Leandro da Silva Duarte

A global meta‐analysis of the relative extent of intraspecific trait variation in plant communities

Recent studies have shown that accounting for intraspecific trait variation (ITV) may better address major questions in community ecology. However, a general picture of the relative extent of ITV compared to interspecific trait variation in plant communities is still missing. Here, we conducted a meta-analysis of the relative extent of ITV within and among plant communities worldwide, using a data set encompassing 629 communities (plots) and 36 functional traits. Overall, ITV accounted for 25% of the total trait variation within communities and 32% of the total trait variation among communities on average. The relative extent of ITV tended to be greater for whole-plant (e.g. plant height) vs. organ-level traits and for leaf chemical (e.g. leaf N and P concentration) vs. leaf morphological (e.g. leaf area and thickness) traits. The relative amount of ITV decreased with increasing species richness and spatial extent, but did not vary with plant growth form or climate. These results highlight global patterns in the relative importance of ITV in plant communities, providing practical guidelines for when researchers should include ITV in trait-based community and ecosystem studies.

What saplings can tell us about forest expansion over natural grasslands

Abstract Questions: 1. Do the species composition, richness and diversity of sapling communities vary significantly in differently sized patches? 2. Do forest patches of different sizes differ in woody plant colonization patterns? Location: São Francisco de Paula, Rio Grande do Sul, Brazil, 29°28′ S, 50°13′ W. Methods: Three woody vegetation types, differing in structural development (patch size) and recovering for 10 years from cattle and burning disturbances, were sampled on grassland. We analysed the composition and complexity of the woody sapling communities, through relative abundance, richness and diversity patterns. We also evaluated recruitment status (residents vs. colonizers) of species in communities occurring in different forest patch size classes. Results: 1. There is a compositional gradient in sapling communities strongly associated with forest patch area. 2. Richness and diversity are positively correlated to patch area, but only in poorly structured patches; large patches present richness and diversity values similar to small patches. 3. Resident to colonizer abundance ratio increases from nurse plants to large patches. The species number proportion between residents and colonizers is similar in small and large patches and did not differ between these patch types. 4. Large patches presented a high number of exclusive species, while nurse plants and small patches did not. Conclusions: Woody plant communities in Araucaria forest patches are associated with patch structure development. Richness and diversity patterns are linked to patch colonization patterns. Generalist species colonize the understorey of nurse plants and small patches; resident species cannot recruit many new individuals. In large patches, sapling recruitment by resident adults precludes the immigration of new species into the patches, limiting richness and diversity. Nomenclature: APG 2003; Anon. 2005).

Phylobetadiversity among Forest Types in the Brazilian Atlantic Forest Complex

Phylobetadiversity is defined as the phylogenetic resemblance between communities or biomes. Analyzing phylobetadiversity patterns among different vegetation physiognomies within a single biome is crucial to understand the historical affinities between them. Based on the widely accepted idea that different forest physiognomies within the Southern Brazilian Atlantic Forest constitute different facies of a single biome, we hypothesize that more recent phylogenetic nodes should drive phylobetadiversity gradients between the different forest types within the Atlantic Forest, as the phylogenetic divergence among those forest types is biogeographically recent. We compiled information from 206 checklists describing the occurrence of shrub/tree species across three different forest physiognomies within the Southern Brazilian Atlantic Forest (Dense, Mixed and Seasonal forests). We analyzed intra-site phylogenetic structure (phylogenetic diversity, net relatedness index and nearest taxon index) and phylobetadiversity between plots located at different forest types, using five different methods differing in sensitivity to either basal or terminal nodes (phylogenetic fuzzy weighting, COMDIST, COMDISTNT, UniFrac and Rao’s H). Mixed forests showed higher phylogenetic diversity and overdispersion than the other forest types. Furthermore, all forest types differed from each other in relation phylobetadiversity patterns, particularly when phylobetadiversity methods more sensitive to terminal nodes were employed. Mixed forests tended to show higher phylogenetic differentiation to Dense and Seasonal forests than these latter from each other. The higher phylogenetic diversity and phylobetadiversity levels found in Mixed forests when compared to the others likely result from the biogeographical origin of several taxa occurring in these forests. On one hand, Mixed forests shelter several temperate taxa, like the conifers Araucaria and Podocarpus. On the other hand, tropical groups, like Myrtaceae, are also very representative of this forest type. We point out to the need of more attention to Mixed forests as a conservation target within the Brazilian Atlantic Forest given their high phylogenetic uniqueness.

Bivalve distribution in hydrographic regions in South America: historical overview and conservation

Based on literature review and malacological collections, 168 native freshwater bivalve and five invasive species have been recorded for 52 hydrographic regions in South America. The higher species richness has been detected in the South Atlantic, Uruguay, Paraguay, and Amazon Brazilian hydrographic regions. Presence or absence data were analysed by Principal Coordinate for Phylogeny-Weighted. The lineage Veneroida was more representative in hydrographic regions that are poorer in species and located West of South America. The Mycetopodidae and Hyriidae lineages were predominant in regions that are richest in species toward the East of the continent. The distribution of invasive species Limnoperna fortunei is not related to species richness in different hydrographic regions there. The species richness and its distribution patterns are closely associated with the geological history of the continent. The hydrographic regions present distinct phylogenetic and species composition regardless of the level of richness. Therefore, not only should the richness be considered to be a criterion for prioritizing areas for conservation, but also the phylogenetic diversity of communities engaged in services and functional aspects relevant to ecosystem maintenance. A plan to the management of this fauna according to particular ecological characteristics and human uses of hydrographic regions is needed.

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.

Impacts of human disturbance in tropical dry forests increase with soil moisture stress

Questions (1) Which disturbances (harvesting, browsing, drought and fire) are important for tree mortality in a tropical dry forest (TDF)? And do these change with size class (juvenile, sapling, adult)? (2) How is mortality and recruitment in a TDF related to soil moisture content (SMC) and does the relationship change for different size classes? (3) Is disturbance-related mortality selectively removing particular species from the TDFs? Location Sonebhadra and Mirzapur districts of Uttar Pradesh, India. Methods We analysed the structure of a TDF in central India in terms of the tree composition of juveniles, saplings and adults at five distinct sites located along a gradient of SMC, and recorded the numbers of individuals in each size class killed by the four disturbance types over two years. We also recorded total stem density and recruitment at each site. We compared annual mortality index (AMI) and its four disturbance components (harvesting, browsing, drought, fire) and annual recruitment index (ARI), against the mean SMC of each site using generalized linear mixed models. Results The impact of all disturbances on total AMI decreased as SMC increased whereas ARI increased as SMC increased. Mortality due to harvesting was substantially greater than other disturbances for adult and sapling trees whereas both harvesting and browsing were important drivers of mortality for juveniles. There was little evidence that particular species were being deliberately selected for harvesting across sites. Conclusion Tree saplings and adults in this TDF were mainly killed by harvesting, indicating that anthropogenic impacts on tree mortality are more important than non-anthropogenic impacts in the TDF, and impacts of all disturbances are more severe with increasing water stress. Thus changes in TDF structure due to harvesting are likely to be more rapid in more arid environments. This article is protected by copyright. All rights reserved.

Phylogenetic composition and structure of tree communities shed light on historical processes influencing tropical rainforest diversity

The Neotropics, Afrotropics and Madagascar have different histories which have influenced their respective patterns of diversity. Based on current knowledge of these histories, we developed the following predictions about the phylogenetic structure and composition of rainforest tree communities: (Hypothesis 1) isolation of Gondwanan biotas generated differences in phylogenetic composition among biogeographical regions; (H2) major Cenozoic extinction events led to lack of phylogenetic structure in Afrotropical and Malagasy communities; (H3) greater angiosperm diversification in the Neotropics led to greater phylogenetic clustering there than elsewhere; (H4) phylogenetic overdispersion is expected near the Andes due to the co-occurrence of magnoliids tracking conserved habitat preferences and recently diversified eudicot lineages. Using abundance data of tropical rainforest tree species from 94 communities in the Neotropics, Afrotropics and Madagascar, we computed net relatedness index (NRI) to assess local phylogenetic structure, i.e. phylogenetic clustering vs. overdispersion relative to regional species pools, and principal coordinates of phylogenetic structure (PCPS) to assess variation in phylogenetic composition across communities. We observed significant differences in phylogenetic composition among biogeographical regions (agreement with H1). Overall phylogenetic structure did not differ among biogeographical regions, but results indicated variation from Andes to Amazon. We found widespread phylogenetic randomness in most Afrotropical and all Malagasy communities (agreement with H2). Most of central Amazonian communities were phylogenetically random, although some communities presented phylogenetic clustering (partial agreement with H3). We observed phylogenetic overdispersion near the Andes (agreement with H4). We were able to identify how differences in lineage composition are related to local phylogenetic co-occurrences across biogeographical regions that have been undergoing different climatic and orographic histories during the past 100 Myr. We observed imprints of the history following Gondwana breakup on phylobetadiversity and local phylogenetic structure of rainforest tree communities in the Neotropics, Afrotropics and Madagascar.

Insect herbivory fluctuations through geological time

Arthropods and land plants are the major macroscopic sources of biodiversity on the planet. Knowledge of the organization and specialization of plant-herbivore interactions, such as their roles in food webs is important for understanding the processes for maintaining biodiversity. A limited number of studies have examined herbivory through geological time. The most have analyzed localities from one restricted interval within a geological period, or a time transition such as the Paleocene-Eocene boundary interval. In the present study, we analyzed the frequency of herbivory and density of damage type (DT) from the Middle Devonian to the early Miocene. The data were compiled from literature sources and focused on studies that describe occurrences of leaves with DTs indicating herbivore consumption as a proportion of the total number of leaves analyzed. The data were standardized based on the DT categories in the Damage Type Guide, and the age of each locality was updated based on the most recent geochronological standard and expressed in millions of years. Temperature and geological age were the best descriptors of the variation in herbivory frequency, which tended to increase at higher temperatures. Two models were equivalent to explain DT density: the interaction between CO2 levels and geological age, and O2 levels and geological age had the same predictive power. The density of DT tended to increase with higher content of atmospheric CO2 and O2 compared to modern values. The frequency of herbivory and the density of DTs appear to be influenced by long-term atmospheric variables.