Figure 1.

Overview on sampling, capture, and chimpanzee population history

(A) Geographic distribution of chimpanzee subspecies and PanAf sampling locations. The western chimpanzee range is shown in blue, Nigeria-Cameroon in pink, central in green, and eastern in orange. The size of the dots represents the number of sequenced samples (n = 828) and color intensity represents the amount of chimpanzee genetic data generated (mega-base pairs of mapped sequence) from each sampling site.

(B) Experimental pipeline. (1) Samples were collected from 48 sampling sites, DNA extracted and screened for amplification success, uniqueness, and relatedness using microsatellites;¹¹ (2) one library per individual²⁴ was prepared; (3) between 10 and 30 libraries were pooled equi-endogenously;²⁵ (4) enrichment for chromosome 21 with target capture methods, between three and five times per library;²⁵ (5) sequencing data were generated with Illumina.

(C) Average coverage on the target region of chromosome 21 for each sample.

(D) Percentage of the target space covered by at least one read.

(E) Heterozygosity estimates per subspecies derived from ANGSD genotype likelihood on PanAf samples with more than 0.5-fold coverage (GL > 0.5×), from snpAD genotype calls on PanAf samples with more than 5-fold coverage, and from GATK genotype calls on previously published whole-genome (WG) chimpanzee samples.⁶

(F) PCA of western (blue) and Nigeria-Cameroon (pink) chimpanzee subspecies. Dark blue diamonds, Bia sampling site in Ghana at the eastern fringe of the extant western chimpanzee range.

(G) PCA of central (green) and eastern (orange) chimpanzee subspecies. Dark orange diamonds, Ngiri sampling site at the western fringe of the eastern chimpanzee distribution. CAR, Central African Republic; DRC, Democratic Republic of Congo; R. Congo, Republic of Congo. See also Figures S3–S13, S29–S39, and Table S4