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New genes as drivers of phenotypic evolution
Open accessAbstract
During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution.
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“These data suggest extensive gene gain in cell lineages associated with early segregation of developmental potential leading to ctenophore-specific traits in structures controlling feeding, locomotion and integrative functions; a finding consistent with proposed 'orphan' genes contributing to variation in early development and evolution of novelties 22,23 .”
From The ctenophore genome and the evolutionary origins of neural systems (2014) · cites this paper as [22]
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Cites
Targeted gene expression as a means of altering cell fates and generating dominant phenotypes
Brand, A. H., & Perrimon, N. (1993) · Development · doi:10.1242/dev.118.2.401 · Cited by 9,510
Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833
Lethality and centrality in protein networks
Jeong, H., Mason, S., Barabási, A., & Oltvai, Z. (2001) · Nature · doi:10.1038/35075138 · Cited by 5,327
(1977) · Cited by 4,052
Post-embryonic cell lineages of the nematode, Caenorhabditis elegans
Sulston, J. E., & Horvitz, H. R. (1977) · Developmental Biology · doi:10.1016/0012-1606(77)90158-0 · Cited by 3,479
Kumarasamy, K. K., Toleman, M. A., Walsh, T. R., Bagaria, J., Butt, F., Balakrishnan, R., Chaudhary, U., Doumith, M., Giske, C. G., Irfan, S., et al. (2010) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(10)70143-2 · Cited by 2,922
King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815
Løvtrup, S., & Gould, S. J. (1978) · Systematic Zoology · doi:10.2307/2412825 · Cited by 2,359
The cytoplasmic body component TRIM5α restricts HIV-1 infection in Old World monkeys
Stremlau, M. H., Owens, C. M., Perron, M. J., Kießling, M. K., Autissier, P., & Sodroski, J. (2004) · Nature · doi:10.1038/nature02343 · Cited by 1,810
Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis
Mi, S., Lee, X., Li, X., Veldman, G. M., Finnerty, H. F., Collins‐Racie, L. A., LaVallie, E. R., Tang, X.-Y., Edouard, P., Howes, S., et al. (2000) · Nature · doi:10.1038/35001608 · Cited by 1,711
Research works printed but not linked: 2
- Coyne, J. A. & Orr, H. A. Speciation (Sinauer Associates Sunderland, 2004).
- Strausfeld, N. J. & Li, Y. Representation of the calyces in the medial and vertical lobes of cockroach mushroom bodies. J. Comp. Neurol. 409, 626–646 (1999). · DOI
Cited by
Sorted by citations
Items 401–429 of 429
Song, J., Qi, Z., He, C. L., Luo, G., Yuan, B., Xiao, S., Yang, Y., Wang, F., Yè, G., Fang, Q., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2512820122 · Cited by 1
“Gene duplication is a fundamental mechanism for expanding gene families ( 1 , 2 ), involving either segments of genes or entire genomes ( 3 – 5 ).”
Evolutionary and functional dynamics of chimeric pseudogenes (φgenes)Preprint
Jadhav, A. R., Sahoo, S., Kuber, Y. L., Varanwal, A., Tanwar, K., Palwankar, S., Chatrasal, G., Mali, A. M., & Bapat, S. (2025) · bioRxiv · doi:10.1101/2025.10.01.679709
Kong, X., Liu, S., Tan, L., Liu, Y., Lin, Z., & Xue, Q. (2025) · Marine Biotechnology · doi:10.1007/s10126-025-10536-8
“…shell formation and identifies potential candidate genes for the development of fast-growing oyster germplasm. gene may retain functions of the parental genes or undergo neofunctionalization under natural selection, acquiring new phenotypes not present in either progenitor (Chen et al. 2013).”
Evolution of life: quantum mechanical interpretations
Ashrafuzzaman, M. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-36368-9.00005-6
(2025) · Elsevier eBooks · doi:10.1016/b978-0-443-15428-7.16001-5
Niu, H., Pang, Y., Xie, L., Yu, Q., 沈玉帮, Li, J., & Xu, X. (2023) · Figshare · doi:10.6084/m9.figshare.22602716
Niu, H., Pang, Y., Xie, L., Yu, Q., 沈玉帮, Li, J., & Xu, X. (2023) · Figshare · doi:10.6084/m9.figshare.22602713
Additional file 1 of Transcriptional and post-transcriptional regulation of young genes in plants
Raxwal, V. K., Singh, S., Agarwal, M., & Říha, K. (2022) · Figshare · doi:10.6084/m9.figshare.20033136
Brohard, S., Frouin, V., Meyer, V., Chalabi, S., Deleuze, J., Floch, É. L., & Battail, C. (2021) · Figshare · doi:10.6084/m9.figshare.14462545
Lal, D., May, P., Pérez‐Palma, E., Samocha, K. E., Kosmicki, J. A., Robinson, E., Møller, R. S., Krause, R., Nürnberg, P., Weckhuysen, S., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11999259
Additional file 2 of Promoter evolution of mammalian gene duplicates
Fraimovitch, E., & Hagai, T. (2024) · Figshare · doi:10.6084/m9.figshare.26582084
Additional file 1 of Promoter evolution of mammalian gene duplicates
Fraimovitch, E., & Hagai, T. (2024) · Figshare · doi:10.6084/m9.figshare.26582081
Tassios, E., de Leuw, J., Nikolaou, C., Kupczok, A., & Vakirlis, N. (2025) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf324 · Cited by 2
“Orphans matter because they frequently underlie unique phenotypic traits (Chen et al. 2013, Khalturin et al. 2009).”
Evolutionary genomic basis of mimicry diversity of Epicopeiidae moths
Li, H., Zhang, Y., Tian, X., Xu, X., Wang, M., Wang, H., Liang, D., & Zhang, P. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag060
“Adaptive evolution of protein-coding genes is a major force driving phenotypic innovation (Chen et al. 2013; Gibert et al. 2019).”
Herráez-Pérez, A., & Zardoya, R. (2026) · BMC Genomics · doi:10.1186/s12864-026-12745-4 · Cited by 1
Kergourlay, V. (2014) · theses.fr (ABES) · doi:10.70675/e1e28f71z48f6z44faz8257z2e125bed3a19
Pan-génome du riz africain cultivé Oryza glaberrima et son ancêtre sauvage Oryza barthii
Monat, C. (2016) · theses.fr (ABES) · doi:10.70675/b06a7cd9z9852z4098z8e4bz49b5437fe1c9
Jadhav, A. R., Sahoo, S., Kuber, Y. L., Hatwar, K., Varanwal, A., Tanwar, K., Palwankar, S., Chatrasal, G., Mali, A. M., & Bapat, S. A. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag375
Chen, Z.-F., Sun, W.-H., Su, L.-Y., Tan, G., Lu, Y., Luo, L., Li, W., Li, C.-X., Tan, Z.-W., Zhao, Z., et al. (2026) · Horticulture Research · doi:10.1093/hr/uhag214
“Lineage diversification and phenotypic innovation in plants often reflect gene family expansion and contraction [ 38].”
A recently evolved Nodulin recruited by NIN for root hair rhizobial infection in Medicago truncatula
Wang, R., Wu, W., Zhang, H., Chai, Y., Wang, H., Liu, Z., Deng, J., Zhao, L., Ji, C., & Liu, C. (2026) · New Phytologist · doi:10.1111/nph.71452
“It is thought that formation of new genes during evolution is an important driver for functional innovation and newly evolved genes have a fundamental role in phenotypic complexity (Innan & Kondrashov, 2010; Chen et al ., 2013; Xia et al ., 2025).”
Saleem, A., Jiang, Y., Xue, J., Cui, Y., Zhou, C., Liu, F., Liu, Y., Yan, Y., & Yang, R. (2026) · Frontiers in Genetics · doi:10.3389/fgene.2026.1856601
“This exploratory observation aligns with emerging paradigms wherein regulatory integration, rather than expression magnitude, may contribute to functional incorporation of young genes into biological networks (Cai and Petrov, 2010; Chen et al., 2013).”
Rapid evolution and functional divergence of the monkeyflower Mimulus lewisii telomerasePreprint
Samo, N., Nguyen, L., Kumawat, S., & Choi, J. Y. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.05.739867
“These adaptive changes have often resulted in functional and phenotypic novelty and many of these examples have become textbook cases of Darwinian evolution (3–5).”
Evolutionary origin of a new gene drives root growth in one desert poplar
Gao, C., Bai, X., Wei, Q., Shao, X., Zhang, P., Zhang, Q., Wang, J., Wan, D., & Liu, J. (2026) · New Phytologist · doi:10.1111/nph.71511
“The emergence of new genes is a major source of evolutionary innovation and contributes to phenotypic and physiological diver-sification across taxa (Long et al ., 2003; Kaessmann, 2010; Chen et al ., 2013, 2023; Muzaffar et al ., 2024; Jin et al ., 2025).”
López‐Pérez, M., & Fernández, F. J. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7382207
TED1 Promotes the Assembly of SCF D3 ‐D14‐D53 to Reinforce Strigolactone Signaling in Rice
Luo, S., Wu, C., Feng, M., Luo, W., Miao, R., Qian, J., Wang, F., Zhou, C., Liu, B., Shao, J., et al. (2026) · Advanced Science · doi:10.1002/advs.77062
“…with plant-specific subunits like CHROMATIN REMODELING 11/17(CHR11/17), METHYL-CPG-BINDING DOMAIN 9 (MBD9), and TUMOR NECROSIS FACTOR RECEPTOR-ASSOCIATED FACTOR 1A/B (TRA1A/B), forming unique complex modules to regulate flowering time, photomorphogenesis, and stress responses [ 55, 78–80 ].”
De novo genes in plants: Origins, mechanisms, and functional implications
Zuo, Z., Chen, R., Lu, Y., & Yang, Z. (2026) · Plant Communications · doi:10.1016/j.xplc.2026.102098
Cao, Y., Zhang, W., Bi, J., Wei, X., Xiong, X., & Liu, X. (2026) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2026.102031
Zhao, K., Guo, Y., Li, J., Jia, Y., Guo, L., Li, H., Wang, J., Wang, S., Chen, Q., Zhou, H., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2602105123
Yao, S., Peng, Z., Liu, G., Huang, K., & Wan, C. (2026) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6c00665
Metadata
- Authors
- Chen, S., Krinsky, B. H., & Long, M.
- Affiliations
- University of Chicago (US)
- Corresponding author
- Long, Manyuan
- Venue
- Nature Reviews Genetics
- Published
- 2013-08-16
- Volume
- 14
- Issue
- 9
- Pages
- 645-660
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC4236023
- OpenAlex
- W2057844822
- Cited by
- 428
- References
- 137
- Citations by year
- 2026: 21 · 2025: 34 · 2024: 64 · 2023: 46 · 2022: 30 · 2021: 28 · 2020: 30 · 2019: 41 · 2018: 22 · 2017: 26 · 2016: 36 · 2015: 17 · 2014: 27 · 2013: 6
- FWCI
- 3.06
- Type
- journal article
- Language
- en
- Update notices
- erratum (2013-08-22)
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- U.S. Public Health Service (1R01100768‑01A1)
- National Institute of General Medical Sciences (R01GM100768, T32GM007197)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- neofunctionalization, novel genes, gene birth, phenotypic evolution, genome evolution, gene duplication, developmental processes, reproduction, brain function, behavior, biodiversity, functional redundancy
- MeSH terms
- Animals, Behavior, Animal, Brain, Biological Evolution, Gene Expression Regulation, Genes, Humans, Phenotype, Plants, Reproduction, Sex Characteristics, Species Specificity, Evolution, Molecular, Biodiversity
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