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The evolution and population diversity of human-specific segmental duplications
Megan Y Dennis1,2, Lana Harshman2, Bradley J Nelson2
1Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA.
Nature Ecology & Evolution
|June 6, 2017
Summary
Human-specific segmental duplications (HSDs) drive human evolution and adaptation. Our study identifies 218 HSDs, revealing their organization and role in human-specific gene expansions and adaptive traits.
Area of Science:
- Genomics
- Evolutionary Biology
- Human Genetics
Background:
- Segmental duplications (SDs) are crucial for human evolution, adaptation, and genomic instability.
- However, their specific roles and evolutionary trajectories, particularly human-specific segmental duplications (HSDs), remain poorly understood.
Purpose of the Study:
- To investigate the evolution, genetic variation, and protein-coding potential of HSDs.
- To identify HSDs and analyze their genomic organization and impact on gene families.
Main Methods:
- Analysis of 322 deeply sequenced archaic and contemporary hominid genomes to identify HSDs.
- Sequencing of 550 human and nonhuman primate genomic clones to reconstruct the evolution of complex HSD regions.
- Bioinformatic analysis to assess gene content, organization, and evolutionary patterns.
Main Results:
- Identification of 218 HSDs, revealing non-random organization associated with ancestral ape duplications (core duplicons).
- Reconstruction of HSD evolution, primarily in an interspersed inverted orientation.
- Discovery of human-specific gene expansions (e.g., TCAF1/2) and ten gene families (e.g., ARHGAP11B, SRGAP2C) with persistent copy number, splicing evidence, and no common disruptive mutations.
Conclusions:
- HSDs are key drivers of human-specific adaptations.
- Specific gene families within HSDs represent strong candidates for the evolution of unique human traits.
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