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
Figures
![Figure 1 The standard random effects approach and samples. A) The standard random effects approach, in which the rates vary randomly over sites but are constant over branches. Different values of are showed in different colors. B) Samples from our new random effects approach [20], used by MEME, in which the rate on each branch is drawn independently of the rate on any other branch. All possible assignments of rates to sites are considered.](/paper-figures/7c0c11683f47469f9d5d29a91ca0dd06/detecting-individual-sites-subject-to-episodic-diversifying-selection-figure-1.jpg)
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
Cited by
Sorted by citations
Items 901–1,000 of 1,003
Faustini, G., Tucciarone, C. M., Legnardi, M., Grassi, L., Berto, G., Drigo, M., Cecchinato, M., & Franzo, G. (2023) · Preventive Veterinary Medicine · doi:10.1016/j.prevetmed.2023.105943 · Cited by 9
Tracy, K. E., Kiemnec‐Tyburczy, K. M., DeWoody, J. A., Parra‐Olea, G., & Zamudio, K. R. (2015) · Immunogenetics · doi:10.1007/s00251-015-0835-4 · Cited by 9
Gardinassi, L. G., Simas, P. V. M., Gomes, D. E., do Bonfim, C. M., Nogueira, F., Garcia, G., Carareto, C. M. A., Rahal, P., & de Souza, F. P. (2012) · Viruses · doi:10.3390/v4112432 · Cited by 9
Analysis of Next-generation Sequencing Data in Virology - Opportunities and Challenges
Kasibhatla, S. M., Waman, V., Kale, M. M., & Kulkarni‐Kale, U. (2016) · InTech eBooks · doi:10.5772/61610 · Cited by 9
The human retinoblastoma susceptibility gene (RB1): an evolutionary story in primates
Viana, M. C., Tavares, W. C., Brant, A. C., Boroni, M., & Seuánez, H. N. (2017) · Mammalian Genome · doi:10.1007/s00335-017-9689-4 · Cited by 9
Parmar, D. R., Mitra, S., Bhadouriya, S., Rao, T., Kunteepuram, V., & Gaur, A. (2017) · Genetica · doi:10.1007/s10709-017-9979-5 · Cited by 10
Parallel evolution of site‐specific changes in divergent caribou lineages
Horn, R. L., Marques, A. J. D., Manseau, M., Golding, B., Klütsch, C. F. C., Abraham, K., & Wilson, P. J. (2018) · Ecology and Evolution · doi:10.1002/ece3.4154 · Cited by 9
Characterization of the β-defensin genes in giant panda
Zhang, Z.-Y., Zhang, H., Li, D., Xiong, T.-Y., & Fang, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-29898-2 · Cited by 9
Mozzi, A., Forni, D., Clerici, M., Cagliani, R., & Sironi, M. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02086 · Cited by 9
Ciceri, G., Canuti, M., Bianchi, S., Gori, M., Piralla, A., Colzani, D., Libretti, M., Frati, E. R., Baggieri, M., Lai, A., et al. (2019) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2019.103943 · Cited by 9
Irwin, D. M. (2019) · Gene · doi:10.1016/j.gene.2019.144296 · Cited by 9
Hwang, E.-H., Kim, G., Oh, H., An, Y. J., Kim, J., Kim, J. H., Hwang, E., Park, J., Hong, J. J., & Koo, B. (2020) · Archives of Virology · doi:10.1007/s00705-020-04653-z · Cited by 9
Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment ErrorsPreprint
Selberg, A., Clark, N. L., Sackton, T. B., Muse, S. V., Lucaci, A. G., Weaver, S., Nekrutenko, A., Chikina, M. D., & Pond, S. L. K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.13.620707 · Cited by 10
Gómez‐Romero, N., Basurto-Alcántara, F. J., & Velázquez-Salinas, L. (2023) · Pathogens · doi:10.3390/pathogens12111361 · Cited by 8
Faustini, G., Poletto, F., Baston, R., Tucciarone, C. M., Legnardi, M., Maso, M. D., Genna, V., Fiorentini, L., Donato, A. D., Perulli, S., et al. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1412615 · Cited by 8
Molecular Evolutionary Analyses of the Fusion Genes in Human Parainfluenza Virus Type 4
Mizukoshi, F., Kimura, H., Sugimoto, S., Kimura, R., Nagasawa, N., Hayashi, Y., Hashimoto, K., Hosoya, M., Shirato, K., & Ryo, A. (2024) · Microorganisms · doi:10.3390/microorganisms12081633 · Cited by 8
Tomás, G., Marandino, A. E., Rodríguez, S., Wallau, G. L., Dezordi, F. Z., de Oliveira, A. L. S., Techera, C., Calleros, L., Grecco, S., Williman, J., et al. (2024) · npj Viruses · doi:10.1038/s44298-024-00078-6 · Cited by 8
Franzo, G., Legnardi, M., Poletto, F., Baston, R., Faustini, G., Cecchinato, M., & Tucciarone, C. M. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1527335 · Cited by 8
Zhang, Y., Guo, J., Yang, Q., Zhuang, T., Xiao, S., & Fang, L. (2025) · Animal Diseases · doi:10.1186/s44149-025-00160-3 · Cited by 8
Global Evolution and Transmission Dynamics of Enterovirus D68
Xiao, M., Han, Z., Ma, X., Ji, T., Yan, D., Wang, D., Zhu, S., Lu, H., Cong, R., Wang, X., et al. (2025) · Journal of Medical Virology · doi:10.1002/jmv.70497 · Cited by 8
The genetic foundations of convergent traits
Allard, J. B., & Kumar, S. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00933-7 · Cited by 13
Garzón‐Ospina, D., López, C., Cadavid, L. F., Patarroyo, M. E., & Patarroyo, M. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079731 · Cited by 8
Freitas, L. A., & Nery, M. F. (2022) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2022.105271 · Cited by 7
Teng, L., Liang, M., Wang, C., Li, Y., Urbach, J. M., Kobe, B., Xing, Q., Han, W., & Ye, N. (2023) · The Plant Journal · doi:10.1111/tpj.16131 · Cited by 8
Acontia, a Specialised Defensive Structure, Has Low Venom Complexity in Calliactis polypus
Smith, H. L., Prentis, P. J., Bryan, S. E., Norton, R. S., & Broszczak, D. A. (2023) · Toxins · doi:10.3390/toxins15030218 · Cited by 8
Hilbert, Z. A., Haffener, P. E., Young, H., Schwiesow, M. J. W., Leffler, E. M., & Elde, N. C. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad119 · Cited by 10
Zhang, M., He, D., Liu, Y., Gong, Y., Dong, W., Chen, Y., & Ma, S. (2023) · Virology Journal · doi:10.1186/s12985-023-02179-9 · Cited by 8
Ramírez-Medina, E., Velázquez-Salinas, L., Rai, A., Espinoza, N., Valladares, A., Silva, E. B., Burton, L., Spinard, E. J., Meyers, A., Risatti, G. R., et al. (2023) · Viruses · doi:10.3390/v15102134 · Cited by 8
Solarte-Murillo, L. V., Reyes, H., Ojeda, L., Cárcamo, J. G., Pontigo, J. P., & Loncoman, C. (2024) · Viruses · doi:10.3390/v16040556 · Cited by 8
Foko, L. P. K., Hawadak, J., Moukoko, C. E. E., Das, A., & Singh, V. (2024) · Gene · doi:10.1016/j.gene.2024.148744 · Cited by 7
From emergence to endemicity of highly pathogenic H5 avian influenza viruses in Taiwan
Li, Y., Ko, H., Hughes, J., Liu, M., Lin, Y., Hampson, K., & Brunker, K. (2024) · Nature Communications · doi:10.1038/s41467-024-53816-y · Cited by 8
Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary
Bay, R. A., & Bielawski, J. P. (2013) · Journal of Molecular Evolution · doi:10.1007/s00239-013-9549-0 · Cited by 8
Huang, B.-H., Chen, Y.-W., Huang, C., Gao, J., & Liao, P. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0759-0 · Cited by 8
State aggregation for fast likelihood computations in molecular evolution
Davydov, I. I., Robinson‐Rechavi, M., & Salamin, N. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw632 · Cited by 8
Caraballo, D. A., Buzzi, L. I., Modenutti, C. P., Acosta-Montalvo, A., Castro, O., & Rossi, M. S. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.400868 · Cited by 8
Marichannegowda, M. H., Mengual, M., Kumar, A., Giorgi, E. E., Tu, J. J., Martinez, D. R., Romero-Severson, E. O., Li, X., Feng, L., Permar, S. R., et al. (2020) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100315 · Cited by 8
Evolution of the recombination regulator PRDM9 in minke whales
Damm, E., Ullrich, K. K., Amos, W., & Odenthal-Hesse, L. (2022) · BMC Genomics · doi:10.1186/s12864-022-08305-1 · Cited by 8
Kim, H. N., Yoon, S., Lim, C. S., Lee, C. K., & Yoon, J. H. (2022) · Journal of Clinical Virology · doi:10.1016/j.jcv.2022.105213 · Cited by 9
The Diversity and Spatiotemporally Evolutionary Dynamic of Atypical Porcine Pestivirus in China
Ma, H., Li, W., Zhang, M., Yang, Z., Lin, L., Ghonaim, A. H., & He, Q. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.937918 · Cited by 8
Garzón‐Ospina, D., & Buitrago, S. P. (2022) · Primates · doi:10.1007/s10329-022-01019-8 · Cited by 8
Romero, V., Arias‐Almeida, B., & Aguiar, S. A. (2022) · BMC Genomics · doi:10.1186/s12864-022-09071-w · Cited by 7
Cassidy, H., Lizarazo, E., Schuele, L., van Leer‐Buter, C., & Niesters, H. G. M. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1088770 · Cited by 8
Quispe-Ricalde, M. A., Castelán-Sánchez, H. G., Meza-Rodríguez, P. M., Dávila‐Ramos, S., Sierra, J. L., Batista‐García, R. A., Concha-Velasco, F., Lucana, S. F., Cruz, J. D. S., Zea, V., et al. (2023) · Archives of Virology · doi:10.1007/s00705-022-05645-x · Cited by 8
Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses
Escalera‐Zamudio, M., Pond, S. L. K., de la Viña, N. M., Gutiérrez, B., Inward, R. P. D., Thézé, J., van Dorp, L., Castelán-Sánchez, H. G., Bowden, T. A., Pybus, O. G., et al. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad076 · Cited by 6
Genetic diversity comparison of the DQA gene in European rabbit (Oryctolagus cuniculus) populations
Magalhães, V., Abrantes, J., Muñoz‐Pajares, A. J., & Esteves, P. J. (2015) · Immunogenetics · doi:10.1007/s00251-015-0866-x · Cited by 9
Garzón‐Ospina, D., Forero-Rodríguez, J., & Patarroyo, M. A. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0830-x · Cited by 8
Insights into intercontinental spread of Zika virus
Liang, D., Leung, R. K. K., Lee, S. S., & Kam, K. M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0176710 · Cited by 8
Minaya, M., Korom, M., Wang, H., Belshe, R. B., & Morrison, L. A. (2017) · PLoS ONE · doi:10.1371/journal.pone.0176687 · Cited by 8
Li, J., Yang, C., Ran, J., Jiang, X., Du, H., Li, Z., Liu, Y., & Zhang, L. (2018) · 3 Biotech · doi:10.1007/s13205-018-1504-8 · Cited by 9
Banguera‐Hinestroza, E., Ferrada, E., Sawall, Y., & Flot, J. (2019) · Genes · doi:10.3390/genes10050324 · Cited by 8
Bassano, I., Ong, S. H., Sanz-Hernández, M., Vinkler, M., Kebede, A., Hanotte, O., Onuigbo, E. B., Fife, M. S., & Kellam, P. (2019) · BMC Genomics · doi:10.1186/s12864-019-5621-5 · Cited by 8
Phylodynamic and transmission pattern of rabies virus in China and its neighboring countries
Wang, L., Wu, X., Bao, J., Song, C., & Du, J. (2019) · Archives of Virology · doi:10.1007/s00705-019-04297-8 · Cited by 8
Evidence of CPV2c introgression into Croatia and novel insights into phylogeny and cell tropism
Novosel, D., Tuboly, T., Balka, G., Szeredi, L., Lojkić, I., Jungić, A., Acinger-Rogić, Ž., Aït-Ali, T., & Cságola, A. (2019) · Scientific Reports · doi:10.1038/s41598-019-53422-9 · Cited by 8
Mendes, T., Silva, L., Almeida, D., & Antunes, A. (2020) · Genomics · doi:10.1016/j.ygeno.2020.01.023 · Cited by 8
Nyamota, R., Owino, V., Murungi, E. K., Villinger, J., Otiende, M. Y., Masiga, D. K., Thuita, J. K., Lekolool, I., & Jeneby, M. M. (2020) · Journal of Medical Primatology · doi:10.1111/jmp.12461 · Cited by 8
Mathioudakis, M. M., Maliogka, V. I., Candresse, T., Nickel, O., Fajardo, T. V. M., Budzyńska, D., Hasiów‐Jaroszewska, B., & Katis, N. I. (2021) · Plants · doi:10.3390/plants10050917 · Cited by 8
Bowman, J. D., & Lynch, V. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.27.582135 · Cited by 9
Positive Selection Drives the Evolution of the Structural Maintenance of Chromosomes (SMC) Complexes
Forni, D., Mozzi, A., Sironi, M., & Cagliani, R. (2024) · Genes · doi:10.3390/genes15091159 · Cited by 6
Interaction of chikungunya virus glycoproteins with macrophage factors controls virion production
Yao, Z., Ramachandran, S., Huang, S., Kim, E. J., Jami‐Alahmadi, Y., Kaushal, P., Bouhaddou, M., Wohlschlegel, J. A., & Li, M. M. H. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00193-3 · Cited by 7
Zheng, X., Cao, F., Yu, Y., Yu, X., Zhou, Y., Cheng, S., Qiu, X., Ao, L., Yang, X., Sun, Z., et al. (2025) · Viruses · doi:10.3390/v17040526 · Cited by 7
Li, Y.-Y., Chen, K.-F., Fan, C., Li, H., Zhen, H.-Q., Zhu, Y.-Q., Wang, B., Huang, Y., & Li, G. (2025) · Animals · doi:10.3390/ani15152312 · Cited by 7
Guzmán, M., Cádiz, L., Sáenz, L., Hidalgo, H., & Verdugo, C. (2025) · Viruses · doi:10.3390/v17081111 · Cited by 7
The auxin gatekeepers: Evolution and diversification of the YUCCA family
Vijayanathan, M., Faryad, A., Abeywickrama, T. D., Christensen, J. M., & Neilson, E. H. J. (2025) · The Plant Journal · doi:10.1111/tpj.70563 · Cited by 7
Lamb, K. D., Hughes, J., Lytras, S., Young, F., Koci, O., Herzig, J. C., Lovell, S. C., Grove, J., Yuan, K., & Robertson, D. L. (2026) · Nature Communications · doi:10.1038/s41467-026-69569-9 · Cited by 20
Bartocillo, A. M. F., Nishita, Y., Abramov, A. V., & Masuda, R. (2021) · Mammal Research · doi:10.1007/s13364-021-00561-y · Cited by 7
Kalaiyarasu, S., Mishra, N., Subramaniam, S., Moorthy, D., Sudhakar, S. B., Singh, V. P., & Sanyal, A. (2023) · Viruses · doi:10.3390/v15030733 · Cited by 7
Zhao, X., Dai, C., Qian, S., Tang, Q., Li, L., Hao, Y.-J., Zhou, Z.-J., Ge, X.-Y., Gong, C., & Yuan, J.-F. (2023) · Microbiology spectrum · doi:10.1128/spectrum.00810-23 · Cited by 6
Chacón, J. L., Chacón, R. D., Sánchez-Llatas, C. J., Morin-Lagos, J. G., Astolfi‐Ferreira, C. S., & Ferreira, A. J. P. (2023) · Avian Pathology · doi:10.1080/03079457.2023.2228725 · Cited by 7
Moreira, F. R. R., de Menezes, M. T., Salgado‐Benvindo, C., Whittaker, C., Cox, V. A., Chandradeva, N., de Paula, H. H. S., Martins, A. F., das Chagas, R. R., Brasil, R. D. V., et al. (2023) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0011536 · Cited by 7
Sistrom, M., Andrews, H., & Edwards, D. L. (2024) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0011459 · Cited by 7
Towards the Exploration and Evolution of Insulin-like Venoms in Actiniaria (Sea anemones)
Delgado, A., Sozanski, K. S., & Daly, M. (2024) · Marine Drugs · doi:10.3390/md22030136 · Cited by 7
Gladue, D. P., Gomez-Lucas, L., Largo, E., Ramírez-Medina, E., Torralba, J., Queralt-Martín, M., Alcaraz, A., Velázquez-Salinas, L., Nieva, J. L., & Borca, M. V. (2024) · Journal of Virology · doi:10.1128/jvi.00231-24 · Cited by 7
Molecular characterization of canine circovirus based on the Capsid gene in Thailand
Dankaona, W., Nooroong, P., Poolsawat, N., Srionrod, N., Techangamsuwan, S., & Anuracpreeda, P. (2024) · BMC Veterinary Research · doi:10.1186/s12917-024-04120-w · Cited by 7
Kwak, J. S., León‐Tapia, M. Á., Diblasi, C., Manousi, D., Grønvold, L., Sandvik, G. K., & Saitou, M. (2024) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkae162 · Cited by 9
Huang, S., Girdner, J., Nguyen, L. P., Sandoval, C., Fregoso, O. I., Enard, D., & Li, M. M. H. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1011836 · Cited by 7
Adero, J., Wokorach, G., Stomeo, F., Yao, N. K., Machuka, E., Njuguna, J. N., Byarugaba, D. K., Kreuze, J. F., Yencho, G. C., Otema, M. A., et al. (2024) · Pathogens · doi:10.3390/pathogens13100833 · Cited by 7
On the ancestry and evolution of the extinct dire wolf
Gedman, G. L., Morrill, K. M., Oppenheimer, J., Hyseni, C., Cassatt‐Johnstone, M., Lucaci, A. G., Alexandre, N. M., Troy, W., Chao, J. C., Fedrigo, O. D., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101306 · Cited by 14
Nataraj, R., Ashok, A. K., Dey, A. A., & Kesavardhana, S. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.00948-25 · Cited by 7
Rai, D. K., Lawrence, P., Pauszek, S. J., Piccone, M. E., Knowles, N. J., & Rieder, E. A. (2015) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s37223 · Cited by 7
Neves, F., Abrantes, J., & Esteves, P. J. (2016) · Innate Immunity · doi:10.1177/1753425916647471 · Cited by 7
Getchell, R. G., Cornwell, E. R., Bogdanowicz, S. M., Andrés, J. Á., Batts, W. N., Kurath, G., Breyta, R. B., Choi, J., Farrell, J. M., & Bowser, P. R. (2017) · Diseases of Aquatic Organisms · doi:10.3354/dao03171 · Cited by 7
Evolutionary Analysis of Pectin Lyases of the Genus Colletotrichum
Lara-Márquez, A., Oyama, K., Zavala-Páramo, M. G., Villa-Rivera, M. G., Conejo-Saucedo, U., & Cano-Camacho, H. (2017) · Journal of Molecular Evolution · doi:10.1007/s00239-017-9812-x · Cited by 7
White, N. D., Batz, Z. A., Braun, E. L., Braun, M. J., Carleton, K. L., Kimball, R. T., & Swaroop, A. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13496 · Cited by 7
An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias
Latrille, T., & Lartillot, N. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac005 · Cited by 7
Bouchiba, Y., Esque, J., Cottret, L., Maréchaux, M., Gaston, M., Gasciolli, V., Keller, J., Nouwen, N. P., Gully, D., Arrighi, J., et al. (2022) · Protein Science · doi:10.1002/pro.4327 · Cited by 7
Genome-Wide Reassortment Analysis of Influenza A H7N9 Viruses Circulating in China during 2013–2019
He, D., Wang, X., Wu, H., Wang, X., Yan, Y., Li, Y., Zhan, T., Hao, X., Hu, J., Hu, S., et al. (2022) · Viruses · doi:10.3390/v14061256 · Cited by 7
Luo, H., Luo, S., Fang, W., Lin, Q., Chen, X., & Zhou, X. (2022) · BMC Genomics · doi:10.1186/s12864-022-08904-y · Cited by 7
Widespread convergent evolution of alpha-neurotoxin resistance in African mammals
Drabeck, D. H., Holt, J., & McGaugh, S. E. (2022) · Biology Letters · doi:10.1098/rsbl.2022.0361 · Cited by 7
Molecular evolution analysis of three species gyroviruses in China from 2018 to 2019
Yan, T., Zhao, M., Sun, Y., Zhang, S., Zhang, X., Liu, Q., Li, Y., & Cheng, Z. (2023) · Virus Research · doi:10.1016/j.virusres.2023.199058 · Cited by 7
Yadav, S., Chahar, N., Lal, M., & Das, S. (2023) · Plant Gene · doi:10.1016/j.plgene.2023.100424 · Cited by 7
Phylogenetic analysis of rabies surveillance samples from north and northeast Brazil
da Cunha, T. C. A. D. S., da Silva, F. S., da Silva, S. P., Cruz, A. C. R., Paiva, F. A. D. S., Casseb, L. M. N., do Nascimento, A. D. N. S., de Oliveira, I. A. S., Branco, M. D. A. C., de Oliveira, R. A. B., et al. (2023) · Frontiers in Veterinary Science · doi:10.3389/fvets.2023.1257558 · Cited by 7
Accurate detection of convergent mutations in large protein alignments with ConDor
Morel, M., Zhukova, A., Lemoine, F., & Gascuel, O. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae040 · Cited by 3
Jiang, Y., Yu, G., Chai, W., Song, G., & Li, R. (2013) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12062 · Cited by 7
Pseudogenization of CCL14 in the Ochotonidae (pika) family
Neves, F., Abrantes, J., Lissovsky, A. A., & Esteves, P. J. (2015) · Innate Immunity · doi:10.1177/1753425915577455 · Cited by 7
Elbers, J. P., Clostio, R. W., & Taylor, S. S. (2017) · Journal of Heredity · doi:10.1093/jhered/esx034 · Cited by 7
Baillie, S. M., Hemstock, R., Muir, A. M., Krueger, C. C., & Bentzen, P. (2017) · Immunogenetics · doi:10.1007/s00251-017-0996-4 · Cited by 7
Shepherd, F. K., Murtaugh, M. P., Chen, F., Culhane, M. R., & Marthaler, D. (2017) · Pathogens · doi:10.3390/pathogens6040064 · Cited by 7
Tellis, M. B., Gujar, N., & Joshi, R. S. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2018.1497542 · Cited by 7
First assessment of MHC diversity in wild Scottish red deer populations
Pérez‐Espona, S., Goodall-Copestake, W. P., Savirina, A., Bobovikova, J., Molina-Rubio, C., & Pérez-Barbería, F. J. (2019) · European Journal of Wildlife Research · doi:10.1007/s10344-019-1254-x · Cited by 7
Niner, M. D., Stepien, C. A., Gorgoglione, B., & Leaman, D. W. (2020) · Ecology and Evolution · doi:10.1002/ece3.6611 · Cited by 7
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
