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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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Large tandem duplications affect gene expression, 3D organization, and plant–pathogen responsePreprint
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“Althoughwe donot haveevidence concerning their potential ability to be translated or if the resultant protein would be functional, it is tempting to speculate that TDDO-mediated chimeric genes can lead to gene novelty as previously described (Chen et al. 2013).”
A de novo evolved gene in the house mouse regulates female pregnancy cycles
Xie, C., Bekpen, C., Künzel, S., Keshavarz, M., Krebs-Wheaton, R., Škrabar, N., Ullrich, K. K., & Tautz, D. (2019) · eLife · doi:10.7554/elife.44392 · Cited by 49
“There has so far been much focus on de novo genes and other new genes to have male-biased expression and to affect male fertility (Chen et al., 2013; Ellegren and Parsch, 2007; Heinen et al., 2009; Kaessmann, 2010; Long et al., 2013; Reinhardt et al., 2013; Zhao et al., 2014).”
BackgroundLateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites
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“Introduction Novel genes derived from a number of processes; including gene duplications, de novo gene formation, and LGT; contribute to genomic and phenotypic plasticity and can drive adaptive evolution [1].”
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“New genes may arise from pre-existing gene structures through gene duplication, gene fusion, and horizontal gene transfer or may arise de novo from previously noncoding regions (Chen et al. 2013).”
High rate of translocation-based gene birth on the Drosophila Y chromosome
Tobler, R., Nolte, V., & Schlötterer, C. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706502114 · Cited by 43
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“Changes in the gene essentiality are indispensable drivers of organismal evolution (Chen et al. 2013; Carelli et al. PDZ domains network signalling interactions 165 2016).”
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“7,8 Furthermore, it has been shown that novel genes can become essential in a short time span in Drosophila melanogaster .”
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“New genes have been shown to be able to fulfil crucial roles in biological processes after relatively short evolutionary times for different lineages, highlighting their potential importance in biological transitions [14].”
BackgroundRetrotransposons as Drivers of Mammalian Brain Evolution
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“Independently from the mechanisms of their generation, new gene copies have great potential for neofunctionalization favoring phenotypic evolution [79], a property that, contrary to what has been prevailingly thought, is likely to also apply to pseudogenes and retropseudogenes [80].”
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“There is good evidence that amplifications have contributed to the emergence of many different novel phenotypes, from proteins [9,28] to morphologies and body plans [6,29,30] in many taxonomic groups [31–33].”
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“According to Chen et al. (2013), genetic variations are generated in several ways, such as mutation and new gene origination, in addition to meiotic recombination.”
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“In flowering plants, the expansion and/or contraction of gene families have been well documented as crucial driving forces in lineage splitting and function diversifying [84].”
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“Furthermore, both within and between phyla there is evident topology shuffling within key developmental gene networks, especially in terms of co-option of novel or external genes into these regulatory modules, thereby creating novel developmental mechanisms via the cell-to-tissue-level morphogenetic processes they inf…”
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“to reveal the functional relevance of novel genes as drivers of this phenotypic patterning (42).”
BackgroundStress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts
Doughty, T. W., Domenzain, I., Millán-Oropeza, A., Montini, N., de Groot, P. A., Pereira, R., Nielsen, J., Henry, C., Daran, J.-M. G., Siewers, V., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16073-3 · Cited by 37
Dual pathogenicity island transfer by piggybacking lateral transduction
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Rapid functional and evolutionary changes follow gene duplication in yeast
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Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks
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“2015) and otherwise rich substrate for the selection of novel traits (Kaessmann 2010; Tautz and Domazet-Lo so 2011; Chen et al. 2013).”
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“At the other end of the spectrum, there is a growing interest in novel taxonomically restricted genes that are free to evolve new functions without suffering from the constraining effect of pleiotropy (Chen et al., 2013).”
BackgroundMethodInfluentialWu, D., Wang, X., Li, Y., Zeng, L., Irwin, D. M., & Zhang, Y. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu206 · Cited by 36
“New genes, including both duplicated and de novo genes, show a male or testis-bias in expression in animals, and many of them have biological functions associated with reproduction (Kaessmann 2010; Chen et al. 2013; Long et al. 2013).”
BackgroundEvolution of genetic mechanisms regulating cortical neurogenesis
Espinós, A., Ortuño, E. F., Negri, E., & Borrell, V. (2022) · Developmental Neurobiology · doi:10.1002/dneu.22891 · Cited by 38
“Changes that alter the genetic repertoire can be achieved in several ways: alteration of gene copy number with a dosage-dependent effect (Heide et al., 2017), generation of new genes, or mutation of already existing ones, the latter two resulting in neofunctionalization (Chen et al., 2013).”
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“…HSP70 genes play a vital role in maintaining cellular homeostasis to defend against abiotic and biotic stresses (Piano et al., 2002; Franzellitti and Fabbri, 2005; Liu et al., 2014; Cheng et al., 2016; Nie et al., 2017; Nie et al., 2018; Cheng et al., 2019; Clark et al., 2021; Hu et al., 2022).”
BackgroundGene fusion as an important mechanism to generate new genes in the genus Oryza
Zhou, Y., Zhang, C., Zhang, L., Ye, Q., Liu, N., Wang, M., Long, G., Fan, W., Long, M., & Wing, R. A. (2022) · Genome biology · doi:10.1186/s13059-022-02696-w · Cited by 37
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Genomic sources of phenotypic novelty in the evolution of eusociality in insects
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“Novel genes, or genes with no known homology, play an important role in evolutionary novelty as they evolve new molecular functions and cellular localizations, contribute to stress resistance, and can influence development [69,70].”
BackgroundFinck, J., Berdan, E. L., Mayer, F., Ronacher, B., & Geiselhardt, S. (2016) · Scientific Reports · doi:10.1038/srep33695 · Cited by 37
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“A it is generally agreed that the emergence of new, species-specific genes helped drive the phenotypic evolution of humans, just as they have done in other species (1, 2), there is a lack of direct evidence that links these genes to normal human biology and/or to the onset of traits that might be uniquely human in dis…”
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“Natural chimeric genes arise from the fusion of existing sequence elements to create a new open reading frame (ORF) that contributes to novel molecular and cellular functions (Chen et al., 2013; Ding et al., 2012; Long and Langley, 1993).”
BackgroundOrphans and new gene origination, a structural and evolutionary perspective
Light, S., Basile, W., & Elofsson, A. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.05.006 · Cited by 37
“Most of previous reviews have dwelled on recently duplicated genes [34 ,35,36].”
BackgroundOn the Regulatory Evolution of New Genes Throughout Their Life History
Zhang, J., & Zhou, Q. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy206 · Cited by 36
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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