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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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Lu, A., & Guindon, S. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst198 · Cited by 34
Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease
Principi, N., Piralla, A., Zampiero, A., Bianchini, S., Umbrello, G., Scala, A., Bosis, S., Fossali, E. F., Baldanti, F., & Esposito, S. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135640 · Cited by 35
The role of selection in the evolution of marine turtles mitogenomes
Ramos, E. K. D. S., Freitas, L. A., & Nery, M. F. (2020) · Scientific Reports · doi:10.1038/s41598-020-73874-8 · Cited by 34
Comparative Genomics Reveals Early Emergence and Biased Spatiotemporal Distribution of SARS-CoV-2
Chiara, M., Horner, D. S., Gissi, C., & Pesole, G. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab049 · Cited by 37
Beres, S. B., Zhu, L., Pruitt, L., Olsen, R. J., Faili, A., Kayal, S., & Musser, J. M. (2022) · mBio · doi:10.1128/mbio.03618-21 · Cited by 36
Wang, W., He, X., Zhang, Y., Qiao, Y., Shi, J., Chen, R., Chen, J., Xiang, Y., Wang, Z., Chen, G., et al. (2022) · Transboundary and Emerging Diseases · doi:10.1111/tbed.14634 · Cited by 35
Piñana, M., Gónzalez‐Sánchez, A., Andrés, C., Vila, J., Creus‐Costa, A., Prats‐Méndez, I., Arnedo‐Muñoz, M., Saubi, N., Esperalba, J., Rando‐Segura, A., et al. (2024) · Journal of Infection · doi:10.1016/j.jinf.2024.106153 · Cited by 34
Ballinger, M. J., Bruenn, J. A., Kotov, A. A., & Taylor, D. J. (2013) · Virology · doi:10.1016/j.virol.2013.07.032 · Cited by 34
The ‘emergence’ of turnip mosaic virus was probably a ‘gene-for-quasi-gene’ event
Gibbs, A. J., Nguyen, H. D., & Ohshima, K. (2015) · Current Opinion in Virology · doi:10.1016/j.coviro.2014.12.004 · Cited by 34
Lycett, S., Tanya, V. N., Hall, M. D., King, D. P., Mazeri, S., Mioulet, V., Knowles, N. J., Wadsworth, J., Bachanek‐Bankowska, K., Ngwa, V. N., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-41995-4 · Cited by 34
A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum
Castillo, J. A., & Agathos, S. N. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1456-6 · Cited by 34
Takeuchi, J. S., Fukano, K., Iwamoto, M., Tsukuda, S., Suzuki, R., Aizaki, H., Muramatsu, M., Wakita, T., Sureau, C., & Watashi, K. (2018) · Journal of Virology · doi:10.1128/jvi.01432-18 · Cited by 38
Tan, C. Y., Opaskornkul, K., Thanawongnuwech, R., Arshad, S. S., Hassan, L., & Ooi, P. T. (2020) · PLoS ONE · doi:10.1371/journal.pone.0235832 · Cited by 34
Widespread Evolution of Molecular Resistance to Snake Venom α-Neurotoxins in Vertebrates
Khan, M. A., Dashevsky, D., Kerkkamp, H. M. I., Kordiš, D., Bakker, M., Wouters, R. M., van Thiel, J., den Brouw, B. O., Vonk, F. J., Kini, R. M., et al. (2020) · Toxins · doi:10.3390/toxins12100638 · Cited by 35
Genetic diversity and evolution of goose astrovirus in the east of China
Fei, Z., Jiao, A., Xu, M., Wu, J., Wang, Y., Yu, J., Lu, L., Jiang, W., Zhu, G., Sun, W., et al. (2022) · Transboundary and Emerging Diseases · doi:10.1111/tbed.14542 · Cited by 34
Farquharson, K. A., McLennan, E. A., Cheng, Y., Alexander, L., Fox, S., Lee, A. V., Belov, K., & Hogg, C. J. (2022) · iScience · doi:10.1016/j.isci.2022.104474 · Cited by 35
Selection on MHC class II supertypes in the New Zealand endemic Hochstetter’s frog
Lillie, M., Grueber, C. E., Sutton, J. T., Howitt, R., Bishop, P. J., Gleeson, D. M., & Belov, K. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0342-0 · Cited by 33
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Joseph, U., Linster, M., Suzuki, Y., Krauss, S. L., Halpin, R., Vijaykrishna, D., Fabrizio, T. P., Bestebroer, T. M., Maurer‐Stroh, S., Webby, R. J., et al. (2014) · Journal of Virology · doi:10.1128/jvi.02590-14 · Cited by 34
McBee, R. M., Rozmiarek, S. A., Meyerson, N. R., Rowley, P. A., & Sawyer, S. L. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu399 · Cited by 38
IMPACT_S: Integrated Multiprogram Platform to Analyze and Combine Tests of Selection
Maldonado, E., Sunagar, K., Almeida, D., Vasconcelos, V. M., & Antunes, A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0096243 · Cited by 33
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Cagliani, R., Forni, D., Tresoldi, C., Pozzoli, U., Filippi, G., Rainone, V., GIOIA, L. D., Clerici, M., & Sironi, M. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.10.040 · Cited by 34
Rico, Y., Morris‐Pocock, J. A., Zigouris, J., Nocera, J. J., & Kyle, C. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0140170 · Cited by 33
Dib, L., San‐Jose, L. M., Ducrest, A., Salamin, N., & Roulin, A. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18122618 · Cited by 34
A Single Mutation Unlocks Cascading Exaptations in the Origin of a Potent Pitviper Neurotoxin
Whittington, A. C., Mason, A. J., & Rokyta, D. R. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx334 · Cited by 33
Tan, Y., Lam, T. T., Heberlein-Larson, L., Smole, S., Auguste, A. J., Hennigan, S., Halpin, R., Fedorova, N. B., Puri, V., Stockwell, T. B., et al. (2018) · Journal of Virology · doi:10.1128/jvi.00074-18 · Cited by 33
Evolution and Genetic Diversity of Porcine Circovirus 3 in China
Chen, Y., Xu, Q., Chen, H., Luo, X., Wu, Q. H., Tan, C. S., Pan, Q., & Chen, J. (2019) · Viruses · doi:10.3390/v11090786 · Cited by 33
Zeller, M. A., Chang, J., Vincent, A. L., Gauger, P. C., & Anderson, T. K. (2021) · Virus Evolution · doi:10.1093/ve/veab090 · Cited by 33
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Das, S., Sarker, S., Peters, A., Ghorashi, S. A., Phalen, D. N., Forwood, J. K., & Raidal, S. R. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.04.024 · Cited by 33
MacLean, O. A., Lytras, S., Weaver, S., Singer, J. B., Boni, M. F., Lemey, P., Pond, S. L. K., & Robertson, D. L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.28.122366 · Cited by 33
Zimerman, R. A., Ferrareze, P. A. G., Cadegiani, F., Wambier, C. G., Fonseca, D. D. N., de Souza, A. R., Goren, A., Rotta, L. N., Ren, Z., & Thompson, C. E. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.806611 · Cited by 34
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Slimen, H. B., Schaschl, H., Knauer, F., & Suchentrunk, F. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-0896-0 · Cited by 32
Santibáñez‐López, C. E., Kriebel, R., Ballesteros, J. A., Rush, N., Witter, Z. L., Williams, J. R., Janies, D. A., & Sharma, P. P. (2018) · PeerJ · doi:10.7717/peerj.5902 · Cited by 32
Mao, X., & Rossiter, S. J. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106886 · Cited by 32
Bannantine, J. P., Condé, C., Bayles, D. O., Branger, M., & Biet, F. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01701 · Cited by 32
Emerging novel porcine parvoviruses in Europe: origin, evolution, phylodynamics and phylogeography
Cadar, D., Lőrincz, M., Kiss, T., Novosel, D., Podgórska, K., Becskei, Z., Tuboly, T., & Cságola, A. (2013) · Journal of General Virology · doi:10.1099/vir.0.055129-0 · Cited by 32
Ancient and Recent Selective Pressures Shaped Genetic Diversity at AIM2-Like Nucleic Acid Sensors
Cagliani, R., Forni, D., Biasin, M., Comabella, M., Guerini, F. R., Riva, S., Pozzoli, U., Agliardi, C., Caputo, D., Malhotra, S., et al. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu066 · Cited by 35
Solbakken, M. H., Voje, K. L., Jakobsen, K. S., & Jentoft, S. (2017) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2016.2810 · Cited by 31
Khan, A. A., Ali, R. H., & Mirza, B. (2020) · Journal of Molecular Evolution · doi:10.1007/s00239-020-09966-w · Cited by 31
Unraveling the Molecular Evolution of Blood Coagulation Genes in Fishes and Cetaceans
Mariz, J. P. V., & Nery, M. F. (2020) · Frontiers in Marine Science · doi:10.3389/fmars.2020.592383 · Cited by 31
Predicting the mutational drivers of future SARS-CoV-2 variants of concern
Maher, M. C., Bartha, I., Weaver, S., di Iulio, J., Ferri, E., Soriaga, L. B., Lempp, F. A., Hie, B., Bryson, B. D., Berger, B., et al. (2021) · DSpace@MIT (Massachusetts Institute of Technology) · doi:10.34944/dspace/6982 · Cited by 31
Positive Evolutionary Selection On the RIG-I-Like Receptor Genes in Mammals
de Matos, A. L., McFadden, G., & Esteves, P. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081864 · Cited by 31
Impact of spatial dispersion, evolution and selection on Ebola Zaire Virus epidemic waves
Azarian, T., Presti, A. L., Giovanetti, M., Cella, E., Magalis, B. R., Lai, A., Zehender, G., Ciccozzi, M., & Salemi, M. (2015) · Scientific Reports · doi:10.1038/srep10170 · Cited by 34
Molecular Evolution, Diversity, and Adaptation of Influenza A(H7N9) Viruses in China
Lu, J., Raghwani, J., Wu, J., Pryce, R., Bowden, T. A., Thézé, J., Shanqian, H., Song, Y., 邹丽容, Liang, L., et al. (2018) · Emerging infectious diseases · doi:10.3201/eid2410.171063 · Cited by 31
Otieno, J. R., Kamau, E., Oketch, J. W., Ngoi, J. M., Gichuki, A. M., Binter, Š., Otieno, G. P., Ngama, M., Agoti, C. N., Cane, P. A., et al. (2018) · Virus Evolution · doi:10.1093/ve/vey027 · Cited by 31
Ayalew, L. E., Ahmed, K. A., Mekuria, Z. H., Lockerbie, B. P., Popowich, S., Tikoo, S. K., Ojkić, D., & Gomis, S. M. (2020) · Virus Evolution · doi:10.1093/ve/veaa025 · Cited by 31
Sorouri, M., Chang, T., Jesudhasan, P. R. R., Pinkham, C., Elde, N. C., & Hancks, D. C. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3001045 · Cited by 27
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Trujillo, A. L., Hoffman, E. A., Becker, C. G., & Savage, A. E. (2021) · Heredity · doi:10.1038/s41437-020-00402-9 · Cited by 30
Xavier, J., Alcantara, L. C. J., Fonseca, V., Lima, M. T., Castro, E., Fritsch, H. M., de Oliveira, C. S., Guimarães, N. R., Adelino, T., Evaristo, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40099-y · Cited by 31
Kim, M.-K., Seo, J., Kwak, H.-R., Kim, J.-S., Kim, K., Cha, B., & Choi, H.-S. (2014) · Phytopathology · doi:10.1094/phyto-10-13-0275-r · Cited by 31
Natural selection drives the evolution of mitogenomes in Acrossocheilus
Zhao, D., Guo, Y., & Gao, Y. (2022) · PLoS ONE · doi:10.1371/journal.pone.0276056 · Cited by 30
Zehr, J. D., Kosakovsky Pond, S. L., Millet, J. K., Olarte-Castillo, X. A., Lucaci, A. G., Shank, S. D., Ceres, K. M., Choi, A., Whittaker, G. R., Goodman, L. B., et al. (2023) · Virus Evolution · doi:10.1093/ve/vead019 · Cited by 30
Fischer, W., Apetrei, C., Santiago, M. L., Li, Y., Gautam, R., Pandrea, I., Shaw, G. M., Hahn, B. H., Letvin, N. L., Nabel, G. J., et al. (2012) · Journal of Virology · doi:10.1128/jvi.01862-12 · Cited by 30
Baculovirus Molecular Evolution via Gene Turnover and Recurrent Positive Selection of Key Genes
Hill, T., & Unckless, R. L. (2017) · Journal of Virology · doi:10.1128/jvi.01319-17 · Cited by 28
Kammerer, R., Mansfeld, M., Hänske, J., Mißbach, S., He, X., Köllner, B., Mouchantat, S., & Zimmermann, W. (2017) · BMC Genomics · doi:10.1186/s12864-017-4106-7 · Cited by 30
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Stenzel, T., Dziewulska, D., Muhire, B. M., Hartnady, P., Kraberger, S. J., Martin, D. P., & Varsani, A. (2018) · Viruses · doi:10.3390/v10030107 · Cited by 30
Forni, D., Pontremoli, C., Pozzoli, U., Clerici, M., Cagliani, R., & Sironi, M. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy050 · Cited by 30
Subramaniam, S., Sanyal, A., Mohapatra, J. K., Sharma, G. K., BISWAL, J. K., Ranjan, R., Rout, M., Das, B., Bisht, P., Mathapati, B., et al. (2013) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2013.04.027 · Cited by 29
Forni, D., Cagliani, R., Pozzoli, U., Colleoni, M., Riva, S., Biasin, M., Filippi, G., GIOIA, L. D., Gnudi, F., Comi, G. P., et al. (2013) · Immunity · doi:10.1016/j.immuni.2013.04.008 · Cited by 29
Optimization strategies for fast detection of positive selection on phylogenetic trees
Valle, M., Schabauer, H., Pacher, C., Heinz Stockinger, C., Stamatakis, A., Robinson‐Rechavi, M., & Salamin, N. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt760 · Cited by 28
A system-level, molecular evolutionary analysis of mammalian phototransduction
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Nam, K., Lee, K. W., Chung, O., Yim, H., Cha, S., Lee, S.-W., Jun, J., Cho, Y. S., Bhak, J., de Magalhães, J. P., et al. (2017) · Scientific Reports · doi:10.1038/srep40233 · Cited by 31
Cicconardi, F., Marino, D. D., Olimpieri, P. P., Arthofer, W., Schlick-Steiner, B. C., & Steiner, F. M. (2017) · Scientific Reports · doi:10.1038/srep43770 · Cited by 27
Posso-Terranova, A. M., & Andrés, J. Á. (2017) · Evolution · doi:10.1111/evo.13335 · Cited by 29
Awadi, A., Slimen, H. B., Smith, S., Knauer, F., Makni, M., & Suchentrunk, F. (2018) · Scientific Reports · doi:10.1038/s41598-018-29657-3 · Cited by 29
Tan, Y., Pickett, B. E., Shrivastava, S., Gresh, L., Balmaseda, Á., Amedeo, P., Hu, L., Puri, V., Fedorova, N. B., Halpin, R., et al. (2018) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0006670 · Cited by 29
Khan, I., Maldonado, E., Silva, L., Almeida, D., Johnson, W. E., O’Brien, S. J., Zhang, G., Jarvis, E. D., Gilbert, M. T. P., & Antunes, A. (2019) · Diversity · doi:10.3390/d11080131 · Cited by 29
Zimmermann, W., & Kammerer, R. (2021) · BMC Genomics · doi:10.1186/s12864-021-07413-8 · Cited by 29
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Nayyab, S., Gervasi, M. G., Tourzani, D. A., Caraballo, D. A., Jha, K. N., Teves, M. E., Cui, W., Georg, G. I., Visconti, P. E., & Salicioni, A. M. (2021) · Molecular Reproduction and Development · doi:10.1002/mrd.23539 · Cited by 29
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Shaikh, N. Y., & Sunagar, K. (2023) · eLife · doi:10.7554/elife.83761 · Cited by 31
Zeisset, I., & Beebee, T. J. C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100176 · Cited by 29
Deep venomics of the Pseudonaja genus reveals inter- and intra-specific variation
Reeks, T., Lavergne, V., Sunagar, K., Jones, A., Undheim, E. A. B., Dunstan, N. L., Fry, B. G., & Alewood, P. F. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.11.019 · Cited by 29
CenH3 evolution reflects meiotic symmetry as predicted by the centromere drive model
Zedek, F., & Bureš, P. (2016) · Scientific Reports · doi:10.1038/srep33308 · Cited by 29
Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation
Cicconardi, F., Marcatili, P., Arthofer, W., Schlick-Steiner, B. C., & Steiner, F. M. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.04.023 · Cited by 25
Minias, P., Pikus, E., & Anderwald, D. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1338-3 · Cited by 29
Sunagar, K., Fry, B. G., Jackson, T., Casewell, N. R., Undheim, E. A. B., Vidal, N., Ali, S. A., King, G. F., Vasudevan, K., Vasconcelos, V. M., et al. (2013) · PLoS ONE · doi:10.1371/annotation/accecc73-91b2-45d4-bb33-774b1f394ca1 · Cited by 30
de Jong, M., van Oosterhout, C., Hoelzel, A. R., & Janke, A. (2023) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.13010 · Cited by 31
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Sun, J., Duan, X., Hoffmann, A. A., Liu, Y., Garvin, M. R., Chen, L., Hu, G., Zhou, J., Huang, H., Xue, X., et al. (2019) · Molecular Ecology · doi:10.1111/mec.15148 · Cited by 29
Suttie, A., Tok, S., Yann, S., Keo, P., Horm, S. V., Roe, M., Kaye, M., Sorn, S., Holl, D., Tum, S., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0226108 · Cited by 28
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Xiang, B., Chen, L., Cai, J., Liang, J., Lin, Q., Xu, C., Ding, C., Liao, M., & Ren, T. (2020) · Pathogens · doi:10.3390/pathogens9100837 · Cited by 28
Li, Y., Wang, S., Cheng, C., Jiaqi, Z., Supen, W., Hou, X., Liu, X., Xuejiao, Y., & XianPing, L. (2020) · Ecography · doi:10.1111/ecog.05082 · Cited by 27
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Xiao, J., Huang, K., Lu, H., Song, Y., Han, Z., Zhang, M., Li, J., Zhou, X., Chen, J., Yu, Q., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.01958-22 · Cited by 28
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Self-citationPacheco, M. A., Kadakia, E. R., Chaudhary, Z., Perkins, D. J., Kelley, J., Ravishankar, S., Cranfield, M. R., Talundzic, E., Udhayakumar, V., & Escalante, A. A. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02550-18 · Cited by 30
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Despot-Slade, E., Mravinac, B., Širca, S., Castagnone‐Sereno, P., Plohl, M., & Meštrović, N. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa336 · Cited by 27
Gasmi, L., Baek, S., Kim, J. C., Kim, S., Lee, M. R., Park, S. E., Shin, T. Y., Lee, S. J., Parker, B. L., & Kim, J. S. (2021) · Scientific Reports · doi:10.1038/s41598-020-78910-1 · Cited by 32
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
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.
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