Figure 1. (A) The population identify for the newly sequenced sample based on PCA analysis. The arrow shows the sample sequenced in this study. (B) The completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) for the final reference genome. (C) The numbers of unique and sharing SVs for three methods of SVs identification (Vulcan, NanoSV, and SyRI). (D) The number of long SVs (1Kb) within chromosomes. The linear regression was based on the autosomes (“lm” function in R platform, p < 0.001).

Figure 2. The distribution pattern of methylation frequencies across mitochondrial genome, autosomes, and sex chromosomes based on boxplot (A) and density plot (B). Only the “minimum (Q1 -1.5*IQR)”, first quartile [Q1], median, third quartile [Q3] and “maximum (Q3 + 1.5*IQR)” are shown for boxplot.

Figure 3. (A) The methylation frequencies of annotated SNPs within and around protein-coding genes. The tiny black bars show the standard errors. (B) Boxplots for methylation frequencies of SNPs with annotations of impacts on gene structure (following the annotation of SnpEff v5.1). (C) Boxplots for methylation frequencies of SVs from three different tools. (D) The median methylation frequencies across small Indels with different lengths. The formulas show linear regressions of median values against lengths of small Indels (< 50bp).

Figure 4. The distributions of common logarithm of recombination rates for SVs. (A) The boxplot comparisons for duplications, inversions, deletions, and insertions identified from three methods (NanoSV, SyRI, and Vulcan). The “body”, “down1k”, and “up1k” indicate the regions within the SVs, 1Kb downstream of the SVs, and 1Kb upstream of the SVs, respectively. “NS” indicates “non-significant” based on the Wilcoxon rank sum test (p>0.05). The significance levels of 0.05, 0.01, and 0.001 are showed with “*”, “**”, and “***”, respectively. (B) The density distribution of the fine-scale recombination rates for four types of SVs. The “INS”, “INV”, “DUP”, and “DEL” indicate the “insertions”, “inversions”, “duplications”, and “deletions”, respectively.

Figure 5. The selective signals for the Chinese and Indian rhesus macaques based on three complementary methods (F_st,θ _{π_India}/θ _{π_China}, Ihh12, top 5% strongest windows, 100Kb). (A) The distribution of F_st andθ _{π_India}/θ _{π_China} based on comparison between the Chinese and Indian rhesus macaques. The red and blue points show the the candidate selective sweep windows for the Indian and Chinese groups, respectively. (B) The candidate selective sweep signals above the dotted line (top 5% windows) for the Chinese rhesus macaques. The SVs involved gene (TTC28 ) with the highest signal in Ihh12 was shown. (C) The candidate selective sweep signals above the dotted line (top 5% windows) for the Indian rhesus macaques. The SVs involved gene (IL1RAPL2 ) with the highest signal in Ihh12 was shown. (D) The functional enrichment ontology for the Chinese rhesus populations. (E) The percentages of SVs under positive selection. (F) The chromosomal distribution for the 53 positively selected genes with signals of congruent SVs. Note: the horizontal axis shows the X chromosome while the vertical axis shows the number of genes. (G) The linear regression for congruent SVs counts and the SVs under selective sweep (p = 0.4, not significant). The blue point is the outlier (X chromosome).

Supplementary figure 1. The whole genome alignment between CR2 and reference genome of an Indian rhesus macaque (mm10) using minimap2 (-xasm10). The dotplot visualization was based on a R package dotPlotly. The vertical axis shows the CR2 scaffolds while the horizontal axis exhibits the chromosomes of mm10.

Supplementary figure 2. The chromosome-wide methylation frequencies for the Chinese rhesus macaque. The black points show the median values within slide-windows (the window-size of 1Mb).

Supplementary figure 3. The fine-scale recombination rates inferred with pyrho package across chromosomes [33], which using population genomic data of the Chinese and Indian rhesus macaque (27 samples). The vertical axis is the logarithm of median fine-scale recombination rates with base 10 (ρ/Mb, slide-window, 1Mb). The horizontal axis shows the coordinates of chromosomes (Mb).