International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 113 Functional genomics approaches, such as the analysis of gene expression and regulatory elements, have further enriched our understanding of primate evolution. Comparative RNA sequencing has revealed genetic variation and gene expression differences that are consistent with positive selection, shedding light on the genetic basis of species-specific adaptations (Perry et al., 2012). Moreover, the creation of a global catalog of whole-genome diversity from 233 primate species has provided a comprehensive resource for studying the impact of genomic diversity on biological processes, evolutionary divergence, and conservation efforts (Kuderna et al., 2023). 6 Case Studies in Primate Population Genomics 6.1 Population genomics of African great apes (chimpanzees, bonobos, and gorillas) Research on the population genomics of African great apes, including chimpanzees, bonobos, and gorillas, has revealed significant insights into their genetic diversity, structure, and evolutionary dynamics. Chimpanzees and bonobos exhibit complex demographic histories with evidence of ancient admixture. For instance, de Manuel et al. found that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, contributing less than 1% to the central chimpanzee genomes (Manuel et al., 2016). Additionally, studies have shown that chimpanzees have a nucleotide diversity (pi) of 0.134%, which is higher than that of humans but lower than previously thought (Yu et al., 2003). Gorillas, on the other hand, exhibit the highest nucleotide diversity among African apes, with a (pi) value of 0.158% (Yu et al., 2004). The genetic structure of chimpanzee populations has been extensively studied, revealing three distinct populations: western, central, and eastern chimpanzees, with little evidence of gene flow between them (Becquet et al., 2007). Furthermore, Chaisson et al. (2018) systematically discovered structural changes (length>50 base pairs) through improved sequence adjacency and detected 614186 primate deletions, insertions, and reversals, each assigned to a specific primate lineage (Figure 2), providing deeper insights into their evolutionary trajectories. Figure 2 SMRT assemblies and SV analyses (Adopted from Chaisson et al., 2018) Image caption: (Top) Contiguity of the de novo assemblies. (Bottom, left to right) For each ape, SVdetection was done against the human reference genome as represented by a dot plot of an inversion). Human-specific SVs, identified by comparing ape SVs and population genotyping (0/0, homozygous reference),were compared to single-cell gene expression differences [range: low (dark blue) to high (dark red)] in primary and organoid tissues. Each heatmap row is a gene that intersects an insertion or deletion (green), duplication (cyan), or inversion (light green) (Adopted from Chaisson et al., 2018)
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