The evolution and population diversity of human-specific segmental duplications
Open accessAbstract
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed "core duplicons", and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (e.g., TCAF1/2), we highlight ten gene families (e.g., ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing, and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits.
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The SRGAP2 gene family is composed of SRGAP2A, the ancestral gene shared by all mammals, and human-specific duplicates SRGAP2B, SRGAP2C, and SRGAP2D, which emerged through segmental duplications during hominin evolution over the past approximately 2-3 million years.
“This family is composed of SRGAP2A, the ancestral gene shared by all mammals (named SRGAP2 in non-human species), human-specific (HS) gene duplicates SRGAP2B, SRGAP2C, and SRGAP2D, which emerged through segmental duplications during hominin evolution, over the past ∼2–3 million years.25,26”
From Synaptic neoteny of human cortical neurons requires species-specific balancing of SRGAP2-SYNGAP1 cross-inhibition (2024) · cites this paper as [26]
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- Authors
- Dennis, M. Y., Harshman, L., Nelson, B. J., Penn, O., Cantsilieris, S., Huddleston, J., Antonacci, F., Penewit, K., Denman, L., Raja, A., Baker, C., Mark, K., Malig, M., Janke, N., Espinoza, C., Stessman, H. A. F., Nuttle, X., Hoekzema, K., Lindsay-Graves, T. A., Wilson, R. K., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Howard Hughes Medical Institute (US)
- University of Bari Aldo Moro (IT)
- Washington University in St. Louis (US)
- Corresponding author
- Eichler, Evan E.
- ORCID
- Venue
- Nature Ecology & Evolution
- Published
- 2017-02-17
- Volume
- 1
- Issue
- 3
- Pages
- 69-69
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC5450946
- OpenAlex
- W2587990010
- Cited by
- 159
- References
- 80
- Citations by year
- 2026: 11 · 2025: 13 · 2024: 18 · 2023: 22 · 2022: 10 · 2021: 22 · 2020: 27 · 2019: 18 · 2018: 13 · 2017: 5
- FWCI
- 11.62
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- ResearchWorks at the University of Washington (University of Washington) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institute of Mental Health (R01MH101221)
- National Human Genome Research Institute (U41HG007635, R25HG007153, R01HG002385)
- National Institute of Neurological Disorders and Stroke (R00NS083627)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (T32HD007396, U54HD079125)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- segmental duplication, human evolution, gene family expansion, copy number variation, mRNA splicing, genomic instability
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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