Ecological literature offers a myriad of methods for quantifying β diversity. One such method is determining BD total (BD), which, unlike other methods, can be decomposed into meaningful components that indicate how unique a sampling unit is regarding its composition (local contribution) and how unique a species is regarding its occurrence in the community (species contribution). Despite this advantage, the original formulation of the BD metric only assesses taxonomic variation and neglects other important dimensions of biodiversity. We expanded the original formulation of BD to capture variation in the functional and phylogenetic dimensions of community data by computing two new metrics-BD Fun and BD Phy-as well as their respective components that represent the local and species contribution. We tested the statistical performance of these new metrics for capturing variation in functional and phylogenetic composition through simulated communities and illustrated the potential use of these new metrics by analyzing β diversity of stream fish communities. Our results demonstrated that BD Phy and BD Fun have acceptable type I error and great power to detect the effect of deep evolutionary relationships and attributes mediating patterns of β diversity. The empirical example illustrated how BD Phy and BD Fun reveal complementary aspects of β diversity relative to the original BD metric. These new metrics can be used to identify local communities that are of conservation importance because they represent unique functional, phylogenetic, and taxonomic compositions. We conclude that BD Phy and BD Fun are important tools for providing complementary information in the investigation of the structure of biological communities.

Speciation events occurring within biogeographic regions, and historical dispersal between regions influence diversity patterns observed in present-day assemblages. Such assessment has been often performed based on the phylogenetic structure of local assemblages. We underline some issues with that approach, and show that more reliable evaluation of historical events influencing present-day diversity can be achieved by combining phylogenetic diversity to an estimate of species assemblage age based on ancestral range estimation. We apply the new approach to test two concurrent hypotheses—Tropical Niche Conservatism (TNC) and Out of The Tropics (OTT)—which provide alternative explanations to species richness gradients, as possible explanations to higher species richness in tropical assemblages of Tyrannidae birds in relation to temperate ones across the American continent. Tropical assemblages tended to be older and to show higher phylogenetic diversity than temperate ones, suggesting that recent events of historical dispersal carried out by few lineages likely drove species assembly in younger temperate assemblages. This finding provides support to TNC as the most probable explanation to species richness variation in tyrannid assemblages across the Americas. Combining phylogenetic structure measures with a flexible assemblage age metric calculated from ancestral range estimation allows deeper understanding of current diversity gradients.

Biodiversity is inherently multidimensional in nature, differences in evolutionary history, attributes of species, taxonomic composition constitutes a small fraction of whole variation present in this multidimensional space. Despite its multidimensional characteristic, biodiversity has been traditionally measured by assessing its dimensions separately through metrics of diversity. However, assessing multiple dimensions in a common framework opens the possibility of answering interesting questions that, until now, are poorly understood, such as: What dimensions capture most of the variation present in biodiversity among communities? We assess this question by extending the framework of Importance Values (IVs) to three dimensions of variation in biodiversity, functional, taxonomic and phylogenetic, and evaluate which of these captures the most variation in biodiversity space. To address this question we used data from stream fish communities of the Ivinhema River Basin in Brazil. We found that functional and phylogenetic dimensions are more important than the taxonomic dimension (represented by richness) in capturing variation in the biodiversity space formed by these three dimensions together. Furthermore, the IVs of these three dimensions were similar along an altitudinal gradient, indicating similar contributions by a given dimension in different environmental conditions. We highlight the importance of adopting a multidimensional approach when describing biodiversity, since richness (the proxy for taxonomic dimension), despite being the most commonly used, is an incomplete surrogate to capture the variation present in the biodiversity space of stream fish communities.

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Studies on ecological communities often address patterns of species distribution and abundance, but few consider uncertainty in counts of both species and individuals when computing diversity measures. We evaluated the extent to which imperfect detection may influence patterns of taxonomic, functional, and phylogenetic diversity in ecological communities. We estimated the true abundance of fruit‐feeding butterflies sampled in canopy and understory strata in a subtropical forest. We compared the diversity values calculated by observed and estimated abundance data through the hidden diversity framework. This framework evaluates the deviation of observed diversity when compared with diversities derived from estimated true abundances and whether such deviation represents a bias or a noise in the observed diversity pattern. The hidden diversity values differed between strata for all diversity measures, except for functional richness. The taxonomic measure was the only one where we observed an inversion of the most diverse stratum when imperfect detection was included. Regarding phylogenetic and functional measures, the strata showed distinct responses to imperfect detection, despite the tendency to overestimate observed diversity. While the understory showed noise for the phylogenetic measure, since the observed pattern was maintained, the canopy had biased diversity for the functional metric. This bias occurred since no significant differences were found between strata for observed diversity, but rather for estimated diversity, with the canopy being more clustered. We demonstrate that ignore imperfect detection may lead to unrealistic estimates of diversity and hence to erroneous interpretations of patterns and processes that structure biological communities. For fruit‐feeding butterflies, according to their phylogenetic position or functional traits, the undetected individuals triggered different responses in the relationship of the diversity measures to the environmental factor. This highlights the importance to evaluate and include the uncertainty in species detectability before calculating biodiversity measures to describe communities.

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Biodiversity can be represented by different dimensions. While many diversity metrics try to capture the variation of these dimensions they also lead to a ‘fragmentation’ of the concept of biodiversity itself. Developing a unified measure that integrates all the dimensions of biodiversity is a theoretical solution for this problem, however, it remains operationally impossible. Alternatively, understanding which dimensions better represent the biodiversity of a set of communities can be a reliable way to integrate the different diversity metrics. Therefore, to achieve a holistic understand of biological diversity, we explore the concept of dimensionality. We define dimensionality of diversity as the number of complementary components of biodiversity, represented by diversity metrics, needed to describe biodiversity in an unambiguously and effective way. We provide a solution that joins two components of dimensionality – correlation and the variation – operationalized through two metrics, respectively: evenness of eigenvalues (EE) and importance values (IV). Through simulation we show that considering EE and IV together can provide information that is neglected when only EE is considered. We demonstrate how to apply this framework by investigating the dimensionality of South American small mammal communities. Our example evidenced that, for some representations of biological diversity, more attention is needed in the choice of diversity metrics necessary to effectively characterize biodiversity. We conclude by highlighting that this integrated framework provides a better understanding of dimensionality than considering only the correlation component.

Neotropical stream fishes exhibit a complex evolutionary history and encompass both old and recent lineages. Patterns of species diversity of stream fishes are relatively well-studied for Neotropical streams, but not for patterns of clade distribution and historical factors that structure these assemblages, which are the main interests of phylogenetic ecology. Understanding the evolutionary context of communities provides important insights into large-scale mechanisms that structure them. This review aims to: (i) discuss the main concepts of phylogenetic ecology and its application to Neotropical stream fishes; and (ii) highlight the main methods applied in this background. The first section presents the main phylogenetic hypothesis of fishes and discusses how their gaps in Neotropical stream fishes hinder phylogenetic ecology. Afterward, we discuss the main concepts of phylogenetic ecology (phylogenetic signal, community phylogenetic structure, and phylogenetic diversity), as well as gaps and potential applications of these concepts and tools to understand Neotropical stream fish assemblages. The second section introduces the main methods to address the phylogenetic ecology, including a standardized procedure to edit fish phylogenetic trees, comparative methods, and indices and analytical tools to understand community structure and conservation importance. Finally, we discuss the perspectives to the next years to better understand the Neotropical stream fish assemblages in the light of past and current historical processes.