Coarse patterns in the Earth's present climate and geology correspond with distinct constellations of plants and animals. Yet the origin and assembly of these major biomes also reflects unique evolutionary and colonisation histories acted out on a stage of significant global environmental change (Pennington et al. 2004; Sanmartin & Ronquist 2004; Poux et al. 2005; Crisp 2006; Galley & Lindner 2006). An understanding of the historical processes that have produced today's major biomes is not only of intrinsic interest, but is also relevant to the way we manage them under future environmental change (Moritz 1994; Hewitt 2004a, b).
Our capacity to unravel the histories of the Earth's biomes has taken a quantum leap in the last two decades with key developments in both the biological and physical sciences. First, there has been a revolution in phylogenetics: rigorous phylogenies and phylogeographies are now routinely produced using molecular genetic data, often using divergence time dating techniques. These data sets are critical to tests of biome origin and assembly (Crisp 2006). Second, methods and dating techniques in palaeostratigraphy have also improved, providing a more precise palaeochronology for biologists. The integration of findings from biological disciplines with detailed knowledge of the timing and nature of climatic and geological events has provided new perspectives on the evolutionary history of many of the world's biotas.
Most of the research focus on biome assembly has been in the Northern Hemisphere, especially temperate Europe (Hewitt 2001, 2004a Taberlet et al. 1998), western North America (Soltis et al. 1997; Brunsfeld et al. 2001; Cook et al. 2001; Lessa et al. 2003), southeastern North America (Avise 2000; Soltis et al. 2006), the Arctic and Beringia (Weider & Hobaek 2000; Hewitt 2004a; Kadereit et al. 2004; Kadereit & Comes 2005), the European Alps (Tribsch & Schonswetter 2003) and the California Floristic Province (Calsbeek et al. 2003). A growing number of Southern Hemisphere biomes are also being investigated (see Beheregaray 2008), including the Wet Tropics rainforest (Stork & Turton 2008) and temperate eucalypt forests (Sunnucks et al. 2006) of Australia. These studies are painting a general picture of the impacts of geologically recent environmental change on biome assembly and maintenance across the globe, with numerous commonalities emerging as well as idiosyncratic, biome-specific responses. Yet this picture remains incomplete without knowledge of the equivalent patterns and processes in the widespread arid-zone biomes of the planet. Although some individual species have been studied (e.g. Eggert et al. 2002; Zink 2002; Bates et al. 2003; Murphy et al. 2006; Leaché & Mulcahy 2007), synthetic molecular phylogenetic studies of the evolution of arid-zone biotas are yet to be carried out.
An arid biome ideally suited to broad-scale comparative phylogenetic and phylogeographical analysis is the Australian arid zone, here defined as the region of Australia having a moisture index of less than 0.4 (mean annual rainfall divided by evaporation) (Fig. 1). First, it is the largest biome in Australia, and one of the largest deserts in the world, occupying approximately 70% of Australia's 7.5 million square kilometres. Second, the Australian arid zone's physical origins are well understood: while arid environments were probably present in Australia during the Mid-Tertiary, current arid-zone stony and sandy desert landforms are much younger, with their origin in the Early Pliocene and Mid-Pleistocene (Fujioka et al. 2005, 2008). Thus, it is considerably younger than the mesic biomes of Australia's southern, eastern and northern coastlines that stem from the ancestral Mesozoic Gondwanan forests that were widespread until the Mid-Tertiary (Hill 1994; Schodde 2006). Third, the biota of the Australian arid zone is already well described from taxonomic and ecological perspectives (e.g. Barker & Greenslade 1982; Cogger & Cameron 1984; Stafford-Smith & Morton 1990; Dawson & Dawson 2006), with a number of hypotheses already proposed about its evolutionary origins (Schodde 1982; Maslin & Hopper 1982; Cracraft 1986, 1991).
Molecular phylogenetic studies of a diverse array of Australian arid zone plants, invertebrates and vertebrates are beginning to accumulate, and our understanding of the climatic and geological history of the region is continuing to develop. However, a coordinated multispecies approach integrating knowledge from the physical sciences, equivalent to those underway in other regions of the world, is just beginning in Australia. Here we present a synthesis of current knowledge of the history of the Australian arid-zone biota, and the climate and landscape that has harboured it, with an aim to stimulate further coordinated research. First, we review present geological and palaeoclimatic knowledge on the development of the Australian arid zone over the past 20 million years. This provides a vital platform upon which we then proceed to collate the relevant phylogenetic and phylogeographical analyses of arid-zone taxa and look for broad congruence between physical and biological histories. In particular, we consider what light these patterns shed on the processes leading to the origin of the arid-zone biota, as well as the maintenance of that biota as aridity oscillated and intensified over the last two million years. We compare the patterns in the Australian arid zone with those emerging from other biomes, and use these spatio-temporal patterns to generate questions and testable hypotheses to direct future research on the history and conservation of the Australian arid zone.