitochondrial DNA (mtDNA) diversity across its distribution in New Guinea and Australia. Here we investigate the phylogeography of P. breviceps in Australia using data from two mitochondrial genes (ND2 and ND4) and a nuclear gene (ω-globin). Phylogenetic analyses revealed the existence of two divergent mtDNA clades that are distributed over distinct geographical regions, one from coastal New South Wales and south-eastern Queensland and a second over the remaining distributional range of the species in Australia. The two groups generally had distinct ω-globin haplotypes that differed by one or two mutational steps. Analyses of Molecular Variation further supported the presence of at least two populations, accounting for 84.8% of the total mtDNA variation and 44% of the ω-globin variation. The general concordance of phylogeographic and population analyses suggests that population subdivision, possibly resulting from the combined influences of aridification after the Pliocene and uplift of the Great Dividing Range has impacted the evolution of P. breviceps. Our results also show that the geographical distribution of the two evolutionary lineages does not correspond with the distribution of the current morphological subspecies and we further propose that they be considered as separate Evolutionarily Significant Units for the purposes of conservation management.

Fine-scale comparative phylogeography of a sympatric sister species triplet of subterranean diving beetles from a single calcrete aquifer in Western Australia

Calcrete aquifers in the arid Yilgarn region of central Western Australia are a biodiversity hotspot for stygofauna. A distinct pattern of interspecific size class variation among subterranean dytiscid beetle species has been observed in 29 of these aquifers where either two or three small, medium and/or large sympatric species are found that are in some cases sister species. We used a 3.5 km(2) grid of bores to sample dytiscids on a fine-scale and employed a comparative phylogeographical and population genetic approach to investigate the origins of a sympatric sister species triplet of diving beetles from a single aquifer. Mitochondrial DNA sequence data from the Cytochrome oxidase c subunit I gene revealed that all three species have high levels of haplotype diversity with ancient (approximately 1 million years ago) intra-specific coalescence of haplotypes, but low levels of nucleotide diversity. Population analyses provide evidence for multiple expansion events within each species. There was spatial heterogeneity in the distribution of genetic variation and abundance both within and among the three taxa. Population analyses revealed significant fine-scale differentiation with isolation by distance for Paroster macrosturtensis and P. mesosturtensis, but not the smallest species P. microsturtensis. Haplotype network analyses provided limited or no evidence for past population fragmentation within the large and small species, but substantial historical divergence was observed in P. mesosturtensis that was not spatially structured. A patchy population structure with contemporaneous and historical isolation by distance in the three species is likely to have been a significant isolating and diversifying force, preventing us from ruling out a potential role for allopatric divergence during speciation of this beetle sister triplet.

The evolution of sexual and parthenogenetic Warramaba: a window onto Plio-Pleistocene diversification processes in an arid biome

Environmental changes over the Plio-Pleistocene have been key drivers of speciation patterns and genetic diversification in high-latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2-7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio-Pleistocene environmental change on diversification processes in arid Australia.

Australian pirates: systematics and phylogeny of the Australasian pirate spiders (Araneae:Mimetidae), with a description of the Western Australian fauna

Pirate spiders (Mimetidae) are well known for their specialised feeding ecology. They are vagrant araneophagic predators, enter the webs of their prey spiders and exhibit patterns of aggressive mimicry to overcome the web owner. The mimetid fauna of Australia and New Zealand currently consists of 26 species in the following three genera: Australomimetus Heimer, 1986 (18 species), Mimetus Hentz, 1832 (six species), and Ero C.L. Koch, 1836 (two species). The systematic position of the majority of Australasian mimetids was investigated through phylogenetic techniques utilising morphological character systems of 29 exemplar taxa and 87 characters, including the first examination of spinneret structure in species of Australomimetus. The results support an expanded concept for Australomimetus, which, apart from the introduced Ero aphana (Walckenaer, 1802), is found to contain the entire Australian and New Zealand mimetid fauna, also recorded from Asia. The following taxonomic changes are proposed: A. catulli (Heimer, 1989), comb. nov., A. hannemanni (Heimer, 1989), comb. nov., A. japonicus (Uyemura, 1938), comb. nov., A. mendicus (O. P. Cambridge, 1879), comb. nov. and A. sennio (Urquhart, 1891), comb. nov.; Ero luzoniensis Barrion & Litsinger, 1995 is synonymised with Ero aphana, and A. andreae Heimer, 1989 is synonymised with A. daviesianus Heimer, 1986; Mimetus tikaderi Gajbe, 1992 from India is excluded from Mimetidae, and referred to Liocranidae. The Western Australian mimetid fauna is described for the first time and comprises nine species of Australomimetus, including the following five new species: A. diabolicus, sp. nov., A. djuka, sp. nov., A. dunlopi, sp. nov., A. nasoi, sp. nov. and A. stephanieae, sp. nov. Several species-groups of Australomimetus are identified.