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Detecting Individual Sites Subject to Episodic Diversifying Selection
Open accessAbstract
The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. Existing computational techniques, which are designed to identify sites subject to pervasive selection, may fail to recognize sites where selection is episodic: a large proportion of positively selected sites. We present a mixed effects model of evolution (MEME) that is capable of identifying instances of both episodic and pervasive positive selection at the level of an individual site. Using empirical and simulated data, we demonstrate the superior performance of MEME over older models under a broad range of scenarios. We find that episodic selection is widespread and conclude that the number of sites experiencing positive selection may have been vastly underestimated.
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“Positively selected sites were identified using two different methods: the Bayes Empirical Bayes (BEB) analysis from MA (with a cutoff of 0.90) and the Mixed Effects Model of Evolution (MEME) (with the default cutoff of 0.1)34.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [34]
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“However, this test can be misleading because estimates of ! can be increased by processes such as intensification of positive selection when selective pressures vary both along branches and sites (Murrell et al. 2012).”
From RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015) · cites this paper as Murrell et al. 2012
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“Standard methods for estimating the strength and extent of purifying or positive selection from molecular sequence data are not suitable for detecting relaxed selection, because they lack power and can mistake an increase in the intensity of positive selection for relaxation of both purifying and positive selection.”
From RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015) · cites this paper as Murrell et al. 2012
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“To be conservative, we considered as positively selected only sites also detected by the Mixed Effects Model of Evolution (MEME) method34.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [34]
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“This development vastly increased the detectable instances of positive selection (Murrell et al. 2012).”
From RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015) · cites this paper as Murrell et al. 2012
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“Our random effects (Kosakovsky Pond et al. 2011) and mixed effects (Murrell et al. 2012) branch-site models allow detection of individual branches on which only a subset of sites are under positive selection or, conversely, individual sites which are under positive selection on only a subset of branches.”
From RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015) · cites this paper as Murrell et al. 2012
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Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolutionary Rate at the Molecular Level
KIMURA, M. (1968) · Nature · doi:10.1038/217624a0 · Cited by 3,747
Adaptive protein evolution at the Adh locus in Drosophila
McDonald, J. H., & Kreitman, M. (1991) · Nature · doi:10.1038/351652a0 · Cited by 3,313
Self, S., & Liang, K.-Y. (1987) · Journal of the American Statistical Association · doi:10.1080/01621459.1987.10478472 · Cited by 2,861
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
Pond, S. L. K., & Frost, S. D. W. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi105 · Cited by 2,320
Codon-substitution models for heterogeneous selection pressure at amino acid sites
Yang, Z., Nielsen, R., Goldman, N., & Pedersen, A.-M. K. (2000) · Genetics · doi:10.1093/genetics/155.1.431 · Cited by 2,286
Hughes, A. L., & Nei, M. (1988) · Nature · doi:10.1038/335167a0 · Cited by 1,976
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
Nielsen, R., & Yang, Z. (1998) · Genetics · doi:10.1093/genetics/148.3.929 · Cited by 1,622
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Molecular analysis of non structural rotavirus group A enterotoxin gene of bovine origin from India
Malik, Y. S., Kumar, N., Sharma, K. K., Ghosh, S., Bànyai, K., Ganesh, B., Kobayashi, N., & Matthijnssens, J. (2014) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2014.04.004 · Cited by 11
Molecular evolution of candidate male reproductive genes in the brown algal model Ectocarpus
Lipinska, A. P., Damme, E. J. M. V., & Clerck, O. D. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0577-9 · Cited by 11
Singarete, M. E., Grizante, M. B., Milograna, S. R., Nery, M. F., Kin, K., Wagner, G. P., & Kohlsdorf, T. (2015) · Genetics and Molecular Biology · doi:10.1590/s1415-475738320150039 · Cited by 11
Laver, C., & Matsubara, J. A. (2017) · Experimental Eye Research · doi:10.1016/j.exer.2017.03.005 · Cited by 11
Delaye, L., Ruiz‐Ruiz, S., Calderón, E. J., Tarazona, S., Conesa, A., & Moyá, A. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy116 · Cited by 11
Geyer, L. B., Zigler, K. S., Tiozzo, S., & Lessios, H. A. (2020) · Scientific Reports · doi:10.1038/s41598-020-66390-2 · Cited by 11
Wang, C., Zeng, Z.-Q., & Zhuang, W.-Y. (2021) · Microbial Genomics · doi:10.1099/mgen.0.000646 · Cited by 12
Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing
Cassidy, H., Schuele, L., Lizarazo, E., Couto, N., Rossen, J. W. A., Friedrich, A. W., van Leer‐Buter, C., & Niesters, H. G. M. (2022) · Virus Evolution · doi:10.1093/ve/veab109 · Cited by 11
Vuono, E. A., Ramírez-Medina, E., Pruitt, S., Rai, A., Espinoza, N., Spinard, E. J., Valladares, A., Silva, E. B., Velázquez-Salinas, L., Borca, M. V., et al. (2022) · Viruses · doi:10.3390/v14081682 · Cited by 11
Pu, D.-Q., Liu, H.-L., Wu, X.-L., & Chen, Z.-T. (2022) · Genes · doi:10.3390/genes13101881 · Cited by 11
Chong, S. L., Tan, J. L., & Ngeow, Y. F. (2022) · BMC Genomics · doi:10.1186/s12864-022-08941-7 · Cited by 11
Navarro‐López, R., Xu, W., Gómez‐Romero, N., Velázquez-Salinas, L., & Berhane, Y. (2022) · Pathogens · doi:10.3390/pathogens11111284 · Cited by 11
High functional allelic diversity and copy number in both MHC classes in the common buzzard
Winternitz, J. C., Chakarov, N., Rinaud, T., Ottensmann, M., & Krüger, O. (2023) · BMC Ecology and Evolution · doi:10.1186/s12862-023-02135-9 · Cited by 12
Ancient duplication, coevolution, and selection at the MHC class IIA and IIB genes of birds
Minias, P., Edwards, S. V., & Babik, W. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1250824 · Cited by 13
Jagadeeshan, S., Coppard, S. E., & Lessios, H. A. (2015) · Evolution & Development · doi:10.1111/ede.12108 · Cited by 11
Identification of positive selection in disease response genes within members of the Poaceae
Rech, G. E., Vargas, W. A., Sukno, S. A., & Thon, M. R. (2012) · Plant Signaling & Behavior · doi:10.4161/psb.22362 · Cited by 11
Functional evolution of the OAS1 viral sensor: Insights from old world primates
Fish, I. H., & Boissinot, S. (2016) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2016.07.005 · Cited by 11
Huang, B.-H., Chen, Y.-W., Huang, C., Gao, J., & Liao, P. (2016) · Scientific Reports · doi:10.1038/srep39031 · Cited by 10
Multiple major histocompatibility complex class I genes in Asian anurans: Ontogeny and phylogeny
Didinger, C., Eimes, J. A., Lillie, M., & Waldman, B. (2016) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2016.12.003 · Cited by 11
Cuypers, L., Libin, P., Schrooten, Y., Theys, K., Maio, V. C. D., Cento, V., Lunar, M. M., Nevens, F., Poljak, M., Ceccherini‐Silberstein, F., et al. (2017) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2017.05.007 · Cited by 11
Talbot, B., Balvín, O., Vonhof, M. J., Broders, H. G., Fenton, M. B., & Keyghobadi, N. (2017) · Royal Society Open Science · doi:10.1098/rsos.170446 · Cited by 11
Biedrzycka, A., Konopiński, M. K., Hoffman, E. A., Trujillo, A. L., & Zalewski, A. (2019) · Evolutionary Applications · doi:10.1111/eva.12898 · Cited by 11
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Xu, W., Weese, J. S., Ojkić, D., Lung, O., Handel, K., & Berhane, Y. (2020) · Scientific Reports · doi:10.1038/s41598-020-63278-z · Cited by 11
Cestode strobilation: prediction of developmental genes and pathways
Paludo, G. P., Thompson, C. E., Miyamoto, K. N., Guedes, R. L. M., Zaha, A., de Vasconcelos, A. T. R., Cancela, M., & Ferreira, H. B. (2020) · BMC Genomics · doi:10.1186/s12864-020-06878-3 · Cited by 10
Adult survival in migratory caribou is negatively associated with MHC functional diversity
Gagnon, M., Yannic, G., Boyer, F., & Côté, S. D. (2020) · Heredity · doi:10.1038/s41437-020-0347-3 · Cited by 11
Mwangi, P. N., Mogotsi, M. T., Seheri, M. L., Mphahlele, M. J., Peenze, I., Esona, M. D., Kumwenda, B., Steele, A. D., Kirkwood, C. D., Ndze, V. N., et al. (2020) · Vaccines · doi:10.3390/vaccines8040609 · Cited by 11
Emergence and adaptive evolution of influenza D virus
He, W., Lu, M., Xing, G., Shao, Y., Zhang, M., Yang, Y., Li, X., Zhang, L., Li, G., Cao, Z., et al. (2021) · Microbial Pathogenesis · doi:10.1016/j.micpath.2021.105193 · Cited by 11
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High genetic stability of co-circulating human adenovirus type 31 lineages over 59 years
Götting, J., Baier, C., Panagiota, V., Maecker‐Kolhoff, B., Dhingra, A., & Heim, A. (2022) · Virus Evolution · doi:10.1093/ve/veac067 · Cited by 11
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Melillo, D., Varriale, S., Giacomelli, S., Natale, L., Bargelloni, L., Oreste, U., Pinto, M. R., & Coscia, M. R. (2015) · Molecular Immunology · doi:10.1016/j.molimm.2015.03.247 · Cited by 11
ElSayed, A. I., Boulila, M., & Rott, P. (2014) · Journal of Molecular Evolution · doi:10.1007/s00239-014-9630-3 · Cited by 11
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Tao, J., Qi, Q., Kang, M., & Huang, H. (2015) · PLoS ONE · doi:10.1371/journal.pone.0127821 · Cited by 11
Garzón‐Ospina, D., Buitrago, S. P., Ramos, A. E., & Patarroyo, M. A. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00010 · Cited by 11
Králová, T., Albrecht, T., Bryja, J., Hořák, D., Johnsen, A., Lifjeld, J. T., Novotný, M., Sedláček, O., Velová, H., & Vinkler, M. (2018) · Molecular Ecology · doi:10.1111/mec.14724 · Cited by 11
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Coetzer, W. G., Turner, T. R., Schmitt, C. A., & Grobler, J. P. (2018) · PeerJ · doi:10.7717/peerj.4953 · Cited by 10
Johny, J., Diallo, S., Nadachowska‐Brzyska, K., Moliterno, A. A. C., Roy, A., Kalinová, B., Große‐Wilde, E., & Schlyter, F. (2025) · Molecular Ecology · doi:10.1111/mec.17693 · Cited by 10
Wang, D., Zhou, W., He, Q., Bai, Y., Zhang, L., Zhan, Y., Yang, Y., & Wang, N. (2025) · Virulence · doi:10.1080/21505594.2025.2535472 · Cited by 10
Eirin-Lopez, J. M., & Sánchez, L. (2015) · Development Genes and Evolution · doi:10.1007/s00427-015-0491-6 · Cited by 10
Bakiu, R., Korro, K., & Santovito, G. (2015) · The European Zoological Journal · doi:10.1080/11250003.2015.1018352 · Cited by 10
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Palomar, G., Dudek, K., Wielstra, B., Jockusch, E. L., Vinkler, M., Arntzen, J. W., Ficetola, G. F., Matsunami, M., Waldman, B., Těšičký, M., et al. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evaa259 · Cited by 10
Xu, W., & Yang, M. (2021) · Vaccine · doi:10.1016/j.vaccine.2021.01.042 · Cited by 10
Rhen, T., Even, Z., Brenner, A., Lodewyk, A., Das, D., Singh, S. K., & Simmons, R. B. (2021) · Sexual Development · doi:10.1159/000516973 · Cited by 10
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Chiara, M., Horner, D. S., Ferrandi, E., Gissi, C., & Pesole, G. (2023) · Communications Biology · doi:10.1038/s42003-023-04784-4 · Cited by 10
Boulila, M., TIBA, S. B., & Jilani, S. (2013) · Journal of Genetics · doi:10.1007/s12041-013-0211-9 · Cited by 10
Bradley, B. J., Snowdon, C. T., McGrew, W. C., Lawler, R. R., Guevara, E. E., McIntosh, A. M., & O’Connor, T. D. (2016) · American Journal of Primatology · doi:10.1002/ajp.22583 · Cited by 10
Pontremoli, C., Forni, D., Cagliani, R., & Sironi, M. (2018) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2018.06.031 · Cited by 10
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Dömel, J. S., Dietz, L., Macher, T., Rozenberg, A., Mayer, C., Spaak, J. M., Melzer, R. R., & Leese, F. (2020) · Polar Biology · doi:10.1007/s00300-020-02636-z · Cited by 10
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He, D., Gu, M., Wang, X., Wang, X., Li, G., Yan, Y., Gu, J., Zhan, T., Wu, H., Hao, X., et al. (2021) · Viruses · doi:10.3390/v13122524 · Cited by 10
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Paetzold, C., Barke, B. H., & Hörandl, E. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232213881 · Cited by 10
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Guevara, E. E., Veilleux, C. C., Saltonstall, K., Caccone, A., Mundy, N. I., & Bradley, B. J. (2016) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23046 · Cited by 10
Themudo, G. E., & Campos, P. F. (2017) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zlx034 · Cited by 10
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Wei, S., He, X., Wang, D., Jinyou, X., Yang, Y., Yuan, S., Shang, J., & Yang, H. (2019) · Archives of Virology · doi:10.1007/s00705-019-04342-6 · Cited by 9
Sang, S., Chen, P., Li, C., Zhang, A., Wang, Y., & Liu, Q. (2024) · Virus Evolution · doi:10.1093/ve/veae072 · Cited by 9
Tian, F., Zhou, B., Li, X., Zhang, Y., Qi, D., Qi, H., Jiang, H., Zhao, K., & Liu, S. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.125605 · Cited by 9
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Han, Z., Wang, F., Xiao, J., Fu, H., Song, Y., Jiang, M., Lu, H., Li, J., Xu, Y., Zhu, R., et al. (2023) · Virus Evolution · doi:10.1093/ve/vead080 · Cited by 9
Domańska-Blicharz, K., Lisowska, A., Opolska, J., Ruszkowski, J. J., Gogulski, M., & Pomorska‐Mól, M. (2024) · BMC Veterinary Research · doi:10.1186/s12917-024-04277-4 · Cited by 9
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Mah, M. G., Zeller, M. A., Zhang, R., Zhuang, Y., Maro, V. P., Crump, J. A., Rubach, M. P., Ooi, E. E., Low, J. G. H., Wang, D. Y., et al. (2024) · npj Viruses · doi:10.1038/s44298-024-00058-w · Cited by 10
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Salles, M. M. A., Carvalho, A. L. G., Leaché, A. D., Martinez, N., Bauer, F., Motte, M., Espínola, V., Rodrigues, M. T., Piantoni, C., Pie, M. R., et al. (2025) · Molecular Ecology · doi:10.1111/mec.70130 · Cited by 13
Zhang, W., León-Ricardo, B. X., van Schooten, B., Belleghem, S. M. V., Counterman, B. A., McMillan, W. O., Kronforst, M. R., & Papa, R. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz202 · Cited by 9
Tagliamonte, M. S., Yowell, C. A., Elbadry, M. A., Boncy, J., Raccurt, C. P., Okech, B. A., Goss, E. M., Salemi, M., & Dame, J. B. (2020) · mSphere · doi:10.1128/msphere.00937-20 · Cited by 9
Cuy-Chaparro, L., Bohórquez, M. D., Arévalo‐Pinzón, G., Castañeda-Ramírez, J. J., Suárez, C. F., Pabón, L., Ordóñez, D., Gallego-López, G. M., Suarez, C. E., Pérez, D. A. M., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22020714 · Cited by 9
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Metadata
- Authors
- Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Kosakovsky Pond, S. L.
- Affiliations
- Stellenbosch University (ZA)
- University of California San Diego (US)
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-07-12
- Volume
- 8
- Issue
- 7
- Pages
- e1002764
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3395634
- OpenAlex
- W2118982822
- Cited by
- 1,811
- References
- 63
- Citations by year
- 2026: 147 · 2025: 135 · 2024: 169 · 2023: 162 · 2022: 161 · 2021: 183 · 2020: 172 · 2019: 123 · 2018: 115 · 2017: 99 · 2016: 87 · 2015: 100 · 2014: 83 · 2013: 66 · 2012: 9
- FWCI
- 49.72
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- TUScholarShare (Temple University) (submittedVersion, cc-by)
- SUNScholar (Stellenbosch University) (submittedVersion)
- Funders
- National Science Foundation (0714991)
- European Commission
- National Research Foundation
- National Institutes of Health (AI47745, AI74621, AI-36214, AI57167, GM093939)
- Center for AIDS Research, University of Washington
- University of California, San Diego
- National Institute of General Medical Sciences (GM093939, R01GM093939)
- National Institute of Allergy and Infectious Diseases (R01AI057167, AI-74621, AI-47745, AI57167, R21AI047745, AI 43638, R24AI106039, R56AI047745, AI-36214, R01AI047745, U01AI043638, P01AI074621, P30AI036214, T32AI007384)
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- episodic selection, positive selection, memes, protein-coding genes, natural selection
- MeSH terms
- Amino Acids, Animals, Computer Simulation, Models, Theoretical, Phylogeny, Rhodopsin, Selection, Genetic, Vertebrates, Open Reading Frames, Evolution, Molecular, Computational Biology
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