The DOI matches its Crossref record; 63 of the 63 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“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]
The cited source says what the claim attributes to it.
In the citing paper
“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
The cited source says what the claim attributes to it.
In the citing paper
“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
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
Flagged first, then by citations
Cited by
Sorted by citations
Items 401–500 of 1,003
York, J. M., & Zakon, H. H. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac009 · Cited by 27
Decoupled evolution of the Sex Peptide gene family and Sex Peptide Receptor in Drosophilidae
Hopkins, B. R., Angus-Henry, A., Kim, B. Y., Carlisle, J. A., Thompson, A., & Kopp, A. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2312380120 · Cited by 29
Kraberger, S. J., Kumari, S. G., Hamed, A. A., Gronenborn, B., Thomas, J. E., Sharman, M., Harkins, G. W., Muhire, B. M., Martin, D. P., & Varsani, A. (2014) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2014.11.024 · Cited by 27
Two mitochondrial genes under episodic positive selection in subterranean octodontoid rodents
Tomasco, I. H., & Lessa, E. P. (2013) · Gene · doi:10.1016/j.gene.2013.09.097 · Cited by 27
Phylogeographic analysis of rabies viruses in the Philippines
Tohma, K., Saito, M., Kamigaki, T., Tuason, L. T., Demetria, C. S., Orbina, J. R. C., MANALO, D. L., Miranda, M. E., Noguchi, A., Inoue, S., et al. (2014) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2014.01.026 · Cited by 27
Laenen, L., Dellicour, S., Vergote, V., Nauwelaers, I., Coster, S. D., Verbeeck, I., Vanmechelen, B., Lemey, P., & Maes, P. (2016) · Molecular Ecology · doi:10.1111/mec.13887 · Cited by 29
Molecular evolution of key metabolic genes during transitions to C4 and CAM photosynthesis
Goolsby, E. W., Moore, A. J., Hancock, L. P., de Vos, J. M., & Edwards, E. J. (2018) · American Journal of Botany · doi:10.1002/ajb2.1051 · Cited by 27
Cross-species analysis of apical asparagine-rich protein of Plasmodium vivax and Plasmodium knowlesi
Muh, F., Ahmed, M. A., Han, J., Nyunt, M. H., Lee, S., Lau, Y. L., Kaneko, O., & Han, E. (2018) · Scientific Reports · doi:10.1038/s41598-018-23728-1 · Cited by 27
Wu, Z., Mo, C., Zhang, S., & Li, H. (2018) · Scientific Reports · doi:10.1038/s41598-018-26596-x · Cited by 27
Man, J., Harrington, T. A., Lally, K., & Bartlett, M. E. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad220 · Cited by 36
Eco-immunology of fish invasions: the role of MHC variation
Monzón‐Argüello, C., de Leániz, C. G., Gajardo, G., & Consuegra, S. (2014) · Immunogenetics · doi:10.1007/s00251-014-0771-8 · Cited by 26
Batra, V., Maheshwarappa, A., Dagar, K., Kumar, S., Soni, A., Kumaresan, A., Kumar, R., & Datta, T. K. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1535-8 · Cited by 26
Mitogenome evolution in ladybirds: Potential association with dietary adaptation
Yuan, M., Zhang, L., Zhang, Q., Zhang, L., Li, M., Wang, X., Feng, R.-Q., & Tang, P. (2020) · Ecology and Evolution · doi:10.1002/ece3.5971 · Cited by 26
Molecular Epidemiology of B3 and D8 Measles Viruses through Hemagglutinin Phylogenetic History
Bianchi, S., Canuti, M., Ciceri, G., Gori, M., Colzani, D., Dura, M., Pennati, B. M., Baggieri, M., Magurano, F., Tanzi, E., et al. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21124435 · Cited by 26
Zhou, Y., Tan, L. V., Luo, K., Liao, Q., Wang, L., Qiu, Q., Zou, G., Liu, P., Anh, N. T., Hong, N. T. T., et al. (2020) · Virologica Sinica · doi:10.1007/s12250-020-00266-7 · Cited by 26
The spread of Tembusu virus in China from 2010 to 2019
Qiu, G., Cui, Y., Li, Y., Li, Y., & Wang, Y. (2021) · Virus Research · doi:10.1016/j.virusres.2021.198374 · Cited by 26
Improved high‐throughput MHC typing for non‐model species using long‐read sequencing
Cheng, Y., Grueber, C. E., Hogg, C. J., & Belov, K. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13511 · Cited by 26
DeSalle, R., Chicote, J. U., Sun, T., & García‐España, A. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-13 · Cited by 27
Molecular evolution of candidate genes involved in post‐mating‐prezygotic reproductive isolation
Bono, J. M., Matzkin, L. M., Hoang, K. L., & Brandsmeier, L. (2014) · Journal of Evolutionary Biology · doi:10.1111/jeb.12574 · Cited by 23
Population genomics of dengue virus serotype 4: insights into genetic structure and evolution
Waman, V., Kasibhatla, S. M., Kale, M. M., & Kulkarni‐Kale, U. (2016) · Archives of Virology · doi:10.1007/s00705-016-2886-8 · Cited by 26
Wang, S., Liu, C., Wilson, A. B., Zhao, N., Li, X., Zhu, W., Gao, X., Liu, X., & Li, Y. (2017) · Molecular Ecology · doi:10.1111/mec.14242 · Cited by 26
Liu, G., Zhang, H., Sun, G., Zhao, C., Shang, S., Gao, X., Xia, T., & Yang, X. (2017) · BMC Genomics · doi:10.1186/s12864-017-3983-0 · Cited by 26
Boso, G., Buckler-White, A. J., & Kozak, C. A. (2018) · Journal of Virology · doi:10.1128/jvi.00850-18 · Cited by 26
Buckley, J., Kilbride, E. A., Çevik, V., Vicente, J. G., Holub, E. B., & Mable, B. K. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0665-5 · Cited by 25
Stager, M., Cerasale, D. J., Dor, R., Winkler, D. W., & Cheviron, Z. A. (2014) · Gene · doi:10.1016/j.gene.2014.05.019 · Cited by 28
Evolutionary analysis of Tembusu virus: Evidence for the emergence of a dominant genotype
Dai, L., Li, Z., & Pan, T. (2015) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2015.03.004 · Cited by 25
Toll-like receptor variation in the bottlenecked population of the endangered Seychelles warbler
Gilroy, D. L., van Oosterhout, C., Komdeur, J., & Richardson, D. S. (2016) · Animal Conservation · doi:10.1111/acv.12307 · Cited by 23
SILVA, M. C. D. L. D., Chibucos, M. C., Munro, J. B., Daugherty, S., Coelho, M. M., & da Silva, J. C. F. (2020) · Scientific Reports · doi:10.1038/s41598-019-56950-6 · Cited by 25
Rey-Campos, M., Novoa, B., Pallavicini, A., Gerdol, M., & Figueras, A. J. (2020) · Biomolecules · doi:10.3390/biom10060943 · Cited by 25
Genomic diversity in a population of Spodoptera frugiperda nucleopolyhedrovirus
Masson, T., Fabre, M. L., Pidre, M. L., Niz, J. M., Berretta, M. F., Romanowski, V., & Ferrelli, M. L. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.104749 · Cited by 25
Comparative Chloroplast Genomics in Phyllanthaceae Species
Rehman, U., Sultana, N., Abdullah, A., Jamal, A., Muzaffar, M., & Poczai, P. (2021) · Diversity · doi:10.3390/d13090403 · Cited by 27
ASFV Gene A151R Is Involved in the Process of Virulence in Domestic Swine
Ramírez-Medina, E., Vuono, E. A., Pruitt, S., Rai, A., Espinoza, N., Valladares, A., Spinard, E. J., Silva, E. B., Velázquez-Salinas, L., Gladue, D. P., et al. (2022) · Viruses · doi:10.3390/v14081834 · Cited by 25
Genomic and transcriptomic analyses support a silk gland origin of spider venom glands
Zhu, B., Jin, P., Zhang, Y., Shen, Y., Wang, W., & Li, S. (2023) · BMC Biology · doi:10.1186/s12915-023-01581-7 · Cited by 26
Gaballa, A., Wiedmann, M., & Carroll, L. M. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1060519 · Cited by 25
Structural and evolutionary characteristics of fish-specific TLR19
Wang, J., Zhang, Z., Fu, H., Zhang, S., Liu, J., Chang, F., Li, F., Zhao, J., & Yin, D. (2015) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2015.09.005 · Cited by 25
Adaptive Evolution of Toll-Like Receptors (TLRs) in the Family Suidae
Darfour-Oduro, K. A., Megens, H., Roca, A. L., Groenen, M. A. M., & Schook, L. B. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124069 · Cited by 26
Gismondi, M. I., Carrasco, J. M. D., Valva, P., Becker, P. D., Guzmán, C. A., Campos, R. H., & Preciado, M. V. (2013) · Virology · doi:10.1016/j.virol.2013.09.002 · Cited by 25
Chung, D.-H., Västermark, Å., Camp, J. V., McAllister, R. C., Remold, S. K., Chu, Y.-K., Bruder, C. E. G., & Jonsson, C. B. (2013) · Journal of Virology · doi:10.1128/jvi.01394-13 · Cited by 25
Arcà, B., Struchiner, C. J., Pham, V. M., Sferra, G., Lombardo, F., Pombi, M., & Ribeiro, J. M. C. (2013) · Insect Molecular Biology · doi:10.1111/imb.12068 · Cited by 25
Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing
Dyrdak, R., Mastafa, M., Hodcroft, E. B., Neher, R. A., & Albert, J. (2019) · Virus Evolution · doi:10.1093/ve/vez007 · Cited by 25
Emergence and adaptive evolution of Nipah virus
Li, K., Yan, S., Wang, N., He, W., Guan, H., He, C., Wang, Z., Lu, M., He, W., Ye, R., et al. (2019) · Transboundary and Emerging Diseases · doi:10.1111/tbed.13330 · Cited by 25
Navas-Pérez, E., Vicente‐García, C., Mirra, S., Burguera, D., Fernàndez‐Castillo, N., Ferrán, J. L., López-Mayorga, M., Alaiz-Noya, M., Suárez‐Pereira, I., Antón-Galindo, E., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02172-3 · Cited by 26
Relationships between fox populations and rabies virus spread in northern Canada
Nadin‐Davis, S. A., Falardeau, E., Flynn, A., Whitney, H. G., & Marshall, H. D. (2021) · PLoS ONE · doi:10.1371/journal.pone.0246508 · Cited by 25
Essential gene acquisition destabilizes plasmid inheritance
Wein, T., Wang, Y., Barz, M., Stücker, F. T., Hammerschmidt, K., & Dagan, T. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009656 · Cited by 25
Sebastian, W., Sukumaran, S., & Gopalakrishnan, A. (2022) · Heredity · doi:10.1038/s41437-022-00519-z · Cited by 24
Lamaze, F. C., Pavey, S. A., Normandeau, É., Roy, G., Garant, D., & Bernatchez, L. (2014) · Molecular Ecology · doi:10.1111/mec.12684 · Cited by 24
The mammalian complement system as an epitome of host–pathogen genetic conflicts
Cagliani, R., Forni, D., Filippi, G., Mozzi, A., GIOIA, L. D., Pontremoli, C., Pozzoli, U., Bresolin, N., Clerici, M., & Sironi, M. (2016) · Molecular Ecology · doi:10.1111/mec.13558 · Cited by 26
Baquero, L. A., Pérez, D. A. M., Garzón‐Ospina, D., Forero-Rodríguez, J., Ortiz-Suárez, H. D., & Patarroyo, M. A. (2017) · Parasites & Vectors · doi:10.1186/s13071-017-2183-8 · Cited by 24
Tian, R., Xu, S., Chai, S., Yin, D., Zakon, H. H., & Yang, G. (2017) · Journal of Evolutionary Biology · doi:10.1111/jeb.13213 · Cited by 24
Parallel Evolution of Metazoan Mitochondrial Proteins
Klink, G. V., & Bazykin, G. A. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx025 · Cited by 23
Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes
Bose, M. E., Shrivastava, S., He, J., Nelson, M. I., Bera, J., Fedorova, N. B., Halpin, R., Town, C. D., Lorenzi, H., Amedeo, P., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0220057 · Cited by 24
Dömel, J. S., Macher, T., Dietz, L., Duncan, S., Mayer, C., Rozenberg, A., Wolcott, K., Leese, F., & Melzer, R. R. (2019) · Frontiers in Zoology · doi:10.1186/s12983-019-0316-y · Cited by 24
Matsushima, Y., Mizukoshi, F., Sakon, N., Doan, Y. H., Ueki, Y., Ogawa, Y., Motoya, T., Tsukagoshi, H., Nakamura, N., Shigemoto, N., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02189 · Cited by 24
Tagliamonte, M. S., Abid, N., Borocci, S., Sangiovanni, E., Ostrov, D. A., Pond, S. L. K., Salemi, M., Chillemi, G., & Mavian, C. N. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms22010080 · Cited by 23
Potdar, V. A., Vipat, V., Ramdasi, A. Y., Jadhav, S., Pawar-Patil, J., Walimbe, A. M., Patil, S., Choudhury, M. L., Shastri, J. S., Agrawal, S. R., et al. (2021) · The Indian Journal of Medical Research · doi:10.4103/ijmr.ijmr_3418_20 · Cited by 24
Evaluation of an ASFV RNA Helicase Gene A859L for Virus Replication and Swine Virulence
Ramírez-Medina, E., Vuono, E. A., Pruitt, S., Rai, A., Espinoza, N., Velázquez-Salinas, L., Gladue, D. P., & Borca, M. V. (2021) · Viruses · doi:10.3390/v14010010 · Cited by 24
Decena, M. Á., Gálvez, S., Agostini, F., Sancho, R., Contreras‐Moreira, B., Marais, D. L. D., Hernández, P., & Catalán, P. (2021) · Plants · doi:10.3390/plants10122664 · Cited by 24
Fiamenghi, M. B., Bueno, J. G. R., Camargo, A. P., Borelli, G., Carazzolle, M. F., Pereira, G. A. G., dos Santos, L. V., & José, J. (2022) · Biotechnology for Biofuels and Bioproducts · doi:10.1186/s13068-022-02153-7 · Cited by 23
Craveiro, S. R., de Melo, F. L., Ribeiro, Z. M. A., Ribeiro, B. M., Báo, S. N., Inglis, P. W., & Castro, M. E. B. (2013) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2013.08.005 · Cited by 24
de Matos, A. L., McFadden, G., & Esteves, P. J. (2013) · Immunogenetics · doi:10.1007/s00251-013-0740-7 · Cited by 24
Zedek, F., & Bureš, P. (2016) · Annals of Botany · doi:10.1093/aob/mcw186 · Cited by 25
Navarro-Sigüenza, A. G., Vázquez‐Miranda, H., Hernández‐Alonso, G., García-Trejo, E. A., & Sánchez‐González, L. A. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.04.013 · Cited by 24
Three-Finger Toxin Diversification in the Venoms of Cat-Eye Snakes (Colubridae: Boiga)
Dashevsky, D., Debono, J., Rokyta, D. R., Nouwens, A. S., Josh, P. F., & Fry, B. G. (2018) · Journal of Molecular Evolution · doi:10.1007/s00239-018-9864-6 · Cited by 24
Evolution and Diversification of FRUITFULL Genes in Solanaceae
Maheepala, D. C., Emerling, C. A., Rajewski, A. C., Macon, J., Strahl, M., Pabón‐Mora, N., & Litt, A. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00043 · Cited by 22
Michelet, C., Danchin, É., Jaouannet, M., Bernhagen, J., Panstruga, R., Kogel, K., Keller, H., & Coustau, C. (2019) · Genes · doi:10.3390/genes10100740 · Cited by 24
Begum, Y., & Mondal, S. K. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1748717 · Cited by 22
Mazzetto, E., Bortolami, A., Fusaro, A., Mazzacan, E., Maniero, S., Vascellari, M., Beato, M. S., Schiavon, E., Chiapponi, C., Terregino, C., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01136 · Cited by 24
Fluorescence Phenomena in Amyloid and Amyloidogenic Bionanostructures
Apter, B., Lapshina, N., Barhum, H., Fainberg, B. D., Handelman, A., Accardo, A., Diaferia, C., Ginzburg, P., Morelli, G., & Rosenman, G. I. (2020) · Crystals · doi:10.3390/cryst10080668 · Cited by 24
Structure and evolution of the sea star egg receptor for sperm bindin
Hart, M. W. (2013) · Molecular Ecology · doi:10.1111/mec.12251 · Cited by 23
Origin and Evolution of Dishevelled
Dillman, A. R., Minor, P. J., & Sternberg, P. W. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.005314 · Cited by 23
Williams, D. T., Diviney, S. M., Niazi, A., Durr, P. A., Chua, B. H., Herring, B. L., Pyke, A. T., Doggett, S. L., Johansen, C. A., & Mackenzie, J. S. (2015) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0004240 · Cited by 23
Lam, S. D., Bordin, N., Waman, V., Scholes, H., Ashford, P., Sen, N., van Dorp, L., Rauer, C., Dawson, N., Pang, C., et al. (2020) · UCL Discovery (University College London) · Cited by 22
Genetic diversity and evolution of Hantaan virus in China and its neighbors
Li, N., Li, A., Liu, Y., Wu, W., Li, C., Yu, D., Zhu, Y., Li, J., Li, D., Wang, S., et al. (2020) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0008090 · Cited by 23
Kumar, M., Mohapatra, S., Mazumder, P., Singh, A., Honda, R., Lin, C., Kumari, R., Goswami, R., Jha, P. K., Vithanage, M. S., et al. (2020) · Current Pollution Reports · doi:10.1007/s40726-020-00161-5 · Cited by 23
Genetic variation of staphylococcal LukAB toxin determines receptor tropism
Perelman, S. S., James, D. B. A., Boguslawski, K. M., Nelson, C. W., Ilmain, J. K., Zwack, E. E., Prescott, R. A., Mohamed, A., Tam, K., Chan, R., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00890-3 · Cited by 23
Klompen, A. M. L., Kayal, E., Collins, A. G., & Cartwright, P. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab081 · Cited by 23
Niche adaptation promoted the evolutionary diversification of tiny ocean predators
Latorre, F., Deutschmann, I. M., Labarre, A., Obiol, A., Krabberød, A. K., Pelletier, É., Sieracki, M. E., Cruaud, C., Jaillon, O., Massana, R., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2020955118 · Cited by 23
Evolution of host-microbe cell adherence by receptor domain shuffling
Baker, E. P., Sayegh, R., Kohler, K. M., Borman, W., Goodfellow, C. K., Brush, E. R., & Barber, M. F. (2022) · eLife · doi:10.7554/elife.73330 · Cited by 21
Zehr, J. D., Pond, S. L. K., Martin, D. P., Ceres, K., Whittaker, G. R., Millet, J. K., Goodman, L. B., & Stanhope, M. J. (2022) · Viruses · doi:10.3390/v14050853 · Cited by 23
Molecular Evolution of the Capsid Gene in Norovirus Genogroup I
Kobayashi, M., Yoshizumi, S., Kogawa, S., Takahashi, T., Ueki, Y., Shinohara, M., Mizukoshi, F., Tsukagoshi, H., Sasaki, Y., Suzuki, R., et al. (2015) · Scientific Reports · doi:10.1038/srep13806 · Cited by 24
Junqueira, D. M., Tochetto, C., Anderson, T. K., Gava, D., Haach, V., Cantão, M. E., Baker, A. L. V., & Schaefer, R. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1243567 · Cited by 23
Forero-Rodríguez, J., Garzón‐Ospina, D., & Patarroyo, M. A. (2014) · Malaria Journal · doi:10.1186/1475-2875-13-58 · Cited by 23
Sironi, M., Biasin, M., Cagliani, R., Gnudi, F., Saulle, I., Ibba, S. V., Filippi, G., Yahyaei, S., Tresoldi, C., Riva, S., et al. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu193 · Cited by 23
Antigenic Drift Defines a New D4 Subgenotype of Measles Virus
Muñoz-Alía, M. Á., Muller, C. P., & Russell, S. J. (2017) · Journal of Virology · doi:10.1128/jvi.00209-17 · Cited by 23
Li, Y., Bao, H., Zhang, X., Zhai, M., Bao, X., Wang, D., & Zhang, S. (2017) · Journal of Medical Virology · doi:10.1002/jmv.24847 · Cited by 22
Han, C., Li, Q., Zhang, Z., & Huang, J. (2017) · Developmental & Comparative Immunology · doi:10.1016/j.dci.2017.08.007 · Cited by 23
Patterns and rates of viral evolution in HIV-1 subtype B infected females and males
Dapp, M. J., Kober, K. M., Chen, L., Westfall, D. H., Wong, K., Zhao, H. C., Hall, B., Deng, W., Sibley, T. R., Ghorai, S., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0182443 · Cited by 21
Selection, drift, and introgression shape MHC polymorphism in lizards
Sagonas, Κ., Runemark, A., Antoniou, A., Lymberakis, P., Pafilis, P., Valakos, E. D., Poulakakis, N., & Hansson, B. (2018) · Heredity · doi:10.1038/s41437-018-0146-2 · Cited by 23
Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana
Tuteja, R., McKeown, P. C., Ryan, P., Morgan, C. C., Donoghue, M. T. A., Downing, T., O’Connell, M. J., & Spillane, C. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz063 · Cited by 23
Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales
Secaira-Morocho, H., Castillo, J. A., & Driks, A. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000451 · Cited by 25
Episodic positive diversifying selection on key immune system genes in major avian lineages
Antonides, J. D., Mathur, S., & DeWoody, J. A. (2019) · Genetica · doi:10.1007/s10709-019-00081-3 · Cited by 22
Sugar assimilation underlying dietary evolution of Neotropical bats
Camacho, J. J., Rivera, A. B., Peña, V., Morales‐Sosa, P., Robb, S. M. C., Russell, J., Yi, K., Wang, Y., Tsuchiya, D., Murillo‐García, O. E., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02485-7 · Cited by 23
Slimen, H. B., Awadi, A., Tolesa, Z. G., Knauer, F., Alves, P. C., Makni, M., & Suchentrunk, F. (2018) · Journal of Zoological Systematics & Evolutionary Research · doi:10.1111/jzs.12204 · Cited by 22
Kwon, T., Yoo, S. J., Lee, D., Sunwoo, S.-Y., Je, S. H., Park, J. W., Kim, M.-H., Park, C., & Lyoo, Y. S. (2018) · Virus Research · doi:10.1016/j.virusres.2018.11.004 · Cited by 22
Serotonin Receptor 1A Variation Is Associated with Anxiety and Agonistic Behavior in Chimpanzees
Staes, N., Sherwood, C. C., Freeman, H. D., Brosnan, S. F., Schapiro, S. J., Hopkins, W. D., & Bradley, B. J. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz061 · Cited by 22
Doğan, Ö., Schrödl, M., & Chen, Z. (2020) · PeerJ · doi:10.7717/peerj.8603 · Cited by 22
Picard, L., Ganivet, Q., Allatif, O., Cimarelli, A., Guéguen, L., & Etienne, L. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa680 · Cited by 22
Comparative analysis of chloroplast genomes of seven perennial Helianthus species
Azarin, K., Usatov, A. V., Makarenko, M., Khachumov, V., & Алексеевна, Г. В. (2021) · Gene · doi:10.1016/j.gene.2021.145418 · Cited by 22
Jacobsen, M. W., Jensen, N. W., Nygaard, R., Præbel, K., Jónsson, B., Nielsen, N. H., Pujolar, J. M., Fraser, D. J., Bernatchez, L., & Hansen, M. M. (2021) · Ecology Of Freshwater Fish · doi:10.1111/eff.12633 · Cited by 22
Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data
He, K., Liang, C.-H., Zhu, Y., Dunn, P. O., Zhao, A., & Minias, P. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.823686 · Cited by 22
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.
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
