Code and data from: 'Breaking new ground: niche divergence and expansion in ground parrots (Pezoporini: Platycercinae)'

This R project folder contains all of the code and data files necessary to recreate the figures and analyses.Most raw data files are contained in the inputs folder (see below). Occurrence data for P. flaviventris are not included - these must be requested directly from the Department of Biodiversity Conservation and Attractions, Western Australia. Therefore, the project folders contain neither raw nor derived data files that contain locality data for P. flaviventris. The project contains the following folders:1. BioGeoBears: contains input data for the BioGeoBEARS analyses (.txt and DATA files), as well as all outputs from the BioGeoBEARS analyses as described in the Methods and Results sections.2. code: contains all R scripts used to run the analyses and generate the outputs. Scripts are numbered 1-7 corresponding to the same order in which analyses are described in the Methods section. Additionally, six scripts appended with the letter 2 are updated versions of functions from the tidyouwie package.2. inputs: contains the following raw data files:-NVIS_V7_0_AUST_EXT.gdb: 100 m x 100 m (1 Ha) resolution National Vegetation Information System (NVIS) layer v7.0 from the Department of Climate Change, Energy, the Environment and Water (https://www.dcceew.gov.au/environment/land/native-vegetation/national-vegetation-information-system).-PaleoClim/: BIO1–BIO19 paleoclimate layers from the PALEO-PGEM-Series at 1,000-year intervals for the last 5 My, downloaded using the pastclim package v2.1.0 (code/5.paleoclimate.R).-aus.*: shapefile of Australia (not including offshore territories).-Ecoregions2017.*: shapefile of the 2017 global ecoregion classification (Dinerstein E et al. 2017 An ecoregion-based approach to protecting half the terrestrial realm. Bioscience 67, 534–545).-hab_desc.csv: legend for NVIS_V7_0_AUS_EXT.-HARM_*.tif: annual Australia-wide layers from 1750–2020 for average monthly temperatures (°C) for the warmest three months (January, February and March; BIO10), average monthly temperatures (°C) for the coolest three months (June, July and August; BIO11), and total annual rainfall (mm; BIO12), generated at a 0.2 ° resolution using a delta bias correction based on data from PaleoView v1.5.1 and the RCP 4.5 projection from the StableClim database (see details in Tomlinson S et al. 2023 Reconstructing mechanisms of extinctions to guide mammal conservation biogeography. J Biogeogr 50, 1199–1212).-ibra7_regions.*: shapefile of Australia's bioregions (https://www.dcceew.gov.au/environment/land/nrs/science/ibra), used to extract the location of the Nullarbor Plain.-Platycercinae.*: shapefile of Australian platycercine distributions, sourced from BirdLife International and Handbook of the Birds of the World.-region_20km.tif: raster file with an Australian landmass mask.-SWAFR.*: shapefile of the South-West Australian Floristic Region, derived from ibra7_regions.*.3. occ: csv files with cleaned occurrence records for all Australian platycercine parrots apart from P. flaviventris.4. outputs: folder for all outputs generated using the R scripts. The following outputs, which cannot be generated without the missing P. flaviventris occurrence data, are included in the folder and can be used as derived data files for downstream analyses and visualisations:-biogeobears_comparison.csv: summary table of model valuation of BioGeoBEARS models (output from code/6.niche_evolution.R).-biomes.csv: single biome with the largest occupancy mapped to each parrot species (output from code/2.niche_overlap.R).-biomes2.csv: all biomes with at least 25% occupancy mapped to each parrot species (output from code/2.niche_overlap.R).-model_perf.csv: summary table of model comparison of climatic niche models for ground parrots (output from code/4.niche_models.R).-paleo_stack_df.csv: paleoclimatic suitability for ground parrots across Australia from 5 My to the present at 1 Ky timesteps (output from code/5.paleoclimate.R).-parrot_niches.csv: summary table with climatic niche dimensions for Australia playtcerine parrots (output from code/6.niche_evolution.R).-Species_Climate*.RDS: climatic niche models for ground parrots (output from code/4.niche_models.R).-stack_df.csv: climatic suitability for ground parrots across Australia from 1750 to 2020 at annual timesteps (output from code/4.niche_models.R).5. ouwie: contains all OUwie model runs (output from code/6.niche_evolution.R).6. phylogeny: contains pruned_tree.tre, a pruned version of the latest parrot phylogeny (Smith BT, Thom G, Joseph L. 2024 Revised evolutionary and taxonomic synthesis for parrots (Order: Psittaciformes) guided by phylogenomic analysis. Bull Am Mus Nat Hist 468, 1–89), including only Australian platycercine parrots.7. plots: folder for all plotting outputs from the R scripts.8. temp: empty folder for some temporary outputs generated while running code/5.paleoclimate.R.