Data from: Drivers and spatial patterns of avian defaunation in tropical forests
Data files
Mar 24, 2025 version files 329.64 KB
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Bird_RR_data.csv
321.68 KB
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README.md
7.96 KB
Mar 24, 2025 version files 329.64 KB
-
Bird_RR_data.csv
321.68 KB
-
README.md
7.96 KB
Abstract
This repository is organized into three folders: Data, Scripts, and Raster, which contain the CSV files and R scripts created and used throughout this study.
The Data folder contains a CSV file that details changes in bird abundance used to model the impact of hunting. Please note that latitude and longitude have been rounded to one decimal place to protect sensitive data regarding the locations of species subjected to trade and hunting.
| Variables | Type | Description |
|---|---|---|
| Study | Categorical | Numerical study ID where abundance values in hunted and no-hunted forests were extracted |
| Reviewer | Categorical | Person who extracted the data from studies. |
| Order | Categorical | The higher-level taxonomic classification of the bird species. |
| Family | Categorical | Mid-level taxonomic group within the order, representing a more specific classification of the bird species. |
| Species | Categorical | Binomial name of the species extracted from each Study |
| BirdLife_Species | Categorical | Binomial name of the species according to Bird Life nomenclature |
| BirdTree_Species | Categorical | Binomial name of the species according to Jetz et al. (2012) nomenclature (phylogenetic tree) |
| IUCN_Species | Categorical | Binomial name of the species according to IUCN Red List. |
| Hunting | Categorical | Type of hunting motivation retrieved from study: subsistence (S), comercial (C) or a mix of both (SC) |
| RR | Numeric | Abundance response ratio. No units. |
| Hdens | Numeric | Abundance of bird species in hunted site. |
| Udens | Numeric | Abundance of bird species in unhunted site. |
| Traded | Categorical | If bird species is traded as a pet or not. |
| Realm | Categorical | Biogeographic realm where study was conducted |
| Country | Categorical | Country where hunted and unhunted sites are located. |
| Dist_Hunters | Numeric | Distance to nearest hunter access points in kilometes from hunted sites. (>90% of cases are human settlements) |
| TravDist | Numeric | Travel time to major cities from hunted sites (min) |
| PopDens | Numeric | Human population density from hunted sites (n/km2) |
| Stunting | Numeric | Prevalence of cronic malnutrition in children under 5 years old (proxy of poverty, %) in hunted sites. |
| FoodBiomass | Numeric | Livestock biomass (cattle, sheep, goat, pig and chicken) available in hunted sites (ton/km2) |
| Reserve | Categorical | If hunted site is located inside (1) or outside (0) protected areas where hunting activities are banned or restricted. |
| NPP | Numeric | Net Primary Productivity of the hunted forest (kg C/m²/year) |
| CountryNum | Categorical | Country numeric code according to ISO 3166-1 |
| Food | Categorical | If bird species is hunted or not for food consumption. |
| Hunted | Categorical | If bird species is hunted for food consumption or pet trade or not targeted by hunters neither trappers. |
The Scripts folder contains the necessary R scripts for data analysis and visualisation, as well as the generation of defaunation rasters.
The data analysis scripts include:
- RR_BRMS.R (modelling)
- Variable_Importance.R (variance partitioning)
- Cross_Validation.R (model cross-validation)
- MESS.R (Multi-Environmental Surface Similarity analysis)
The raster creation scripts consist of: - AllDefaunation_Map.R
- LargeDefaunation_Map.R
- MediumDefaunation_Map.R
- SmallDefaunation_Map.R
- Pet_Map.R
- Food_Map.R
These correspond to all bird species, large birds, medium-sized birds, small birds, birds subject to the pet trade, and birds hunted for meat consumption, respectively.
Finally, AreaDefaunation.R and Plot_Food_Pet.R are visualisation scripts used to display the defaunated area across different realms and bird communities.
- The Raster folder includes raster maps depicting hunting-induced defaunation for all tropical bird species, along with separate files showing the defaunation index for large-bodied, medium-bodied, and small-bodied bird species. These maps were generated using average model predictions, with a constant response ratio (RR) of 1 for non-hunted species (i.e., assuming no change in abundance for species not affected by hunting). Additionally, raster files related to the pet trade and food consumption report the average defaunation index only for bird species affected by these pressures.
Supplemental Files Description:
- pet_map.tif: Raster map depicting defaunation index for bird species subjected to pet trade. Pixels values depict DI, which ranges from 0 (totally defaunated community) to 1 (intact community). It does not include no-hunted bird species.
- food_map.tif: Raster map depicting defaunation index (DI) for bird species hunted for food consumption. Pixels values depict DI, which ranges from 0 (totally defaunated community) to 1 (intact community). It does not include no-hunted bird species.
- medium_defaunation_map.tif: Raster map depicting defaunation index (DI) for medium-sized bird species. Pixels values depict DI, which ranges from 0 (totally defaunated community) to 1 (intact community). It includes no-hunted bird species, assuming RR=1 (no changes in abundance).
- large_defaunation_map.tif: Raster map depicting defaunation index (DI) for large-sized. Pixels values depict DI, which ranges from 0 (totally defaunated community) to 1 (intact community). It includes no-hunted bird species, assuming RR=1 (no changes in abundance).
- combined_defaunation_map.tif: Raster map depicting defaunation index (DI) for all tropical bird species. Pixels values depict DI, which ranges from 0 (totally defaunated community) to 1 (intact community). It includes no-hunted bird species, assuming RR=1 (no changes in abundance).
- small_defaunation_map.tif: Raster map depicting defaunation index (DI) for small-sized Pixels values depict DI, which ranges from 0 (totally defaunated community) to 1 (intact community). It includes no-hunted bird species, assuming RR=1 (no changes in abundance).
We expanded the dataset of hunting impacts on bird populations from Benítez-López et al. (2017) by supplementing additional bird abundance data from local hunting studies through a systematic search of the literature (see details in Supplementary Methods 1). Our final dataset comprises 2968 abundance estimates for 518 tropical bird species at both hunted and non-hunted sites (control) based on 60 local hunting studies (Figure S1, Table SX). Studies that report potential confounding effects, such as habitat loss and logging were not included in our analysis. Changes in abundance due to hunting pressure were subsequently expressed as the response ratio (RR) between the abundance of each bird species (s) in hunted (Xsh) and non-hunted (Xsc) sites within each study (RR =Xsh/Xsc) (Peres & Palacios, 2007; Benítez-López et al., 2017, 2019) RR = 0 then indicates local extinction; 0 < RR < 1, reduction in abundance; RR ≈ 1, no changes in abundance and RR > 1, increase in abundance.
We compiled the following information from each study: the geographic coordinates of hunted and unhunted sites in each study, the hunter’s access point to the hunted site (i.e. roads, settlements or rivers), and the motivation for hunting (i.e. subsistence, commercial or both). We further compiled information on different predictors often recognised as drivers of hunting pressure, including the distance to access points, human population density, poverty level, and travel time to major cities, as well as information on factors that modulate species responses to hunting pressure, such as net primary productivity or whether hunting activities took place inside or outside protected areas (Peres, 2000; Brashares et al., 2010; Benítez-López et al., 2017, 2019; Whytock et al., 2018; Bogoni et al., 2020; Scabin & Peres, 2021) (Supplementary Table 2).
Please, note that all continuous predictors were scaled and centered around zero with a SD equal to 1 before model fitting.