François Rigal

BAT – Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity

Summary 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. 3. All functions allow the rarefaction of communities. Estimation methods include curve-fitting and nonparametric algorithms. Beta diversity indices include the Jaccard and Sorensen 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.

Integrating landscape disturbance and indicator species in conservation studies.

Successful conservation plans are conditioned by our ability to detect anthropogenic change in space and time and various statistical analyses have been developed to handle this critical issue. The main objective of this paper is to illustrate a new approach for spatial analysis in conservation biology. Here, we propose a two-step protocol. First, we introduce a new disturbance metric which provides a continuous measure of disturbance for any focal communities on the basis of the surrounding landscape matrix. Second, we use this new gradient to estimate species and community disturbance thresholds by implementing a recently developed method called Threshold Indicator Taxa ANalysis (TITAN). TITAN detects changes in species distributions along environmental gradients using indicators species analysis and assesses synchrony among species change points as evidence for community thresholds. We demonstrate our method with soil arthropod assemblages along a disturbance gradient in Terceira Island (Azores, Portugal). We show that our new disturbance metric realistically reflects disturbance patterns, especially in buffer zones (ecotones) between land use categories. By estimating species disturbance thresholds with TITAN along the disturbance gradient in Terceira, we show that species significantly associated with low disturbance differ from those associated with high disturbance in their biogeographical origin (endemics, non-endemic natives and exotics) and taxonomy (order). Finally, we suggest that mapping the disturbance community thresholds may reveal areas of primary interest for conservation, since these may host indigenous species sensitive to high disturbance levels. This new framework may be useful when: (1) both local and regional processes are to be reflected on single disturbance measures; (2) these are better quantified in a continuous gradient; (3) mapping disturbance of large regions using fine scales is necessary; (4) indicator species for disturbance are searched for and; (5) community thresholds are useful to understand the global dynamics of habitats.

Functional biogeography of oceanic islands and the scaling of functional diversity in the Azores

Significance Biogeographic theory builds upon a long history of analyzing species-diversity patterns of remote islands, but no previous studies have attempted to investigate corresponding patterns in functional traits on islands. Our analyses of functional diversity (FD) for spiders and beetles in the Azorean archipelago reveal that FD increases with species richness, which, in turn scales with island area regardless of the taxa and distributional group considered (endemics, natives, and exotics). Our results also support the hypothesis that each group contributes to FD in proportion to their species richness and that, being dominant, exotic species have significantly extended the realized trait space of the Azorean islands. Further analyses in other archipelagos are needed to establish whether our findings are representative of oceanic islands. Analyses of species-diversity patterns of remote islands have been crucial to the development of biogeographic theory, yet little is known about corresponding patterns in functional traits on islands and how, for example, they may be affected by the introduction of exotic species. We collated trait data for spiders and beetles and used a functional diversity index (FRic) to test for nonrandomness in the contribution of endemic, other native (also combined as indigenous), and exotic species to functional-trait space across the nine islands of the Azores. In general, for both taxa and for each distributional category, functional diversity increases with species richness, which, in turn scales with island area. Null simulations support the hypothesis that each distributional group contributes to functional diversity in proportion to their species richness. Exotic spiders have added novel trait space to a greater degree than have exotic beetles, likely indicating greater impact of the reduction of immigration filters and/or differential historical losses of indigenous species. Analyses of species occurring in native-forest remnants provide limited indications of the operation of habitat filtering of exotics for three islands, but only for beetles. Although the general linear (not saturating) pattern of trait-space increase with richness of exotics suggests an ongoing process of functional enrichment and accommodation, further work is urgently needed to determine how estimates of extinction debt of indigenous species should be adjusted in the light of these findings.

Oceanic island biogeography through the lens of the general dynamic model: Assessment and prospect

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 GDMs 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.

Use of arthropod rarity for area prioritisation: insights from the Azorean Islands.

We investigated the conservation concern of Azorean forest fragments and the entire Terceira Island surface using arthropod species vulnerability as defined by the Kattan index, which is based on species rarity. Species rarity was evaluated according to geographical distribution (endemic vs. non endemic species), habitat specialization (distribution across biotopes) and population size (individuals collected in standardized samples). Geographical rarity was considered at ‘global’ scale (species endemic to the Azorean islands) and ‘regional’ scale (single island endemics). Measures of species vulnerability were combined into two indices of conservation concern for each forest fragment: (1) the Biodiversity Conservation Concern index, BCC, which reflects the average rarity score of the species present in a site, and (2) one proposed here and termed Biodiversity Conservation Weight, BCW, which reflects the sum of rarity scores of the same species assemblage. BCW was preferable to prioritise the areas with highest number of vulnerable species, whereas BCC helped the identification of areas with few, but highly threatened species due to a combination of different types of rarity. A novel approach is introduced in which BCC and BCW indices were also adapted to deal with probabilities of occurrence instead of presence/absence data. The new probabilistic indices, termed pBCC and pBCW, were applied to Terceira Island for which we modelled species distributions to reconstruct species occurrence with different degree of probability also in areas from which data were not available. The application of the probabilistic indices revealed that some island sectors occupied by secondary vegetation, and hence not included in the current set of protected areas, may in fact host some rare species. This result suggests that protecting marginal non-natural areas which are however reservoirs of vulnerable species may also be important, especially when areas with well preserved primary habitats are scarce.

A new frontier in biodiversity inventory: a proposal for estimators of phylogenetic and functional diversity

Summary: Complete sampling of all dimensions of biodiversity is a formidable task, even for small areas. Undersampling is the norm, and the underquantification of diversity is a common outcome. Estimators of taxon diversity (TD) are widely used to correct for undersampling. Yet, no similar strategy has been developed for phylogenetic (PD) or functional (FD) diversity. We propose three ways of estimating PD and FD, building on estimators originally developed for TD: (i) correcting PD and FD values based on the completeness of TD; (ii) fitting asymptotic functions to accumulation curves of PD and FD; and (iii) adapting nonparametric estimators to PD and FD data. Using trees as a common framework for the estimation of PD and FD, we tested the approach with European mammal and Azores Islands arthropod data. We demonstrated that different methods were able to considerably reduce the undersampling bias and often correctly estimated true diversity using a fraction of the samples necessary to reach complete sampling. Besides the utility of knowing the true diversity of an assemblage from incomplete samples, the use of estimators may present further advantages. For instance, comparisons between sites or time periods are possible only if either sampling is complete or sampling effort is equivalent and sufficient to allow sensible comparisons. Also, as PD and FD asymptote faster than TD, comparisons between these different dimensions may require unbiased values. The framework now proposed combines taxon, phylogenetic and functional diversity into a single framework, offering a tool for future developments involving these different facets of biological diversity.

Drivers of extinction: the case of Azorean beetles

Oceanic islands host a disproportionately high fraction of endangered or recently extinct endemic species. We report on species extinctions among endemic Azorean beetles following 97% habitat loss since AD 1440. We infer extinctions from historical and contemporary records and examine the influence of three predictors: geographical range, habitat specialization and body size. Of 55 endemic beetle species investigated (out of 63), seven can be considered extinct. Single-island endemics (SIEs) were more prone to extinction than multi-island endemics. Within SIEs restricted to native habitat, larger species were more extinction-prone. We thus show a hierarchical path to extinction in Azorean beetles: species with small geographical range face extinction first, with the larger bodied ones being the most threatened. Our study provides a clear warning of the impact of habitat loss on island endemic biotas.

Particulate Organic Matter Distribution along the Lower Amazon River: Addressing Aquatic Ecology Concepts Using Fatty Acids

One of the greatest challenges in understanding the Amazon basin functioning is to ascertain the role played by floodplains in the organic matter (OM) cycle, crucial for a large spectrum of ecological mechanisms. Fatty acids (FAs) were combined with environmental descriptors and analyzed through multivariate and spatial tools (asymmetric eigenvector maps, AEM and principal coordinates of neighbor matrices, PCNM). This challenge allowed investigating the distribution of suspended particulate organic matter (SPOM), in order to trace its seasonal origin and quality, along a 800 km section of the Amazon river-floodplain system. Statistical analysis confirmed that large amounts of saturated FAs (15:0, 18:0, 24:0, 25:0 and 26:0), an indication of refractory OM, were concomitantly recorded with high pCO2 in rivers, during the high water season (HW). Contrastingly, FAs marker which may be attributed in this ecosystem to aquatic plants (18:2ω6 and 18:3ω3) and cyanobacteria (16:1ω7), were correlated with higher O2, chlorophyll a and pheopigments in floodplains, due to a high primary production during low waters (LW). Decreasing concentrations of unsaturated FAs, that characterize labile OM, were recorded during HW, from upstream to downstream. Furthermore, using PCNM and AEM spatial methods, FAs compositions of SPOM displayed an upstream-downstream gradient during HW, which was attributed to OM retention and the extent of flooded forest in floodplains. Discrimination of OM quality between the Amazon River and floodplains corroborate higher autotrophic production in the latter and transfer of OM to rivers at LW season. Together, these gradients demonstrate the validity of FAs as predictors of spatial and temporal changes in OM quality. These spatial and temporal trends are explained by 1) downstream change in landscape morphology as predicted by the River Continuum Concept; 2) enhanced primary production during LW when the water level decreased and its residence time increased as predicted by the Flood Pulse Concept.

The role of plant fidelity and land-use changes on island exotic and indigenous canopy spiders at local and regional scales

Understanding the processes that lead to successful invasions is essential for the management of exotic species. We aimed to assess the comparative relevance of habitat (both at local and at regional scale) and plant features on the species richness of local canopy spiders of both indigenous and exotic species. In an oceanic island, Azores archipelago, we collected spiders in 97 transects belonging to four habitat types according to the degree of habitat disturbance, four types of plants with different colonisation origin (indigenous vs. exotic), and four types of plants according to the complexity of the vegetation structure. Generalised linear mixed models and linear regressions were performed separately for indigenous and exotic species at the local and regional landscape scales. At the local scale, habitat and plant origin explained the variation in the species richness of indigenous spiders, whereas exotic spider richness was poorly correlated to habitat and plant structure. The surrounding landscape matrix substantially affected indigenous spiders, but did not affect exotic spiders, with the exception of the negative effect exerted by native forests on the richness of exotic species. Our results revealed that the local effect of habitat type, plant origin and plant structure explain variations in the species richness observed at a regional scale. These results shed light on the mechanistic processes behind the role of habitat types in invasions, i.e., plant fidelity and plant structure are revealed as key factors, suggesting that native forests may act as physical barriers to the colonisation of exotic spiders.

Cave microbial community composition in oceanic islands: disentangling the effect of different colored mats in diversity patterns of Azorean lava caves

Processes determining diversity and composition of bacterial communities in island volcanic caves are still poorly understood. Here, we characterized colored microbial mats in 14 volcanic caves from two oceanic islands of the Azores using 16S rRNA gene sequences. Factors determining community diversity (α) and composition (β) were explored, namely colored mats, caves and islands, as well as environmental and chemical characteristics of caves. Additive partitioning of diversity using OTU occurrence showed a greater influence of β-diversity between islands and caves that may relate to differences in rare OTUs (singletons and doubletons) across scales. In contrast, Shannon diversity partitioning revealed the importance of the lowest hierarchical level (α diversity, colored mat), suggesting a dominance of cosmopolitan OTUs (>1%) in most samples. Cosmopolitan OTUs included members involved in nitrogen cycling, supporting the importance of this process in Azorean caves. Environmental and chemical conditions in caves did not show any significant relationship to OTU diversity and composition. The absence of clear differences between mat colors and across scales may be explained by (1) the geological youth of the cave system (cave communities have not had enough time to diverge) or/and (2) community convergence, as the result of selection pressure in extreme environments.