Renato Lima

University of São Paulo | USP · Departamento de Ciências Biológicas (LCB) (ESALQ)

Questions We assess gap size and shape distributions, two important descriptors of the forest disturbance regime, by asking: which statistical model best describes gap size distribution; can simple geometric forms adequately describe gap shape; does gap size or shape vary with forest type, gap age or the method used for gap delimitation; and how si...

In stable populations with constant demographic rates, size distributions reflect size-dependent patterns of growth and mortality. However, population growth can also affect size distributions, which may not be aligned with current growth and mortality. Using 25 y of demographic data from the 50-ha Barro Colorado Island plot, we examined how inters...

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...

Endemic species are important for biodiversity conservation. Yet, quantifying endemism remains challenging because endemism concepts can be too strict (i.e., pure endemism) or too subjective (i.e., near endemism). We propose a data-driven approach to objectively estimate the proportion of records inside a given the target area (i.e., endemism level...

Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, biogeography, macroecology and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For...

Despite the progress in the measurement and accessibility of plant trait information, acquiring sufficiently complete data from enough species to answer broad‐scale questions in plant functional ecology and biogeography remains challenging. A common way to overcome this challenge is by imputation, or ‘gap‐filling' of trait values. This has proven a...

One goal of ecological restoration is species conservation, so selecting tree species from local floras in restoration plantings is important to restore native species populations and avoid biotic homogenization. We evaluated if species planted to restore the Brazilian Atlantic Forest adequately represent the tree flora from local reference forests...

Tree monocultures constitute an increasing fraction of the global tree cover and are the dominant tree‐growing strategy of forest landscape restoration commitments. Their advantages to produce timber are well known, but their value for biodiversity is highly controversial and context dependent. Therefore, understanding whether, and in which conditi...

Biodiversity is declining globally, yet many biodiversity hotspots still lack comprehensive species conservation assessments. Using multiple International Union for Conservation of Nature (IUCN) Red List criteria to evaluate extinction risks and millions of herbarium and forest inventory records, we present automated conservation assessments for al...

Biodiversity is declining globally, yet many biodiversity hotspots still lack comprehensive species conservation assessments. Using multiple International Union for Conservation of Nature (IUCN) Red List criteria to evaluate extinction risks and millions of herbarium and forest inventory records, we present automated conservation assessments for al...

Investigating which species are planted in active restoration initiatives is useful for identifying underrepresented species and functional groups, which in turn can inform and improve the practice and policies of forest resto�ration. The Atlantic Forest is one of the global hotspots for biodiversity conservation and a region where many forest re...

Designing multispecies systems with suitable climatic affinity and identifying species' vulnerability under human‐driven climate change are current challenges to achieve successful adaptation of natural systems. To address this problem, we need to (1) identify groups of species with climatic similarity under climate scenarios and (2) identify areas...

For more than three decades, major efforts in sampling and analyzing tree diversity in South America have focused almost exclusively on trees with stems of at least 10 and 2.5 cm diameter, showing highest species diversity in the wetter western and northern Amazon forests. By contrast, little attention has been paid to patterns and drivers of diver...

Species under milder climates (e.g., warm and wet) tend to experience lower variability in temperature and rainfall regimes and might occur in narrower climatic ranges than species that tolerate harsher conditions (e.g., cold or dry climates). Thus, tree species that occur under harsh conditions should have a broader climatic range, being a small s...

Aim Locally abundant species are typically widespread, while locally scarce species are geographically restricted—the so‐called abundance‐occupancy relationships (AORs). AORs help explain the drivers of species rarity and community assembly, but little is known about how variation around such relationship is driven by species traits and niche‐based...

Understanding the mechanisms controlling forest carbon storage is crucial to support "nature-based" solutions for climate change mitigation. We used a dataset of 892 Atlantic Forest inventories to assess the direct and indirect effects of environmental conditions, human impacts, tree community proprieties, and sampling methods on tree above-ground...

Data on tropical forests are in high demand. But ground forest measurements are hard to sustain and the people who make them are extremely disadvantaged compared to those who use them. We propose a new approach to forest data that focuses on the needs of data originators, and ensures users and funders contribute properly.

Climate change is one of the main drivers of species extinction in the twentyfirst-century. Here, we (1) quantify potential changes in species’ bioclimatic area of habitat (BAH) of 135 native potential agroforestry species from the Brazilian flora, using two different climate change scenarios (SSP2-4.5 and SSP5-8.5) and dispersal scenarios, where s...

In tropical semi-deciduous forests, where 20-50 % of canopy trees shed their leaves in the dry season, species with varying degrees of leaf deciduousness share the same space and resources. Here, we describe the tree community in a 10.24-ha plot to assess whether small-scale variation in canopy structure and soil conditions are associated with chan...

Species co-occurrences in local communities can arise independent or dependent on species’ niches. However, the role of niche-dependent processes has not been thoroughly deciphered when generalized to biogeographical scales, probably due to combined shortcomings of data and methodology. Here, we explored the influence of environmental filtering and...

Aim Here we examine the functional profile of regional tree species pools across the latitudinal distribution of Neotropical moist forests, and test trait–climate relationships among local communities. We expected opportunistic strategies (acquisitive traits, small seeds) to be overrepresented in species pools further from the equator, but also in...

Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, bio-geography, macro-ecology, and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time....

The Atlantic Forest is one of the most important biodiversity hotspots, yet only a few studies have attempted to summarize tree diversity patterns across its full extent. With the increasing availability of primary biodiversity data, such a synthesis is potentially feasible; however, a critical assessment of the available information is needed to u...

Many authors have tried to explain the shape of the species abundance distribution (SAD). Some of them have suggested that sampling spatial scale is an important factor shaping SADs. These suggestions, however, did not consider the indirect and well-known effect of sample size, which increases as samples are combined to generate SADs at larger spat...

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...

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia...

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia...

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia...

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia...

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia...

Endemic species are essential for setting conservation priorities. Yet, quantifying endemism remains challenging because endemism concepts can be too strict (i.e. pure endemism) or too subjective (i.e. near endemism). We use a data-driven approach to objectively estimate the proportion of records outside a given the target area (i.e. endemism level...

Many authors have tried to explain the shape of the species abundance distribution (SAD). Some of them have suggested that sampling scale is an important factor shaping SADs. These suggestions, however, did not consider the indirect and well-known effect of sample size, which increases as samples are combined to generate SADs at larger scales. Here...

Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia...

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...

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...

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...

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...

Overabundant bamboos often affect negatively forest structure and ecological process such as seed rain, seedling establishment, survival, and growth. We tested the prediction that the bird community, seed rain profile, seedling and sapling establishment, and tree demography are altered in Guadua tagoara patches, a large-sized woody bamboo native fr...

Assessing the conservation value of restoration plantings is critical to support the global forest landscape restoration movement. We assessed the implications of tree species selection in the restoration of Brazil's Atlantic Forest regarding carbon stocking and species conservation. This assessment was based on a comprehensive dataset of seedling...

Carbon storage is widely acknowledged as one of the most valuable forest ecosystem services. Deforestation, logging, fragmentation, fire, and climate change have significant effects on tropical carbon stocks; however, an elusive and yet undetected decrease in carbon storage may be due to defaunation of large seed dispersers. Many large tropical tre...

Fig. S1. Distribution function of seed size diameter (mm) dispersed by the major frugivores in the Atlantic forest, Brazil. Fig. S2. Maximum tree height by class of species according to its seed diameter and wood density. Fig. S3. Relationship between wood density and seed diameter by dispersal mode. Fig. S4. Relationships between abiotic variables...

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...

In forestry, the description of tree sizes is commonly performed by fitting statistical models to diameter distributions. However, there is little agreement on which models are more flexible to this end, especially in tropical forests. Here we provide the simultaneous evaluation at species and subplot levels of 10 models using large data sets from...

The composition and diversity of Cerrado were evaluated in three different sites in eastern Mato Grosso do Sul, one of the most threatened and poorly studied areas in the Brazilian Cerrado. Vascular species were surveyed along trails in different Cerrado physiognomies, with special regard to shrub and tree species. Additionally, in the areas of cer...

Aims: The coastal Brazilian rainforest on white-sand (restinga) ranks among the most fragmented forest types in the tropics, owing to both the patchy distribution of sandy soils and widespread coastal development activities. Here we study the environmental and evolutionary determinants of a forest tree assemblage at a single restinga forest in Sout...

Pattern description – search for trends or non-random arrangements in communities, has a long history in plant ecology. Commonly, the structure and diversity of plant communities are described based on their size class distribution (SDD), spatial distribution (SSD) and species abundance distribution (SAD). This is because there is an underlying ass...

With fast growth rates and clonal reproduction, bamboos can rapidly invade forest areas, drastically changing their original structure. In the Brazilian Atlantic Forest, where recent mapping efforts have shown that woody bamboos dominate large areas, the present study assessed the differences in soil and vegetation between plots dominated (>90% of...

In the Montane and Submontane Rain Forest of the Carlos Botelho State Park - PECB (ca. 37,000 ha) the composition, richness and geographical distribution of native, vascular forest species was evaluated. The analysis of 1143 species of 140 families supported the pattern found for other forests of Eastern Brazil, showing high species richness of Myr...

Located in the Serra de Paranapiacaba, South of São Paulo State, the Carlos Botelho State Park (PECB) shelters more than 37,000 ha of Atlantic Forest in one of the most important and large remnants of this Biome in Brazil. In the Park the Montane and Submontane rain forests are the predominant types of forests. Aiming to organize the available flor...

This work presents an analysis of the vegetation of the Carlos Botelho State Park (a 37.644,36 hectares conservation unit located in the Vale do Ribeira do Iguape Region, São Paulo state, southeastern Brazil) as a contribution for the elaboration of its Management Plan. Field data were obtained through a Rapid Ecological Assessment – REA, carried o...

We assessed the structure, diversity and distribution of tree species in a 10.24-ha permanent plot of high Restinga forest (HRF) in southeastern Brazil. We sampled 15,040 individuals belonging to 45 families, 87 genera and 116 species (density= 1,468 trees ha-1, and basal area= 28.0 m2 ha-1). Mean richness was lower than other types of tropical for...

We present a review of more than 30 years of ecological restoration in the Brazilian part of the Atlantic Forest. Based on what has been done in this biome, we try to summarize the main findings and challenges for restoration in this highly threatened forest biome. We found that many past experiences did not result in self-perpetuating forests, for...

This study aimed to characterize the structure of the herb stratum in relation to light availability in the Submontane Atlantic Rain Forest at the Carlos Botelho State Park, SP, Brazil. Fortyone 10 x10 m plots were established under the closed canopy (18 plots), small and medium canopy gaps (11) and large canopy gaps dominated by Guadua tagoara (Ne...

In the Atlantic Montane Rain Forest of south-eastern Brazil, a field study was carried out to describe the forest disturbance regime, analyse canopy gap composition and evaluate the influence of habitat parameters on gap tree species composition. We characterized canopy gaps considering the group of variables as follows: area, type and number of tr...

A study was carried out to characterize the general pattern of tree mortality and damage in an old-growth semideciduous seasonal forest in the Caetetus Ecological Station, southeastern Brazil, and to assess species-specific patterns of mode and frequency of disturbances. We counted all disturbance events promoted by trees or parts of them larger th...

The canopy disturbance regime and the influence of gap methods on the interpretation of forest structure and dynamics were evaluated in a tropical semi-deciduous forest in south-eastern Brazil. We encountered a gap density of 11.2 gaps ha−1 and an average size which varied from 121 to 333 m2 depending on the gap delimitation method considered (mini...

In a 10.24 ha permanent plot of Tropical Lower Montane Atlantic Rain Forest in the Carlos Botelho State Park (Sete Barras, SP, Brazil), this study aimed to describe the canopy disturbance regime and to assess natural regeneration under different light regimes. In order to do so, the plot was completely surveyed for canopy gaps that were measured an...

In the Atlantic Montane Rain Forest of South-eastern Brazil, a study was carried out to describe and evaluate canopy gap colonization. Gap composition by herb species was assessed through their soil coverage and woody species by measuring and identifying all individuals taller than one meter. Gap structure (gap size, number and diameter of treefall...