New genes as drivers of phenotypic evolution
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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.
“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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Retrogenes Reveal the Direction of Sex-Chromosome Evolution in Mosquitoes
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Network rewiring is an important mechanism of gene essentiality change
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Rapidly Evolving Genes and Genetic Systems
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Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome
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Genetic characterization of ms (3) K81, a paternal effect gene of Drosophila melanogaster.
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Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition
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Retrogenes Moved Out of the Z Chromosome in the Silkworm
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Maternal activation of gap genes in the hover fly Episyrphus
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bicoid occurrence and Bicoid‐dependent hunchback regulation in lower cyclorrhaphan flies
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Demasculinization of the Anopheles gambiae X chromosome
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Self-citationFrequent Recent Origination of Brain Genes Shaped the Evolution of Foraging Behavior in Drosophila
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Role of Testis-Specific Gene Expression in Sex-Chromosome Evolution of Anopheles gambiae
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Drosophila melanogaster p24 trafficking proteins have vital roles in development and reproduction
Saleem, S., Schwedes, C. C., Ellis, L. L., Grady, S. T., Adams, R. L., Johnson, N., Whittington, J. R., & Carney, G. E. (2012) · Mechanisms of Development · doi:10.1016/j.mod.2012.04.002 · Cited by 23 · see citing works
The evolutionary history of the SAL1 gene family in eutherian mammals
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Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila
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A role for convergent evolution in the secretory life of cells
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Evolutionary interactions between sex chromosomes and autosomes
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The ctenophore genome and the evolutionary origins of neural systems
Moroz, L. L., Kocot, K. M., Citarella, M. R., Dosung, S., Norekian, T. P., Povolotskaya, I. S., Grigorenko, A. P., Dailey, C., Berezikov, E., Buckley, K. M., et al. (2014) · Nature · doi:10.1038/nature13400 · Cited by 716 · see citing works
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The impact of transposable elements in adaptive evolution
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“…et al., 2009; Figure 4), fruit flies (Zhang, Dean, Brunet, & Long, 2004), apes and human (Baertsch, Diekhans, Kent, Haussler, & Brosius, 2008; Rosso et al., 2008), Arabidopsis (Matsuno et al., 2009) and many other organisms (Carelli et al., 2016; Chen et al., 2013; Kubiak & Makałowska, 2017).”
New Gene Evolution: Little Did We Know
Long, M., VanKuren, N. W., Chen, S., & Vibranovski, M. D. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133301 · Cited by 307 · see citing works
“However, studies in the past decade have found numerous young genes with important, and sometimes essential, functions at the molecular, cellular, and individual level (27).”
BackgroundSelf-citationOss, S. B. V., & Carvunis, A. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008160 · Cited by 302 · see citing works
Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies
Patalano, S., Vlasova, A. V., Wyatt, C. D. R., Ewels, P., Ferreira, F. C., Ferreira, P. G., Asher, C. L., Jurkowski, T. P., Segonds-Pichon, A., Bachman, M., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1515937112 · Cited by 239 · see citing works
“There is a debate over the relative roles for core sets of conserved genes (42–48) and taxon-restricted genes (TRGs) (5, 44, 47, 49, 50) in the evolution of convergent phenotypes (7, 44, 46).”
BackgroundHarpur, B., Kent, C. F., Molodtsova, D., Lebon, J., Alqarni, A., Owayss, A., & Zayed, A. (2014) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1315506111 · Cited by 229 · see citing works
“Taxonomically restricted genes (TRGs) have been the subject of recent attention because they are predicted to be drivers of phenotypic evolution (30).”
BackgroundCoregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals
Lan, X., & Pritchard, J. K. (2016) · Science · doi:10.1126/science.aad8411 · Cited by 189 · see citing works
microRNAs in the Same Clusters Evolve to Coordinately Regulate Functionally Related Genes
Wang, Y., Luo, J., Zhang, H., & Lü, J. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw089 · Cited by 187 · see citing works
“Similar to protein-coding genes, the origin of young miRNA genes is usually achieved by duplication (Kim and Nam 2006; Bartel 2009; Marco et al. 2013) or de novo formation (Lu, Shen, et al. 2008; Chen et al. 2013; Long et al. 2013; Marco et al. 2013; Meunier et al. 2013).”
Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development
Paralkar, V. R., Mishra, T., Luan, J. Y., Yao, Y., Kossenkov, A. V., Anderson, S. M., Dunagin, M. C., Pimkin, M., Gore, M., Sun, D. K., et al. (2014) · Blood · doi:10.1182/blood-2013-12-544494 · Cited by 184 · see citing works
Climbing the social ladder: the molecular evolution of sociality
Rehan, S. M., & Toth, A. L. (2015) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2015.05.004 · Cited by 180 · see citing works
Divergent Transcription: A Driving Force for New Gene Origination?
Wu, X., & Sharp, P. A. (2013) · Cell · doi:10.1016/j.cell.2013.10.048 · Cited by 171 · see citing works
“Tandem duplication, retroposition, and recombination of existing genes or gene fragments are the major mechanisms for new gene origination (Chen et al., 2013; Long et al., 2013).”
Jin, J., He, K., Tang, X., Li, Z., Lv, L., Zhao, Y., Luo, J., & Gao, G. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv058 · Cited by 165 · see citing works
“Novel genes can rapidly integrate into existing networks and effectively drive the evolution of phenotypes (Chen et al. 2010, 2013).”
BackgroundWitt, E., Benjamin, S., Svetec, N., & Zhao, L. (2019) · eLife · doi:10.7554/elife.47138 · Cited by 160 · see citing works
“Natural selection may not only preserve testis-bias and function of novel genes, but also shape expression and function in somatic tissues for others (Chen et al., 2010; Chen et al., 2013; Zhou et al., 2008).”
BackgroundShang, J., Tian, J., Cheng, H., Yan, Q., Li, L., Jamal, A., Xu, Z., Xiang, L., Saski, C. A., Jin, S., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02088-y · Cited by 152 · see citing works
Evolutionary origin and diversification of epidermal barrier proteins in amniotes
Strasser, B., Mlitz, V., Hermann, M., Rice, R. H., Eigenheer, R. A., Alibardi, L., Tschachler, E., & Eckhart, L. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu251 · Cited by 135 · see citing works
“Although any model for the evolution of EDC genes must include speculative elements, a key role of gene duplications and fusions, as demonstrated for other cases of gene origin (Long et al. 2003; Chen et al. 2013) is supported by the results of the present study.”
ResultThe life history of retrocopies illuminates the evolution of new mammalian genesPreprint
Carelli, F., Hayakawa, T., Go, Y., Imai, H., Warnefors, M., & Kaessmann, H. (2016) · Genome Research · doi:10.1101/gr.198473.115 · Cited by 113 · see citing works
“In addition tomutations that alter sequences or activities of preexisting genes (Necsulea and Kaessmann 2014), new genes with novel functions are thought to have substantially contributed to phenotypic evolution (Kaessmann 2010; Chen et al. 2013).”
BackgroundThe genomic architecture and molecular evolution of ant odorant receptorsPreprint
McKenzie, S. K., & Kronauer, D. J. C. (2018) · Genome Research · doi:10.1101/gr.237123.118 · Cited by 119 · see citing works
“New genes provide abundant raw material for evolution to act upon and are likely instrumental in the phenotypic adaptation of organisms (Long et al. 2003, 2013; Demuth and Hahn 2009; Chen et al. 2013).”
BackgroundSilva, C. D., Zamperin, G., Ferrarini, A., Minio, A., Molin, A. D., Venturini, L., Buson, G., Tononi, P., Avanzato, C., Zago, E. D., et al. (2013) · The Plant Cell · doi:10.1105/tpc.113.118810 · Cited by 115 · see citing works
“Although genes that are not conserved in a certain species are often assumed to be dispensable or redundant for development or survival, there is now evidence to indicate that such genes may have a strong impact on phenotype (Chen et al., 2013); therefore, we named them varietal genes.”
BackgroundLiu, J., Shi, C., Shi, C., Li, W., Zhang, Q., Zhang, Y., Li, K., Lü, H., Shi, C., Zhu, S., et al. (2019) · Molecular Plant · doi:10.1016/j.molp.2019.10.017 · Cited by 115 · see citing works
Yang, L., Wang, Y., Zhang, Z., & He, S. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu279 · Cited by 106 · see citing works
“Orphan Genes in G. pachycheilus In the past few years, substantial progress has demonstrated that lineage-specific new genes can rapidly evolve indispensable biological roles and make a contribution to lineage-specific phenotype and adaptation (Chen et al. 2013).”
BackgroundThe evolution of duplicate gene expression in mammalian organsPreprint
Guschanski, K., Warnefors, M., & Kaessmann, H. (2017) · Genome Research · doi:10.1101/gr.215566.116 · Cited by 105 · see citing works
Functional Proteins from Short Peptides: Dayhoff's Hypothesis Turns 50
Romero, M. L. R., Rabin, A., & Tawfik, D. S. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201609977 · Cited by 103 · see citing works
Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers
Liang, M., Chen, W., LaFountain, A. M., Liu, Y., Peng, F., Xia, R., Bradshaw, H. D., & Yuan, Y. (2023) · Science · doi:10.1126/science.adf1323 · Cited by 102 · see citing works
New genes drive the evolution of gene interaction networks in the human and mouse genomes
Zhang, W., Landback, P., Gschwend, A. R., Shen, B., & Long, M. (2015) · Genome biology · doi:10.1186/s13059-015-0772-4 · Cited by 98 · see citing works
“New genes provide important genetic novelties responsible for biological diversity in organisms [1], and are often the genetic basis for lineage- or species-specific components in important biological processes and structures [2, 3].”
BackgroundSelf-citationDe Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints
Smock, R. G., Yadid, I., Dym, O., Clarke, J., & Tawfik, D. S. (2016) · Cell · doi:10.1016/j.cell.2015.12.024 · Cited by 95 · see citing works
“The birth of new proteins is essential to the diversity of life, particularly in cellular signaling and immunity (Chen et al., 2013).”
BackgroundJasper, W. C., Linksvayer, T. A., Atallah, J., Friedman, D., Chiu, J. C., & Johnson, B. R. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu292 · Cited by 92 · see citing works
“Highly Expressed TRGs To avoid analyzing TRGs that are spurious ORFs (DomazetLoso and Tautz 2003; Chen et al. 2013), or simply genes of minor importance, we began by identifying and analyzing all those TRGs that are highly expressed in at least one of the ten tissues.”
BackgroundThe placenta as a model for understanding the origin and evolution of vertebrate organs
Griffith, O. W., & Wagner, G. P. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0072 · Cited by 91 · see citing works
Mechanisms of protein evolution
Jayaraman, V., Toledo‐Patiño, S., Noda‐García, L., & Laurino, P. (2022) · Protein Science · doi:10.1002/pro.4362 · Cited by 85 · see citing works
“65,121–123 Such segments might also comprise the starting material for novel proteins (Figure 3c, d).(124,125) It is important to highlight the fact that, although phenotypic mutations are not heritable as such, the potential to make them can be.”
BackgroundGene coevolution and regulation lock cyclic plant defence peptides to their targets
Gilding, E. K., Jackson, M. A., Poth, A. G., Henriques, S. T., Prentis, P. J., Mahatmanto, T., & Craik, D. J. (2015) · New Phytologist · doi:10.1111/nph.13789 · Cited by 89 · see citing works
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“19, 20 and Supplementary Method 9).”
Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N. M., Zhu, W. Z., Wang, Z., et al. (2019) · National Science Review · doi:10.1093/nsr/nwz064 · Cited by 82 · see citing works
“Genome duplication has led to the duplication of HOX genes [22], as well as the emergence of many new genes [51].”
BackgroundMolecular and cellular evolution of corticogenesis in amniotes
Cárdenas, A., & Borrell, V. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-019-03315-x · Cited by 82 · see citing works
Oppenheim, S. J., Baker, R. H., Simon, S., & DeSalle, R. (2014) · Insect Molecular Biology · doi:10.1111/imb.12154 · Cited by 81 · see citing works
“Novel genes can arise in many ways (e.g. gene duplication, lateral gene transfer, de novo gene creation from noncoding regions of DNA) and may rapidly acquire adaptive functional roles (Ranz & Parsch, 2012; Chen et al., 2013).”
BackgroundNew Insights on Intermediary Metabolism for a Better Understanding of Nutrition in Teleosts
Panserat, S., Marandel, L., Seiliez, I., & Cassy, S. (2018) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-115250 · Cited by 81 · see citing works
De novo genes with an lncRNA origin encode unique human brain developmental functionality
An, N. A., Zhang, J., Mo, F., Luan, X., Tian, L., Shen, Q. S., Li, X., Li, C., Zhou, F., Zhang, B., et al. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01925-6 · Cited by 80 · see citing works
Identification of pathogenic variant enriched regions across genes and gene familiesPreprint
Pérez‐Palma, E., May, P., Iqbal, S., Niestroj, L., Du, J., Heyne, H., Lal, J. C., O’Donnell‐Luria, A., Nürnberg, P., Palotie, A. V., et al. (2019) · Genome Research · doi:10.1101/gr.252601.119 · Cited by 76 · see citing works
A Zea genus-specific micropeptide controls kernel dehydration in maize
Yu, Y., Li, W., Liu, Y., Liu, Y., Zhang, Q., Ouyang, Y., Wenya, D., Xue, Y., Zou, Y., Yan, J., et al. (2024) · Cell · doi:10.1016/j.cell.2024.10.030 · Cited by 73 · see citing works
Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulationPreprint
Werner, M. S., Sieriebriennikov, B., Prabh, N., Loschko, T., Lanz, C., & Sommer, R. J. (2018) · Genome Research · doi:10.1101/gr.234872.118 · Cited by 72 · see citing works
“For the increasing number of identified new genesthatprovide important biological function (BurkiandKaessmann2004;Caietal.2008;Rossoetal.2008;Chen et al. 2010, 2013b; Reinhardt et al. 2013; Mayer et al. 2015; Santos et al. 2017), the evolutionary path from origin to integration into gene networks…”
Fukushima, K., & Pollock, D. D. (2020) · Nature Communications · doi:10.1038/s41467-020-18090-8 · Cited by 70 · see citing works
New genes often acquire male-specific functions but rarely become essential in DrosophilaPreprint
Kondo, S., Vedanayagam, J., Mohammed, J., Eizadshenass, S., Kan, L., Pang, N., Aradhya, R., Siepel, A. C., Steinhauer, J., & Lai, E. C. (2017) · Genes & Development · doi:10.1101/gad.303131.117 · Cited by 69 · see citing works
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Wang, L., Lei, T., Han, G., Yue, J., Zhang, X., Yang, Q., Ruan, H., Gu, C., Zhang, Q., Qian, T., et al. (2021) · The Plant Journal · doi:10.1111/tpj.15394 · Cited by 68 · see citing works
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New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos
Jin, G., Ma, P., Wu, X., Gu, L., Long, M., Zhang, C., & Li, D.-Z. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab288 · Cited by 63 · see citing works
“We know little about the genetic basis underlying the appearance of phenotypic novelties, despite a link between the innovations and genomic novelty in general and new genes in particular that has long been hypothesized (Chen et al. 2013; Erwin 2021).”
BackgroundSelf-citationTowards reconstructing the ancestral brain gene-network regulating caste differentiation in ants
Qiu, B., Larsen, R. S., Chang, N., Wang, J., Boomsma, J. J., & Zhang, G. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0689-x · Cited by 64 · see citing works
Phytochemical variation in treetops: causes and consequences for tree-insect herbivore interactions
Lämke, J., & Unsicker, S. B. (2018) · Oecologia · doi:10.1007/s00442-018-4087-5 · Cited by 64 · see citing works
The importance of genomic novelty in social evolution
Sumner, S. (2013) · Molecular Ecology · doi:10.1111/mec.12580 · Cited by 63 · see citing works
“Such analyses are revealing a general role for novel (e.g. taxonomically restricted) genes in phenotypic innovations across the animal kingdom (Chen et al. 2013).”
BackgroundInfluentialThe goddard and saturn genes are essential for Drosophila male fertility and may have arisen de novo
Gubala, A. M., Schmitz, J. F., Kearns, M. J., Vinh, T. T., Bornberg‐Bauer, E., Wolfner, M. F., & Findlay, G. D. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx057 · Cited by 63 · see citing works
“Likewise, it is possible these genes arose through horizontal gene transfer followed by divergence, rather than from noncoding sequence, since this is another source for newly evolved genes (Chen et al. 2013).”
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“…enabled the exploration of evolutionary developmental (evo-devo) theories as to how highly complex behavioral traits may emerge from a genetic functional architecture, which can be at once widely conserved (Rittschof et al. 2014) and pleiotropically constrained (Carroll 2008; Chen et al. 2013).”
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“A recent survey of the functional roles of new genes across various taxa offers evidence for the rapid recruitment of new genes into gene networks underlying a wide range of phenotypes including reproduction, behavior and development (Chen et al. 2013).”
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“LINEs are recognized as a source of gene duplications and implicated in genetic novelty where duplicated genes can evolve new functions (38, 77).”
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“It is expected that through the course of evolution there will have arisen both genetic and structural novelties, as well as reversals and losses (Chen et al., 2013; Jenner, 2004), the latter impossible to code in relational trees based on morphological characters (Strausfeld and Andrew, 2011).”
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“Among settings and conditions conducive to gene emergence and rapid gene evolution (Chen et al., 2013), the testis is a particularly facile environment (Zhao et al., 2014).”
Adaptive evolution of testis-specific, recently evolved, clustered miRNAs inDrosophila
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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 48 · see citing works
“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].”
BackgroundDurand, É., Gagnon‐Arsenault, I., Hallin, J., Hatin, I., Dubé, A. K., Nielly‐Thibault, L., Namy, O., & Landry, C. R. (2019) · Genome Research · doi:10.1101/gr.239822.118 · Cited by 46 · see citing works
“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 · see citing works
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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).”
Computational Identification of Novel Genes: Current and Future Perspectives
Klasberg, S., Bitard‐Feildel, T., & Mallet, L. (2016) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s39950 · Cited by 43 · see citing works
“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].”
BackgroundExperimental Evolution of Innovation and Novelty
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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.”
BackgroundYue, J., Wang, R., Ma, X., Liu, J., Lu, X., Thakar, S. B., An, N., Liu, J., Xia, E., & Liu, Y. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.03.022 · Cited by 40 · see citing works
“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].”
BackgroundStudying evolution of the primary body axis in vivo and in vitro
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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…”
BackgroundSingh, P. P., Reeves, G. A., Contrepois, K., Papsdorf, K., Miklas, J. W., Ellenberger, M., Hu, C., Snyder, M. P., & Brunet, A. (2024) · Cell · doi:10.1016/j.cell.2024.04.048 · Cited by 40 · see citing works
Transcriptome analysis reveals rod/cone photoreceptor specific signatures across mammalian retinas
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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 · see citing works
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).”
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“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
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“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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BackgroundGene fusion as an important mechanism to generate new genes in the genus Oryza
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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].”
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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
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“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 · see citing works
- 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 › Agricultural and Biological Sciences › Plant Science › 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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