Plio-Pleistocene diversification and biogeographic barriers in southern Australia reflected in the phylogeography of a widespread and common lizard species.

Palaeoclimatic events and biogeographical processes since the mid-Tertiary have played an important role in shaping the evolution and distribution of Australian fauna. However, their impacts on fauna in southern and arid zone regions of Australia are not well understood. Here we investigate the phylogeography of an Australian scincid lizard, Tiliqua rugosa, across southern Australia using mitochondrial DNA (mtDNA) and 11 nuclear DNA markers (nuDNA), including nine anonymous nuclear loci. Phylogenetic analyses revealed three major mtDNA lineages within T. rugosa, geographically localised north and south of the Murray River in southern Australia, and west of the Nullarbor Plain. Molecular variance and population analyses of both mtDNA and nuDNA haplotypes revealed significant variation among the three populations, although potential introgression of nuDNA markers was also detected for the Northern and Southern population. Coalescent times for major mtDNA lineages coincide with an aridification phase, which commenced after the early Pliocene and increased in intensity during the Late Pliocene-Pleistocene. Species distribution modelling and a phylogeographic diffusion model suggest that the range of T. rugosa may have contracted during the Last Glacial Maximum and the locations of optimal habitat appear to coincide with the geographic origin of several distinct mtDNA lineages. Overall, our analyses suggest that Plio-Pleistocene climatic changes and biogeographic barriers associated with the Nullarbor Plain and Murray River have played a key role in shaping the present-day distribution of genetic diversity in T. rugosa and many additional ground-dwelling animals distributed across southern Australia.

Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales).

Relatively little is known about species-level genetic diversity in flowering plants outside the eudicots and monocots, and it is often unclear how to interpret genetic patterns in lineages with whole-genome duplications. We addressed these issues in a polyploid representative of Hydatellaceae, part of the water-lily order Nymphaeales. We examined a transcriptome of Trithuria submersa for evidence of recent whole-genome duplication, and applied transcriptome-derived microsatellite (expressed-sequence tag simple-sequence repeat (EST-SSR)) primers to survey genetic variation in populations across its range in mainland Australia. A transcriptome-based Ks plot revealed at least one recent polyploidization event, consistent with fixed heterozygous genotypes representing underlying sets of homeologous loci. A strong genetic division coincides with a trans-Nullarbor biogeographic boundary. Patterns of 'allelic' variation (no more than two variants per EST-SSR genotype) and recently published chromosomal evidence are consistent with the predicted polyploidization event and substantial homozygosity underlying fixed heterozygote SSR genotypes, which in turn reflect a selfing mating system. The Nullarbor Plain is a barrier to gene flow between two deep lineages of T. submersa that may represent cryptic species. The markers developed here should also be useful for further disentangling species relationships, and provide a first step towards future genomic studies in Trithuria.

Preservation of Terrestrial Microorganisms and Organics Within Alteration Products of Chondritic Meteorites from the Nullarbor Plain, Australia.

Meteorites that fall to Earth quickly become contaminated with terrestrial microorganisms. These meteorites are out of chemical equilibrium in the environments where they fall, and equilibration promotes formation of low-temperature alteration minerals that can entomb contaminant microorganisms and thus preserve them as microfossils. Given the well-understood chemistry of meteorites and their recent discovery on Mars by rovers, a similarly weathered meteorite on Mars could preserve organic and fossil evidence of a putative past biosphere at the martian surface. Here, we used several techniques to assess the potential of alteration minerals to preserve microfossils and biogenic organics in terrestrially weathered ordinary chondrites from the Nullarbor Plain, Australia. We used acid etching of ordinary chondrites to reveal entombed fungal hyphae, modern biofilms, and diatoms within alteration minerals. We employed synchrotron X-ray fluorescence microscopy of alteration mineral veins to map the distribution of redox-sensitive elements of relevance to chemolithotrophic organisms, such as Mn-cycling bacteria. We assessed the biogenicity of fungal hyphae within alteration veins using a combination of Fourier-transform infrared spectroscopy and pyrolysis gas chromatography-mass spectrometry, which showed that alteration minerals sequester and preserve organic molecules at various levels of decomposition. Our combined analyses results show that fossil microorganisms and the organic molecules they produce are preserved within calcite-gypsum admixtures in meteorites. Furthermore, the distributions of redox-sensitive elements (e.g., Mn) within alteration minerals are localized, which qualitatively suggests that climatically or microbially facilitated element mobilization occurred during the meteorite's residency on Earth. If returned as part of a sample suite from the martian surface, ordinary chondrites could preserve similar, recognizable evidence of putative past life and/or environmental change.

Eukaryotic Colonization of Micrometer-Scale Cracks in Rocks: A "Microfluidics" Experiment Using Naturally Weathered Meteorites from the Nullarbor Plain, Australia.

The advent of microfluidics has revolutionized the way we understand how microorganisms propagate through microporous spaces. Here, we apply this understanding to the study of how endolithic environmental microorganisms colonize the interiors of sterile rock. The substrates used for our study are stony meteorites from the Nullarbor Plain, Australia; a semiarid limestone karst that provides an ideal setting for preserving meteorites. Periodic flooding of the Nullarbor provides a mechanism by which microorganisms and exogenous nutrients may infiltrate meteorites. Our laboratory experiments show that environmental microorganisms reach depths greater than 400 µm by propagating through existing brecciation, passing through cracks no wider than the diameter of a resident cell (i.e., ∼5 µm). Our observations are consistent with the propagation of these eukaryotic cells via growth and cell division rather than motility. The morphology of the microorganisms changed as a result of propagation through micrometer-scale cracks, as has been observed previously for bacteria on microfluidic chips. It has been suggested that meteorites could have served as preferred habitats for microorganisms on ancient Mars. Based on our results, the depths reached by terrestrial microorganisms within meteorites would be sufficient to mitigate against the harmful effects of ionizing radiation, such as UV light, in Earth's deserts and potentially on Mars, if similar processes of microbial colonization had once been active there. Thus, meteorites landing in ancient lakes on Mars, that later dried out, could have been some of the last inhabited locations on the surface, serving as refugia before the planet's surface became inhospitable. Finally, our observations suggest that terrestrial microorganisms can colonize very fine cracks within meteorites (and potentially spaceships and rovers) on unexpectedly short timescales, with important implications for both recognition of extraterrestrial life in returned geological samples and planetary protection.

What's under the hood? Phylogeny and taxonomy of the snake genera Parasuta Worrell and Suta Worrell (Squamata: Elapidae), with a description of a new species from the Pilbara, Western Australia.

Despite decades of phylogenetic studies, the generic and species-level relationships of some Australian elapid snakes remain problematic. The morphologically conservative genus Parasuta comprises small nocturnal snakes with a particularly obfuscated taxonomic history. Here we provide a molecular phylogenetic analysis of all currently recognised species including members of the sister genus Suta and provide new morphological data that lead to a taxonomic revision of generic and species boundaries. We failed to find support for monophyly of Parasuta or Suta, instead supporting previous evidence that these two genera should be combined. Our species-level investigations revise the boundaries between P. gouldii (Gray) and P. spectabilis (Krefft) resulting in recognition that both P. spectabilis bushi (Storr) and P. spectabilis nullarbor (Storr) are conspecific with P. gouldii. We also find the Pilbara population of P. monachus (Storr) to be specifically distinct. As a consequence of this information, we synonymise Parasuta with its senior synonym Suta, redescribe S. gouldii, S. monachus and S. spectabilis to clarify morphological and geographical boundaries and describe S. gaikhorstorum sp. nov., which differs from all other described Suta species, including the geographically proximate and similar-looking S. monachus, by a combination of molecular genetic markers, morphometric attributes, details of colouration and scalation. The recognition of S. gaikhorstorum sp. nov. adds to the growing list of the many endemic reptiles from this exceptionally diverse biotic region. We also designate a lectotype for S. spectabilis from the original syntype series, highlight a distinctive population from the Great Victoria Desert in Western Australia and comment on further unresolved issues regarding the relationships between S. dwyeri (Worrell) and S. nigriceps (Gȕnther).

Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers.

Finding fresh, sterilized rocks provides ecologists with a clean slate to test ideas about first colonization and the evolution of soils de novo. Lava has been used previously in first colonizer studies due to the sterilizing heat required for its formation. However, fresh lava typically falls upon older volcanic successions of similar chemistry and modal mineral abundance. Given enough time, this results in the development of similar microbial communities in the newly erupted lava due to a lack of contrast between the new and old substrates. Meteorites, which are sterile when they fall to Earth, provide such contrast because their reduced and mafic chemistry commonly differs to the surfaces on which they land; thus allowing investigation of how community membership and structure respond to this new substrate over time. We conducted 16S rRNA gene analysis on meteorites and soil from the Nullarbor Plain, Australia. We found that the meteorites have low species richness and evenness compared to soil sampled from directly beneath each meteorite. Despite the meteorites being found kilometers apart, the community structure of each meteorite bore more similarity to those of other meteorites (of similar composition) than to the community structure of the soil on which it resided. Meteorites were dominated by sequences that affiliated with the Actinobacteria with the major Operational Taxonomic Unit (OTU) classified as Rubrobacter radiotolerans. Proteobacteria and Bacteroidetes were the next most abundant phyla. The soils were also dominated by Actinobacteria but to a lesser extent than the meteorites. We also found OTUs affiliated with iron/sulfur cycling organisms Geobacter spp. and Desulfovibrio spp. This is an important finding as meteorites contain abundant metal and sulfur for use as energy sources. These ecological findings demonstrate that the structure of the microbial community in these meteorites is controlled by the substrate, and will not reach homeostasis with the Nullarbor community, even after ca. 35,000 years. Our findings show that meteorites provide a unique, sterile substrate with which to test ideas relating to first-colonizers. Although meteorites are colonized by microorganisms, the microbial population is unlikely to match the community of the surrounding soil on which they fall.

A species assemblage approach to comparative phylogeography of birds in southern Australia.

We present a novel approach to investigating the divergence history of biomes and their component species using single-locus data prior to investing in multilocus data. We use coalescent-based hierarchical approximate Bayesian computation (HABC) methods (MsBayes) to estimate the number and timing of discrete divergences across a putative barrier and to assign species to their appropriate period of co-divergence. We then apply a coalescent-based full Bayesian model of divergence (IMa) to suites of species shown to have simultaneously diverged. The full Bayesian model results in reduced credibility intervals around divergence times and allows other parameters associated with divergence to be summarized across species assemblages. We apply this approach to 10 bird species that are wholly or patchily discontinuous in semi-arid habitats between Australia's southwest (SW) and southeast (SE) mesic zones. There was substantial support for up to three discrete periods of divergence. HABC indicates that two species wholly restricted to more mesic habitats diverged earliest, between 594,382 and 3,417,699 years ago, three species from semi-arid habitats diverged between 0 and 1,508,049 years ago, and four diverged more recently, between 0 and 396,843 years ago. Eight species were assigned to three periods of co-divergence with confidence. For full Bayesian analyses, we accounted for uncertainty in the two remaining species by analyzing all possible suites of species. Estimates of divergence times from full Bayesian divergence models ranged between 429,105 and 2,006,355; 67,172 and 663,837; and 24,607 and 171,085 for the earliest, middle, and most recent periods of co-divergence, respectively. This single-locus approach uses the power of multitaxa coalescent analyses as an efficient means of generating a foundation for further, targeted research using multilocus and genomic tools applied to an understudied biome.