Cited by 195Chromosomal and Genetic VariationsEvolution and Genetic DynamicsGenome Rearrangement Algorithms

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

Kondrashov, Fyodor A., Kondrashov, Alexey S.·2006·Journal of Theoretical Biology

DOI 10.1016/j.jtbi.2005.08.033

Open this paper in CoChat — free account

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.

Integrity signals

Registry

Crossref · 10.1016/j.jtbi.2005.08.033

Cites

150 of 150 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Evolution by Gene Duplication
Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833
The Neutral Theory of Molecular Evolution
Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,687
The Neutral Theory of Molecular Evolution
Kimura, M. (1983) · Cambridge University Press eBooks · doi:10.1017/cbo9780511623486 · Cited by 6,300
The Evolutionary Fate and Consequences of Duplicate Genes
Lynch, M., & Conery, J. S. (2000) · Science · doi:10.1126/science.290.5494.1151 · Cited by 4,988
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971
α-Synuclein Locus Triplication Causes Parkinson's Disease
Singleton, A. B., Farrer, M., Johnson, J., Singleton, A., Hague, S., Kachergus, J., Hulihan, M., Peuralinna, T., Dutra, A., Nussbaum, R., et al. (2003) · Science · doi:10.1126/science.1090278 · Cited by 4,383
Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316
Preservation of Duplicate Genes by Complementary, Degenerative Mutations
Force, A., Lynch, M., Pickett, F. B., Amores, A., Yan, Y.-L., & Postlethwait, J. (1999) · Genetics · doi:10.1093/genetics/151.4.1531 · Cited by 3,529
Adaptive protein evolution at the Adh locus in Drosophila
McDonald, J. H., & Kreitman, M. (1991) · Nature · doi:10.1038/351652a0 · Cited by 3,313
A census of human cancer genes
Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., & Stratton, M. R. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1299 · Cited by 3,184
Detection of large-scale variation in the human genome
Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892
Large-scale copy number polymorphism in the human genome
Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M., et al. (2004) · Science · doi:10.1126/science.1098918 · Cited by 2,557
The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana
Cannon, S. B., Mitra, A., Baumgarten, A. M., Young, N. D., & May, G. (2004) · BMC Plant Biology · doi:10.1186/1471-2229-4-10 · Cited by 2,415
The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms
Kaeberlein, M., McVey, M., & Guarente, L. (1999) · Genes & Development · doi:10.1101/gad.13.19.2570 · Cited by 2,253
α-synuclein locus duplication as a cause of familial Parkinson's disease
Chartier-Harlin, M.-C., Kachergus, J., Roumier, C., Mouroux, V., Douay, X., Lincoln, S., Levecque, C., Larvor, L., Andrieux, J., Hulihan, M., et al. (2004) · The Lancet · doi:10.1016/s0140-6736(04)17103-1 · Cited by 2,029
Human Gene Mutation Database (HGMD®): 2003 update
Stenson, P., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N., Abeysinghe, S. S., Krawczak, M., & Cooper, D. (2003) · Human Mutation · doi:10.1002/humu.10212 · Cited by 1,887
Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans
Tissenbaum, H. A., & Guarente, L. (2001) · Nature · doi:10.1038/35065638 · Cited by 1,603
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
Kellis, M., Birren, B. W., & Lander, E. S. (2004) · Nature · doi:10.1038/nature02424 · Cited by 1,500
Genome-wide analysis of DNA copy-number changes using cDNA microarrays
Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D., & Brown, P. O. (1999) · Nature Genetics · doi:10.1038/12640 · Cited by 1,416
Recent Segmental Duplications in the Human Genome
Bailey, J. A., Gu, Z., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W., & Eichler, E. E. (2002) · Science · doi:10.1126/science.1072047 · Cited by 1,355
Estimate of the Mutation Rate per Nucleotide in Humans
Nachman, M. W., & Crowell, S. L. (2000) · Genetics · doi:10.1093/genetics/156.1.297 · Cited by 1,226
The molecular basis of insecticide resistance in mosquitoes
Hemingway, J., Hawkes, N. J., McCarroll, L., & Ranson, H. (2004) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2004.03.018 · Cited by 1,183
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors
Pollack, J. R., Sørlie, T., Perou, C. M., Rees, C. A., Jeffrey, S. S., Lønning, P. E., Tibshirani, R. J., Botstein, D., Børresen‐Dale, A., & Brown, P. O. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162471999 · Cited by 1,167
The Influence of CCL3L1 Gene-Containing Segmental Duplications on HIV-1/AIDS Susceptibility
Gonzalez, E., Kulkarni, H. R., Bolivar, H., Mangano, A. M., Sanchez, R., Catano, G., Nibbs, R. J. B., Freedman, B. I., Quinones, M. P., Bamshad, M. J., et al. (2005) · Science · doi:10.1126/science.1101160 · Cited by 1,145
Causal relation between α-synuclein locus duplication as a cause of familial Parkinson's disease
Ibáñez, P., Bonnet, A. M., Débarges, B., Lohmann, E., Tison, F., Agid, Y., Dürr, A., Brice, A., & Pollak, P. (2004) · The Lancet · doi:10.1016/s0140-6736(04)17104-3 · Cited by 1,063
Genome architecture, rearrangements and genomic disorders
Stankiewicz, P., & Lupski, J. R. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02592-1 · Cited by 944
The origin of new genes: Glimpses from the young and old
Long, M., Betrán, E., Thornton, K., & Wang, W. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1204 · Cited by 933
Duplication and Divergence: The Evolution of New Genes and Old Ideas
Taylor, J. S., & Raes, J. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.092831 · Cited by 924
Mefloquine resistance in Plasmodium falciparum and increased pfmdr1 gene copy number
Price, R. N., Uhlemann, A., Brockman, A., McGready, R. M., Ashley, E. A., Phaipun, L., Patel, R., Laing, K. G., Looareesuwan, S., White, N. J., et al. (2004) · The Lancet · doi:10.1016/s0140-6736(04)16767-6 · Cited by 849
Selection in the evolution of gene duplications
Kondrashov, F. A., Rogozin, I. B., Wolf, Y. I., & Koonin, E. V. (2002) · Genome biology · doi:10.1186/gb-2002-3-2-research0008 · Cited by 774
Self-citation
Evolution of genetic redundancy
Nowak, M. A., Boerlijst, M. C., Cooke, J., & Smith, J. M. (1997) · Nature · doi:10.1038/40618 · Cited by 760
Dosage sensitivity and the evolution of gene families in yeast
Papp, B., Pál, C., & Hurst, L. D. (2003) · Nature · doi:10.1038/nature01771 · Cited by 753
Comparison of kindreds with parkinsonism and α‐synuclein genomic multiplications
Farrer, M. J., Kachergus, J. M., Forno, L. S., Lincoln, S., Wang, D., Hulihan, M., Maraganore, D. M., Gwinn, K. A., Wszołek, Z. K., Dickson, D. W., et al. (2004) · Annals of Neurology · doi:10.1002/ana.10846 · Cited by 711
Chromosome 21 and Down syndrome: from genomics to pathophysiology
Antonarakis, S. E., Lyle, R., Dermitzakis, E. T., Reymond, A., & Deutsch, S. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1448 · Cited by 703
Adaptive protein evolution in Drosophila
Smith, N. G. C., & Eyre‐Walker, A. (2002) · Nature · doi:10.1038/4151022a · Cited by 677
The early stages of duplicate gene evolution
Moore, R. C., & Purugganan, M. D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2535513100 · Cited by 640
Genome-wide analysis of DNA copy number variation in breast cancer using DNA microarrays
Pollack, J. R., Perou, C. M., Sørlie, T., Alizadeh, A. A., Rees, C. A., Eise, M. B., Pergamenschikov, A., Williams, C. F., van de Rijn, M., Jeffrey, S. S., et al. (1999) · Nature Genetics · doi:10.1038/14385 · Cited by 632
GENE AMPLIFICATION
Stark, G. R., & Wahl, G. M. (1984) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.53.070184.002311 · Cited by 583
Amplification of the multidrug resistance gene in some chloroquine-resistant isolates of P. falciparum
Foote, S. J., Thompson, J. K., Cowman, A. F., & Kemp, D. J. (1989) · Cell · doi:10.1016/0092-8674(89)90330-9 · Cited by 573
Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease
Shaw, C. A. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh073 · Cited by 493
An Alu Transposition Model for the Origin and Expansion of Human Segmental Duplications
Bailey, J. A., Liu, G., & Eichler, E. E. (2003) · The American Journal of Human Genetics · doi:10.1086/378594 · Cited by 445
High-Resolution Analysis of DNA Copy Number Using Oligonucleotide MicroarraysPreprint
Bignell, G. R., Huang, J. H., Greshock, J. D., Watt, S., Butler, A. P., West, S., Grigorova, M., Jones, K. W., Wei, W., Stratton, M. R., et al. (2004) · Genome Research · doi:10.1101/gr.2012304 · Cited by 396
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
Hwang, D. G., & Green, P. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404142101 · Cited by 390
Genomic microarrays in human genetic disease and cancer
Albertson, D. G., & Pinkel, D. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg261 · Cited by 371
α-Synuclein in blood and brain from familial Parkinson disease with SNCA locus triplication
Miller, D. W., Hague, S., Clarimón, J., Baptista, M., Gwinn, K. A., Cookson, M., & Singleton, A. (2004) · Neurology · doi:10.1212/01.wnl.0000127517.33208.f4 · Cited by 356
Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast
Papp, B., Pál, C., & Hurst, L. D. (2004) · Nature · doi:10.1038/nature02636 · Cited by 353
Amplification of an Esterase Gene Is Responsible for Insecticide Resistance in a California Culex Mosquito
Mouchès, C., Pasteur, N., Bergé, J. B., Hyrien, O., Michel Raymond, A., Vincent, B. R. D. S., de Silvestri, M., & Georghiou, G. P. (1986) · Science · doi:10.1126/science.3755546 · Cited by 350
Rapid divergence in expression between duplicate genes inferred from microarray data
Gu, Z., Nicolae, D. L., Lu, H. H.-S., & Li, W. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02837-8 · Cited by 346
Direct estimates of human per nucleotide mutation rates at 20 loci causing mendelian diseases
Kondrashov, A. S. (2002) · Human Mutation · doi:10.1002/humu.10147 · Cited by 336
Self-citation
The Part Played by Recurrent Mutation in Evolution
Haldane, J. B. S. (1933) · The American Naturalist · doi:10.1086/280465 · Cited by 319
The altered evolutionary trajectories of gene duplicates.
Lynch, M., & Katju, V. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.09.001 · Cited by 315
Ancient Phylogenetic Relationships
Gribaldo, S., & Philippe, H. (2002) · Theoretical Population Biology · doi:10.1006/tpbi.2002.1593 · Cited by 314
Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment
Brown, C. J., Todd, K., & Rosenzweig, R. F. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026009 · Cited by 305
Segmental duplications: an 'expanding' role in genomic instability and disease
Emanuel, B. S., & Shaikh, T. H. (2001) · Nature Reviews Genetics · doi:10.1038/35093500 · Cited by 303
Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels
Britten, R. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.172510699 · Cited by 296
Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian EvolutionPreprint
Hardison, R. C., Roskin, K. M., Yang, S., Diekhans, M., Kent, W. J., Weber, R., Elnitski, L., Li, J., O'Connor, M., Kolbe, D., et al. (2003) · Genome Research · doi:10.1101/gr.844103 · Cited by 281
Whole genome DNA copy number changes identified by high density oligonucleotide arrays
Huang, J., Wei, W., Zhang, J., Liu, G., Bignell, G. R., Stratton, M. R., Futreal, P. A., Wooster, R., Jones, K. W., & Shapero, M. H. (2004) · Human Genomics · doi:10.1186/1479-7364-1-4-287 · Cited by 279
Klinefelter Syndrome
Smyth, C. M., & Bremner, W. J. (1998) · Archives of Internal Medicine · doi:10.1001/archinte.158.12.1309 · Cited by 244
Divergence in the Spatial Pattern of Gene Expression Between Human Duplicate GenesPreprint
Makova, K. D., & Li, W. (2003) · Genome Research · doi:10.1101/gr.1133803 · Cited by 232
Asymmetric Sequence Divergence of Duplicate GenesPreprint
Conant, G. C., & Wagner, A. (2003) · Genome Research · doi:10.1101/gr.1252603 · Cited by 232
Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments
Koszul, R., Caburet, S., Dujon, B., & Fischer, G. (2003) · The EMBO Journal · doi:10.1038/sj.emboj.7600024 · Cited by 227
Genotype—environment interactions and the estimation of the genomic mutation rate inDrosophila melanogaster
Kondrashov, A. S., & Houle, D. (1994) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1994.0166 · Cited by 225
Self-citation
Alteration in Copy Numbers of Genes as a Mechanism for Acquired Drug Resistance
Yasui, K., Mihara, S., Zhao, C. N., Okamoto, H. H., Saito-Ohara, F., Tomida, A., Funato, T., Yokomizo, A., Naito, S., Imoto, I., et al. (2004) · Cancer Research · doi:10.1158/0008-5472.can-3263-2 · Cited by 218
Rapid evolution of expression and regulatory divergences after yeast gene duplication
Gu, X., Zhang, Z., & Huang, W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409186102 · Cited by 208
Oncogene amplification in solid tumors
Schwab, M. (1999) · Seminars in Cancer Biology · doi:10.1006/scbi.1999.0126 · Cited by 207
Enhanced Copper Tolerance in Silene vulgaris (Moench) Garcke Populations from Copper Mines Is Associated with Increased Transcript Levels of a 2b-Type Metallothionein Gene
Hoof, N. A. L. M. V., Hassinen, V. H., Hakvoort, H. W. J., Ballintijn, K. F., Schat, H., Verkleij, J. A. C., Ernst, W. H. O., Kärenlampi, S. O., & Tervahauta, A. I. (2001) · PLANT PHYSIOLOGY · doi:10.1104/pp.126.4.1519 · Cited by 201
A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications
Kondrashov, F. A., & Koonin, E. V. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.05.001 · Cited by 200
Self-citation
Protection against zinc toxicity by metallothionein and zinc transporter 1
Palmiter, R. D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401022101 · Cited by 197
Molecular analyses of unrelated Charcot-Marie-Tooth (CMT) disease patients suggest a high frequency of the CMTIA duplication.
Wise, C. A., Garcia, C. A., Davis, S. N., Heju, Z., Pentao, L., Patel, P. I., & Lupski, J. R. (1993) · PubMed · Cited by 191
Metallothionein Gene Duplications and Metal Tolerance in Natural Populations of Drosophila melanogaster
Maroni, G., Wise, J., Young, J. E., & Otto, E. (1987) · Genetics · doi:10.1093/genetics/117.4.739 · Cited by 190
Duplicated genes evolve slower than singletons despite the initial rate increase
Jordan, I. K., Wolf, Y. I., & Koonin, E. V. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-22 · Cited by 189
Gene duplication and biased functional retention of paralogs in bacterial genomes
Gevers, D., Vandepoele, K., Simillion, C., & de Peer, Y. V. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.02.007 · Cited by 186
Evolutionary origins and maintenance of redundant gene expression during metazoan development
Cooke, J., Nowak, M. A., Boerlijst, M. C., & Smith, J. M. (1997) · Trends in Genetics · doi:10.1016/s0168-9525(97)01233-x · Cited by 181
Genome Architecture Catalyzes Nonrecurrent Chromosomal Rearrangements
Stankiewicz, P., Shaw, C. J., Dapper, J. D., Wakui, K., Shaffer, L. G., Withers, M. A., Elizondo, L. I., Park, S. S., & Lupski, J. R. (2003) · The American Journal of Human Genetics · doi:10.1086/374385 · Cited by 181
FITNESS COSTS OF INSECTICIDE RESISTANCE IN NATURAL BREEDING SITES OF THE MOSQUITO CULEX PIPIENS
Bourguet, D., Guillemaud, T., Chevillon, C., & Michel Raymond, A. (2004) · Evolution · doi:10.1111/j.0014-3820.2004.tb01579.x · Cited by 177
Preferential Duplication of Conserved Proteins in Eukaryotic Genomes
Davis, J. C., & Petrov, D. A. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020055 · Cited by 174
16 The evolution of gene duplicates
Otto, S. P., & Yong, P. J. (2002) · Advances in genetics · doi:10.1016/s0065-2660(02)46017-8 · Cited by 173
Molecular biology and evolution of resistance of toxicants
Taylor, M. F. J., & Feyereisen, R. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025633 · Cited by 172
An overview of the evolution of overproduced esterases in the mosquito Culex pipiens
Michel Raymond, A., Chevillon, C., Guillemaud, T., Lenormand, T., & Pasteur, N. (1998) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1998.0322 · Cited by 172
Meta‐Analysis of gross insertions causing human genetic disease: Novel mutational mechanisms and the role of replication slippage
Chen, J., Chuzhanova, N. A., Stenson, P. D., Férec, C., & Cooper, D. N. (2005) · Human Mutation · doi:10.1002/humu.20133 · Cited by 166
Somatic alterations in the human cancer genome
Weir, B. A., Zhao, X., & Meyerson, M. M. (2004) · Cancer Cell · doi:10.1016/j.ccr.2004.11.004 · Cited by 166
Large-Scale Variation Among Human and Great Ape Genomes Determined by Array Comparative Genomic HybridizationPreprint
Locke, D. P., Segraves, R., Carbone, L., Archidiacono, N., Albertson, D. G., Pinkel, D., & Eichler, E. E. (2003) · Genome Research · doi:10.1101/gr.1003303 · Cited by 161
Invasion and maintenance of a gene duplication.
Clark, A. G. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.8.2950 · Cited by 152
The Structure and Early Evolution of Recently Arisen Gene Duplicates in the Caenorhabditis elegans Genome
Katju, V., & Lynch, M. (2003) · Genetics · doi:10.1093/genetics/165.4.1793 · Cited by 151
Low Nucleotide Diversity in Chimpanzees and Bonobos
Ning, Y., Jensen‐Seaman, M. I., Chemnick, L. G., Kidd, J. R., Deinard, A. S., Ryder, O. A., Kídd, K. K., & Li, W. (2003) · Genetics · doi:10.1093/genetics/164.4.1511 · Cited by 150
Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma
Man, T., Lu, X.-Y., Jaeweon, K., Perlaky, L., Harris, C. P., Shah, S. K., Ladanyi, M., Gorlick, R. G., Lau, C. C., & Rao, P. H. (2004) · BMC Cancer · doi:10.1186/1471-2407-4-45 · Cited by 147
The Molecular Pathogenesis of Pelizaeus-Merzbacher Disease
Garbern, J. Y., Cambi, F., Shy, M. E., & Kamholz, J. A. (1999) · Archives of Neurology · doi:10.1001/archneur.56.10.1210 · Cited by 146
Very Low Gene Duplication Rate in the Yeast Genome
Gao, L., & Innan, H. (2004) · Science · doi:10.1126/science.1102033 · Cited by 145
Different evolutionary patterns between young duplicate genes in the human genome
Zhang, P., Gu, Z., & Li, W. (2003) · Genome biology · doi:10.1186/gb-2003-4-9-r56 · Cited by 145
Duplication of the proteolipid protein gene is the major cause of Pelizaeus‐Merzbacher disease
Sistermans, E. A., de Coo, I. F. M., de Wijs, I. J., & van Oost, B. A. (1998) · Neurology · doi:10.1212/wnl.50.6.1749 · Cited by 144
Increased gene dosage of Ink4a/Arf results in cancer resistance and normal agingPreprint
Matheu, A., Pantoja, C., Efeyan, A., Criado, L. M., Martín‐Caballero, J., Flores, J. M., Klatt, P., & Serrano, M. (2004) · Genes & Development · doi:10.1101/gad.310304 · Cited by 140
Mechanisms of drug resistance in Leishmania
Ouellette, M., & Papadopoulou, B. (1993) · Parasitology Today · doi:10.1016/0169-4758(93)90135-3 · Cited by 133
Patterns of Segmental Duplication in the Human Genome
Zhang, L. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh262 · Cited by 132
Identification of a 3.0-kb Major Recombination Hotspot in Patients with Sotos Syndrome Who Carry a Common 1.9-Mb Microdeletion
Visser, R., Shimokawa, O., Harada, N., Kinoshita, A., Ohta, T., Niikawa, N., & Matsumoto, N. (2004) · The American Journal of Human Genetics · doi:10.1086/426950 · Cited by 130
Evolution of cis-regulatory elements in duplicated genes of yeast
Papp, B., Pál, C., & Hurst, L. D. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(03)00174-4 · Cited by 126
A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture
Mehan, M. R., Freimer, N. B., & Ophoff, R. A. (2004) · Human Genomics · doi:10.1186/1479-7364-1-5-335 · Cited by 121
Genome-Wide Amplifications Caused by Chromosomal Rearrangements Play a Major Role in the Adaptive Evolution of Natural Yeast
Infante, J. J., Dombek, K. M., Rebordinos, L. G., Cantoral, J. M., & Young, E. T. (2003) · Genetics · doi:10.1093/genetics/165.4.1745 · Cited by 121
Analysis of Segmental Duplications and Genome Assembly in the MousePreprint
Bailey, J. A., Church, D. M., Ventura, M., Rocchi, M., & Eichler, E. E. (2004) · Genome Research · doi:10.1101/gr.2238404 · Cited by 120
Frequency of new copy number variation in humans
van Ommen, G. B. (2005) · Nature Genetics · doi:10.1038/ng0405-333 · Cited by 116
Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species
Wang, W., Yu, H., & Long, M. (2004) · Nature Genetics · doi:10.1038/ng1338 · Cited by 114
Pathological Consequences of Sequence Duplications in the Human GenomePreprint
Mazzarella, R. A., & Schlessinger, D. (1998) · Genome Research · doi:10.1101/gr.8.10.1007 · Cited by 109
Insecticide resistance genes confer a predation cost on mosquitoes, Culex pipiens
BERTICAT, C., DURON, O., HEYSE, D., & RAYMOND, M. (2004) · Genetical Research · doi:10.1017/s0016672304006792 · Cited by 108
Role of gene duplication in evolution
Ohta, T. (1989) · Genome · doi:10.1139/g89-048 · Cited by 105
Context of deletions and insertions in human coding sequences
Kondrashov, A. S., & Rogozin, I. B. (2004) · Human Mutation · doi:10.1002/humu.10312 · Cited by 104
Self-citation
Amplification of the multidrug resistance gene pfmdr1 in Plasmodium falciparum has arisen as multiple independent events.
Triglia, T., Foote, S. J., Kemp, D. J., & Cowman, A. F. (1991) · Molecular and Cellular Biology · doi:10.1128/mcb.11.10.5244 · Cited by 103
A genomic rearrangement resulting in a tandem duplication is associated with split hand-split foot malformation 3 (SHFM3) at 10q24
de Mollerat, X. J. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg212 · Cited by 101
BAC microarray analysis of 15q11–q13 rearrangements and the impact of segmental duplications
Locke, D. P., Segraves, R., Nicholls, R. D., Schwartz, S., Pinkel, D., Albertson, D. G., & Eichler, E. E. (2004) · Journal of Medical Genetics · doi:10.1136/jmg.2003.013813 · Cited by 101
Unexpected survival in a case of prenatally diagnosed non‐mosaic trisomy 22: Clinical report and review of the natural history
Tinkle, B. T., Walker, M. E., Blough, R. I., Saal, H. M., & Hopkin, R. J. (2003) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.10216 · Cited by 98
APPEARANCE AND SWEEP OF A GENE DUPLICATION: ADAPTIVE RESPONSE AND POTENTIAL FOR NEW FUNCTIONS IN THE MOSQUITOCULEX PIPIENS
Lenormand, T., Guillemaud, T., Bourguet, D., & Michel Raymond, A. (1998) · Evolution · doi:10.1111/j.1558-5646.1998.tb02250.x · Cited by 95
Similar Rates but Different Modes of Sequence Evolution in Introns and at Exonic Silent Sites in Rodents: Evidence for Selectively Driven Codon Usage
Chamary, J., & Hurst, L. D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh087 · Cited by 94
The androgen receptor gene and its influence on the development and progression of prostate cancer
Montgomery, J. S., Price, D. K., & Figg, W. D. (2001) · The Journal of Pathology · doi:10.1002/1096-9896(200109)195:2 · Cited by 92
Parkinson's disease and dementia with Lewy bodies: a difference in dose?
Singleton, A., & Gwinn, K. A. (2004) · The Lancet · doi:10.1016/s0140-6736(04)17117-1 · Cited by 87
Charcot-Marie-Tooth Disease and Related Inherited Neuropathies
Murakami, T., Garcia, C. A., Reiter, L. T., & Lupski, J. R. (1996) · Medicine · doi:10.1097/00005792-199609000-00001 · Cited by 86
Developmental Gene Amplification and Origin Regulation
Tower, J. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.37.110801.143851 · Cited by 85
Esterase gene amplification in Culex pipiens
Guillemaud, T., Makate, N., Michel Raymond, A., Hirst, B., & Callaghan, A. (1997) · Insect Molecular Biology · doi:10.1046/j.1365-2583.1997.00186.x · Cited by 82
Thiourea as a Key Reagent for the Preparation of Aliphatic Sulphonyl Chlorides and Bromides
Johnson, T. B., & Sprague, J. M. (1936) · Science · doi:10.1126/science.83.2161.528-a · Cited by 82
Polymorphically duplicated genes: their relevance to phenotypic variation in humans
Buckland, P. R. (2003) · Annals of Medicine · doi:10.1080/07853890310001276 · Cited by 78
THIOUREA AS A KEY REAGENT FOR THE PREPARATION OF ALIPHATIC SULPHONYL CHLORIDES AND BROMIDES
Johnson, T., & Sprague, J. M. (1936) · Science · doi:10.1126/science.83.2161.528 · Cited by 73
Evolution of antibiotic resistance gene function
Koch, A. L. (1981) · Microbiological Reviews · doi:10.1128/mr.45.2.355-378.1981 · Cited by 66
Zinc- and arsenic-resistant strains of Thiobacillus ferrooxidans have increased copy numbers of chromosomal resistance genes
Kondratyeva, T. F., Muntyan, L. N., & Karavaiko, G. I. (1995) · Microbiology · doi:10.1099/13500872-141-5-1157 · Cited by 64
Glyphosate selection of gene amplification in suspension cultures of 3 plant species
Widholm, J. M., Chinnala, A. R., Ryu, J., Song, H., Eggett, T., & Brotherton, J. E. (2001) · Physiologia Plantarum · doi:10.1034/j.1399-3054.2001.1120411.x · Cited by 57
Indel-Based Evolutionary Distance and Mouse–Human DivergencePreprint
Ogurtsov, A. Y., Sunyaev, S. R., & Kondrashov, A. S. (2004) · Genome Research · doi:10.1101/gr.2450504 · Cited by 57
Self-citation
Structure and expression of a tandem duplication of the Drosophila metallothionein gene.
Otto, E., Young, J. E., & Maroni, G. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.16.6025 · Cited by 56
Study of Intrachromosomal Duplications Among the Eukaryote Genomes
Achaz, G., Netter, P., & Coissac, É. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003774 · Cited by 53
Amplification and overexpression of genes in 17p11.2∼p12 in osteosarcoma
van Dartel, M., & Hulsebos, T. J. M. (2004) · Cancer Genetics and Cytogenetics · doi:10.1016/j.cancergencyto.2004.03.007 · Cited by 52
Charcot-Marie-Tooth Polyneuropathy: Duplication, Gene Dosage, and Genetic Heterogeneity
Lupski, J. R. (1999) · Pediatric Research · doi:10.1203/00006450-199902000-00001 · Cited by 52
The evolutionary history of human chromosome 7
Müller, S., Finelli, P., Neusser, M., & Wienberg, J. (2004) · Genomics · doi:10.1016/j.ygeno.2004.05.005 · Cited by 49
Appearance and Sweep of a Gene Duplication: Adaptive Response and Potential for New Functions in the Mosquito Culex pipiens
Lenormand, T., Guillemaud, T., Bourguet, D., & Michel Raymond, A. (1998) · Evolution · doi:10.2307/2411343 · Cited by 46
Polymorphisms and fluctuations in copy number of amplified esterase genes in Culex pipiens mosquitoes
Callaghan, A., Guillemaud, T., Makate, N., & Michel Raymond, A. (1998) · Insect Molecular Biology · doi:10.1111/j.1365-2583.1998.00077.x · Cited by 45
Role of the locus and of the resistance gene on gene amplification frequency in methotrexate resistant Leishmania tarentolae
Kündig, C., Leblanc, E., Papadopoulou, B., & Ouellette, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.18.3653 · Cited by 37
DNA Amplification in DNA Puff II/9A of Sciara coprophilaPreprint
Gerbi, S. A., Liang, C., Wu, N., DiBartolomeis, S. M., Bienz-Tadmor, B., Smith, H. S., & Urnov, F. D. (1993) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1993.058.01.055 · Cited by 37
Sex and U
Kondrashov, A. S. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(00)02188-0 · Cited by 36
Self-citation
Estimation of the abundance of the cadmium resistance gene cadA in microbial communities in polluted estuary water
Oger, C., Berthe, T., Quillet, L., Barray, S., Chiffoleau, J.-F., & Petit, F. (2001) · Research in Microbiology · doi:10.1016/s0923-2508(01)01246-3 · Cited by 35
Evolution of antibiotic resistance gene function.
Koch, A. L. (1981) · Microbiological Reviews · doi:10.1128/mmbr.45.2.355-378.1981 · Cited by 33
Genome-wide profiling of gene amplification and deletion in cancer.
Kashiwagi, H., & Uchida, K. (2000) · PubMed · Cited by 31
Implications of Gene Amplification for Evolution and Management of Insecticide Resistance
Tabashnik, B. E. (1990) · Journal of Economic Entomology · doi:10.1093/jee/83.4.1170 · Cited by 30
Regulatory Sequences for the Amplification and Replication of the Ribosomal DNA Minichromosome in Tetrahymena thermophila
Blomberg, P., Randolph, C., Yao, C.-H., & Yao, M.-C. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.12.7237 · Cited by 28
Plasticity of human chromosome 3 during primate evolution
Tsend‐Ayush, E., Grützner, F., Yue, Y., Grossmann, B., Hänsel, U., Sudbrak, R., & Haaf, T. (2003) · Genomics · doi:10.1016/j.ygeno.2003.08.012 · Cited by 26
Distribution of short paired duplications in mammalian genomes
Thomas, E. E., Srebro, N., Sebat, J. L., Navin, N. E., Healy, J., Mishra, B., & Wigler, M. H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403727101 · Cited by 26
Clusters of Identical New Mutations Can Account for the “Overdispersed” Molecular Clock
Huai, H., & Woodruff, R. C. (1997) · Genetics · doi:10.1093/genetics/147.1.339 · Cited by 21
On the formation of amplified nucleoli during early Xenopus oogenesis
Mais, C. (2002) · Journal of Structural Biology · doi:10.1016/s1047-8477(02)00526-9 · Cited by 20
Detection of DNA copy number abnormality by microarray expression analysis
Zhou, X. C., Cole, S. W., Hu, S., & Wong, D. T. (2004) · Human Genetics · doi:10.1007/s00439-004-1087-9 · Cited by 18
Amplification of a gene for metallothionein by tandem repeat in a strain of cadmium-resistant yeast cells
Tohoyama, H., SHIRAISHI, E., AMANO, S., Inouhe, M., Joho, M., & Murayama, T. (1996) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1996.tb08060.x · Cited by 16
Overproduction by gene amplification of the multifunctional arom protein confers glyphosate tolerance to a plastid-free mutant of Euglena gracilis
Reinbothe, S., Ortel, B., & Parthier, B. (1993) · Molecular and General Genetics MGG · doi:10.1007/bf00276940 · Cited by 14
Different age distribution patterns of human, nematode, and Arabidopsis duplicate genes
Zhang, P., Min, W., & Li, W. (2004) · Gene · doi:10.1016/j.gene.2004.08.001 · Cited by 11
The evolution of gene number: are heritable and non-heritable errors equally important?
Pál, C., & Hurst, L. D. (2000) · Heredity · doi:10.1046/j.1365-2540.2000.00725.x · Cited by 11
[Gene amplification in prokaryote and eukaryote systems].
Velkov, V. V. (1982) · PubMed · Cited by 10
Her-2/neuGene Amplification in Familial vs Sporadic Breast Cancer
Espinosa, A. B., Tabernero, M. D., García-Macías, M. C., Primo, D., Gómez-Bernal, A., Cruz, J. J., Ramos, M., de Mora, J. F., Alonso, A. G., & Órfão, A. (2003) · American Journal of Clinical Pathology · doi:10.1309/5h778w5k75cmm03w · Cited by 9
Her-2/neu Gene Amplification in Familial vs Sporadic Breast Cancer; Impact on the Behavior of the Disease
Ana B. Espinosa, P., Tabernero, M. D., García-Macías, M. C., Primo, D., Gómez-Bernal, A., Juan J. Cruz, M. P., Ramos, M., de Mora, J. F., Alonso, A. G., & Órfão, A. (2003) · American Journal of Clinical Pathology · doi:10.1309/5h77-8w5k-75cm-m03w · Cited by 6
Amplification of ribosomal genes and formation of extrachromosomal nucleoli in oocytes of starfish Henricia hayashi (Asteroidea: Echinasteridae)
Gaginskaya, E. R., Kasyanov, V. L., & Kogan, G. L. (1988) · Cell Differentiation · doi:10.1016/0045-6039(88)90036-x · Cited by 4

Research works printed but not linked: 2

Serebrovsky, 1938, Genes scute and achaete in Drosophila melanogaster and a hypothesis of gene divergency, C. R. Acad. Sci. URSS., 19, 77
Velkov, 1982, Gene amplification in prokaryotic and eukaryotic systems, Genetika, 18, 529

Sorted by citations

The evolution of gene duplications: classifying and distinguishing between models
Innan, H., & Kondrashov, F. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2689 · Cited by 1,338
“However, as data from eukaryotes became more widely available, authors started to relate dosage and gene duplications in multicellular organism”
BackgroundSelf-citation
Turning a hobby into a job: How duplicated genes find new functions
Conant, G. C., & Wolfe, K. H. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2482 · Cited by 1,281
“Duplicate gene pairs can also be preserved by selection for increased gene dosag”
Background
Adaptive laboratory evolution—Principles and applications for biotechnology
Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827
“Whereas there is an ongoing debate about the long-term fixation of gene duplications, either by their selective advantage under selection pressure, or by selective neutrality and fixation by random drift, they are a prerequisite for the development of novel molecular functions [129-131].”
Background
Gene duplication as a mechanism of genomic adaptation to a changing environment
Kondrashov, F. A. (2012) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2012.1108 · Cited by 663
Self-citation
Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates
Hahn, M. W. (2009) · Journal of Heredity · doi:10.1093/jhered/esp047 · Cited by 428
“Multiple authors have also recently proposed that this is a major force in duplicate gene retention (Kondrashov et al. 2002; Kondrashov and Kondrashov 2006; Sugino and Innan 2006).”
Background

See all 195

Authors: Kondrashov, F. A., & Kondrashov, A. S.
Affiliations: National Center for Biotechnology Information (US)
Corresponding author: Kondrashov, Fyodor A.
Kondrashov, Alexey S.
ORCID: 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)
DOI: 10.1016/j.jtbi.2005.08.033
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
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Role of selection in fixation of gene duplications

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks