Multi-Species Phylogeography of Arid-Zone Sminthopsinae (Marsupialia: Dasyuridae) Reveals Evidence of Refugia and Population Expansion in Response to Quaternary Change

Historical population contraction and expansion events associated with Pleistocene climate change are important drivers of intraspecific population structure in Australian arid-zone species. We compared phylogeographic patterns among arid-adapted Dasyuridae (Sminthopsis and Planigale) with close phylogenetic relationships and similar ecological roles to investigate the drivers of phylogeographic structuring and the importance of historical refugia. We generated haplotype networks for two mitochondrial (control region and cytochrome b) and one nuclear (omega-globin) gene from samples distributed across each species range. We used Φ_ST to test for a genetic population structure associated with the four Pilbara subregions, and we used expansion statistics and Bayesian coalescent skyline analysis to test for signals of historical population expansion and the timing of such events. Significant population structure associated with the Pilbara and subregions was detected in the mitochondrial data for most species, but not with the nuclear data. Evidence of population expansion was detected for all species, and it likely began during the mid-late Pleistocene. The timing of population expansion suggests that these species responded favorably to the increased availability of arid habitats during the mid-late Pleistocene, which is when previously patchy habitats became more widespread. We interpret our results to indicate that the Pilbara region could have acted as a refugium for small dasyurids.

Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid zone Specialist: The Yellow-Footed Rock-Wallaby

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogalexanthopusxanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x.xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.

Snails in the desert: Assessing the mitochondrial and morphological diversity and the influence of aestivation behavior on lineage differentiation in the Australian endemic Granulomelon Iredale, 1933 (Stylommatophora: Camaenidae)

Progressive aridification since the mid-Miocene has had a significant influence on the evolution of the biota in the arid zone of central Australia. Especially moisture sensitive groups, such as snails, are often restricted to topographically complex areas, which have acted as refugia in an otherwise inhospitable environment. This historical fragmentation is deemed to be a potent agent of allopatric lineage diversification. Camaenid land snails are amongst only a few terrestrial gastropods that have managed to survive in the arid zone probably due to their ability to escape desiccation through aestivation. Here, we present the first study of the mitochondrial lineage differentiation in an endemic land snail genus from the Australian 'Red Centre', Granulomelon Iredale, 1933. Exposing significant incongruence between mtDNA phylogeny and morphology-based taxonomy, we completely revise the species and genus level taxonomy of this camaenid group. We demonstrate that this genus contains three species, G. grandituberculatum, G. adcockianum and G. squamulosum, which have so far been assigned to different genera: Granulomelon Iredale, 1933 (junior synonym: Baccalena Iredale, 1937), Basedowena Iredale, 1937 and Pleuroxia Ancey, 1887. Two of these species are widespread comprising multiple divergent mitochondrial lineages. Based on a molecular clock estimate, these lineages diverged approximately during the mid-Pleistocene, a period of particularly severe aridification. The phylogeographic patterns are consistent with an isolation-by-distance model in one species but not the other. We suggest that these differences can be attributed to their distinctive aestivation behavior.

On the biogeography of Centipeda: a species-tree diffusion approach

Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging due to the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms of geography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plant genus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampled from its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previously published substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipeda correlates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral species show a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly and southerly groups since ∼840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event (∼20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the Great Victoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. The result indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. This study contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers a significant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult to describe geography in terms of discrete areas.

Past and present distribution of Dasycercus: toward a better understanding of the identity of specimens in cave deposits and the conservation status of the currently recognised species D. blythi and D. cristicauda (Marsupialia : Dasyuridae)

Maps of the distribution of the two currently recognised species of Dasycercus, D. blythi and D. cristicauda have been prepared following correct identification based on tail morphology of specimens in the modern collections of all Australian museums. Localities in which the remains of Dasycercus have been found in cave deposits have also been mapped and an attempt made to determine the specific identity of some of these specimens. Following examination of larger samples of each species, differences in the premolar dentition were found to no longer be diagnostic. Most cave specimens could not be assigned to species on the basis of some dental measurements. DNA sequences could provide a means for establishing the identity of the cave specimens. Correct identification of specimens, together with knowledge of the search effort underlying the known distribution and persistence of the species in localities over their ranges, is essential for assessment of their conservation status.

Multiple biogeographical barriers identified across the monsoon tropics of northern Australia: phylogeographic analysis of the brachyotis group of rock-wallabies

The monsoon tropics of northern Australia are a globally significant biodiversity hotspot, but its phylogeography is poorly known. A major challenge for this region is to understand the biogeographical processes that have shaped the distribution and diversity of taxa, without detailed knowledge of past climatic and environmental fluctuations. Although molecular data have great potential to address these questions, only a few species have been examined phylogeographically. Here, we use the widely distributed and abundant short-eared rock-wallaby (Petrogale brachyotis; n = 101), together with the sympatric monjon (P. burbidgei; n = 11) and nabarlek (P. concinna; n = 1), to assess historical evolutionary and biogeographical processes in northern Australia. We sequenced ∼1000 bp of mitochondrial DNA (control region, ND2) and ∼3000 bp of nDNA (BRCA1, ω-globin and two anonymous loci) to investigate phylogeographic structuring and delineate the time-scale of diversification within the region. Our results indicate multiple barriers between the Top End (Northern Territory) and Kimberley (Western Australia), which have caused divergence throughout the Plio-Pleistocene. Eight geographically discrete and genetically distinct lineages within the brachyotis group were identified, five of which are separated by major river valleys (Ord, Victoria, Daly), arid lowlands and discontinuous sandstone ranges. It is likely that these barriers have similarly influenced genetic structure in other monsoonal biota.

Evolution of arid zone birds in Australia: leapfrog distribution patterns and mesic-arid connections in quail-thrush (Cinclosoma, Cinclosomatidae)

The quail-thrush, Cinclosoma, include between five and seven species distributed broadly across arid and semi-arid inland Australia, mesic forests of south-eastern Australia and New Guinea. It has been suggested that the arid zone species of quail-thrush arose from forest ancestors as Australia changed from a warm wet climate to a cooler drier climate since the late-Miocene. We generated multilocus (mitochondrial ND2 and eight nuclear loci) gene and species trees with complete taxon sampling of Cinclosoma to investigate evolutionary relationships and species status of some taxa. Topologies reconstructed in congruent, highly-resolved gene trees and species trees that supported the recognition of seven species. Ancestral state reconstruction and divergence time estimates suggest that arid-adapted taxa radiated in parallel with a drying climate and changing habitat. A 'leapfrog' distribution in phenotypes of arid zone taxa was likely a result of ancestral retention of inconspicuous (or camouflaged) plumage patterns. A specimen-based report from 1968 of hybridization between non-sister taxa Cinclosoma castanotum and Cinclosoma marginatum was verified using molecular analysis on specimens collected at the same locality 40 years later. We discuss the implications of hybridization to the evolution of this species group.

Cryptic grey-bellied dunnart (Sminthopsis griseoventer) discovered in South Australia: genetic, morphological and subfossil analyses show the value of collecting voucher material

The assumption that almost all mammal species are known to science has led to a recent trend away from collecting voucher specimens/tissues during field studies. Here we present a case study of a recently discovered cryptic marsupial (Sminthopsis griseoventer) in South Australia (SA) and show how such collections can contribute to rigorous biodiversity and biogeographic assessments. Morphological and genetic (allozyme and mitochondrial control region (CR) sequence data) analyses, including ancient DNA analyses of type material, were applied to 188 voucher specimens and 94 non-vouchered tissues of Sminthopsis held at the SA Museum. These data were used to confirm the presence of S. griseoventer in SA, validate means of identifying it morphologically and describe recent and pre-European distributions. Pelage differences between S. griseoventer and S. dolichura enabled their identification, but external measurements overlapped considerably. Subfossil S. griseoventer were identified from seven deposits and confirmed that in the past the species was more widespread in SA. CR divergences (>1.8%) among Western Australian and SA S. griseoventer suggested its long-term presence in SA. Discrepancies between the mitochondrial and allozyme affinities of S. aitkeni and S. griseoventer, coupled with the lack of obvious morphological differences, indicate that a taxonomic reappraisal of these species is warranted. The study strongly demonstrates an ongoing need for the routine collection of mammal voucher material in biological and environmental impact surveys.

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.

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

The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.

Conservation status and biogeography of Australia's terrestrial mammals

This paper attempts to identify and explain patterns in the biogeography of Australia’s indigenous terrestrial mammals at the time of European settlement (before modern extinctions), and also compares species’ pre-European and current status by region. From subfossil, historical and contemporary sources, we compiled data on the past geographic range and present status of mammals for Australia’s 85 biogeographic regions. Of the 305 indigenous species originally present, 91 have disappeared from at least half of the bioregions in which they occurred before European settlement. Thirty-nine extant species ‘persist’ in less than 25% of their original bioregions; 28 of these are marsupials and 11 are rodents. Twenty-two of the original 305 species are extinct, a further eight became restricted to continental islands, and 100 have become extinct in at least one bioregion. Over the same period, 26 species of exotic mammals established wild populations and now occupy from one to 85 bioregions. When we classified the bioregions in terms of their original species composition, the 3-group level in the dendrogram approximated the Torresian, Eyrean and Bassian subregions proposed by Spencer in 1898, while the 4-group level separated southern semiarid Eyrean bioregions, including those in south-west Australia, from the arid Eyrean bioregions. The classification dendrogram showed geographically (and statistically) discrete clustering down to the 19-group level, suggesting that all four subregions can be further divided on the basis of their mammal faunas. Variation partitioning showed 66% of the biogeographical pattern can be explained by environmental factors (related to temperature and precipitation), the spatial position of each bioregion (a third-order polynomial of latitude and longitude), the area of each bioregion, and the richness of species in each bioregion. In addition to the marked distributional changes that indigenous mammals have experienced over the last 200 years, the 49% of variation explainable by temperature and precipitation implies further shifts with global climate change.