International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 108-119 http://ecoevopublisher.com/index.php/ijmeb 109 This study is to summarize the current knowledge on primate population genomics, focusing on the diversity, population structure, and evolutionary dynamics of primate species. By synthesizing findings from recent genomic studies, this study will provide a comprehensive overview of the genetic variation within and between primate populations and the evolutionary forces shaping this diversity. Additionally, this study will explore the implications of these findings for understanding human evolution and for the conservation of primate species, and identify future research directions and challenges in the field of primate population genomics, emphasizing the need for continued advancements in genomic technologies and analytical methods. 2 Genetic Diversity in Primates 2.1 Intraspecific genetic variation Genetic diversity within primate species varies significantly, influenced by factors such as population size, habitat fragmentation, and evolutionary history. For instance, rhesus macaques (Macaca mulatta) exhibit a high level of nucleotide diversity, approximately 2.5 times greater than that observed in humans. This diversity includes over 43.7 million single-nucleotide variants, which have implications for both functional and non-functional genomic regions (Xue et al., 2016). Prado-Martinez et al. (2013) found that chimpanzees, particularly the common chimpanzee, display significant genetic diversity, with distinct genetic populations identified within the species. For example, the Nigeria-Cameroon/western and central/eastern populations of common chimpanzees are genetically distinct, highlighting the complex population history and gene flow within this species. In macaques, whole-genome sequencing has revealed extensive genetic variation, including numerous variants that affect protein sequences and gene regulation, underscoring the species’ utility as a model for human disease studies (Xue et al., 2016). Similarly, studies on lemurs have shown that even critically endangered species like the black and white ruffed lemur and Coquerel’s sifaka maintain high levels of genetic diversity, suggesting that conservation efforts can be effective if timely (Perry et al., 2012). 2.2 Interspecific genetic variation Comparative genomic studies have provided insights into the genetic differences between various primate species. For instance, humans and chimpanzees, despite sharing 98.7% of their genomic DNA, exhibit significant differences in gene expression patterns, particularly in the brain, which may underlie the distinct cognitive and behavioral traits observed between the species (Enard et al., 2002). Additionally, the genetic diversity observed in great apes, including gorillas and orangutans, has been linked to their population history and varying levels of inbreeding, which affect their susceptibility to diseases and overall genetic health. Great apes, such as chimpanzees and gorillas, show extensive genetic variation, with evidence of gene flow and distinct population structures within species. In contrast, New World monkeys and Old World monkeys exhibit different patterns of genetic diversity and evolutionary pressures. For example, the genetic diversity in rhesus macaques, an Old World monkey, is shaped by a large and fluctuating population size, which has led to higher levels of nucleotide diversity compared to humans (Xue et al., 2016). These differences highlight the varied evolutionary trajectories and selective pressures experienced by different primate lineages. 2.3 Factors influencing genetic diversity Mutation, recombination, and genetic drift are fundamental forces shaping genetic diversity in primates. Mutations introduce new genetic variants, while recombination shuffles these variants, creating new combinations of alleles. Genetic drift, particularly in small populations, can lead to significant changes in allele frequencies over time. For example, the high level of genetic polymorphism observed in the common ancestor of the African ape clade (Homo-Pan-Gorilla) suggests that genetic drift played a significant role in shaping the genetic landscape of these species. Population size, habitat fragmentation, and gene flow are critical factors influencing genetic diversity. Large populations tend to maintain higher levels of genetic diversity due to a greater number of breeding individuals and reduced effects of genetic drift. Conversely, habitat fragmentation can isolate populations, reducing gene flow and
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