CSIRO PUBLISHING www.publish.csiro.au/journals/is Invertebrate Systematics, 2008, 22, 195–203 Subterranean archipelago: mitochondrial DNA phylogeography of stygobitic isopods (Oniscidea : Haloniscus) from the Yilgarn region of Western Australia Steven J. B. Cooper A,B,F , Kathleen M. Saint A , Stefano Taiti C , Andrew D. Austin B,D and William F. Humphreys E A Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia. B Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, South Australia 5005, Australia. C Istituto per lo Studio degli Ecosistemi, CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy. D School of Earth and Environmental Sciences, The University of Adelaide, South Australia 5005, Australia. E Western Australian Museum, Collections and Research Centre, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia. F Corresponding author. Email: cooper.steve@saugov.sa.gov.au Abstract. The arid Yilgarn region of Western Australia contains numerous isolated calcrete aquifers, within which a diverse subterranean fauna has been discovered. Genetic and morphological studies of subterranean dytiscid beetles and amphipods have suggested that individual calcretes are equivalent to closed island habitats, which have been isolated for millions of years. Here we test this ‘subterranean island’ hypothesis further by phylogeographic analyses of subterranean oniscidean isopods (Haloniscus), using mitochondrial DNA (mtDNA) sequence data derived from the cytochrome c oxidase subunit I gene. Phylogenetic and population genetic analyses provided evidence for significant phylogeographic structuring of isopod populations, with evidence for at least 24 divergent mtDNA lineages, each restricted in their distribution to a single calcrete aquifer. The high level of divergence among calcrete populations (generally >25%) and several mtDNA lineages within calcretes (>16%) suggests that each lineage is likely to represent a distinct species. These analyses, together with comparative phylogeographic data from dytiscid beetles and amphipods, provide strong support for the ‘subterranean island’ hypothesis, applying to both air-breathing and fully aquatic arthropod groups. The finding of several epigean lineages that grouped with stygobitic Haloniscus populations, and the overall phylogeographic structure of populations, suggests that the majority of stygobitic species evolved within individual calcretes following independent colonisation by epigean ancestors. Additional keywords: cytochrome c oxidase subunit I (COI), Isopoda, stygofauna. Introduction Previous morphological and molecular genetic studies have that cladogenesis coincided with a major period of aridity of the identified a unique and diverse subterranean aquatic inverte- Australian continent in the Pliocene (~5–10 million years ago, brate fauna (known collectively as stygofauna) within calcrete Bowler 1976; Stein and Robert 1986). These analyses led to the (limestone) aquifers of the arid Yilgarn region of central proposal that calcrete aquifers (henceforth referred to as ‘cal- Western Australia (Fig. 1). The fauna comprises ~100 water cretes’) are equivalent to closed island habitats, which have had beetle species (Dytiscidae, Watts and Humphreys 1999, 2000; little or no gene flow between them for millions of years. This 2001, 2003; 2004, 2006) and a variety of crustacean species in hypothesis is significant because it suggests that each of the groups such as Bathynellacea (Cho 2005; Cho et al. 2006a, ~200 major calcretes in the Yilgarn region contains unique, 2006b), Isopoda (Taiti and Humphreys 2001), Amphipoda locally endemic, stygobitic species. In a region where ground- (J. Bradbury, unpubl. data), Copepoda (Karanovic 2004) and water and the calcrete itself is heavily utilised for mining oper- Ostracoda (Karanovic and Marmonier 2002). ations, such a proposal has major conservation and Taxonomic and molecular genetic studies (Cooper et al. environmental management implications, with drawdown of 2002; Leys et al. 2003) of the dytiscid fauna showed that species groundwater below the level of the calcrete (~10 m) likely to be are restricted in their distributions to single calcrete aquifers and a significant threat to unique stygobitic species. © CSIRO 2008 10.1071/IS07039 1445-5226/08/020195