Alexandre Oliveira

University of São Paulo | USP · Department of Ecology (IB)

Tree diversity and composition in Amazonia are known to be strongly determined by the water supplied by precipitation. Nevertheless, within the same climatic regime, water availability is modulated by local topography and soil characteristics (hereafter referred to as local hydrological conditions), varying from saturated and poorly drained to well...

Context Tropical forests are great reservoirs of carbon but they still suffer high rates of deforestation despite their importance. Yet, large uncertainty remains about the effects of landscape-level forest loss on biomass of forest remnants, and how these effects vary with disturbance intensity at larger regional scales. Objectives We evaluated w...

Tropical forests are being deforested worldwide, and the remaining fragments are suffering from biomass and biodiversity erosion. Quantifying this erosion is challenging because ground data on tropical biodiversity and biomass are often sparse. Here, we use an unprecedented dataset of 1819 field surveys covering the entire Atlantic Forest biodivers...

Tropical forests are being deforested worldwide, and the remaining fragments are suffering from biomass and biodiversity erosion. Quantifying this erosion is challenging because ground data on tropical biodiversity and biomass are often sparse. Here, we use an unprecedented dataset of 1,819 field surveys covering the entire Atlantic Forest biodiver...

Aim Forest fragmentation is among the principal causes of global biodiversity loss, yet how it affects mutualistic interactions between plants and animals at large spatial scale is poorly understood. In particular, tropical forest regeneration depends on animal‐mediated seed dispersal, but the seed‐dispersing animals face rapid decline due to fores...

Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a n...

Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturba...

Climate is widely recognised as an important determinant of the latitudinal diversity gradient. However, most existing studies make no distinction between direct and indirect effects of climate, which substantially hinders our understanding of how climate constrains biodiversity globally. Using data from 35 large forest plots, we test hypothesised...

Trophic rewilding has been suggested as a restoration tool to restore ecological interactions and reverse defaunation and its cascading effects on ecosystem functioning. One of the ecological processes that has been jeopardized by defaunation is animal-mediated seed dispersal. Here, we propose an approach that combines joint species distribution mo...

The aim of this study was to characterize the structure and composition of the tree and shrub community in a 77-ha fragment of Restinga forest in Caraguatatuba, São Paulo, Brazil. In this fragment, forty 20 × 20-m plots (1.6 ha) were systematically allocated and all trees with a stem diameter at breast height (DBH) ≥4.8 cm were sampled. Sixteen plo...

DNA barcoding helps to identify species, especially when identification is based on parts of organisms or life stages such as seeds, pollen, wood, roots or juveniles. However, the implementation of this approach strongly depends on the existence of complete reference libraries of DNA sequences. If such a library is incomplete, DNA-based identificat...

Aim To examine the contribution of large‐diameter trees to biomass, stand structure, and species richness across forest biomes. Location Global. Time period Early 21st century. Major taxa studied Woody plants. Methods We examined the contribution of large trees to forest density, richness and biomass using a global network of 48 large (from 2 t...

Despite the general recognition that fragmentation can reduce forest biomass through edge effects, a systematic review of the literature does not reveal a clear role of edges in modulating biomass loss. Additionally, the edge effects appear to be constrained by matrix type, suggesting that landscape composition has an influence on biomass stocks. T...

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and Ma...

Belongs to paper Species Distribution Modelling: Contrasting presence-only models with plot abundance data by Gomes et al.

Comparing the results of modelling the area of occupancy with MaxEnt and with inverse distance weighting (IDW). Analysis results for the predicted area of occupancy as calculated by Maxent and IDW methods. The analyses were conducted for 170 of all 227 hyperdominant species that had MaxEnt’s predicted environmental suitability significantly differ...

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and Ma...

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and Ma...

Differences between the proportion of taxa in the SP tree flora and the proportion of taxa with barcoding sequences with DNA barcodes per family and genus.

The priority index for future sequencing efforts for tree species in the state of São Paulo, Brazil.

Tree community surveys used to obtain species abundances for the São Paulo tree flora.

Primers and PCR protocols used to obtain the DNA sequences.

The full list of the São Paulo tree flora, including their life form, geographical distribution, threat status at state-level and the source of the record.

List of GenBank accessions found for the São Paulo tree flora.

Tropical forests account for a quarter of the global carbon storage and a third of the terrestrial productivity. Few studies have teased apart the relative importance of environmental factors and forest attributes for ecosystem functioning, especially for the tropics. This study aims to relate aboveground biomass (AGB) and biomass dynamics (i.e., n...

Past human influences on Amazonian forest The marks of prehistoric human societies on tropical forests can still be detected today. Levis et al. performed a basin-wide comparison of plant distributions, archaeological sites, and environmental data. Plants domesticated by pre-Columbian peoples are much more likely to be dominant in Amazonian forests...

The extent to which pre-Columbian societies altered Amazonian landscapes is hotly debated. We performed a basin-wide analysis of pre-Columbian impacts on Amazonian forests by overlaying known archaeological sites in Amazonia with the distributions and abundances of 85 woody species domesticated by pre-Columbian peoples. Domesticated species are fiv...

We analyze forest structure, diversity, and dominance in three large-scale Amazonian forest dynamics plots located in Northwestern (Yasuni and Amacayacu) and central (Manaus) Amazonia, to evaluate their consistency with prevailing wisdom regarding geographic variation and the shape of species abundance distributions, and to assess the robustness of...

Disentangling the mechanisms that shape community assembly across diversity gradients is a central matter in ecology. While many studies have explored community assembly through species average trait values, there is a growing understanding that intraspecific trait variation (ITV) can also play a critical role in species coexistence. Classic biodiv...

This file contains data belonging to the article "Intraspecific leaf trait variability along a boreal-to-tropical community diversity gradient" by Cristina C. Bastias, Claire Fortunel, Fernando Valladares, Christopher Baraloto, Raquel Benavides, William Cornwell, Lars Markesteijn, Alexandre A. de Oliveira, Jeronimo B.B Sansevero, Marcel C. Vaz, Nat...

Species ranks at sample size of 20 individuals per species (ITV) vs species ranks at sample size of 5 individuals (rarefied ITV) in order to detect bias in the ITV estimate by a small sample size. R2 close to 1 means no bias (i.e. similar ITV values obtained for a species using 20 individuals and using 5 individuals). (TIF)

Boxplot of the ITV values for leaf size grouped in 7 categories of sample size per species (No. of individuals). n: number of observations in each category. (TIF)

Community accumulation curves at sample size of 5 individuals. Dashed lines are 95% confident. (TIF)

Linear regression models of the median values of trait overlap (panel A, B) and the proportion of low (less than 0.25; panel C, D) and high (> 0.75; panel E, F) values of degree of trait overlap between species for each forest community against species richness for both leaf size (left) and SLA (right). Trait similarity was calculated by kernel den...

Species ranks at sample size of 10 individuals per species (ITV) vs species ranks at sample size of 5 individuals (rarefied ITV) in order to detect bias in the ITV estimate by a small sample size. R2 close to 1 means no bias (i.e. similar ITV values obtained for a species using 10 individuals and using 5 individuals). (TIF)

Boxplot of the ITV values for SLA grouped in 7 categories of sample size per species (No. of individuals). n: number of observations in each category. (TIF)

In a study specifically designed to quantify the production of seedlings grown from seeds collected in Restinga, we found only six from 122 surveyed nurseries in São Paulo state producing local seedlings. Total number of commercially produced seedlings was relatively low. Thus, we compared it with the number of legally committed seedlings to restor...

Interspecific interactions are considered to be important structuring forces in early successional vegetation. Whereas competition seems to prevail in less severe environments, facilitation tends to increase in importance in harsh environments. Hence, facilitation is expected to play an important role in degraded tropical areas with high irradiance...

Biological invasions pose a significant threat to biodiversity, especially on oceanic islands. One of the primary explanations for the success of plant invaders is direct suppression of competitors. However, indirect interactions can also be important, although they are often overlooked in studies on biological invasion. The shrub Leucaena leucocep...

Raw data from germination nursery experiment of Erythrina velutina: litter. (CSV)

Raw data from germination field experiment of Erythrina velutina. (CSV)

Nursery germination analysis: R code. (R)

Raw data from native species ocurrence in invaded and non invaded plots in Fernando de Noronha island. (CSV)

Raw data from germination nursery experiment of Erythrina velutina: soil. (CSV)

Raw data from field experiment of Erythrina velutina seedlings growth. (CSV)

Native species occurence analysis: R code. (R)

Field survival analysis: R code. (R)

Raw data from Leucaena leucocephala abundance rank in Fernando de Noronha island. (CSV)

Field germination analysis: R code. (R)

List of models compared for field experiment of Erythrina velutina germination. The models were binomial generalised linear mixed models (GLMMs) with germination as the response variable, the presence of Leucaena leucocephala (leu), Capparis flexuosa (cap) or litter (lit) and their interactions as fixed predictor variables and the blocks as a rando...

Raw data from field experiment of Erythrina velutina seedlings survival. (CSV)

Field growth analysis: R code. (R)

Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land...

Tropical forests are globally important, but it is not clear whether biodiversity enhances carbon storage and sequestration in them. We tested this relationship focusing on components of functional trait biodiversity as predictors.Data are presented for three rain forests in Bolivia, Brazil and Costa Rica. Initial above-ground biomass and biomass i...

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened...

Estimates of extinction risk for Amazonian plant and animal species are rare, and not often incorporated into land-use policy and conservation planning. Here we overlay spatial distribution models with historical and projected deforestation to show that at least 40% and up to 64% of all Amazonian tree species are likely to qualify as globally threa...

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened...

We aimed to determine the role of soil nutrients in the herbaceous-tree boundary in a tropical mangrove forest. We assembled plots in this boundary such that each was initially covered by ~50% of each life form. We added NPK to three of the plots monthly and monitored them, along with the control plots, for 18 mo. In plots with added NPK, mangrove...

The structure of the Atlantic Forest (AF) has been studied for almost 70 years. However, the related existing knowledge is spread over hundreds of documents, many of them unpublished and/or difficult to access. Synthesis initiatives are available, but they are restricted to only a few parts or types of the AF or are focused on species occurrence. H...

The stress gradient hypothesis (SGH) postulates how the balance between plant competition and facilitation shifts along environmental gradients. Early formulations of the SGH predicted that facilitation should increase monotonically with stress. However, a recent theoretical refinement of the SGH postulates stronger facilitation under moderate stre...

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characteriz...

Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+ (Reducing Emissions from Deforestation and Forest Degradation). Though broad-scale mapping is based primarily on remote sensing data, the accuracy of resulting for...