DOI: 10.5061/dryad.jm63xsjmv
title: Data from: Life-history strategies drive plant species richness patterns in the Atlantic Forest hotspot

description: Aim: The underlying processes driving the origin and spatial variation of
 species richness stand as one of the most fundamental and enigmatic
 questions in ecology. Here, we assess the roles of water availability,
 energy availability, climatic seasonality, physiological tolerance,
 historical climate stability, topographic heterogeneity, and the
 mid-domain effect in shaping spatial richness variation among various
 plants of the Atlantic Forest. Location: Atlantic Forest Hotspot, South
 America. Taxon: 14,037 species of vascular plants (angiosperms and
 gymnosperms), including trees, lianas, shrubs, subshrubs, terrestrial
 herbs and epiphytic herbs. Methods: We employed stacked ecological niche
 modeling to estimate species richness across different plant life forms.
 We then applied spatial models and hierarchical partitioning to assess the
 role and significance of each hypothesis in explaining species diversity
 variation. Results: Spatial richness variation in the Atlantic Forest
 results from the interplay of multiple drivers, with effects differing
 among plant life forms. Overall, regions with higher energy availability,
 lower temperature seasonality, higher temperature stability but lower
 precipitation stability over the last 21,000 years, and more complex
 topography harbored more species. However, the effects of water stress and
 cold sensitivity contrasted among life forms. Main
 conclusions: Observed species richness variation among life forms
 is primarily rooted in their life-history strategies. Trees and lianas
 exhibited lower sensitivity to water stress but were less tolerant to cold
 extremes, whereas subshrubs and terrestrial herbs showed the opposite
 pattern, with lower tolerance to water stress but greater cold tolerance.
 Shrubs and epiphytic herbs displayed an intermediate pattern, combining
 the reduced sensitivity to water stress of trees and lianas with the
 higher cold tolerance of subshrubs and terrestrial herbs. Our study
 deepens the understanding of the factors shaping Atlantic Forest diversity
 and opens new pathways for predicting and managing large-scale impacts of
 human activities.
description: # Data from: Life-history strategies drive plant species richness patterns
 in the Atlantic Forest hotspot
 [https://doi.org/10.5061/dryad.jm63xsjmv](https://doi.org/10.5061/dryad.jm63xsjmv) ## Description of the data and file structure The data contains all the information and reproducible R scripts to generate the results and figures associated with the paper. Species distributions were estimated using ecological niche modeling. Presence-absence matrices were generated by stacking individual species models. Richness maps and statistical analyses were then conducted to evaluate the drivers of plant species richness across the Atlantic Forest. All analyses were conducted using R (version ≥ 4.2). ### Files and variables #### File: Richness_AF_Data.zip **Description of the data and file structure:**  **scripts:** A folder containing reproducible R scripts required to perform the analyses and generate the figures included in the paper: * **0 - Plots of hypothesis.R**\ Generates conceptual figures illustrating the hypotheses evaluated in the study. * **1 - Get PAM from Models.R**\ Generates the species Presence–Absence Matrix (PAM) from ecological niche model predictions. * **2 - Richness by lifeform.R**\ Calculates spatial species richness for each plant life form using modeled species. * **2.2 - Richness by lifeform_PAMwithOcurrences.R**\ Calculates species richness including both modeled and non-modeled species. * **3 - Generate explanatory variables to model richness.R**\ Generates environmental predictor variables used in richness modeling. * **4 - Prepare explanatory variables to model richness.R**\ Prepares and combines environmental variables into raster layers for spatial modeling. * **5 - Fit INLA spatial models.R**\ Fits spatial models to evaluate the effects of environmental predictors on species richness. * **6 - Spatial correlation between life forms richness.R**\ Calculates spatial correlations among richness patterns of different plant life forms. * **7 - Plot results and generate figures.R**\ Generates all figures presented in the manuscript from the analysis outputs. **Data:** A folder containing the primary results and supporting datasets: * Hypothesis/: contains figures illustrating the main hypotheses proposed to explain broad-scale patterns in species richness (referenced in Table 1 of the paper). * INLA_models/: includes the models fitted to estimate the drivers of plant species richness across the Atlantic Forest. Import into R with `readRDS()`. * Variables/: folder containing: * Correlation_variables.rds: correlation matrix of the explanatory variables. Import into R with `readRDS().` * Explanatory_Variables.tiff: raster variables used to estimate the drivers of plant species richness (import into R with `terra::rast()`): * Bio02: Mean Diurnal Range. Represents the mean difference between daily maximum and minimum temperature. Units: °C. * Bio06: Minimum Temperature of Coldest Month. Represents the lowest monthly temperature. Units: °C * Bio15: Precipitation Seasonality. Measures variability in monthly precipitation across the year. Units: coefficient of variation (%) * PET (Potential Evapotranspiration): Represents atmospheric demand for water. Units: mm/year. * Aridity Index: Ratio between precipitation and potential evapotranspiration, indicating water availability. Units: unitless. * Prec_stab\ Precipitation Stability. Measures long-term temporal stability in precipitation since the Last Glacial Maximum. Higher values indicate more stable conditions. Units: unitless index * Temp_stab (Temperature Stability): Measures long-term temporal stability in temperature since the Last Glacial Maximum. Higher values indicate more stable conditions. Units: unitless index. * Topo_het (Topographic Heterogeneity): Represents variation in elevation within each spatial cell. Higher values indicate greater terrain complexity. Units: meters (standard deviation of elevation) * Binarized_*models*_v2.tif: raster file showing the predicted distribution (presence/absence) of 10,341 plant species in the Atlantic Forest, estimated using Ecological Niche Modelling. Import into R with `terra::rast().` * Ecoregions_af.gpkg: a spatial vector file representing the ecoregions within the Atlantic Forest. Import into R with `terra::vect().` * GrowthForm_Final.txt: a text file containing the consensus plant growth forms, sourced from Engemann et al. (2016). Import into R with `data.table::fread().`Columns: * FAMILY_STD: standardized plant family name. * SPECIES_STD: standardized species scientific name. * GROWTHFORM_STD: standardized growth form classification. * GROWTHFORM_DIV: alternative growth form classification * ID: unique identifier for each species record. * CONSENSUS: final consensus growth form classification used in the analyses. * SOURCES: number of independent sources supporting the growth form classification. * Misiones_checklist_native_endemic_species.csv: A CSV file listing native plant species found in the portion of the Atlantic Forest located in Misiones Province, Argentina. Import into R with `data.table::fread().`Columns: * FAMILIA: plant family name * GENERO: genus name * EPITETO ESPECIFICO: species epithet * SIGLA SP.: author abbreviation for the species name * SUBESPECIE: subspecies name, if applicable * SIGLA SSP: author abbreviation for the subspecies name * VARIEDAD: variety name, if applicable * SIGLA VAR.: author abbreviation for the variety name * FORMA: form name, if applicable * SIGLA FOR.: author abbreviation for the form name * EN ARGENTINA: presence in Argentina (Si/No) * EN BRASIL: presence in Brazil (Si/No) * EN CHILE: presence in Chile (Si/No) * EN PARAGUAY: presence in Paraguay (Si/No) * EN URUGUAY: presence in Uruguay (Si/No) * HABITO: plant growth habit (e.g., tree, shrub, herb) * STATUS: species status (e.g., native) * PROV. FITOG.: phytogeographic province(s) where the species occurs * ALTURA MINIMA: minimum elevation of occurrence (meters above sea level) * ALTURA MAXIMA: maximum elevation of occurrence (meters above sea level) * DIST. ARGENTINA: distribution within Argentina (province codes) * Occurrences.gz: compressed data table with records of 14,037 plant species confirmed in the Atlantic Forest across the Neotropics. Import into R with `data.table::fread()`. Columns: * species: species scientific name. * x: longitude in decimal degrees (WGS84) * y: latitude in decimal degrees (WGS84) - Occurrences_rasterized.tiff: Raster file indicating pixels where records exist for species excluded from the niche models due to having fewer than 10 occurrences. Import into R with `terra::rast().` - PAM.gzip: A compressed Presence-Absence Matrix (PAM) for 10,341 plant species across the Atlantic Forest. This matrix was generated through stacked ecological niche modeling. Import into R with `data.table::fread()`. - PAM_with_occurrences.gz: Same as *PAM.gzip*, but also including the occurrences of non-modeled species. Import into R with `data.table::fread()`. - Richness_by_lifeforms.rds: R list containing the spatial richness of each life form across the Atlantic Forest. Import into R with `readRDS().` * Richness_by_lifeform_withOccurrences.rds: R list with the spatial richness of each life form, including both modeled and non-modeled species. Import into R with `readRDS().` * Richness_correlations.rds: Correlation matrix of richness across life forms. Import into R with `readRDS().` * Richness_correlations_with_Undersampled.rds: Same as *Richness_correlations.rds*, but including both modeled and non-modeled species. Import into R with `readRDS().` * SpeciesData_v2.gzip: A compressed data table containing detailed information about the 14,037 plant species analyzed in the study.  Import into R with `data.table::fread()`. Columns: * species: species scientific name * family: plant family name * origin: species origin status in Brazil (e.g., Native) * habitat: primary habitat type (e.g., Terrestrial) * endemism: endemism status in Brazil (Endemic or Non-endemic) * source_occurrence: source indicating that the species occurs in the Atlantic Forest (florabr or misiones checklist) * genus: genus name * lifeForm: plant growth form (e.g., Tree, Shrub, Herb, Liana) * n: total number of occurrence records compiled for the species in the Neotropic. * n_in_af: number of occurrence records located within the Atlantic Forest * modeled: logical variable indicating whether the species was included in ecological niche modeling (TRUE/FALSE)