1. Novel algorithms have been recently developed to estimate alpha and partition beta diversity in all their dimensions (taxon, phylogenetic and functional diversity -TD, PD and FD), whether communities are completely sampled or not. 2.The R package BAT -Biodiversity Assessment Tools -performs a number of analyses based on either species identities (TD) or trees depicting species relationships (PD and FD). Functions include building randomized accumulation curves for alpha and beta diversity, alpha diversity estimation from incomplete samples and the partitioning of beta diversity in its replacement and richness difference components. All functions allow the rarefaction of communities. Estimation methods include curve-fitting andnon-parametric algorithms. Beta diversity indices include the Jaccard and Sørensen families of measures and deal with both incidence and abundance data. Two auxiliary functions that allow judging the efficiency of the algorithms are also included. 4.Several examples are shown using the data included in the package, which demonstrate the usefulness of the different methods. The BAT package constitutes an open platform for further development of new biodiversity assessment tools.

Aim To propose a unified framework for quantifying taxon (Tb), phylogenetic (Pb) and functional (Fb) beta diversity via pairwise comparisons of communities, which allows these types of beta diversity to be partitioned into ecologically meaningful additive components.Location Global, with case studies in Europe and the Azores archipelago.Methods Using trees as a common representation for taxon, phylogenetic and functional diversity, we partition total beta diversity (b total ) into its replacement (turnover, b repl ) and richness difference (b rich ) components according to which part of a global tree was shared by or unique to communities that were being compared. We demonstrate the application of this framework using artificial and empirical examples (mammals in Europe and epigean arthropods in the Azores).Results Our empirical examples show that comparing Pb and Fb with the most commonly used Tb revealed previously hidden patterns of beta diversity.More importantly, we demonstrate that partitioning Pb total and Fb total into their respective b repl and b rich components facilitates the detection of more complex patterns than using the overall coefficients alone, further elucidating the different forces operating in community assembly. Main conclusionsThe methods presented here allow the integration and full comparison of Tb, Pb and Fb. They provide a tool for effectively disentangling the replacement (turnover) and richness difference components of the different biodiversity facets within the same methodological framework.

The general dynamic model of oceanic island biogeography (GDM) has added a new dimension to theoretical island biogeography in recognizing that geological processes are key drivers of the evolutionary processes of diversification and extinction within remote islands. It provides a dynamic and essentially non-equilibrium framework generating novel predictions for emergent diversity properties of oceanic islands and archipelagos. Its publication in 2008 coincided with, and spurred on, renewed attention to the dynamics of remote islands. We review progress, both in testing the GDM's predictions and in developing and enhancing ecological-evolutionary understanding of oceanic island systems through the lens of the GDM. In particular, we focus on four main themes: (i) macroecological tests using a space-for-time rationale; (ii) extensions of theory to islands following different patterns of ontogeny; (iii) the implications of GDM dynamics for lineage diversification and trait evolution; and (iv) the potential for downscaling GDM dynamics to local-scale ecological patterns and processes within islands. We also consider the implications of the GDM for understanding patterns of non-native species diversity. We demonstrate the vitality of the field of island biogeography by identifying a range of potentially productive lines for future research.