The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesicadapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.

Aim The mesic biome, encompassing both rain forest and open sclerophyllous forests, is central to understanding the evolution of Australia's terrestrial biota and has long been considered the ancestral biome of the continent. Our aims are to review and refine key hypotheses derived from palaeoclimatic data and the fossil record that are critical to understanding the evolution of the Australian mesic biota. We examine predictions arising from these hypotheses using available molecular phylogenetic and phylogeographical data. In doing so, we increase understanding of the mesic biota and highlight data deficiencies and fruitful areas for future research.Location The mesic biome of Australia, along the eastern coast of Australia, and in the south-east and south-west, including its rain forest and sclerophyllous, often eucalypt-dominated, habitats.Methods We derived five hypotheses based on palaeoclimatic and fossil data regarding the evolution of the Australian mesic biota, particularly as it relates to the mesic biome. We evaluated predictions formulated from these hypotheses using suitable molecular phylogenies of terrestrial plants and animals and freshwater invertebrates.Results There was support for the ancestral position of mesic habitat in most clades, with support for rain forest habitat ancestry in some groups, while evidence of ancestry in mesic sclerophyllous habitats was also demonstrated for some plants and herpetofauna. Contraction of mesic habitats has led to extinction of numerous lineages in many clades and this is particularly evident in the rain forest component. Species richness was generally higher in sclerophyllous clades than in rain forest clades, probably due to higher rates of net speciation in the former and extinction in the latter. Although extinction has been prominent in rain forest communities, tropical rain forests appear to have experienced extensive immigration from northern neighbours. Pleistocene climatic oscillations have left genetic signatures at multiple levels of divergence and with complex geographical structuring, even in areas with low topographical relief and few obvious geographical barriers.Main conclusions Our review confirms long-held views of the ancestral position of the Australian mesic biome but also reveals new insights into the complexity of the processes of contraction, fragmentation, extinction and invasion during the evolution of this biome.

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.