José Carvalho

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.

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.

Spatial Factors Play a Major Role as Determinants of Endemic Ground Beetle Beta Diversity of Madeira Island Laurisilva

The development in recent years of new beta diversity analytical approaches highlighted valuable information on the different processes structuring ecological communities. A crucial development for the understanding of beta diversity patterns was also its differentiation in two components: species turnover and richness differences. In this study, we evaluate beta diversity patterns of ground beetles from 26 sites in Madeira Island distributed throughout Laurisilva – a relict forest restricted to the Macaronesian archipelagos. We assess how the two components of ground beetle beta diversity (βrepl – species turnover and βrich - species richness differences) relate with differences in climate, geography, landscape composition matrix, woody plant species richness and soil characteristics and the relative importance of the effects of these variables at different spatial scales. We sampled 1025 specimens from 31 species, most of which are endemic to Madeira Island. A spatially explicit analysis was used to evaluate the contribution of pure environmental, pure spatial and environmental spatially structured effects on variation in ground beetle species richness and composition. Variation partitioning showed that 31.9% of species turnover (βrepl) and 40.7% of species richness variation (βrich) could be explained by the environmental and spatial variables. However, different environmental variables controlled the two types of beta diversity: βrepl was influenced by climate, disturbance and soil organic matter content whilst βrich was controlled by altitude and slope. Furthermore, spatial variables, represented through Moran’s eigenvector maps, played a significant role in explaining both βrepl and βrich, suggesting that both dispersal ability and Madeira Island complex orography are crucial for the understanding of beta diversity patterns in this group of beetles.

Biogeographic patterns of spiders in coastal dunes along a gradient of mediterraneity

The Iberian Peninsula is recognized for its high levels of species richness, rarity and endemicity. Our main aim was to study biogeographic patterns of spiders in coastal dunes along a gradient of mediterraneity. Distance-decay of similarity, nestedness and co-occurrence metrics were used to explore spider’ distribution patterns. A similarity analysis was performed in order to obtain a hierarchical classification of sites. Indicator species analysis was conducted to identify indicator species for the various clustering levels of the site typology. The differentiation among assemblages was further explored by non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM). Assemblages’ similarity among sites decreased with climatic/geographic distance. The observed values of nestedness metrics (T and NODF) were not significant, while the co-occurrence metrics (C-score and Checkerboard units) were higher than expected by chance. Cluster analysis showed that spider’ assemblages were structured along a gradient from North to South, forming four geographically distinct clusters. ANOSIM tests and NMDS supported the biogeographic patterns identified by cluster analysis. Several indicator species were found for the different levels of the hierarchic site typology. Spider assemblages revealed a high degree of biogeographical structure along the Atlantic coast of the Iberian Peninsula. The coast is a “biogeographic crossroad”, encompassing faunistic elements of different origins. The hierarchic typology of sites is generally consistent with the major biogeographic regions and the thermoclimatic belts recognized for the region. Our results indicate that the climatic gradient and historic factors played a key role in the current spiders’ biogeographic patterns.

Influence of herbaceous cover, shelter and land cover structure on wild rabbit abundance in NW Portugal

The European wild rabbitOryctolagus cuniculus (Linnaeus, 1758) populations in the Iberian Peninsula has suffered a serious decline. Therefore, the knowledge about the factors that influence rabbit distribution and abundance is of major interest for conservation and management programmes. Rabbit relative abundance was evaluated by pellet counting in relation to herbaceous ground cover, shelter availability (tall scrub cover and gaps in rocks) and land cover structure in the Peneda-Gerês National Park (PGNP), NW Portugal. Rabbit abundance was higher at intermediate levels of herbaceous cover, but no significant statistical differences were detected. A strong association between the abundance index and tall scrub cover was verified, and when this cover was rare, an association with gaps in rocks was observed. At the land cover level, rabbit abundance was associated with high interspersion sites of rocks with matorral and high interspersion sites of tall scrubland. Evidence from this study highlighted the importance of shelter and the interspersion of open/shelter habitats for rabbits. This pattern could be interpreted as an anti-predator strategy. Therefore, management actions should favour the growing and establishing of tall scrub patches and the selective cutting in highly continuous areas of tall scrub vegetation.

Development of a Larvicidal Nanoemulsion with Pterodon emarginatus Vogel Oil.

Pterodon emarginatus Vogel is a Brazilian species that belongs to the family Fabaceae, popularly known as sucupira. Its oil has several biological activities, including potent larvicidal property against Aedes aegypti. This insect is the vector of dengue, a tropical disease that has been considered a critical health problem in developing countries, such as Brazil. Most of dengue control methods involve larvicidal agents suspended or diluted in water and making active lipophilic natural products available is therefore considered a technological challenge. In this context, nanoemulsions appear as viable alternatives to solve this major problem. The present study describes the development of a novel nanoemulsion with larvicidal activity against A. aegypti along with the required Hydrophile Lipophile Balance determination of this oil. It was suggested that the mechanism of action might involve reversible inhibition of acetylcholinesterase and our results also suggest that the P. emarginatus nanoemulsion is not toxic for mammals. Thus, it contributes significantly to alternative integrative practices of dengue control, as well as to develop sucupira based nanoproducts for application in aqueous media.

Determinants of spider species richness in coastal dunes along a gradient of mediterraneity

Abstract.  1. The Iberian Peninsula is one of the most relevant areas in terms of species richness, rarity and endemism in the Mediterranean Basin. Using spiders as a model, we studied the relative importance of environmental and non‐environmental spatial variation along a gradient of mediterraneity on the western coast of the Iberian Peninsula.

Optimal inventorying and monitoring of taxon, phylogenetic and functional diversity

1. Inventorying requires comprehensive sampling, while monitoring should build on it and focus on as few components as possible to detect changes in time or space. To sample or acquire information for both purposes can therefore be viewed as different processes, herewith called α-sampling and β-sampling. Biodiversity covers species, their genetic diversity and the way they interact in communities and ecosystems. Quantifying these aspects leads to the need to study taxon (TD), phylogenetic (PD) and functional diversity (FD). Here we propose and test a method for the optimization of sampling protocols to inventorying and monitoring TD, PD and FD for a wide range of taxa. 2. We used spiders as a case-study, although the same optimization procedure could be applied to any taxon requiring a combination of sampling methods. Spiders were sampled in multiple sites in the Iberian Peninsula. PD and FD were measured as the sum of the length of branches on a phylogenetic or functional tree. To reach the optimal combination of methods for inventory, we followed an iterative procedure optimizing the accumulation curve of diversity values. Optimal monitoring in space or time required minimizing the difference between sampled and true β-diversity. We used a framework that disentangles species replacement and richness differences contributions to overall β-diversity. 3. For α-diversity, the optimal combination of 24 samples for TD, PD and FD allowed sampling more than 50% of real diversity. For β-diversity, the optimal combination of six samples for all measures allowed reaching a bias (difference between sampled and true diversity) below 0.08. 4. The widespread use of similar sampling protocols worldwide and regular repetition in time can have a major impact on the scope and usefulness of global monitoring projects. In addition, the comparable sampling of biodiversity in space and/or time allows reusing of data collected for specific purposes, potentiating a synergistic effect among different projects. This makes data useful much beyond their initial plan. We strongly advocate the optimization, standardization and widespread adoption of sampling protocols for all taxa at a global level, for both inventory and monitoring of all levels of biodiversity: taxon, phylogenetic and functional.

Modeling directional spatio-temporal processes in island biogeography

Abstract A key challenge in island biogeography is to quantity the role of dispersal in shaping biodiversity patterns among the islands of a given archipelago. Here, we propose such a framework. Dispersal within oceanic archipelagos may be conceptualized as a spatio‐temporal process dependent on: (1) the spatial distribution of islands, because the probability of successful dispersal is inversely related to the spatial distance between islands and (2) the chronological sequence of island formation that determines the directional asymmetry of dispersal (hypothesized to be predominantly from older to younger islands). From these premises, directional network models may be constructed, representing putative connections among islands. These models may be translated to eigenfunctions in order to be incorporated into statistical analysis. The framework was tested with 12 datasets from the Hawaii, Azores, and Canaries. The explanatory power of directional network models for explaining species composition patterns, assessed by the Jaccard dissimilarity index, was compared with simpler time‐isolation models. The amount of variation explained by the network models ranged from 5.5% (for Coleoptera in Hawaii) to 60.2% (for Pteridophytes in Canary Islands). In relation to the four studied taxa, the variation explained by network models was higher for Pteridophytes in the three archipelagos. By the contrary, small fractions of explained variation were observed for Coleoptera (5.5%) and Araneae (8.6%) in Hawaii. Time‐isolation models were, in general, not statistical significant and explained less variation than the equivalent directional network models for all the datasets. Directional network models provide a way for evaluating the spatio‐temporal signature of species dispersal. The method allows building scenarios against which hypotheses about dispersal within archipelagos may be tested. The new framework may help to uncover the pathways via which species have colonized the islands of a given archipelago and to understand the origins of insular biodiversity.

Global Island Monitoring Scheme (GIMS): a proposal for the long-term coordinated survey and monitoring of native island forest biota

Islands harbour evolutionary and ecologically unique biota, which are currently disproportionately threatened by a multitude of anthropogenic factors, including habitat loss, invasive species and climate change. Native forests on oceanic islands are important refugia for endemic species, many of which are rare and highly threatened. Long-term monitoring schemes for those biota and ecosystems are urgently needed: (i) to provide quantitative baselines for detecting changes within island ecosystems, (ii) to evaluate the effectiveness of conservation and management actions, and (iii) to identify general ecological patterns and processes using multiple island systems as repeated ‘natural experiments’. In this contribution, we call for a Global Island Monitoring Scheme (GIMS) for monitoring the remaining native island forests, using bryophytes, vascular plants, selected groups of arthropods and vertebrates as model taxa. As a basis for the GIMS, we also present new, optimized monitoring protocols for bryophytes and arthropods that were developed based on former standardized inventory protocols. Effective inventorying and monitoring of native island forests will require: (i) permanent plots covering diverse ecological gradients (e.g. elevation, age of terrain, anthropogenic disturbance); (ii) a multiple-taxa approach that is based on standardized and replicable protocols; (iii) a common set of indicator taxa and community properties that are indicative of native island forests’ welfare, building on, and harmonized with existing sampling and monitoring efforts; (iv) capacity building and training of local researchers, collaboration and continuous dialogue with local stakeholders; and (v) long-term commitment by funding agencies to maintain a global network of native island forest monitoring plots.