Genome-wide copy number variation drives adaptive evolution in Macaca mulatta populations
Yun Liu1, Lin Zhang1, Xianlin Jin1
1Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China.
Current Zoology
|June 26, 2026
Summary
Copy number variations (CNVs) reveal significant genomic diversity in rhesus macaques. This study maps CNVs, uncovering adaptations related to immunity, metabolism, and body size across populations.
Area of Science:
- Genomics
- Evolutionary Biology
- Primate Genetics
Background:
- Copy number variation (CNV) is a key driver of genomic diversity within species.
- CNV remains underexplored in rhesus macaque (Macaca mulatta) populations.
- Understanding CNV is crucial for characterizing intraspecific variation and adaptation.
Purpose of the Study:
- To comprehensively map copy number variations (CNVs) across the rhesus macaque genome.
- To investigate the role of CNVs in population structure and adaptation in Macaca mulatta.
- To identify CNV-associated genes related to phenotypic traits and environmental adaptation.
Main Methods:
- Whole-genome sequencing of 8 M. m. lasiotis individuals, integrated with 6 existing genomes for a total of 60 rhesus macaque genomes.
- Read-depth based approach for copy number variation (CNV) detection and mapping.
- Hierarchical clustering and comparative genomic analyses to assess population structure and identify differentiated CNVRs.
Main Results:
- Identified approximately 59.6 Mb (2.2% of the reference genome) with CNV, comprising 1,272 nonoverlapping CNV regions (CNVRs).
- CNV-derived population structure showed discordance with SNV-based phylogenies.
- Highly differentiated CNVRs between Indian and Chinese populations were enriched for immune response and xenobiotic metabolism genes.
- Subspecies-specific CNVRs were linked to environmental adaptation and phenotypic variation, with notable gene copy number differences in M. m. tcheliensis.
- Six body size-associated genes exhibited significant CNV across subspecies.
Conclusions:
- CNVs play a significant role in shaping the genomic architecture and adaptive traits of rhesus macaques.
- CNV patterns provide insights into subspecies adaptation to specific environments and selective pressures.
- This study establishes a foundational resource for future research on structural variation in Macaca mulatta population genetics.
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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