The systematics and biogeographic history of Australian arid zone oniscidean isopods (Philosciidae)

Abstract

Groundwater-dependent ecosystems in the Australian arid zone consist of highly diverse and relictual endemic invertebrates with complex evolutionary histories. Recent molecular phylogenetic studies on Haloniscus isopods, in particular, have identified significant levels of short-range endemicity, revealed extensive diversity with 26 new putative species, and have uncovered preliminary findings for a pattern of a shared evolutionary history amongst Haloniscus species from disparate and isolated groundwater regions. However, molecular datasets were restricted to either a single mitochondrial (cytochrome “c” oxidase subunit I (COI)) or two genes (COI and 18S rRNA), which resulted in poor topological resolution for internal branches, and evolutionary connections were not assessed in detail with divergence dating analyses. In this study, we aimed to generate a substantial and informative phylogenomic dataset with a transcriptome-based exon capture approach to examine the evolution and biogeographic history of Haloniscus from three major Australian arid zone groundwater-dependent ecosystems: subterranean calcrete aquifers of the Yilgarn region in Western Australia and Ngalia Basin region, Northern Territory, and surface springs fed by the Great Artesian Basin in South Australia. In Chapter 2, we generated an effective methodological framework to infer an isopod-specific orthologous marker set and bait design targeting 469 single-copy protein-coding genes, provided empirical data and post-processing scripts to improve future exon capture experiments, and produced a well-resolved Haloniscus isopod phylogeny for further phylogenetic and biogeographic inference. In Chapter 3, we implemented this dataset, together with additional phylogenetic analyses, divergence time dating and ancestral area reconstructions, to highlight significant historical connections between Haloniscus from the three groundwater regions and the influence of two major aridification intervals, one in the late Miocene and a second, following a temporary return to warmer and wetter conditions, in the Pliocene, on the isolation and ensuing diversification of the fauna. These findings contribute key insights into the biogeographic history of the Australian continent, and provide support for important hypotheses regarding the aridification of Australia. Lastly, in Chapter 4, we described four new species of Haloniscus, presented a revised generic diagnosis and key to the genus, transferred the genus from Scyphacidae to Philosciidae, and also transferred two species from Andricophiloscia to Haloniscus. The exploitation of groundwater for industrial, agricultural, and domestic uses represents a serious threat to these important taxa, and the formal documentation and naming of species (beyond just molecular results) is critical to the successful conservation management of these climate relicts and their refugial ecosystems.