Molecular systematics and biodiversity of oniscidean isopods in the groundwater calcretes of central Western Australia.

Groundwater calcrete aquifers of central Western Australia have been shown to contain a high diversity of stygobiont (subterranean aquatic) invertebrates, with each species confined to an individual calcrete and the entire system resembling a 'subterranean archipelago' containing hundreds of isolated calcretes. Here, we utilised alternative sampling techniques above the water table and uncovered a significant fauna of subterranean terrestrial oniscidean isopods from the calcretes. We explored the diversity and evolution of this fauna using molecular analyses based on one mitochondrial gene, Cytochrome C Oxidase Subunit I (COI), two Ribosomal RNA genes (28S and 18S), and one protein coding nuclear gene, Lysyl-tRNA Synthetase (LysRS). The results from 12 calcretes showed the existence of 36 divergent DNA lineages belonging to four oniscidean families (Paraplatyarthridae, Armadillidae, Stenoniscidae and Philosciidae). Using a combination of phylogenetic and species delimitation methods, we hypothesized the occurrence of at least 27 putative new species of subterranean oniscideans, of which 24 taxa appeared to be restricted to an individual calcrete, lending further support to the "subterranean island hypothesis". Three paraplatyarthrid species were present on adjacent calcretes and these exceptions possessed more ommatidia and body pigments compared with the calcrete-restricted taxa, and are likely to represent troglophiles. The occurrence of stenoniscid isopods in the calcretes of central Western Australia, a group previously only known from the marine littoral zone, suggests a link to the marine inundation of the Eucla basin during the Late Eocene. The current oniscidean subterranean fauna consists of groups known to be subtropical, littoral and benthic, reflecting different historical events that have shaped the evolution of the fauna in the calcretes.

Evolution of endoglucanase genes in subterranean and surface isopod crustaceans from Central Western Australia.

Recent studies have identified a significant number of endogenous cellulase genes in various arthropods, including isopods, allowing them to process hydrocarbons efficiently as a food source. While this research has provided insight into underlying gene-level processes in cellulose decomposition by arthropods, little is known about the existence and expression of cellulase genes in species from cave environments where carbohydrates are sparse. To investigate whether endogenous cellulase genes are maintained in subterranean species, we sequenced the transcriptomes of two subterranean paraplatyarthrid isopod species from calcrete (carbonate) aquifers of central Western Australia and a related surface isopod species. Seven protein-coding open-reading frames associated with endoglucanase genes were identified in all species. Orthology inference analyses, using a wide range of cellulase sequences from available databases, supported the endogenous origin of the putative endoglucanase genes. Selection analyses revealed that these genes are primarily subject to purifying selection in most of the sites for both surface and subterranean isopod species, indicating that they are likely to encode functional peptides. Furthermore, evolutionary branch models supported the hypothesis of an adaptive shift in selective pressure acting on the subterranean lineages compared with the ancestral lineage and surface species. Branch-site models also revealed a few amino acid sites on the subterranean branches to be under positive selection, suggesting the acquisition of novel adaptations to the subterranean environments. These findings also imply that hydrocarbons exist in subsurface aquifers, albeit at reduced levels, and have been utilized by subterranean isopods as a source of energy for millions of years.

Pilbarana, a new subterranean amphipod genus (Hadzioidea: Eriopisidae) of environmental assessment importance from the Pilbara, Western Australia.

The Pilbara and nearby regions in north-western Western Australia have an exceptionally high diversity of short-range endemic invertebrates inhabiting threatened groundwater-dependent habitats. Amphipod crustaceans, in particular, are dominant in these communities, but are poorly understood taxonomically, with many undescribed species. Recent molecular phylogenetic analyses of Pilbara eriopisid amphipods have, nonetheless, uncovered a previously unknown biodiversity. In this study, we formally establish a new genus, Pilbarana Stringer & King gen. nov., and describe two new species, P. grandis Stringer & King sp. nov. from Cane River Conservation Park and P. lowryi Stringer & King sp. nov. from the Fortescue River Basin near the Hamersley Range, using a combination of molecular and morphological data. The new genus is similar morphologically to the two additional Western Australian eriopisid genera, Nedsia Barnard & Williams, 1995 and Norcapensis Bradbury & Williams, 1997, but represents a genetically divergent, reciprocally monophyletic lineage, which can be differentiated by its vermiform body shape, the presence of an antennal sinus, and by the length and form of the antennae and uropods. This research signifies an important contribution to knowledge of Pilbara subterranean communities and has critical implications for future environmental impact assessments and conservation management.

Taxonomy of Paraplatyarthrus Javidkar and King (Isopoda: Oniscidea: Paraplatyarthridae) with description of five new species from Western Australia, and comments on Australian Trichorhina Budde-Lunde, 1908 (Platyarthridae).

The oniscidean fauna of Australia is generally poorly known but recent sampling has revealed a new family, Paraplatyarthridae, found in both terrestrial and groundwater calcretes of central Western Australia. The family was initially described based on a new genus and species, Paraplatyarthrus subterraneus Javidkar and King, 2015. Here we describe an additional five Paraplatyarthrus species from the Yilgarn region of Western Australia, based on both morphological and molecular evidence (COI divergences). Four species are subterranean: P. crebesconiscus Javidkar and King sp. nov., P. cunyuensis Javidkar and King sp. nov., P. occidentoniscus Javidkar and King sp. nov., and P. pallidus Javidkar and King sp. nov., and one is a surface species, P. nahidae Javidkar and King sp. nov. A key to their identification is provided along with information on their distribution. In addition, type material of the two described Australian species of Platyarthridae, Trichorhina australiensis Wahrberg, 1922 from Western Australia and T. tropicalis Lewis, 1998 from Queensland, are examined. Morphological reassessment of type material shows T. australiensis belongs to Paraplatyarthrus (comb. nov.) and that T. tropicalis is correctly placed in Trichorhina, confirming that the genus and family Platyarthridae occur in Australia.

The Evolution of Epigean and Stygobitic Species of Koonunga Sayce, 1907 (Syncarida: Anaspidacea) in Southern Australia, with the Description of Three New Species.

Three new species of Koonunga were discovered in surface and subterranean waters in southern Australia, and were defined using mtDNA analyses and morphology. The new species are: Koonunga hornei Leijs & King; K. tatiaraensis Leijs & King and K. allambiensis Leijs & King. Molecular clock analyses indicate that the divergence times of the species are older than the landscape that they currently inhabit. Different scenarios explaining this apparent discrepancy are discussed in the context of the palaeography of the area. A freshwater epigean origin for Koonunga is considered the most likely hypothesis, whereby some lineages made the transition to the subterranean environment within the last few million years influenced by significant climatic cooling/drying. We discuss the possibility that one stygobitic lineage secondarily regained some of its body pigmentation as adaptation to increased photic conditions after cave collapse and forming of cenotes during the last glacial maximum.