Aim To detect centres of vascular plant endemism at a continental scale by analysis of specimen‐based distributional data and to relate any pattern to environmental factors and history. Location Australia. Methods Presence of 8468 seed plant species‐level taxa throughout continental Australia and Tasmania was mapped on a 1° grid to visualize the pattern of species richness. This sample comprises half the known flora. Three indices of endemism were calculated but we preferred one that is unrelated to species richness, so that these two concepts could be distinguished in practice. Centres of endemism were detected by simple mapping and by spatial autocorrelation analysis (SAC). Linear regression was used to examine the relationship of the patterns of species richness and endemism to latitude, topography and climate. Results Both species richness and endemism vary greatly across the continent but in most cases the same centres were high in both richness and endemism. Twelve distinct centres were identified. The major centres of both diversity and endemism are south‐west western Australia, the Border Ranges between New South Wales and Queensland, the Wet Tropics near Cairns, Tasmania and the Iron‐McIlwraith Range of eastern Cape York Peninsula. The last centre appears to be more significant than recognized by past authors. Whether this is a true Australian centre of endemism, or is largely an outlier of the flora of Papua New Guinea, is explored. Another centre, in the Adelaide–Kangaroo Island region, has been overlooked altogether by previous authors. Regression analysis did not find a simple climatic explanation of the observed patterns. There was a suggestion that topographic variation within the 1° cells may be positively correlated with endemism, which is consistent with mountainous regions functioning as refugia. One clear result is that all the major centres of endemism are near‐coastal. A likely explanation is that Pleistocene expansions of the central desert have been a powerful limitation on the viability of refugia for narrowly endemic species. All the centres of endemism lie outside the estimated limits of the expanded arid zone at the last glacial maximum (18,000 yr BP). In particular, the ‘Central Australian Mountain Ranges centre of plant diversity and endemism’ of Boden & Given (1995) is detected as a strong centre of species richness, but not at all as a centre of endemism. This is despite good sampling of this region. Main conclusions Endemism can be distinguished from species richness by using an appropriate index and mapping of such indices can detect centres of endemism. This study demonstrates the value of specimen based distributional data, such as is held in state herbaria and museums.

How and why organisms are distributed as they are has long intrigued evolutionary biologists. The tendency for species to retain their ancestral ecology has been demonstrated in distributions on local and regional scales, but the extent of ecological conservatism over tens of millions of years and across continents has not been assessed. Here we show that biome stasis at speciation has outweighed biome shifts by a ratio of more than 25:1, by inferring ancestral biomes for an ecologically diverse sample of more than 11,000 plant species from around the Southern Hemisphere. Stasis was also prevalent in transocean colonizations. Availability of a suitable biome could have substantially influenced which lineages establish on more than one landmass, in addition to the influence of the rarity of the dispersal events themselves. Conversely, the taxonomic composition of biomes has probably been strongly influenced by the rarity of species' transitions between biomes. This study has implications for the future because if clades have inherently limited capacity to shift biomes, then their evolutionary potential could be strongly compromised by biome contraction as climate changes.

We present a new, broadly applicable measure of the spatial restriction of phylogenetic diversity, termed phylogenetic endemism (PE). PE combines the widely used phylogenetic diversity and weighted endemism measures to identify areas where substantial components of phylogenetic diversity are restricted. Such areas are likely to be of considerable importance for conservation. PE has a number of desirable properties not combined in previous approaches. It assesses endemism consistently, independent of taxonomic status or level, and independent of previously defined political or biological regions. The results can be directly compared between areas because they are based on equivalent spatial units. PE builds on previous phylogenetic analyses of endemism, but provides a more general solution for mapping endemism of lineages. We illustrate the broad applicability of PE using examples of Australian organisms having contrasting life histories: pea-flowered shrubs of the genus Daviesia (Fabaceae) and the Australian species of the Australo-Papuan tree frog radiation within the family Hylidae.

The Australian fossil record shows that from ca. 25 Myr ago, the aseasonal-wet biome (rainforest and wet heath) gave way to the unique Australian sclerophyll biomes dominated by eucalypts, acacias and casuarinas. This transition coincided with tectonic isolation of Australia, leading to cooler, drier, more seasonal climates. From 3 Myr ago, aridification caused rapid opening of the central Australian arid zone. Molecular phylogenies with dated nodes have provided new perspectives on how these events could have affected the evolution of the Australian flora. During the Mid-Cenozoic (25-10 Myr ago) period of climatic change, there were rapid radiations in sclerophyll taxa, such as Banksia, eucalypts, pea-flowered legumes and Allocasuarina. At the same time, taxa restricted to the aseasonal-wet biome (Nothofagus, Podocarpaceae and Araucariaceae) did not radiate or were depleted by extinction. During the Pliocene aridification, two Eremean biome taxa (Lepidium and Chenopodiaceae) radiated rapidly after dispersing into Australia from overseas. It is clear that the biomes have different histories. Lineages in the aseasonal-wet biome are species poor, with sister taxa that are species rich, either outside Australia or in the sclerophyll biomes. In conjunction with the fossil record, this indicates depletion of the Australian aseasonal-wet biome from the Mid-Cenozoic. In the sclerophyll biomes, there have been multiple exchanges between the southwest and southeast, rather than single large endemic radiations after a vicariance event. There is need for rigorous molecular phylogenetic studies so that additional questions can be addressed, such as how interactions between biomes may have driven the speciation process during radiations. New studies should include the hitherto neglected monsoonal tropics.

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.

Aim This paper reviews the biogeography of the Australian monsoon tropical biome to highlight general patterns in the distribution of a range of organisms and their environmental correlates and evolutionary history, as well as to identify knowledge gaps.Location Northern Australia, Australian Monsoon Tropics (AMT). The AMT is defined by areas that receive more than 85% of rainfall between November and April.Methods Literature is summarized, including the origin of the monsoon climate, present-day environment, biota and habitat types, and phylogenetic and geographical relationships of selected organisms.Results Some species are widespread throughout the AMT while others are narrow-range endemics. Such contrasting distributions correspond to presentday climates, hydrologies (particularly floodplains), geological features (such as sandstone plateaux), fire regimes, and vegetation types (ranging from rain forest to savanna). Biogeographical and phylogenetic studies of terrestrial plants (e.g. eucalypts) and animals (vertebrates and invertebrates) suggest that distinct bioregions within the AMT reflect the aggregated effects of landscape and environmental history, although more research is required to determine and refine the boundaries of biogeographical zones within the AMT. Phylogenetic analyses of aquatic organisms (fishes and prawns) suggest histories of associations with drainage systems, dispersal barriers, links to New Guinea, and the existence of Lake Carpentaria, now submerged by the Gulf of Carpentaria. Complex adaptations to the landscape and climate in the AMT are illustrated by a number of species.Main conclusions The Australian monsoon is a component of a single global climate system, characterized by a dominant equator-spanning Hadley cell. Evidence of hot, seasonally moist climates dates back to the Late Eocene, implying that certain endemic elements of the AMT biota have a long history. Vicariant differentiation is inferred to have separated the Kimberley and Arnhem Land bioregions from Cape York Peninsula/northern Queensland. Such older patterns are overlaid by younger events, including dispersal from Southeast Asia, and range expansions and contractions. Future palaeoecological and phylogenetic investigations will illuminate the evolution of the AMT biome. Understanding the biogeography of the AMT is essential to provide a framework for ecological studies and the sustainable development of the region.

The classification of the legume family proposed here addresses the long‐known non‐monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near‐complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well‐supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community‐endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade‐based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

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