Cited by 1,698Chromosomal and Genetic VariationsEvolution and Genetic DynamicsGenomics and Phylogenetic Studies

The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.

The Origins of Genome Complexity

Lynch, Michael, Conery, John S.·2003·Science

Open this paper in CoChat — free account

Abstract

Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.

Integrity signals

Registry

Crossref · 10.1126/science.1089370

Cites

32 of 32 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
Self-citation
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
Self-citation
Rates of spontaneous mutation
Drake, J. W., Charlesworth, B., Charlesworth, D., & Crow, J. F. (1998) · Genetics · doi:10.1093/genetics/148.4.1667 · Cited by 1,932
Global Dispersal of Free-Living Microbial Eukaryote Species
Finlay, B. J. (2002) · Science · doi:10.1126/science.1070710 · Cited by 1,832
The Probability of Duplicate Gene Preservation by Subfunctionalization
Lynch, M., & Force, A. G. (2000) · Genetics · doi:10.1093/genetics/154.1.459 · Cited by 1,559
Self-citation
Mobile DNA II
(2007) · Wiley eBooks · doi:10.1128/9781555817954 · Cited by 1,311
Alternative splicing: increasing diversity in the proteomic world
Graveley, B. R. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(00)02176-4 · Cited by 1,228

Flagged first, then by citations

Show all 32 references

Research works printed but not linked: 2

B. Charlesworth, in Population Genetics and Molecular Evolution, T. Ohta, K. Aoki, Eds. (Japan Sci. Soc. Press, Tokyo, 1985), pp. 213–232.
T. R. Gregory, Biol. Rev.76, 65 (2001).

Sorted by citations

Items 101–200 of 1,001

Effect of 5'UTR introns on gene expression in Arabidopsis thaliana
Chung, B., Simons, C., Firth, A. E., Brown, C. M., & Hellens, R. P. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-120 · Cited by 249
The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans
Denver, D. R., Morris, K., Streelman, J. T., Kim, S. K., Lynch, M., & Thomas, W. K. (2005) · Nature Genetics · doi:10.1038/ng1554 · Cited by 248
Self-citation
The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader
Youssef, N. H., Couger, M. B., Struchtemeyer, C. G., Liggenstoffer, A. S., Prade, R. A., Najar, F. Z., Atiyeh, H. K., Wilkins, M. R., & Elshahed, M. S. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00821-13 · Cited by 255
Diversity and geographic distribution of ciliates (Protista: Ciliophora)
Foissner, W., Chao, A., & Katz, L. A. (2007) · Biodiversity and Conservation · doi:10.1007/s10531-007-9254-7 · Cited by 247
On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
Wolf, Y. I., & Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-14 · Cited by 235
“However, moderate genome increase, e.g., by duplication of parts of the genome, or by recombination, can be fixed via genetic drift in small populations [ 9 ].”
Background
A GENERAL MULTIVARIATE EXTENSION OF FISHER'S GEOMETRICAL MODEL AND THE DISTRIBUTION OF MUTATION FITNESS EFFECTS ACROSS SPECIES
Martin, G., & Lenormand, T. (2006) · Evolution · doi:10.1111/j.0014-3820.2006.tb01169.x · Cited by 243
Complex Spliceosomal Organization Ancestral to Extant Eukaryotes
Collins, L., & Penny, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi091 · Cited by 240
The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host–cell interaction genes
Cho, N., Kim, H., Lee, J., Kim, S.-Y., Kim, J., Cha, S., Kim, S.-Y., Darby, A. C., Fuxelius, H., Yin, J., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611553104 · Cited by 234
Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo
Yao, H., Lu, X., Chen, Q., Xu, K., Chen, Y. Z., Cheng, M., Chen, K., Cheng, L., Weng, T.-H., Shi, D., et al. (2020) · Cell Discovery · doi:10.1038/s41421-020-00226-1 · Cited by 241
Evolutionary Conservation of MicroRNA Regulatory Circuits: An Examination of MicroRNA Gene Complexity and Conserved MicroRNA-Target Interactions through Metazoan Phylogeny
Lee, C.-T., Risom, T., & Strauss, W. M. (2007) · DNA and Cell Biology · doi:10.1089/dna.2006.0545 · Cited by 240
Genomic Consequences of Outcrossing and Selfing in Plants
Wright, S., Ness, R. W., Foxe, J. P., & Barrett, S. C. H. (2008) · International Journal of Plant Sciences · doi:10.1086/523366 · Cited by 232
Patterns of Intron Loss and Gain in Plants: Intron Loss-Dominated Evolution and Genome-Wide Comparison of O. sativa and A. thaliana
Roy, S. W., & Penny, D. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl159 · Cited by 225
Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate
Roscoe, B. P., Thayer, K. M., Zeldovich, K. B., Fushman, D., & Bolon, D. N. A. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.01.032 · Cited by 231
Protein Family Expansions and Biological Complexity
Vogel, C., & Chothia, C. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020048 · Cited by 227
Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes
Hou, Y., & Lin, S. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006978 · Cited by 225
Evolution of genome architecture
Koonin, E. V. (2008) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2008.09.015 · Cited by 223
Deletional Bias across the Three Domains of Life
Kuo, C., & Ochman, H. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp016 · Cited by 220
Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution
Cavalier‐Smith, T. (2010) · Biology Direct · doi:10.1186/1745-6150-5-7 · Cited by 223
MACROEVOLUTION AND MACROECOLOGY THROUGH DEEP TIME
BUTTERFIELD, N. J. (2007) · Palaeontology · doi:10.1111/j.1475-4983.2006.00613.x · Cited by 267
Bursts of transposable elements as an evolutionary driving force
Belyayev, A. (2014) · Journal of Evolutionary Biology · doi:10.1111/jeb.12513 · Cited by 221
Understanding Randomness and its Impact on Student Learning: Lessons Learned from Building the Biology Concept Inventory (BCI)
Garvin-Doxas, K., & Klymkowsky, M. W. (2008) · CBE—Life Sciences Education · doi:10.1187/cbe.07-08-0063 · Cited by 216
Giant lungfish genome elucidates the conquest of land by vertebrates
Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, J. M., Irisarri, I., Wong, W. Y., Nowoshilow, S., Kneitz, S., Kawaguchi, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03198-8 · Cited by 211
Root of the Tree: The Significance, Evolution, and Origins of the Ribosome
Bowman, J. C., Petrov, A. S., Frenkel-Pinter, M., Penev, P. I., & Williams, L. D. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00742 · Cited by 197
The causes of epistasis
de Visser, J. A. G. M., Cooper, T. F., & Elena, S. F. (2011) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2011.1537 · Cited by 213
In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae
Macas, J., Novák, P., Pellicer, J., Čížková, J., Koblížková, A., Neumann, P., Fuková, I., Doležel, J., Kelly, L. J., & Leitch, I. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0143424 · Cited by 214
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
Abascal, F., Corvelo, A., Cruz, F., Villanueva‐Cañas, J. L., Vlasova, A. V., Marcet‐Houben, M., Martínez‐Cruz, B., Cheng, J. Y., Prieto, P., Quesada, V., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1090-1 · Cited by 221
Multiple roles of the coding sequence 5′ end in gene expression regulation
Tuller, T., & Zur, H. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1313 · Cited by 206
RESURRECTING THE ROLE OF TRANSCRIPTION FACTOR CHANGE IN DEVELOPMENTAL EVOLUTION
Lynch, V. J., & Wagner, G. P. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00440.x · Cited by 206
Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility
Denise, R., Abby, S. S., & Rocha, E. P. C. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000390 · Cited by 205
Evolution of the Cichlid Visual Palette through Ontogenetic Subfunctionalization of the Opsin Gene Arrays
Spady, T. C., Parry, J. W. L., Robinson, P. R., Hunt, D. M., Bowmaker, J. K., & Carleton, K. L. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl014 · Cited by 207
Evidence for Widespread Degradation of Gene Control Regions in Hominid Genomes
Keightley, P. D., Lercher, M. J., & Eyre‐Walker, A. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030042 · Cited by 198
Preservation of duplicate genes by originalization
Xue, C., & Fu, Y. (2008) · Genetica · doi:10.1007/s10709-008-9311-5 · Cited by 197
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication
Chapman, B., Bowers, J., Feltus, F. A., & Paterson, A. H. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507782103 · Cited by 198
How Do J-Proteins Get Hsp70 to Do So Many Different Things?
Craig, E. A., & Marszałek, J. (2017) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2017.02.007 · Cited by 197
Animals and the invention of the Phanerozoic Earth system
Butterfield, N. J. (2011) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2010.11.012 · Cited by 195
Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals
Lan, X., & Pritchard, J. K. (2016) · Science · doi:10.1126/science.aad8411 · Cited by 194
Environmental drivers of a microbial genomic transition zone in the ocean’s interior
Mende, D. R., Bryant, J. A., Aylward, F. O., Eppley, J. M., Nielsen, T., Karl, D. M., & DeLong, E. F. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0008-3 · Cited by 203
Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps?
van Baarlen, P., van Belkum, A., Summerbell, R. C., Crous, P. W., & Thomma, B. P. H. J. (2007) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2007.00065.x · Cited by 201
Alternative splicing and the evolution of phenotypic novelty
Bush, S. J., Chen, L., Tovar-Corona, J. M., & Urrutia, A. O. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0474 · Cited by 200
Revisiting horizontal transfer of transposable elements in Drosophila
Loreto, É. L. S., Carareto, C. M. A., & Capy, P. (2008) · Heredity · doi:10.1038/sj.hdy.6801094 · Cited by 192
Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes
Keller, I., Bensasson, D., & Nichols, R. A. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030022 · Cited by 188
RNA velocity unraveled
Gorin, G., Fang, M., Chari, T., & Pachter, L. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010492 · Cited by 186
Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon
PATERSON, A., Chapman, B., Kissinger, J. C., Bowers, J., Feltus, F. A., & Estill, J. C. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.09.003 · Cited by 186
Intron Size, Abundance, and Distribution within Untranslated Regions of Genes
Hong, X., Scofield, D. G., & Lynch, M. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl111 · Cited by 190
Self-citation
Three distinct modes of intron dynamics in the evolution of eukaryotesPreprint
Carmel, L., Wolf, Y. I., Rogozin, I. B., & Koonin, E. V. (2007) · Genome Research · doi:10.1101/gr.6438607 · Cited by 182
Long-term evolution of transposable elements
Rouzic, A. L., Boutin, T., & Capy, P. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0705238104 · Cited by 182
Circular RNA Splicing
Eger, N., Schoppe, L., Schuster, S., Laufs, U., & Boeckel, J. (2018) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-1426-1_4 · Cited by 184
Is oxygen limitation in warming waters a valid mechanism to explain decreased body sizes in aquatic ectotherms?
Audzijonytė, A., Barneche, D. R., Baudron, A., Belmaker, J., Clark, T. D., Marshall, C. T., Morrongiello, J. R., & van Rijn, I. (2018) · Global Ecology and Biogeography · doi:10.1111/geb.12847 · Cited by 180
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
Makarova, K. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki775 · Cited by 180
The Extinction Dynamics of Bacterial Pseudogenes
Kuo, C., & Ochman, H. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001050 · Cited by 186
Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians
Tenaillon, M. I., Hufford, M. B., Gaut, B. S., & Ross‐Ibarra, J. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr008 · Cited by 177
Dynamics of transposable elements: towards a community ecology of the genome
Venner, S., Feschotte, C., & Biémont, C. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.05.003 · Cited by 181
Evolution of bird genomes—a transposon's‐eye view
Kapusta, A., & Suh, A. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13295 · Cited by 178
Transposons, Genome Size, and Evolutionary Insights in Animals
Canapa, A., Barucca, M., Biscotti, M. A., Forconi, M., & Olmo, E. (2015) · Cytogenetic and Genome Research · doi:10.1159/000444429 · Cited by 164
Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity
Chen, L., Bush, S. J., Tovar-Corona, J. M., Castillo-Morales, A., & Urrutia, A. O. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu083 · Cited by 173
Diversity and evolution of the animal virome
Harvey, E., & Holmes, E. C. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00665-x · Cited by 178
Reductive genome evolution at both ends of the bacterial population size spectrum
Batut, B., Knibbe, C., Marais, G. A. B., & Daubin, V. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3331 · Cited by 164
A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes
Csürös, M., Rogozin, I. B., & Koonin, E. V. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002150 · Cited by 168
Copy Number Variation Shapes Genome Diversity in Arabidopsis Over Immediate Family Generational Scales
DeBolt, S. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq033 · Cited by 172
Why Transcription Factor Binding Sites Are Ten Nucleotides Long
Stewart, A. J., Hannenhalli, S. S., & Plotkin, J. B. (2012) · Genetics · doi:10.1534/genetics.112.143370 · Cited by 174
Genomic Confirmation of Hybridisation and Recent Inbreeding in a Vector-Isolated Leishmania Population
Rogers, M. B., Downing, T., Smith, B. A., Imamura, H., Sanders, M. J., Svobodová, M., Volf, P., Berriman, M., Cotton, J. A., & Smith, D. F. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004092 · Cited by 167
Theory of prokaryotic genome evolution
Sela, I., Wolf, Y. I., & Koonin, E. V. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1614083113 · Cited by 165
Dynamics of genomic innovation in the unicellular ancestry of animals
Grau‐Bové, X., Torruella, G., Donachie, S. P., Suga, H., Leonard, G., Richards, T. A., & Ruiz‐Trillo, I. (2017) · eLife · doi:10.7554/elife.26036 · Cited by 171
Gene gain and loss across the metazoan tree of life
Fernández, R., & Gabaldón, T. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-019-1069-x · Cited by 165
Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees
Lloréns, C., Fuentes, A. M.-P., Bernad, L., Botella, H., & Moyá, A. (2009) · Biology Direct · doi:10.1186/1745-6150-4-41 · Cited by 161
Constraints and plasticity in genome and molecular-phenome evolution
Koonin, E. V., & Wolf, Y. I. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2810 · Cited by 167
Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
de Souza, F. S. J., Franchini, L. F., & Rubinstein, M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst045 · Cited by 170
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
Åkerborg, Ö., Sennblad, B., Arvestad, L., & Lagergren, J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806251106 · Cited by 161
Viruses and mobile elements as drivers of evolutionary transitions
Koonin, E. V. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0442 · Cited by 161
Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?
Lee, H., Zhang, Z., & Krause, H. M. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.09.006 · Cited by 164
Evolutionary temperature compensation of carbon fixation in marine phytoplankton
Barton, S., Jenkins, J., Buckling, A. G. J., Schaum, C., Smirnoff, N., Raven, J. A., & Yvon‐Durocher, G. (2020) · Ecology Letters · doi:10.1111/ele.13469 · Cited by 160
The mode and tempo of genome size evolution in eukaryotesPreprint
Oliver, M. J., Petrov, D. A., Ackerly, D. D., Falkowski, P. G., & Schofield, O. (2007) · Genome Research · doi:10.1101/gr.6096207 · Cited by 159
New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation
McLysaght, A., & Guerzoni, D. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0332 · Cited by 161
Marine Protists Are Not Just Big Bacteria
Keeling, P. J., & del Campo, J. (2017) · Current Biology · doi:10.1016/j.cub.2017.03.075 · Cited by 162
Prevalence of intron gain over intron loss in the evolution of paralogous gene families
Babenko, V. N. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh686 · Cited by 156
Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
Goodstadt, L., & Ponting, C. P. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020133 · Cited by 154
Genome Size and the Phenotype
Greilhuber, J., & Leitch, I. J. (2012) · Springer eBooks · doi:10.1007/978-3-7091-1160-4_20 · Cited by 154
The evolution of nuclear genome structure in seed plants
Kellogg, E. A., & Bennetzen, J. L. (2004) · American Journal of Botany · doi:10.3732/ajb.91.10.1709 · Cited by 151
The Considerable Genome Size Variation of Hordeum Species (Poaceae) Is Linked to Phylogeny, Life Form, Ecology, and Speciation Rates
Jakob, S. S., Meister, A., & Blattner, F. R. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh092 · Cited by 151
The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity
Hanschen, E. R., Marriage, T. N., Ferris, P. J., Hamaji, T., Toyoda, A., Fujiyama, A., Neme, R., Noguchi, H., Minakuchi, Y., Suzuki, M., et al. (2016) · Nature Communications · doi:10.1038/ncomms11370 · Cited by 160
Origin of Spliceosomal Introns and Alternative SplicingPreprint
Irimia, M., & Roy, S. W. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016071 · Cited by 155
Factors driving effective population size and pan-genome evolution in bacteria
Bobay, L., & Ochman, H. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1272-4 · Cited by 158
Using Population Genetic Theory and DNA Sequences for Species Detection and Identification in Asexual Organisms
Birky, C. W., Adams, J. M., Gemmel, M., & Perry, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010609 · Cited by 149
Comparative genomics of 10 new Caenorhabditis species
Stevens, L., Félix, M., Beltran, T., Braendle, C., Caurcel, C., Fausett, S. R., Fitch, D. H. A., Frézal, L., Gosse, C., Kaur, T., et al. (2019) · Evolution Letters · doi:10.1002/evl3.110 · Cited by 144
The Evolution of Bacterial Genome Architecture
Bobay, L., & Ochman, H. (2017) · Frontiers in Genetics · doi:10.3389/fgene.2017.00072 · Cited by 166
Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain
Zhao, J., Favero, D. S., Peng, H. F., & Neff, M. M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219277110 · Cited by 146
Comparative evolutionary genetics of spontaneous mutations affecting fitness in rhabditid nematodes
Baer, C. F., Shaw, F. H., Steding, C. E., Baumgartner, M., Hawkins, A., Houppert, A. S., Mason, N., Reed, M., Simonelic, K., Woodard, W., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406056102 · Cited by 146
Self-citation
Complex early genes
Roy, S. W., & Gilbert, W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408355101 · Cited by 146
Are There Laws of Genome Evolution?
Koonin, E. V. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002173 · Cited by 144
Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution
Arkhipova, I. R. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy083 · Cited by 141
Did Genetic Drift Drive Increases in Genome Complexity?
Whitney, K. D., & Garland, T. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001080 · Cited by 142
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
Coyne, R. S., Hannick, L. I., Shanmugam, D., Hostetler, J. B., Brami, D., Joardar, V., Johnson, J. H., Radune, D., Singh, I., Badger, J. H., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-10-r100 · Cited by 143
Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements
Naville, M., Henriet, S., Warren, I. A., Sumić, S., Reeve, M., Volff, J., & Chourrout, D. (2019) · Current Biology · doi:10.1016/j.cub.2019.01.080 · Cited by 142
The Repatterning of Eukaryotic Genomes by Random Genetic Drift
Lynch, M., Bobay, L., Catania, F., Goût, J.-F., & Rho, M. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082410-101412 · Cited by 148
Self-citation
Energetics and genetics across the prokaryote-eukaryote divide
Lane, N. J. (2011) · Biology Direct · doi:10.1186/1745-6150-6-35 · Cited by 144
Horizontal Transposon Transfer in Eukarya: Detection, Bias, and Perspectives
Wallau, G. L., Ortiz, M. F., & Loreto, É. L. S. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs055 · Cited by 151
Physical foundations of biological complexity
Wolf, Y. I., Katsnelson, M. I., & Koonin, E. V. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1807890115 · Cited by 155
Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin’s Paradox
Buffalo, V. (2021) · eLife · doi:10.7554/elife.67509 · Cited by 146
On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements
Bourgeois, Y., & Boissinot, S. (2019) · Genes · doi:10.3390/genes10060419 · Cited by 149
Complexity, simplicity, and epidemiology
Pearce, N., & Merletti, F. (2006) · International Journal of Epidemiology · doi:10.1093/ije/dyi322 · Cited by 140

Authors: Lynch, M., & Conery, J. S.
Affiliations: University of Oregon (US)
Corresponding author: Lynch, Michael
ORCID: Lynch, Michael
Conery, John S.
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2003-11-21
Volume: 302
Issue: 5649
Pages: 1401-1404
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.1089370
OpenAlex: W1988714210
Cited by: 1,698
References: 32
Citations by year: 2026: 63 · 2025: 70 · 2024: 95 · 2023: 53 · 2022: 58 · 2021: 82 · 2020: 80 · 2019: 70 · 2018: 70 · 2017: 71 · 2016: 89 · 2015: 65 · 2014: 68 · 2013: 77 · 2012: 90
FWCI: 69.03
Type: journal article
Language: en
Open access: closed
Locations: Science (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 › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: genome complexity, eukaryotic genome evolution, gene duplication, spliceosomal introns, mobile genetic elements, population size reduction, organism size, effective population size, prokaryotes, multicellularity, phenotypic complexity
MeSH terms: Alleles, Animals, Bacteria, Body Constitution, Fungi, Humans, Introns, Invertebrates, Mutation, Phylogeny, Plants, Population Density, Recombination, Genetic, Selection, Genetic, Genetic Variation, Vertebrates, Genome, Spliceosomes, Evolution, Molecular, Interspersed Repetitive Sequences, Gene Duplication, Gene Silencing, Genetic Drift, Eukaryota

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

The Origins of Genome Complexity

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