Understanding spatial patterns of biodiversity is critical for conservation planning, particularly given rapid habitat loss and human-induced climatic change. Diversity and endemism are typically assessed by comparing species ranges across regions. However, investigation of patterns of species diversity alone misses out on the full richness of patterns that can be inferred using a phylogenetic approach. Here, using Australian Acacia as an example, we show that the application of phylogenetic methods, particularly two new measures, relative phylogenetic diversity and relative phylogenetic endemism, greatly enhances our knowledge of biodiversity across both space and time. We found that areas of high species richness and species endemism are not necessarily areas of high phylogenetic diversity or phylogenetic endemism. We propose a new method called categorical analysis of neo-and paleoendemism (CANAPE) that allows, for the first time, a clear, quantitative distinction between centres of neo-and paleo-endemism, useful to the conservation decision-making process.

Aim Biodiversity studies typically use species, or more recently phylogenetic diversity (PD), as their analysis unit and produce a single map of observed diversity. However, observed biodiversity is not necessarily an indicator of significant biodiversity and therefore should not be used alone. By applying a small number of additional metrics to PD, with associated statistical tests, we can determine whether more or less of the phylogeny occurs in an area, whether branch lengths in an area are longer or shorter, and whether more long or short-branched endemism occurs in an area, than expected under a null model. Location Australian continent.Methods We used a phylogeny sampling 90% of Australia's angiosperm genera, and 3.4 million georeferenced plant specimens downloaded from Australia's Virtual Herbarium (AVH), to calculate PD, relative phylogenetic diversity (RPD) and relative phylogenetic endemism (RPE). Categorical analysis of neo-and palaeo-endemism (CANAPE) and randomization tests were performed to determine statistical significance.Results We identify several combinations of significant PD and endemism across the continent that are not seen using observed diversity patterns alone. Joint interpretation of these combinations complements the previous interpretations of Australia's plant evolutionary history. Of conservation concern, only 42% of the significant endemism cells found here overlap with existing nature reserves.Main conclusions These spatial phylogenetic methods are feasible to apply to a whole flora at the continental scale. Observed richness or PD is inadequate to fully understand the patterns of biodiversity. The combination of statistical tests applied here can be used to better explain biodiversity patterns and the evolutionary and ecological processes that have created them. The spatial phylogenetic methods used in this paper can be also be used to identify conservation priorities at any geographical scale or taxonomic level.

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The largest digitized dataset of land plant distributions in Australia assembled to date (750,741 georeferenced herbarium records; 6,043 species) was used to partition the Australian continent into phytogeographical regions. We used a set of six widely distributed vascular plant groups and three non-vascular plant groups which together occur in a variety of landscapes/habitats across Australia. Phytogeographical regions were identified using quantitative analyses of species turnover, the rate of change in species composition between sites, calculated as Simpson's beta. We propose six major phytogeographical regions for Australia: Northern, Northern Desert, Eremaean, Eastern Queensland, Euronotian and South-Western. Our new phytogeographical regions show a spatial agreement of 65% with respect to previously defined phytogeographical regions of Australia. We also confirm that these new regions are in general agreement with the biomes of Australia and other contemporary biogeographical classifications. To assess the meaningfulness of the proposed phytogeographical regions, we evaluated how they relate to broad scale environmental gradients. Physiographic factors such as geology do not have a strong correspondence with our proposed regions. Instead, we identified climate as the main environmental driver. The use of an unprecedentedly large dataset of multiple plant groups, coupled with an explicit quantitative analysis, makes this study novel and allows an improved historical bioregionalization scheme for Australian plants. Our analyses show that: (1) there is considerable overlap between our results and older biogeographic classifications; (2) phytogeographical regions based on species turnover can be a powerful tool to further partition the landscape into meaningful units; (3) further studies using phylogenetic turnover metrics are needed to test the taxonomic areas.

Aim  Acacia is the largest genus of plants in Australia with over 1000 species. A subset of these species is invasive in many parts of the world including Africa, the Americas, Europe, the Middle East, Asia and the Pacific region. We investigate the phylogenetic relationships of the invasive species in relation to the genus as a whole. This will provide a framework for studying the evolution of traits that make Acacia species such successful invaders and could assist in screening other species for invasive potential. Location  Australia and global. Methods  We sequenced four plastid and two nuclear DNA regions for 110 Australian Acacia species, including 16 species that have large invasive ranges outside Australia. A Bayesian phylogenetic tree was generated to define the major lineages of Acacia and to determine the phylogenetic placement of the invasive species. Results  Invasive Acacia species do not form a monophyletic group but do form small clusters throughout the phylogeny. There are no taxonomic characters that uniquely describe the invasive Acacia species. Main conclusions  The legume subfamily Mimosoideae has a high percentage of invasive species and the Australian Acacia species have the highest rate of all the legumes. There is some evidence of phylogenetic clumping of invasive species of Acacia in the limited sampling presented here. This phylogeny provides a framework for further testing of the evolution of traits associated with invasiveness in Acacia.

Summary Understanding changes of biodiversity across the landscape underlies biogeography and ecology and is important in land management and conservation. Measures of species and phylogenetic turnover used to estimate the rate of change of assemblages between sets of locations are more often influenced by wide‐ranging taxa. Transition zones between regions that are associated with range‐restricted taxa can be obscured by wide‐ranging taxa that span them. We present a set of new range‐weighted metrics of taxon and phylogenetic turnover, as modifications of conventional metrics, where the range‐restricted components of the assemblages are assigned greater weight in the calculations. We show how these metrics are derived from weighted endemism and phylogenetic endemism and demonstrate their properties using a continent‐wide data set of Australian Acacia. The range‐weighted metrics result in better delineated transition zones between regions, in that the rate of turnover is steeper than with conventional turnover measures. These metrics provide important complementary information for the interpretation of spatial turnover patterns derived from conventional turnover metrics. Additionally, the phylogenetic variant incorporates information about phylogenetic relatedness while also not saturating at high values of turnover, thus remaining useful for comparisons over greater distances than conventional turnover metrics.

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Aim To develop a biogeographical regionalization of Australian Acacia species and to investigate their environmental correlates. Location Australia. Methods We used a previously published framework for delineating biogeographical regions. We calculated species turnover patterns of 1020 Australian Acacia species with distributions estimated from 171,758 georeferenced herbarium records aggregated to 100 km × 100 km cells (868 across Australia). An agglomerative cluster analysis using a matrix of pairwise Simpson's beta (βsim) dissimilarity values was applied. Eleven environmental variables at the same resolution as the aggregated herbarium records were used to explore the correlates of the βsim patterns using a non‐metric multidimensional scaling (NMDS) analysis. We also used an ANOVA to test the significance of the environmental changes between each pair of biogeographical regions. Results Five major Acacia biogeographical regions were proposed. These bioregions were broadly similar to the biomes of Australia. A new subdivision of the Eremaean biome was proposed for Acacia. The most influential environmental variables for the individual bioregions were: (1) temperature seasonality and topographic flatness for the south‐western temperate bioregion; (2) precipitation during the coldest quarter of the year for the south‐eastern temperate bioregion; (3) annual precipitation, annual mean temperature and precipitation seasonality for the monsoonal bioregion; and (4) percentage of sand in the top 30 cm of the soil, rock grain size, annual mean radiation and annual mean temperature for the Eremaean south and north regions. The NMDS analysis provided support for the observed biogeographical patterns. The statistical test showed a highly significant difference between the environments of the proposed bioregions. Climatic variables were consistent predictors across regions, whereas the influence of soils and topographic features varied among bioregions. Main conclusions The major Acacia biogeographical regions correspond well to historical bioregionalizations, suggesting that the environmental drivers of diversification in Acacia are broadly similar to those that act on the flora as a whole. Climate seasonality combined with annual values and non‐climatic factors provide support for the proposed biogeographical regionalization for Acacia.