Vanderlei J. Debastiani

SYNCSA—R tool for analysis of metacommunities based on functional traits and phylogeny of the community components

SUMMARY SYNCSA is an R package for the analysis of metacommunities based on functional traits and phylogeny of the community components. It offers tools to calculate several matrix correlations that express trait-convergence assembly patterns, trait-divergence assembly patterns and phylogenetic signal in functional traits at the species pool level and at the metacommunity level. AVAILABILITY AND IMPLEMENTATION SYNCSA is a package for the R environment, under a GPL-2 open-source license and freely available on CRAN official web server for R (http://cran.r-project.org). CONTACT vanderleidebastiani@yahoo.com.br.

Land Use Explains the Distribution of Threatened New World Amphibians Better than Climate

Background We evaluated the direct and indirect influence of climate, land use, phylogenetic structure, species richness and endemism on the distribution of New World threatened amphibians. Methodology/Principal Findings We used the WWF’s New World ecoregions, the WWFs amphibian distributional data and the IUCN Red List Categories to obtain the number of threatened species per ecoregion. We analyzed three different scenarios urgent, moderate, and the most inclusive scenario. Using path analysis we evaluated the direct and indirect effects of climate, type of land use, phylogenetic structure, richness and endemism on the number of threatened amphibians in New World ecoregions. In all scenarios we found strong support for direct influences of endemism, the cover of villages and species richness on the number of threatened species in each ecoregion. The proportion of wild area had indirect effects in the moderate and the most inclusive scenario. Phylogenetic composition was important in determining the species richness and endemism in each ecoregion. Climate variables had complex and indirect effects on the number of threatened species. Conclusion/Significance Land use has a more direct influence than climate in determining the distribution of New World threatened amphibians. Independently of the scenario analyzed, the main variables influencing the distribution of threatened amphibians were consistent, with endemism having the largest magnitude path coefficient. The importance of phylogenetic composition could indicate that some clades may be more threatened than others, and their presence increases the number of threatened species. Our results highlight the importance of man-made land transformation, which is a local variable, as a critical factor underlying the distribution of threatened amphibians at a biogeographic scale.

Discriminating the effects of phylogenetic hypothesis, tree resolution and clade age estimates on phylogenetic signal measurements

Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure.

Evolutionary Models and Phylogenetic Signal Assessment via Mantel Test

Abstract Phylogenetically closely related species tend to be more similar to each other than to more distantly related ones, a pattern called phylogenetic signal. Appropriate tests to evaluate the association between phylogenetic relatedness and trait variation among species are employed in a myriad of eco-evolutionary studies. However, most tests available to date are only suitable for datasets describing continuous traits, and are most often applicable only for single trait analysis. The Mantel test is a useful method to measure phylogenetic signal for multiple (continuous, binary and/or categorical) traits. However, the classical Mantel test does not incorporate any evolutionary model (EM) in the analysis. Here, we describe a new analytical procedure, which incorporates explicitly an evolutionary model in the standard Mantel test (EM-Mantel). We run numerical simulations to evaluate its statistical properties, under different combinations of species pool size, trait type and number. Our results showed that EM-Mantel test has appropriate type I error and acceptable power, which increases with the strength of phylogenetic signal and with species pool size but depended on trait type. EM-Mantel test is a good alternative for measuring phylogenetic signal in binary and categorical traits and for datasets with multiple traits.

Untangling the Tangled Bank: A Novel Method for Partitioning the Effects of Phylogenies and Traits on Ecological Networks

Understanding how evolutionary and ecological processes shape species interaction networks remains as one of the main challenges in eco-evolutionary studies. Here, we present an integrative analytical framework to partition the effects of phylogenies and functional traits on the structure of ecological networks. The method combines fuzzy set theory and matrix correlation, implemented under a Monte Carlo framework. We designed a simulation study in order to estimate the accuracy of the methods proposed here, measuring Type I Error rates. The simulation study shows that the method is accurate, i.e., incorrectly rejecting a true null hypothesis in ~5% of the cases and falling within the confidence interval. We illustrate our framework using data from a seed dispersal network from southern Brazil. Our analyses suggest that birds must have specific traits in order to consume their plant resources, and that phylogenetic resemblance has no explanatory power for species traits and species interactions in this seed-dispersal network.

Recurrent patterns of phylogenetic habitat filtering in woody plant communities across phytogeographically distinct grassland-forest ecotones

The phylogenetic relationship among species may influence the mechanisms controlling local community assembly in ecological time. We analyzed the degree of recurrence of phylogenetic structure patterns in woody plant communities distributed along grassland-forest ecotones, across different vegetation types in southern Brazil, and the effect of phylogenetic pool size used to assess such patterns. Species frequency in quadrats distributed along grassland-forest ecotones was surveyed in different phytogeographic regions, where forests tend to expand over grasslands. We used principal coordinates of phylogenetic structure (PCPS) to evaluate the structure within vegetation quadrats divided into three habitat categories: grassland, forest edge and forest interior. Furthermore, phylogenetic structure measures were computed using different phylogenetic pool sizes. Our analyses showed consistent patterns in relation to habitat categories and to different phylogenetic pool sizes. Basal clades of angiosperms were as...

HaploVectors: an integrative analytical tool for phylogeography

Phylogeographic approaches are commonly used to understand historical-biogeographic patterns in the distribution of haplotypes. However, the emphasis of most tools lies on describing spatial patterns of genetic variation and assess how large are haplotypic differences among populations. An evaluation of the relative influence of environmental factors compared to pure neutral process of haplotypic distribution - a question of great interest for molecular ecologists - is less investigated, in part because appropriate tools are lacking. Here, we introduce HaploVectors, a flexible tool that allows exploring phylogeographical patterns and discriminating biogeographic, neutral and environmental factors acting to shape genetic distribution across space. Haplovectors are variables that summarize the major gradients of haplotypic distribution across a set of localities and allow weighting haplotypic frequencies by the number of mutational steps using a fuzzy weighting approach. HaploVectors is presented as an R package for computing haplotypic eigenvectors and performing null model- based tests. Investigation of HaploVectors using empirical datasets showed that the method is useful to uncover hidden patterns of haplotypic distribution, not easily detected using traditional methods. Using a plant species as study case, we demonstrate by means of HaploVectors that, even though the distribution of plant haplotypes was associated with different biogeographic regions of the Brazilian Cerrado biome, such association was not mediated by evolutionary relationships among haplotypes. The applicability of HaploVectors is broad, ranging from the pure pattern exploration and discrimination of genetic populations, to a hypothesis-testing framework that uses null-models to understand the influence of environmental factors on haplotypic distribution.

Constraints on the functional trait space of aquatic invertebrates in bromeliads

Functional traits are commonly used in predictive models that link environmental drivers and community structure to ecosystem functioning. A prerequisite is to identify robust sets of continuous axes of trait variation, and to understand the ecological and evolutionary constraints that result in the functional trait space occupied by interacting species. Despite their diversity and role in ecosystem functioning, little is known of the constraints on the functional trait space of invertebrate biotas of entire biogeographic regions. We examined the ecological strategies and constraints underlying the realized trait space of aquatic invertebrates, using data on 12 functional traits of 852 taxa collected in tank bromeliads from Mexico to Argentina. Principal Component Analysis was used to reduce trait dimensionality to significant axes of trait variation, and the proportion of potential trait space that is actually occupied by all taxa was compared to null model expectations. Permutational Analyses of Variance were used to test whether trait combinations were clade‐dependent. The major axes of trait variation represented life‐history strategies optimizing resource use and antipredator adaptations. There was evidence for trophic, habitat, defence and life‐history niche axes. Bromeliad invertebrates only occupied 16%–23% of the potential space within these dimensions, due to greater concentrations than predicted under uniform or normal distributions. Thus, despite high taxonomic diversity, invertebrates only utilized a small number of successful ecological strategies. Empty areas in trait space represented gaps between major phyla that arose from biological innovations, and trait combinations that are unviable in the bromeliad ecosystem. Only a few phylogenetically distant genera were neighbouring in trait space. Trait combinations aggregated taxa by family and then by order, suggesting that niche conservatism was a widespread mechanism in the diversification of ecological strategies.

Analyzing community‐weighted trait means across environmental gradients: should phylogeny stay or should it go?

Functional traits mediate ecological responses of organisms to the environment, determining community structure. Community-weighted trait means (CWM) are often used to characterize communities by combining information on species traits and distribution. Relating CWM variation to environmental gradients allows for evaluating species sorting across the metacommunity, either based on correlation tests or ordinary least squares (OLS) models. Yet, it is not clear if phylogenetic signal in both traits and species distribution affect those analyses. On one hand, phylogenetic signal might indicate niche conservatism along clade evolution, reinforcing the environmental signal in trait assembly patterns. On the other hand, it might introduce phylogenetic autocorrelation to mean trait variation among communities. Under this latter scenario, phylogenetic signal might inflate type I error in analysis relating CWM variation to environmental gradients. We explore multiple ways phylogenetic history may influence analysis relating CWM to environmental gradients. We propose the concept of neutral trait diffusion, which predicts that for a functional trait x, CWM variation among local communities does not deviate from the expectation that x evolved according to a neutral evolutionary process. Based on this framework we introduce a graphical tool called neutral trait diffusion representation (NTDR) that allows for the evaluation of whether it is necessary to carry out phylogenetic correction in the trait prior to analyzing the association between CWM and environmental gradients. We illustrate the NTDR approach using simulated traits, phylogenies and metacommunities. We show that even under moderate phylogenetic signal in both the trait used to define CWM and species distribution across communities, OLS models relating CWM variation to environmental gradients lead to inflated type I error when testing the null hypothesis of no association between CWM and environmental gradient. To overcome this issue, we propose a phylogenetic correction for OLS models and evaluate its statistical performance (type I error and power). Phylogeny-corrected OLS models successfully control for type I error in analysis relating CWM variation to environmental gradients but may show decreased power. Combining the exploratory tool of NTDR and phylogenetic correction in traits, when necessary, guarantees more precise inferences about the environmental forces driving trait-mediated species sorting across metacommunities.

Loss of generalist plant species and functional diversity decreases the robustness of a seed dispersal network

Understanding cascading effects of species loss has become a major challenge for ecologists. Traditionally, the robustness of ecological networks has been evaluated based on simulation studies where primary extinctions occur at random or as a function of species specialization, ignoring other important biological factors. Here, we estimate the robustness of a seed dispersal network from a grassland–forest mosaic in southern Brazil, simulating distinct scenarios of woody plant species extinction, including scenarios where species are eliminated based on their evolutionary and functional distinctiveness. Our results suggest that the network is more robust when species are eliminated based on their evolutionary uniqueness, followed by random extinctions, the extinction of the most specialist species, functional distinctiveness and, at last, when the most generalist species are sequentially eliminated. Our results provide important information for grassland–forest mosaic management, as they indicate that loss of generalist species and functional diversity makes the system more likely to collapse.