The DOI matches its Crossref record; 150 of the 150 references it cites were found in a registry or an index.
Role of selection in fixation of gene duplications
Abstract
New genes commonly appear through complete or partial duplications of pre-existing genes. Duplications of long DNA segments are constantly produced by rare mutations, may become fixed in a population by selection or random drift, and are subject to divergent evolution of the paralogous sequences after fixation, although gene conversion can impede this process. New data shed some light on each of these processes. Mutations which involve duplications can occur through at least two different mechanisms, backward strand slippage during DNA replication and unequal crossing-over. The background rate of duplication of a complete gene in humans is 10(-9)-10(-10) per generation, although many genes located within hot-spots of large-scale mutation are duplicated much more often. Many gene duplications affect fitness strongly, and are responsible, through gene dosage effects, for a number of genetic diseases. However, high levels of intrapopulation polymorphism caused by presence or absence of long, gene-containing DNA segments imply that some duplications are not under strong selection. The polymorphism to fixation ratios appear to be approximately the same for gene duplications and for presumably selectively neutral nucleotide substitutions, which, according to the McDonald-Kreitman test, is consistent with selective neutrality of duplications. However, this pattern can also be due to negative selection against most of segregating duplications and positive selection for at least some duplications which become fixed. Patterns in post-fixation evolution of duplicated genes do not easily reveal the causes of fixations. Many gene duplications which became fixed recently in a variety of organisms were positively selected because the increased expression of the corresponding genes was beneficial. The effects of gene dosage provide a unified framework for studying all phases of the life history of a gene duplication. Application of well-known methods of evolutionary genetics to accumulating data on new, polymorphic, and fixed duplication will enhance our understanding of the role of natural selection in the evolution by gene duplication.
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“Examples for adaptive cross-protection are also available for S. cerevisiae where cobalt resistance also improved tolerance for other metal ions and pulsed cobalt stress exposure during laboratory evolution even resulted in evolutionary cross-protection to thermal and oxidative stress [114].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [114]
In the citing paper
“Other studies used ethylmethanesulfonate (EMS) treated Bacillus boroniphilus to select for increased boron resistance [88] or EMS-treated S. cerevisiae in order to achieve increased nutrient utilization and stress resistance [95,113,114].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [114]
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“Alternatively, positive selection might also favor the enhanced expression levels of initial SSD duplicates prior to mutations (Otto and Yong, 2002; Kondrashov and Kondrashov, 2006), leading to the classical result, Π⋆SSD = s⋆ (C).”
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“…and this retention is thought to occur through three dominant routes (Kuzmin, Taylor, and Boone 2021): (1) by providing dosage amplification (Kondrashov and Kondrashov 2006) or backup compensation (Nowak et al. 1997) (2) by allowing subfunctionalization, i.e. the partitioning of functions…”
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Topological Metrics in Blast Data Mining: Plasmid and Nitrogen-Fixing Proteins Case Studies
Lió, P., Brilli, M., & Fani, R. (2008) · Communications in computer and information science · doi:10.1007/978-3-540-70600-7_16
“Several nitrogen fixation proteins are part of paralogous families [19] and are related to enzymes involved in the biosynthesis of photosynthetic pigments (i.”
BackgroundAnanko, G. G. (2011) · Journal of Molecular Evolution · doi:10.1007/s00239-011-9482-z
“This inference agrees with the known facts on the role of gene duplications as the main supplier of material for adaptive evolution (Ohno 1970; Kondrashov and Kondrashov 2006).”
BackgroundResultA diffusion model for the fate of tandem gene duplicates in diploids
O’Hely, M. (2007) · Theoretical Population Biology · doi:10.1016/j.tpb.2007.01.003
Differential expression of recent gene duplicates in developmental tissues of Arabidopsis thaliana
Owens, S. M. (2009) · OhioLink ETD Center (Ohio Library and Information Network)
EVOLUTION OF PROTEIN INTERACTION NETWORKS THROUGH GENE DUPLICATION
D’Antonio, M. (2011) · Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) · doi:10.13130/d-antonio-matteo_phd2011
“An environmental change occurs and the duplication of a particular gene gives a selective advantage because of its increased dosage (Kondrashov and Kondrashov, 2006) (Figure 7D).”
BackgroundComputational analysis of genetic interaction network structures and gene properties
Koch, E. N. (2017) · University of Minnesota Digital Conservancy (University of Minnesota)
Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishesPreprint
Gu, L., & Xia, C. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/265538
Parallel evolution of toxin resistance in a predator-prey system
Alvarez, S. H. (2015)
Song, J. T., Han, X., & Lin, K. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.31.017467
“However, many basic features of the 79 evolution by gene duplication remain unknown[33, 35].”
BackgroundA GATA factor radiation in Caenorhabditis rewired the endoderm specification networkPreprint
Darragh, A. C., Weinstein, R., Bloom, J., & Rifkin, S. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.20.492851
“…1998; Eyre-Walker and Keightley 1999; Denver et al. 2004; Haag-Liautard et al. 2007), neofunctionalization (Ohno 1970), subfunctionalization (Hughes 1994; Force et al. 1999; Lynch and Force 2000), and redundancy (Ohno 1970; Nei et al. 2000; Piontkivska et al. 2002; Kondrashov and Kondrashov 2006).”
Radiation and diversification of GATA-domain-containing proteins in the genus CaenorhabditisPreprint
Darragh, A. C., & Rifkin, S. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.20.492891
Aristova, E. O., Volkhin, I. A., Denisova, A. A., Nikitin, P., & Petrukhin, E. R. (2025) · Molecular Biology · doi:10.1134/s0026893324700687
Genetic Novelty and Short-Term Evolutionary Dynamics in Drosophila yakuba mayottensisPreprint
Turner, B. A., Titus‐McQuillan, J. E., Yassin, A., & Rogers, R. L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.10.658671
“These structural changes can accelerate the introduction of genetic novelty by altering genome architecture, reshuffling regulatory networks, and creating novel gene combinations [20–23].”
Étude de l'histoire évolutive des gènes dans les génomes de vertébrés
Péres, A. (2015) · theses.fr (ABES) · doi:10.70675/48d1b8e7z25eez400fzaef9zbe8da8ab3bcc
Carvalho, A. F. P. (2021) · theses.fr (ABES) · doi:10.70675/c6b25a92z329cz4e32za110z1b3dadd1a6a0
Huang, W., Tang, X., Jiang, H., Deng, Y., Lu, T., Peng, J., Sun, Y., Li, X., Wang, X., Peng, B., et al. (2026) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2026.105674
Theoretical analyses of the expansion of gene families implicated in dominant diseases
Malaguti, G. (2014) · theses.fr (ABES) · doi:10.70675/a5ddf9bazb4a3z45baza29ez873b8419fb22
“Alternatively, positive selection might also favor the enhanced expression levels of initial SSD duplicates prior to mutations [138,139], leading to the classical result, Π? SSD = s? (A.”
BackgroundAlways read the introduction : integrating regulatory and coding sequence evolution in yeast
Evangelisti, A. M. (2010) · UNM’s Digital Repository (University of New Mexico)
Metadata
- Authors
- Kondrashov, F. A., & Kondrashov, A. S.
- Affiliations
- National Center for Biotechnology Information (US)
- Corresponding author
- Kondrashov, Fyodor A.
- Kondrashov, Alexey S.
- Venue
- Journal of Theoretical Biology
- Publisher
- Elsevier BV
- Published
- 2006-03
- Volume
- 239
- Issue
- 2
- Pages
- 141-151
- ISSN
- 0022-5193 (ISSN-L)
- OpenAlex
- W2018486257
- Cited by
- 195
- References
- 150
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 3 · 2023: 6 · 2022: 9 · 2021: 4 · 2020: 6 · 2019: 7 · 2018: 10 · 2017: 12 · 2016: 6 · 2015: 11 · 2014: 11 · 2013: 10 · 2012: 13
- FWCI
- 1.01
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Theoretical Biology (publishedVersion)
- PubMed (publishedVersion)
- 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 › Genetics › Genome Rearrangement Algorithms
- Keywords
- gene duplication, natural selection, paralogs, gene conversion, unequal crossover, replication slippage, McDonald-Kreitman test, gene dosage effect, positive selection
- MeSH terms
- Animals, Humans, Mutation, Selection, Genetic, Genome, Gene Dosage, Evolution, Molecular, Gene Duplication
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