Data files available here related to the above study include genotypes for wild and captive chimpanzees, geographic information on sampled wild populations in Cameroon, and population allele frequency files for the wild chimpanzee samples.

Note: Wild chimpanzee sampling locations were generalized to a single population coordinate within a single grid cell of 1 km², where fecal samples were collected. Fecal samples were obtained from areas of chimpanzee presence, including nests, footprints, feeding sites, and vocalizations. All fecal sample collection was over a decade ago.

Description of the data and file structure

There are three files consisting of captive chimpanzee genotypes derived from whole-genome sequencing:

• captivechimpanzee_wgs_snps_autosomes.vcf.gz, which contains all genotyped SNPs
• captivechimpanzee_wgs_snps_autosomes_LD-HW-MAF_filtered.vcf, consisting of linkage disequilibrium-pruned, Hardy-Weinberg and minor allele frequency-filtered sites in captivechimpanzee_wgs_snps_autosomes.vcf.gz
• captivechimpanzee_wgs_snps_autosomes_LD-HW-MAF_filtered_neutralloci.vcf, consisting of intergenic sites that were not in selection scan outlier windows, i.e, putatively neutral sites.

Wild chimpanzee genotypes

These genotypes were called from sequence data generated from a capture array, described in our associated preprint:

• wildchimpanzees_capturearray_neutral.vcf, a subset of sites in captivechimpanzee_wgs_snps_autosomes_LD-HW-MAF_filtered_neutralloci.vcf
• wildchimpanzees_capturearray_outlier.vcf, genotypes at a subset of sites in outlier windows from whole-genome selection scans that presumably carry the imprint of positive selection.

Merged captive and wild chimpanzee samples

This genotype file includes captive and wild chimpanzee samples for genomic positions in the capture array SNPs, i.e., the sites in both wildchimpanzees_capturearray_neutral.vcf and wildchimpanzees_capturearray_outlier.vcf:

• captive_and_wild_chimpanzees_merged_capturearray_positions.vcf

Population ID information

• cameroon_wild_chimpanzee_id_to_population.txt, contains genetic population id information for color-coding PCA plots
• cameroon_wild_chimpanzee_samplinglocality_and_environmentaldata.xlsx, contains wild chimpanzee sample IDs, and associated geographic population information, including remotely sensed environmental variables and lat-long coordinates. Explanations for environmental variable abbreviations are below. Unless noted otherwise, temperature and precipitation variables that start with "bio" are in degrees Celsius x 10 and mm, respectively.
  • bio_01: annual mean temperature (degree C), from WorldClim
  • bio_02: mean diurnal range (i.e, mean of monthly (max temp - min temp)), from WorldClim
  • bio_03: Isothermality (bio_02/bio_07) (×100), from WorldClim
  • bio_04: temperature seasonality (standard deviation of monthly temperature x 100), from WorldClim
  • bio_05: maximum temperature of the warmest month, from WorldClim
  • bio_06: minimum temperature of the warmest month, from WorldClim
  • bio_07: temperature annual range, from WorldClim
  • bio_08: mean temperature of the wettest quarter, from WorldClim
  • bio_09: mean temperature of the driest quarter, from WorldClim
  • bio_10: mean temperature of the warmest quarter, from WorldClim
  • bio_11: mean temperature of the coldest quarter, from WorldClim
  • bio_12: annual precipitation (mm), from WorldClim
  • bio_13: precipitation of the wettest month, from WorldClim
  • bio_14: precipitation of the driest month, from WorldClim
  • bio_15: precipitation seasonality (coefficient of variation), from WorldClim
  • bio_16: precipitation of the wettest quarter, from WorldClim
  • bio_17: precipitation of the driest quarter, from WorldClim
  • bio_18: precipitation of the warmest quarter, from WorldClim
  • bio_19: precipitation of the coldest quarter, from WorldClim
  • mdllafrica: Moderate Resolution Imaging Spectroradiometer (MODIS) Land Cover, from Dimiceli et al. (2011)
  • ndvi_brn: maximum NDVI of the least green season, from Carroll et al. (2004)
  • ndvi_grnbrn: NDVI seasonality, from Carroll et al. (2004)
  • ndvi_grn: maximum NDVI of the greening season, from Carroll et al. (2004)
  • ndvi_max: maximum annual NDVI, from Carroll et al. (2004)
  • ndvi_mean: mean annual NDVI, from Carroll et al. (2004)
  • qscat_mean: QuikSCAT backscatterometer (mean) – measure of surface moisture from radar remote sensing (see Long et al. 2001)
  • qscat_std: QuikSCAT backscatterometer (standard deviation of QuikSCAT backscatterometer)– measure of moisture variation (see Long et al. 2001)
  • slope_deg: slope (in degrees)
  • srtm_hgt: elevation obtained from the Shuttle Radar Topography Mission (SRTM), from WorldClim
  • srtm_std: slope (ruggedness) derived obtained from WorldClim SRTM
  • treecover: % tree cover derived from MODIS, from Dimiceli et al. (2011)

Wild population allele frequencies

• wildchimpanzee_cameroon_pop_allele_frequencies.tar contains allele frequency information for capture array genotypes for all 16 geographic populations used in our analyses. Allele frequencies were calculated with vcftools using the --freq2 switch.