Cave animals have historically attracted the attention of evolutionary biologists because of their bizarre 'regressive' characters and convergent evolution. However, understanding of their biogeographic and evolutionary history, including mechanisms of speciation, has remained elusive. In the last decade, molecular data have been obtained for subterranean taxa and their surface relatives, which have allowed some of the classical debates on the evolution of cave fauna to be revisited. Here, we review some of the major studies, focusing on the contribution of phylogeography in the following areas: biogeographic history and the relative roles of dispersal and vicariance, colonization history, cryptic species diversity and modes of speciation of cave animals. We further consider the limitations of current research and prospects for the future. Phylogeographic studies have confirmed that cave species are often cryptic, with highly restricted distributions, but have also shown that their divergence and potential speciation may occur despite the presence of gene flow from surface populations. Significantly, phylogeographic studies have provided evidence for speciation and adaptive evolution within the confines of cave environments, questioning the assumption that cave species evolved directly from surface ancestors. Recent technical developments involving 'next generation' DNA sequencing and theoretical developments in coalescent and population modelling are likely to revolutionize the field further, particularly in the study of speciation and the genetic basis of adaptation and convergent evolution within subterranean habitats. In summary, phylogeographic studies have provided an unprecedented insight into the evolution of these unique fauna, and the future of the field should be inspiring and data rich.

Abstract. Australia was historically considered a poor prospect for subterranean fauna but, in reality, the continent holds a great variety of subterranean habitats, with associated faunas, found both in karst and non-karst environments. This paper critically examines the diversity of subterranean fauna in several key regions for the mostly arid western half of Australia. We aimed to document levels of species richness for major taxon groups and examine the degree of uniqueness of the fauna. We also wanted to compare the composition of these ecosystems, and their origins, with other regions of subterranean diversity world-wide. Using information on the number of 'described' and 'known' invertebrate species (recognised based on morphological and/or molecular data), we predict that the total subterranean fauna for the western half of the continent is 4140 species, of which~10% is described and 9% is 'known' but not yet described. The stygofauna, water beetles, ostracods and copepods have the largest number of described species, while arachnids dominate the described troglofauna. Conversely, copepods, water beetles and isopods are the poorest known groups with less than 20% described species, while hexapods (comprising mostly Collembola, Coleoptera, Blattodea and Hemiptera) are the least known of the troglofauna. Compared with other regions of the world, we consider the Australian subterranean fauna to be unique in its diversity compared with the northern hemisphere for three key reasons: the range and diversity of subterranean habitats is both extensive and novel; direct faunal links to ancient Pangaea and Gondwana are evident, emphasising their early biogeographic history; and Miocene aridification, rather than Pleistocene post-ice age driven diversification events

Calcrete aquifers in the arid Yilgarn region of central Western Australia are a biodiversity hotspot for stygofauna. A distinct pattern of interspecific size class variation among subterranean dytiscid beetle species has been observed in 29 of these aquifers where either two or three small, medium and/or large sympatric species are found that are in some cases sister species. We used a 3.5 km(2) grid of bores to sample dytiscids on a fine-scale and employed a comparative phylogeographical and population genetic approach to investigate the origins of a sympatric sister species triplet of diving beetles from a single aquifer. Mitochondrial DNA sequence data from the Cytochrome oxidase c subunit I gene revealed that all three species have high levels of haplotype diversity with ancient (approximately 1 million years ago) intra-specific coalescence of haplotypes, but low levels of nucleotide diversity. Population analyses provide evidence for multiple expansion events within each species. There was spatial heterogeneity in the distribution of genetic variation and abundance both within and among the three taxa. Population analyses revealed significant fine-scale differentiation with isolation by distance for Paroster macrosturtensis and P. mesosturtensis, but not the smallest species P. microsturtensis. Haplotype network analyses provided limited or no evidence for past population fragmentation within the large and small species, but substantial historical divergence was observed in P. mesosturtensis that was not spatially structured. A patchy population structure with contemporaneous and historical isolation by distance in the three species is likely to have been a significant isolating and diversifying force, preventing us from ruling out a potential role for allopatric divergence during speciation of this beetle sister triplet.

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