DOI: 10.5061/dryad.12jm63z7v
title: Phylogenetic endemism and ancestral area inference reveal historical refugia in the Greater Cape Floristic Region

description: Aim: Refugial areas and habitats are thought to have played a key role in
 facilitating both the emergence and persistence of floristic diversity in
 the Greater Cape Floristic Region (GCFR) of South Africa. While refugial
 areas may be identified using a diversity of biological proxies (e.g.,
 narrow-range endemism; paleoendemism), there is a shortage of studies in
 the GCFR that apply these approaches at the species level and in
 a comparative manner across multiple clades. Location: GCFR, South Africa.
 Time Period: Cenozoic. Major Taxa Studied: Protea, Leucadendron,
 Pentameris, Restionoideae. Methods: We quantify and compare the spatial
 distribution of phylogenetic endemism (PE) in four Cape-centric plant
 clades, two clades of shallow-rooted graminoids (Poales) and two of
 deep-rooted shrubs (Proteales). For each clade, we also quantify the
 phylogenetic effect on PE (PPE), a metric describing the contribution of
 evolutionarily distinctive species (paleoendemics) to PE. Spatial moving
 average regression models are used to assess the influence of climate
 stability and topography on the distributions of PE and PPE. Finally, we
 use ancestral area inference to complement these analyses, on the premise
 that refugial areas are more likely to be resolved as ancestral. Results:
 Both PE and PPE are concentrated in the southwestern GCFR, a pattern
 consistent with the long-term climate stability and steep relief of this
 mountainous region. In addition, ancestral area inference resolves the
 southwestern GCFR as a likely area of origin for all clades examined.
 Spatial patterns of PE and PPE nevertheless vary between clades, with PE
 centres more diffusely and broadly distributed in Proteales than in
 Poales. Main Conclusions: Our study indicates that stable climate and
 topography have played an important refugial role in shaping patterns of
 diversity and endemism in the GCFR, but that functionally distinct clades
 (i.e., shallow-rooted graminoids versus deep-rooted shrubs) differ in
 terms of the location and dispersion of areas that have served as
 historical refugia. We attribute this variation to trait-dependent
 differences in their climate sensitivity.
description: See manuscript related to this dataset for a detailed description
 of the methodology.
description: # Phylogenetic endemism and ancestral area inference reveal historical
 refugia in the Greater Cape Floristic Region van Blerk, J.J.; Verboom,
 G.A.; Cramer, M.D.; Lamberton, L. **Description of the data and file
 structure** **File: Phylogenetic_endemism_paper_data.zip** **Folders**
 **DATA Climate stability index (past)** csi_past.tif Used for the spatial
 moving average models determining whether phylogenetic endemism (PE) and
 the phylogenetic effect on PE (PPE) corresponds with areas of high climate
 stability since the Pliocene. **DATA Environmental layers** * **Chelsa
 bioclimatic data** File 1: CHELSA_bio10_01.tif File 2: CHELSA_bio10_02.tif
 File 3: CHELSA_bio10_03.tif File 4: CHELSA_bio10_04.tif File 5:
 CHELSA_bio10_05.tif File 6: CHELSA_bio10_06.tif File 7:
 CHELSA_bio10_07.tif File 8: CHELSA_bio10_08.tif File 9:
 CHELSA_bio10_09.tif File 10: CHELSA_bio10_011.tif File 11:
 CHELSA_bio10_011.tif File 12: CHELSA_bio10_012.tif File 13:
 CHELSA_bio10_013.tif File 14: CHELSA_bio10_014.tif File 15:
 CHELSA_bio10_015.tif File 16: CHELSA_bio10_016.tif File 17:
 CHELSA_bio10_017.tif File 1:8 CHELSA_bio10_018.tif File 19:
 CHELSA_bio10_019.tif All of the different possible bioclimatic variables
 for the globe to be used in the species distribution modelling. * **DEM**
 aspect_240_card.tif File containing the aspect as 8 cardinal directions of
 the direction in which the slope is facing. Used in the species
 distribution modelling. dem_240m.tif File containing the digital elevation
 model, with the height above sea level in metres. Used in the species
 distribution modelling. slope_240m.tif File containing the angle of the
 slope of the ground. Used in the species distribution modelling. * **Fire
 frequency data** Fire_per_year.tif File containing the number of fires per
 year. Used in the species distribution modelling. FIRM_average.tif File
 containing the average number of fires per year. Used in the species
 distribution modelling. * **NDVI** NDVI_annual_average.tif File containing
 the NDVI average over the year. Used in the species distribution
 modelling. NDVI_max.tif File containing the maximum NDVI in a year. Used
 in the species distribution modelling. NDVI_min.tif File containing the
 minimum NDVI in a year. Used in the species distribution modelling.
 NDVI_range.tif File containing the range of NDVI values over a year. Used
 in the species distribution modelling. * **Soils** EC_mS_m.tif File
 containing the electrical conductivity of the soil for the GCFR region.
 Used in species distribution modelling. Ext_K_cmol_kg.tif File containing
 the extractable potassium of the soil for the GCFR region. Used in species
 distribution modelling. Ext_Na_cmol_kg.tif File containing the extractable
 sodium of the soil for the GCFR region. Used in species distribution
 modelling. Ext_P_mg_kg.tif File containing the extractable magnesium of
 the soil for the GCFR region. Used in species distribution modelling.
 pH.tif File containing the PH levels of the soil for the GCFR region. Used
 in species distribution modelling. Total_C_%.tif File containing the total
 carbon percentage of the soil for the GCFR region. Used in species
 distribution modelling. Total_N_%.tif File containing the total nitrogen
 percentage of the soil for the GCFR region. Used in species distribution
 modelling. * **worldclim** wind speed (m s^-1^) 30seconds (can be
 downloaded at https://www.worldclim.org/). Used in the species
 distribution modelling. **DATA GCFR polygons** * **GCFR outer polygon**
 gcfr_soil_buf.shx gcfr_soil_buf.dbf gcfr_soil_buf.prj gcfr_soil_buf.shp
 All shape files for the outer polygon (perimeter polygon) of the GCFR
 region. Used as region of interest for species distribution modelling and
 PE analysis. * **GCFR regions** GCFR_regions.shp GCFR_regions.shx
 GCFR_regions.dbf GCFR_regions.prj All shape files for the focal regions
 (SW, NW, AP, LB, KM, SE, EC) used within the GCFR.  Weimarck, H. (1941).
 Phytogeographical groups, centres and intervals within the Cape
 flora. *Lund, Leipzig*. **DATA Phylogenies** Protea.tre Phylogeny of all
 the *Protea* species analysed. Used in the calculations of PE and PPE.
 Restionoideae.tre Phylogeny of all the Restionoideae species analysed.
 Used in the calculations of PE and PPE. Leucadendron.tre Phylogeny of all
 the *Leucadendron* species analysed. Used in the calculations of PE and
 PPE. Pentameris.tre Phylogeny of all the *Pentameris* species analysed.
 Used in the calculations of PE and PPE. **DATA Species distributions** *
 **Pentameris**  Pentameris.xlsx Excel workbook file containing
 *Pentameris* spp. names, observation locations (longitude and latitude)
 and location notes for each observation. Empty cells represent unknown
 values.  Used in species distribution modelling.  * **Protea and
 Leucadendron** occ_sp.shx occ_sp.dbf        occ_sp.prj occ_sp.shp Shape
 files containing the locations of all Proteaceae species locations
 including the *Protea* and the *Leucadendron* genera. Used in species
 distribution modelling. Proteaceae_names_codes.csv CSV file containing the
 name codes (CODE or occs_CODE) and species names (genus, species) of all
 the species contained in the occ_sp.shp file. Column names (CODE or
 occs_CODE) are linked to shapefile attributes and used to separate the
 locations of *Protea* and *Leucadendron* from the other species in the
 above dataset. * **Restionoideae** linder_restio.csv CSV file containing
 the names and observation locations (longitude & latitude) of the
 Restionoideae species analysed. Used in the species distribution
 modelling.  **RESULT Reconstructed Ancestral Regions (on phylogenies)**
 Fig S4_Pentameris_DEC_node_labels Fig S5_Pentameris_DEC_node_probs Fig
 S6_Restionoideae_DECj_node_labels Fig S7_Restionoideae_DECj_node_probs Fig
 S8_Protea_DEC_node_labels Fig S9_Protea_DEC_node_probs Fig
 S10_Leucadendron_DECj_node_labels Fig_S11_Leucadendron_DECj_node_probs
 These image files show the reconstructed ancestral regions on phylogenies
 which were used to produce Figure 3 in the manuscript. **RESULT Spatial PE
 and PPE** Leucadendron_PE_PPE_spatial.csv Pentameris_PE_PPE_spatial.csv
 Protea_PE_PPE_spatial.csv Restionoideae_PE_PPE_spatial.csv These spatial
 data-frames contain the PE (phylogenetic endemism) and PPE (the
 phylogenetic effect on PE) data for each pentad along with the geometries
 for each pentad. Used to produce Figure 2 in the manuscript. **Notes on
 file use** Shapefiles are a common format for vector-based geographic
 information system (GIS) data. They can be opened and used in any GIS
 software and in R or Python. A shapefile consists of multiple file types
 beyond the .shp (specifically, .cpg, .dbf, .prj, .sbn, and .sbx). The user
 only interacts directly with the .shp file but the other files need to be
 in the same directory. Tag Image File Format (.tif) files are common
 format raster-based geographic information system (GIS) data. They can be
 opened and used in any GIS software and in R or Python. Pixels within the
 .tif files have associated values that are used in analyses. Tree (.tre)
 files are common formats for storing phylogenetic trees. They can be
 imported into R using various packages (e.g., "ape").  Comma
 separated value (.csv) files are spreadsheets with information separated
 by commas. CSV files may be imported into GIS software, Microsoft excel, R
 or Python.  Excel workbooks (.xlsx) are spreadsheets that are most easily
 viewed in Microsoft excel but can be imported into R or Python.