Land cover and climate change as drivers of bird species abundance in South Africa

Dataset: Data/ReportingRates.csv
Description
This dataset contains species × pentad × year reporting rates (a proxy for relative abundance) derived from Southern African Bird Atlas Project 2 (SABAP2) full-protocol checklists for 2008–2020. For each species–pentad–year combination the file provides the number of full-protocol checklists (TotalEntries), the number of checklists recording the species (ObservedCount), and the reporting rate (ReportingRate = ObservedCount / TotalEntries), together with land-cover proportions (five classes) and four climatic metrics. Land cover was derived from the ESA Climate Change Initiative (CCI) annual layers (300 m, 2008–2020), reclassified into Croplands/Agricultural, Natural Vegetation, Built-up Areas, Water Bodies, and Sparse Vegetation/Bare Ground, and summarized per pentad by zonal statistics in ArcGIS Pro v3.1. Climate variables were obtained from TerraClimate (~4 km, 2008–2020), aggregated to annual values (annual total precipitation, annual mean maximum and minimum temperature, and mean Palmer Drought Severity Index (PDSI)) and averaged across pixels within each pentad. Taxonomic identifiers (common group, common species, genus and species epithet) are included.

Goal of the analyses
To quantify the impact of land cover and climate on relative bird abundance, and to determine the relative contributions of these environmental factors to changes in South African reporting rates (a proxy for relative abundance) between 2008 and 2020.

Key metadata
Title: ReportingRates.csv
Geographic coverage: South Africa (211 SABAP2 pentads selected; pentad = 5′ × 5′ grid cell ≈ 61 km²)
Spatial resolution: Pentad level (~61 km²)
Temporal coverage: 2008–2020 (inclusive)
Number of pentads used: 211
Primary data sources / provenance: SABAP2 full-protocol checklists; ESA CCI Land Cover (300 m; 2008–2020); TerraClimate (~4 km; 2008–2020)
Inclusion criteria: Pentads with ≥4 full-protocol SABAP2 checklists per year (2008–2020)
File format: CSV (comma-separated)
Date created: 10 September 2025
Concise notes on columns and units
Land-cover fields (Cropland, Natural_Vegetation, Sparse_veg_bare_ground, Water, Built_up) are expressed as percent cover of the pentad and should sum approximately to 100% (small differences may arise from classification or excluded classes).
ppt_mean = annual precipitation total (millimetres).
tmax_mean, tmin_mean = annual mean maximum and minimum temperature (°C).
pdsi_mean = annual mean Palmer Drought Severity Index (unitless; negative = drier conditions).
ReportingRate is a proportion bounded between 0 and 1 (ObservedCount / TotalEntries). Values of 0 or 1 can be valid given checklist counts.
Occupancy is binary (1 = species recorded at least once in that pentad–year; 0 = not recorded).
Ref, Common_Group, Common_Species, Genus, Species provide taxonomic identifiers . SpeciesName is a combined human-readable label.
Dataset: Data/combined_avonet.csv (Species traits / AVONET-derived)
Description
Morphological and life-history traits for 431 study species extracted from the AVONET database. Includes continuous functional traits (beak culmen length, beak width, beak depth, tarsus length, wing length, body mass, and geographic range size) and categorical ecological attributes (primary habitat association, habitat density, migration strategy, trophic level, trophic niche, primary lifestyle).

Columns (original → cleaned; type; units / example; description)
Species1 → Scientific_Name; character; e.g., Accipiter melanoleucus; full species binomial.
Species_Name → Common_Name; character; e.g., Black Sparrowhawk; common (vernacular) name.
Family1 → Family; character; e.g., Sylviidae; taxonomic family.
Order1 → Order; character; e.g., Passeriformes; taxonomic order.
Beak_Length_Culmen_1 → Beak_Culmen_mm; numeric; mm; culmen length (bill tip → skull base).
Beak_Length_Nares_1 → Beak_NaresLength_mm; numeric; mm; length to nares (verify definition if used).
Beak_Width_1 → Beak_Width_mm; numeric; mm; bill width at anterior nares.
Beak_Depth_1 → Beak_Depth_mm; numeric; mm; bill depth at anterior nares.
Tarsus_Length_1 → Tarsus_mm; numeric; mm; tarsometatarsus length.
Wing_Length_1 → Wing_mm; numeric; mm; carpal joint → tip of longest primary (unflattened).
Kipps_Distance_1 → Kipps_Distance_mm; numeric; mm; Kipp’s distance (wing shape metric, if present).
Secondary1_1 → Secondary_Length_mm; numeric; mm; secondary feather length (if present).
Hand_Wing.Index_1 → Hand_Wing_Index; numeric; unitless; hand–wing index (flight morphology).
Tail_Length_1 → Tail_mm; numeric; mm; tail length.
Mass_1 → Mass_g; numeric; g; species mean body mass (male+female).
Habitat_1 → Habitat; factor/character; e.g., Grassland, Woodland; primary habitat association.
Habitat_Density_1 → Habitat_Density; integer / ordered; 1 = dense; 2 = semi-open; 3 = open.
Migration_1 → Migration; integer / ordered; 1 = sedentary; 2 = partial/short-distance; 3 = long-distance.
Trophic_Level_1 → Trophic_Level; character/factor; e.g., Herbivore, Carnivore; broad feeding guild.
Trophic_Niche_1 → Trophic_Niche; character/factor; e.g., Invertivore, Frugivore; finer diet category.
Primary_Lifestyle_1 → Primary_Lifestyle; character/factor; Aerial, Terrestrial, Insessorial, Aquatic, Generalist.
Range_Size → Range_km2; numeric; km²; mapped breeding/resident range (excl. vagrants).
Dataset: Spatial data / Shapefile: SA Pentads_4 each year.shp (211 assessed pentads)
Description
GIS polygon layer representing the 211 SABAP2 pentads retained for analysis (each pentad ≈ 5′ × 5′ ≈ 61 km²). Pentads were selected because they met the study criterion of ≥4 full-protocol SABAP2 checklists per year between 2008 and 2020. This layer was used to compute zonal summaries of ESA CCI land-cover and TerraClimate climate variables and to map the geographic distribution of sampled pentads.

Key metadata
Filename: SA Pentads_4 each year.shp
Geometry: Polygon; feature count: 211
CRS (recommended): WGS 84 (EPSG:4326) — record actual CRS used for area calculations if different.
Typical pentad area: ≈ 61 km² (varies with latitude)
Files to distribute: .shp, .shx, .dbf, .prj, optional .cpg, plus exported figure SA Pentads Map.jpeg