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Chen J, Landback P, Arsala D, Guzzetta A, Xia S, Atlas J, Sosa D, Zhang YE, Cheng J, Shen B, Long M. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567139. [PMID: 38045239 PMCID: PMC10690195 DOI: 10.1101/2023.11.14.567139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are genetic novelties pivotal in mammalian evolution. Their phenotypic impacts and evolutionary pattern over time, however, remain elusive in humans due to the technical and ethical complexities in functional studies. By combining human gene age dating and Mendelian disease phenotyping, our research reveals a gradual increase in disease gene proportions with gene age. Logistic regression modeling indicates that this increase could be related to longer protein lengths and higher burdens of deleterious de novo germline variants (DNVs) for older genes. We also find a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (~0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Notably, young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit disease-related functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. We further reveal a logistic growth pattern of pleiotropy over evolutionary time, indicating a diminishing marginal growth of new functions for older genes due to intensifying selective constraints over time. We propose a "pleiotropy-barrier" model that delineates higher potentials of phenotypic innovation for young genes than for older genes, a process subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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Affiliation(s)
- Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Patrick Landback
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Alexander Guzzetta
- Department of Pathology, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Jared Atlas
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Yong E. Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingqiu Cheng
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
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Chen J. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. RESEARCH SQUARE 2023:rs.3.rs-3632644. [PMID: 38045389 PMCID: PMC10690325 DOI: 10.21203/rs.3.rs-3632644/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are structural novelties pivotal in mammalian evolution. Their phenotypic impact on humans, however, remains elusive due to the technical and ethical complexities in functional studies. Through combining gene age dating with Mendelian disease phenotyping, our research reveals that new genes associated with disease phenotypes steadily integrate into the human genome at a rate of ~ 0.07% every million years over macroevolutionary timescales. Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures between young and old genes. Notably, young genes show significant enrichment in the male reproductive system, indicating strong sexual selection. Young genes also exhibit functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, bipedal locomotion, and color vision. Our findings further reveal increasing levels of pleiotropy over evolutionary time, which accompanies stronger selective constraints. We propose a "pleiotropy-barrier" model that delineates different potentials for phenotypic innovation between young and older genes subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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Poo MM. Editorial of non-human primate research. Natl Sci Rev 2023; 10:nwad326. [PMID: 38179259 PMCID: PMC10766141 DOI: 10.1093/nsr/nwad326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Affiliation(s)
- Mu-ming Poo
- Scientific Director, CAS Center for Excellence for Brain Science and Intelligence TechnologyChina
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