Extended Data Fig. 5: The fixed variants, genetic differentiation regions, and inversions between MFA and MMU.

(a) Principal component analysis (PCA) of three macaque populations. The first component (18.6%, x-axis) separates MFA (red) and MMU, while the second component (11%, y-axis) distinguishes CMMU (Chinese rhesus macaque) and IMMU (Indian rhesus macaque). The macaque individuals are clustered according to each population. Newly sequenced samples in this study are marked in color, while the samples from the previous study are marked in gray. (b) Lineage-specific fixed genetic variation. The length distribution of fixed INDELs and SVs are shown in the left panel (INDEL: 2-20 bp (top), SV: 50-500 bp (bottom)) and right (INDEL: 20-50 bp (top), SV: 500-10000 bp (bottom)). Notable peaks for Alu and L1 are at 300 bp and 6000 bp. A fixed SNV in PLA2G3 (c) and a fixed SV in EHBP1L1 (d) result in amino acid differences between MFA and MMU. (e) A genetic differentiation region associated with SRCAP and PHKG2. The gene models, π diversity, F_ST, and XP-EHH across the genomic region are shown from top to bottom. The dotted lines indicate the bottom 5% threshold from π diversity, the top 5% from F_ST, and the top 5% from XP-EHH, respectively. (f, g) Fixed missense variants of SRCAP (f) and PHKG2 (g) result in amino acid differences between MFA and MMU. (h) The syntenic relationship of the inversion with the longest length (4 Mbp) within macaques, with the gene annotation above. (i) The heatmap shows the DEGs within the 500 kbp flanking regions of macaque inversion (≥10 kbp) breakpoints (Z-score of rlog-transformed counts). Each row represents a gene and each column represents a tissue.