The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
APE: Analyses of Phylogenetics and Evolution in R language
Abstract
Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
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?
Maximum likelihood ancestral trait reconstruction using a continuous time Markov model of evolution was implemented for categorical traits.
“we implemented maximum likelihood ancestral trait reconstruction using a continuous time Markov model of evolution; a framework that has been commonly applied to categorical traits (Pagel 1994; Pupko et al. 2000; Paradis et al. 2004).”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Paradis et al. 2004
Many ancestral likelihood inference methods model the probability of phenotype change as a function of branch length.
“many ancestral likelihood inference methods model the probability of phenotype change as a function of branch length (Pagel 1994; Pupko et al. 2000; Paradis et al. 2004).”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Paradis et al. 2004
Reconstruction certainty depends on inferred phylogeny branch lengths, which are related to evolutionary rates.
“Reconstruction certainty, among many factors, depends on inferred phylogeny branch lengths which are related to evolutionary rates.”
From RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution (2024) · cites this paper as Paradis et al. 2004
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
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793
A nonparametric approach to estimating divergence times in the absence of rate constancy.
Sanderson, M. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025731 · Cited by 1,156 · cited 2×
“…models (Nee et al. , 1994; Pybus & Harvey, 2000), population-genetic analysis (Nee et al. , 1995; Strimmer & Pybus, 2001), non-parametric smoothing of evolutionary rates (Sanderson, 1997), and estimation of groups of genes in phylogenetic trees using Klastorin’s method (Misawa & Tajima, 2000).”
Flagged first, then by citations
Research works printed but not linked: 4
- Harvey,P.H. and Pagel,M.D. (1991) The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford.
- Nee,S., Holmes,E.C., Rambaut,A. and Harvey,P.H. (1995) Inferring population history from molecular phylogenies. Phil. Trans. R. Soc. Lond. B, 349, 25-31.
- Nee,S., May,R.M. and Harvey,P.H. (1994) The reconstructed evolu- tionary process. Phil. Trans. R. Soc. Lond. B, 344, 305-311.
- Pybus,O.G. and Harvey,P.H. (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond B, 267, 2267-2272.
Cited by
Sorted by citations
Comprehensive Integration of Single-Cell Data
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
Ratnasingham, S., & Hebert, P. D. N. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066213 · Cited by 2,301
The delayed rise of present-day mammals
Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L., & Purvis, A. (2007) · Nature · doi:10.1038/nature05634 · Cited by 2,082
Salt-responsive gut commensal modulates TH17 axis and disease
Wilck, N., Matus, M. G., Kearney, S. M., Olesen, S. W., Forslund, K., Bartolomaeus, H., Haase, S., Mähler, A., Balogh, A., Markó, L., et al. (2017) · Nature · doi:10.1038/nature24628 · Cited by 1,310
The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., et al. (2011) · Nature · doi:10.1038/nature10532 · Cited by 1,248
Host and viral traits predict zoonotic spillover from mammals
Olival, K. J., Hosseini, P. R., Zambrana-Torrelio, C., Ross, N., Bogich, T. L., & Daszak, P. (2017) · Nature · doi:10.1038/nature22975 · Cited by 1,130
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.020 · Cited by 1,006
The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
Barbosa-Morais, N. L., Irimia, M., Pan, Q., Xiong, H. Y., Gueroussov, S., Lee, L. J., Slobodeniuc, V., Kutter, C., Watt, S., Çolak, R., et al. (2012) · Science · doi:10.1126/science.1230612 · Cited by 1,063
Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance
Rosshart, S. P., Vassallo, B. G., Angeletti, D., Hutchinson, D. S., Morgan, A. P., Takeda, K., Hickman, H. D., McCulloch, J. A., Badger, J. H., Ajami, N. J., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.016 · Cited by 862
Monaco, G., Lee, B., Xu, W., Mustafah, S., Hwang, Y. Y., Carré, C., Burdin, N., Visan, L., Ceccarelli, M., Poidinger, M., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.041 · Cited by 958
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis
Shin, J., Berg, D. A., Zhu, Y., Shin, J. Y., Song, J., Bonaguidi, M. A., Enikolopov, G., Nauen, D. W., Christian, K. M., Ming, G.-L., et al. (2015) · Cell Stem Cell · doi:10.1016/j.stem.2015.07.013 · Cited by 784
Assessing the root of bilaterian animals with scalable phylogenomic methods
Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G. W., Edgecombe, G. D., Martinez, P., Baguñà, J., Bailly, X., Jondelius, U., et al. (2009) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2009.0896 · Cited by 747
Androgen Receptor Pathway-Independent Prostate Cancer Is Sustained through FGF Signaling
Bluemn, E. G., Coleman, I. M., Lucas, J. M., Coleman, R. T., Hernandez-Lopez, S., Tharakan, R., Bianchi-Frias, D., Dumpit, R. F., Kaipainen, A., Corella, A. N., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.09.003 · Cited by 744
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702
The evolution of social monogamy in mammals
Lukas, D., & Clutton-Brock, T. H. (2013) · Science · doi:10.1126/science.1238677 · Cited by 678
A genome-wide transcriptomic analysis of protein-coding genes in human blood cells
Uhlen, M., Karlsson, M. J., Zhong, W., Tebani, A., Pou, C., Mikes, J., Lakshmikanth, T., Forsström, B., Edfors, F., Odeberg, J., et al. (2019) · Science · doi:10.1126/science.aax9198 · Cited by 594
Efficient comparative phylogenetics on large trees
Louca, S., & Doebeli, M. (2018) · Bioinformatics · doi:10.1093/bioinformatics/btx701 · Cited by 564
Progressive Cactus is a multiple-genome aligner for the thousand-genome era
Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586
“Finally, the ‘consensus’ tree was produced as a strict consensus of the Jarvis and Prum trees (collapsing all groupings that were not the same in both trees) using the ape::consensus method from the APE R package 44 .”
Heintz‐Buschart, A., Pandey, U., Wicke, T., Sixel‐Döring, F., Janzen, A., Sittig‐Wiegand, E., Trenkwalder, C., Oertel, W. H., Mollenhauer, B., & Wilmes, P. (2018) · Movement Disorders · doi:10.1002/mds.27105 · Cited by 554
Lauder, A. P., Roche, A. M., Sherrill-Mix, S., Bailey, A., Laughlin, A. L., Bittinger, K., Leite, R., Elovitz, M. A., Parry, S., & Bushman, F. D. (2016) · Microbiome · doi:10.1186/s40168-016-0172-3 · Cited by 539
Nagy, C., Maitra, M., Tanti, A., Suderman, M., Théroux, J.-F., Davoli, M. A., Perlman, K., Yerko, V., Wang, Y. C., Tripathy, S. J., et al. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0621-y · Cited by 532
Association of host genome with intestinal microbial composition in a large healthy cohort
GEM Project Research Consortium, Turpin, W., Espin-Garcia, O., Xu, W., Silverberg, M. S., Kevans, D., Smith, M. I., Guttman, D. S., Griffiths, A., Panaccione, R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3693 · Cited by 460
Campione, N. E., & Evans, D. C. (2012) · BMC Biology · doi:10.1186/1741-7007-10-60 · Cited by 475
Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut
Roager, H. M., Hansen, L. B. S., Bahl, M. I., Frandsen, H. L., Carvalho, V., Gøbel, R. J., Dalgaard, M. D., Plichta, D. R., Sparholt, M. H., Vestergaard, H., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.93 · Cited by 449
Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., et al. (2019) · Science · doi:10.1126/science.aav6202 · Cited by 441
Open MEE : Intuitive, open‐source software for meta‐analysis in ecology and evolutionary biology
Wallace, B. C., Lajeunesse, M. J., Dietz, G., Dahabreh, I. J., Trikalinos, T. A., Schmid, C. H., & Gurevitch, J. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12708 · Cited by 421
Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts
Mollentze, N., & Streicker, D. G. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1919176117 · Cited by 387
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements
Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., et al. (2022) · Science · doi:10.1126/science.abk3112 · Cited by 411
Shah, F., Nicolás, C., Bentzer, J., Ellström, M., Smits, M., Rineau, F., Canbäck, B., Floudas, D., Carleer, R., Lackner, G., et al. (2016) · New Phytologist · doi:10.1111/nph.13722 · Cited by 394
Selectivity determinants of GPCR–G-protein binding
Flock, T., Hauser, A. S., Lund, N., Gloriam, D. E., Balaji, S., & Babu, M. M. (2017) · Nature · doi:10.1038/nature22070 · Cited by 384
A new time tree reveals Earth history’s imprint on the evolution of modern birds
Claramunt, S., & Cracraft, J. (2015) · Science Advances · doi:10.1126/sciadv.1501005 · Cited by 383
SIRT6 is responsible for more efficient DNA double-strand break repair in long-lived species
Tian, X., Firsanov, D., Zhang, Z., Cheng, Y., Luo, L., Tombline, G., Tan, R., Simon, M., Henderson, S., Steffan, J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.043 · Cited by 353
Developmental barcoding of whole mouse via homing CRISPR
Kalhor, R., Kalhor, K., Mejia, L., Leeper, K., Graveline, A., Mali, P., & Church, G. M. (2018) · Science · doi:10.1126/science.aat9804 · Cited by 363
Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
Heintz-Buschart, A., May, P., Laczny, C. C., Lebrun, L. A., Bellora, C., Krishna, A., Wampach, L., Schneider, J. G., Hogan, A., de Beaufort, C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.180 · Cited by 316
Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet
Bisanz, J. E., Upadhyay, V., Turnbaugh, J. A., Ly, K., & Turnbaugh, P. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.06.013 · Cited by 333
The seven deadly sins of comparative analysis
FRECKLETON, R. P. (2009) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2009.01757.x · Cited by 339
The evolution of the social brain: anthropoid primates contrast with other vertebrates
Shultz, S., & Dunbar, R. I. M. (2007) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2007.0693 · Cited by 344
Diversity versus disparity and the radiation of modern cetaceans
Slater, G. J., Price, S. A., Santini, F., & Alfaro, M. E. (2010) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2010.0408 · Cited by 312
Elevation alters ecosystem properties across temperate treelines globally
Mayor, J. R., Sanders, N. J., Classen, A. T., Bardgett, R. D., Clément, J.-C., Fajardo, A., Lavorel, S., Sundqvist, M. K., Bahn, M., Chisholm, C., et al. (2017) · Nature · doi:10.1038/nature21027 · Cited by 325
Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils
Schirrmeister, B. E., Gugger, M., & Donoghue, P. C. J. (2015) · Palaeontology · doi:10.1111/pala.12178 · Cited by 304
Morphological innovation, diversification and invasion of a new adaptive zone
Dumont, E. R., Dávalos, L. M., Goldberg, A., Santana, S. E., Rex, K., & Voigt, C. C. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2011.2005 · Cited by 297
Ctenophore relationships and their placement as the sister group to all other animals
Whelan, N. V., Kocot, K. M., Moroz, T. P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L. L., & Halanych, K. M. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0331-3 · Cited by 263
A genetic, genomic, and computational resource for exploring neural circuit function
Davis, F. P., Nern, A., Picard, S., Reiser, M. B., Rubin, G. M., Eddy, S. R., & Henry, G. L. (2020) · eLife · doi:10.7554/elife.50901 · Cited by 268
Dannemann, M., Andrés, A. M., & Kelso, J. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.015 · Cited by 249
Unexpected patterns of fisheries collapse in the world's oceans
Pinsky, M. L., Jensen, O. P., Ricard, D., & Palumbi, S. R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1015313108 · Cited by 267
Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
Arcila, D., Ortí, G., Vari, R., Armbruster, J. W., Stiassny, M. L. J., Ko, K. D., Sabaj, M. H., Lundberg, J., Revell, L. J., & Betancur-R., R. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-016-0020 · Cited by 243
Genomic diversity and evolution of the head crest in the rock pigeon
Shapiro, M. D., Kronenberg, Z., Li, C., Domyan, E. T., Pan, H., Campbell, M., Tan, H., Huff, C. D., Hu, H., Vickrey, A. I., et al. (2013) · Science · doi:10.1126/science.1230422 · Cited by 265
How does cognition evolve? Phylogenetic comparative psychology
MacLean, E. L., Matthews, L. J., Hare, B. A., Nunn, C. L., Anderson, R. C., Aureli, F., Brannon, E. M., Call, J., Drea, C. M., Emery, N. J., et al. (2012) · Animal Cognition · doi:10.1007/s10071-011-0448-8 · Cited by 260
Speciation and introgression between Mimulus nasutus and Mimulus guttatus
Brandvain, Y., Kenney, A. M., Flagel, L., Coop, G., & Sweigart, A. L. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004410 · Cited by 259
Wallen, Z. D., Appah, M., Dean, M. N., Sesler, C. L., Factor, S. A., Molho, E., Zabetian, C. P., Standaert, D. G., & Payami, H. (2020) · npj Parkinson s Disease · doi:10.1038/s41531-020-0112-6 · Cited by 252
Gut microbiome heritability is nearly universal but environmentally contingent
Grieneisen, L., Dasari, M., Gould, T. J., Björk, J. R., Grenier, J.-C., Yotova, V., Jansen, D., Gottel, N., Gordon, J. B., Learn, N. H., et al. (2021) · Science · doi:10.1126/science.aba5483 · Cited by 243
EVIDENCE FOR COEVOLUTION OF SOCIALITY AND RELATIVE BRAIN SIZE IN THREE ORDERS OF MAMMALS
Pérez-Barbería, F. J., Shultz, S., & Dunbar, R. I. M. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00229.x · Cited by 241
BODDY, A. M., McGOWEN, M. R., SHERWOOD, C. C., GROSSMAN, L. I., GOODMAN, M., & WILDMAN, D. E. (2012) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2012.02491.x · Cited by 207
Gene flow contributes to diversification of the major fungal pathogen Candida albicans
Ropars, J., Maufrais, C., Diogo, D., Marcet-Houben, M., Perin, A., Sertour, N., Mosca, K., Permal, E., Laval, G., Bouchier, C., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04787-4 · Cited by 197
Species coexistence and the dynamics of phenotypic evolution in adaptive radiation
Tobias, J. A., Cornwallis, C. K., Derryberry, E. P., Claramunt, S., Brumfield, R. T., & Seddon, N. (2014) · Nature · doi:10.1038/nature12874 · Cited by 199
Fabre, P. H., Rodrigues, A., & Douzery, E. J. P. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.08.004 · Cited by 211
Miho, E., Yermanos, A., Weber, C. R., Berger, C. T., Reddy, S. T., & Greiff, V. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.00224 · Cited by 189
Ritual human sacrifice promoted and sustained the evolution of stratified societies
Watts, J., Sheehan, O., Atkinson, Q. D., Bulbulia, J., & Gray, R. D. (2016) · Nature · doi:10.1038/nature17159 · Cited by 188
Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression
Contrepois, K., Coudereau, C., Benayoun, B. A., Schuler, N., Roux, P.-F., Bischof, O., Courbeyrette, R., Carvalho, C., Thuret, J.-Y., Ma, Z., et al. (2017) · Nature Communications · doi:10.1038/ncomms14995 · Cited by 191
Regulation of genetic flux between bacteria by restriction–modification systems
Oliveira, P. H., Touchon, M., & Rocha, E. P. C. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603257113 · Cited by 166
Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015) · doi:10.1101/013946 · Cited by 172
Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum
Sepúlveda, V. E., Márquez, R., Turissini, D. A., Goldman, W. E., & Matute, D. R. (2017) · mBio · doi:10.1128/mbio.01339-17 · Cited by 175
Nahar, R., Zhai, W., Zhang, T., Takano, A., Khng, A. J., Lee, Y. Y., Liu, X., Lim, C. H., Koh, T. P. T., Aung, Z. W., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02584-z · Cited by 173
Huang, Z. Y. X., de Boer, W. F., van Langevelde, F., Olson, V., Blackburn, T. M., & Prins, H. H. T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054341 · Cited by 161
Primate Prefrontal Cortex Evolution: Human Brains Are the Extreme of a Lateralized Ape Trend
Smaers, J. B., Steele, J., Case, C. R., Cowper, A., Amunts, K., & Zilles, K. (2011) · Brain, Behavior and Evolution · doi:10.1159/000323671 · Cited by 160
Wang, C., Shen, J., Liu, J., Qin, H., Yuan, Q., Fan, F., Hu, Y., Wang, J., Wei, W., Li, Y., et al. (2019) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2019.05.012 · Cited by 152
Zhou, X., Adamowicz, S. J., Jacobus, L. M., DeWalt, R. E., & Hebert, P. D. (2009) · Frontiers in Zoology · doi:10.1186/1742-9994-6-30 · Cited by 153
SHULTZ, S., & DUNBAR, R. I. M. (2010) · Biological Journal of the Linnean Society · doi:10.1111/j.1095-8312.2010.01427.x · Cited by 151
Human and rat gut microbiome composition is maintained following sleep restriction
Zhang, S. L., Bai, L., Goel, N., Bailey, A., Jang, C. J., Bushman, F. D., Meerlo, P., Dinges, D. F., & Sehgal, A. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620673114 · Cited by 139
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Stankowski, S., Chase, M. A., Fuiten, A. M., Rodrigues, M. F., Ralph, P. L., & Streisfeld, M. A. (2019) · PLOS Biology · doi:10.1371/journal.pbio.3000391 · Cited by 134
Origins and genetic legacies of the Caribbean Taino
Schroeder, H., Sikora, M., Gopalakrishnan, S., Cassidy, L. M., Maisano Delser, P., Sandoval Velasco, M., Schraiber, J. G., Rasmussen, S., Homburger, J. R., Ávila-Arcos, M. C., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1716839115 · Cited by 126
Ecological drivers of song evolution in birds: Disentangling the effects of habitat and morphology
Derryberry, E. P., Seddon, N., Derryberry, G. E., Claramunt, S., Seeholzer, G. F., Brumfield, R. T., & Tobias, J. A. (2018) · Ecology and Evolution · doi:10.1002/ece3.3760 · Cited by 120
Eastwick, P. W. (2009) · Psychological Bulletin · doi:10.1037/a0016845 · Cited by 116
Shultz, S., & Dunbar, R. I. M. (2010) · Journal of Comparative Psychology · doi:10.1037/a0018894 · Cited by 116
Feo, T. J., Field, D. J., & Prum, R. O. (2015) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2014.2864 · Cited by 113
Donovan, M., Mackey, C. S., Platt, G. N., Rounds, J., Brown, A. N., Trickey, D. J., Liu, Y., Jones, K. M., & Wang, Z. (2020) · Neurobiology of Stress · doi:10.1016/j.ynstr.2020.100278 · Cited by 85
Are disease reservoirs special? Taxonomic and life history characteristics
Plourde, B. T., Burgess, T. L., Eskew, E. A., Roth, T. M., Stephenson, N., & Foley, J. E. (2017) · PLOS ONE · doi:10.1371/journal.pone.0180716 · Cited by 95
Graptoloid diversity and disparity became decoupled during the Ordovician mass extinction
Bapst, D. W., Bullock, P. C., Melchin, M. J., Sheets, H. D., & Mitchell, C. E. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113870109 · Cited by 94
Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism
Hazzouri, K. M., Khraiwesh, B., Amiri, K. M. A., Pauli, D., Blake, T., Shahid, M., Mullath, S. K., Nelson, D., Mansour, A. L., Salehi-Ashtiani, K., et al. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00156 · Cited by 91
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
Studer, R. A., Penel, S., Duret, L., & Robinson-Rechavi, M. (2008) · Genome Research · doi:10.1101/gr.076992.108 · Cited by 84
A new Jurassic scansoriopterygid and the loss of membranous wings in theropod dinosaurs
Wang, M., O’Connor, J. K., Xu, X., & Zhou, Z. (2019) · Nature · doi:10.1038/s41586-019-1137-z · Cited by 82
Andreu-Sánchez, S., Blanco-Míguez, A., Wang, D., Golzato, D., Manghi, P., Heidrich, V., Fackelmann, G., Zhernakova, D. V., Kurilshikov, A., Valles-Colomer, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.04.014 · Cited by 81
Microbial embryonal colonization during pipefish male pregnancy
Beemelmanns, A., Poirier, M., Bayer, T., Kuenzel, S., & Roth, O. (2019) · Scientific Reports · doi:10.1038/s41598-018-37026-3 · Cited by 78
Smaers, J. B., Dechmann, D. K. N., Goswami, A., Soligo, C., & Safi, K. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1212181109 · Cited by 79
Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species
Wells, K., Morand, S., Wardeh, M., & Baylis, M. (2020) · Global Ecology and Biogeography · doi:10.1111/geb.13045 · Cited by 65
Jäkel, C., Bergmann, F., Toth, R., Assenov, Y., van der Duin, D., Strobel, O., Hank, T., Klöppel, G., Dorrell, C., Grompe, M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01118-x · Cited by 69
Gouy, A., & Excoffier, L. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz306 · Cited by 63
Zhai, B., Liao, C., Jaggavarapu, S., Tang, Y., Rolling, T., Ning, Y., Sun, T., Bergin, S. A., Gjonbalaj, M., Miranda, E., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03183-4 · Cited by 62
Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds
Alhaddad, H., Khan, R., Grahn, R. A., Gandolfi, B., Mullikin, J. C., Cole, S. A., Gruffydd-Jones, T. J., Häggström, J., Lohi, H., Longeri, M., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053537 · Cited by 62
FOTH, C., BRUSATTE, S. L., & BUTLER, R. J. (2012) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2012.02479.x · Cited by 61
Common evolutionary origin of acoustic communication in choanate vertebrates
Jorgewich-Cohen, G., Townsend, S. W., Padovese, L. R., Klein, N., Praschag, P., Ferrara, C. R., Ettmar, S., Menezes, S., Varani, A. P., Serano, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33741-8 · Cited by 59
Davesne, D., Meunier, F. J., Schmitt, A. D., Friedman, M., Otero, O., & Benson, R. B. J. (2019) · Biological Reviews · doi:10.1111/brv.12505 · Cited by 57
Distinct evolutionary patterns of brain and body size during adaptive radiation
Gonzalez-Voyer, A., Winberg, S., & Kolm, N. (2009) · Evolution · doi:10.1111/j.1558-5646.2009.00705.x · Cited by 52
Balanoff, A. M., Smaers, J. B., & Turner, A. H. (2016) · Journal of Anatomy · doi:10.1111/joa.12403 · Cited by 46
Functional Morphometric Analysis of the Furcula in Mesozoic Birds
Close, R. A., & Rayfield, E. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036664 · Cited by 44
<tt>windex</tt> : Analyzing Convergent Evolution Using the Wheatsheaf Index in R
Arbuckle, K., & Minter, A. (2015) · Evolutionary Bioinformatics · doi:10.4137/ebo.s20968 · Cited by 45
Stanisavljević, S., Čepić, A., Bojić, S., Veljović, K., Mihajlović, S., Đedović, N., Jevtić, B., Momčilović, M., Lazarević, M., Mostarica Stojković, M., et al. (2019) · Scientific Reports · doi:10.1038/s41598-018-37505-7 · Cited by 43
Virtual ancestor reconstruction: Revealing the ancestor of modern humans and Neandertals
Mounier, A., & Mirazón Lahr, M. (2016) · Journal of Human Evolution · doi:10.1016/j.jhevol.2015.11.002 · Cited by 42
Metadata
- Authors
- Paradis, E., Claude, J., & Strimmer, K.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-01-22
- Volume
- 20
- Issue
- 2
- Pages
- 289-290
- ISSN
- 1367-4811
- 1367-4803
- Cited by
- 11,335
- References
- 2
- Language
- en
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
