Phylogenomics: The beginning of incongruence?
Open accessAbstract
Until recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of different tree reconstruction methods on different partitions of the concatenated supergene leads to well-resolved, but real (i.e. statistically significant) incongruences. Gathering a large amount of data is not sufficient to produce reliable trees, given the current limitation of tree reconstruction methods, especially when the quality of data is poor. We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
Additional sources of systematic error include poor taxon or character sampling, large amounts of missing data, and model misspecification.
“Additional sources of systematic error include poor taxon or character sampling (10,14,15), large amounts of missing data (16), and model misspecification (16,17).”
From Error, signal, and the placement of Ctenophora sister to all other animals (2015) · cites this paper as [15]
Cites
1 retracted
RETRACTED ARTICLE: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
Jobb, G., von Haeseler, A., & Strimmer, K. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-18 · Cited by 1,109 · see citing works
RetractedMrBayes 3: Bayesian phylogenetic inference under mixed models
Ronquist, F., & Huelsenbeck, J. P. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg180 · Cited by 28,956 · see citing works
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,698 · see citing works
PAUP^* : Phylogenetic Analysis Using Parsimony (and other methods) 4.0b8
Swofford, D. L. (2001) · Cited by 12,789 · see citing works
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
Castresana, J. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026334 · Cited by 10,447 · see citing works
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
Edgar, R. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-113 · Cited by 8,948 · see citing works
PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
Cummings, M. P. (2004) · Dictionary of Bioinformatics and Computational Biology · doi:10.1002/0471650129.dob0522 · Cited by 5,229 · see citing works
An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis
Hillis, D. M., & Bull, J. J. (1993) · Systematic Biology · doi:10.2307/2992540 · Cited by 3,452 · see citing works
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
Felsenstein, J. (1978) · Systematic Biology · doi:10.1093/sysbio/27.4.401 · Cited by 3,221 · see citing works
Wooding, S. (2004) · The American Journal of Human Genetics · doi:10.1086/383584 · Cited by 3,093 · see citing works
Maddison, W. P. (1997) · Systematic Biology · doi:10.1093/sysbio/46.3.523 · Cited by 3,060 · see citing works
Cases in which parsimony or compatibility methods will be positively misleading.
Felsenstein, J. (1978) · Systematic Zoology · doi:10.2307/2412923 · Cited by 2,230 · see citing works
Genome-scale approaches to resolving incongruence in molecular phylogenies.
Rokas, A., Williams, B. L., King, N., & Carroll, S. B. (2003) · Nature · doi:10.1038/nature02053 · Cited by 1,512 · see citing works
Phylogenomics and the reconstruction of the tree of life
Delsuc, F., Brinkmann, H., & Philippe, H. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1603 · Cited by 1,228 · see citing works
Self-citationRecovering evolutionary trees under a more realistic model of sequence evolution.
Lockhart, P. J., Steel, M., Hendy, M. D., & Penny, D. (1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040136 · Cited by 964 · see citing works
The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
Douzery, E. J. P., Snell, E. A., Bapteste, E., Delsuc, F., & Philippe, H. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403984101 · Cited by 638 · see citing works
Self-citationMUST, a computer package of Management Utilities for Sequences and Trees
Philippe, H. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.22.5264 · Cited by 600 · see citing works
Self-citationPhilippe, H., Lartillot, N., & Brinkmann, H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi111 · Cited by 551 · see citing works
Self-citationComparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability
Douady, C. J. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg042 · Cited by 507 · see citing works
Genome-scale phylogeny and the detection of systematic biases.
Phillips, M. J., Delsuc, F., & Penny, D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh137 · Cited by 450 · see citing works
Self-citationRokas, A., & Carroll, S. B. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi121 · Cited by 424 · see citing works
Molecular phylogenetics: state-of-the-art methods for looking into the past
Whelan, S., Lió, P., & Goldman, N. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02272-7 · Cited by 413 · see citing works
An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics
Brinkmann, H., van der Giezen, M., Zhou, Y., de Raucourt, G. P., & Philippe, H. (2005) · Systematic Biology · doi:10.1080/10635150500234609 · Cited by 281 · see citing works
Self-citationLeebens‐Mack, J., Raubeson, L. A., Cui, L., Kuehl, J. V., Fourcade, M. H., Chumley, T. W., Boore, J. L., Jansen, R. K., & dePamphilis, C. W. (2005) · eScholarship (California Digital Library) · Cited by 271 · see citing works
Early–branching or fast–evolving eukaryotes? An answer based on slowly evolving positions
Philippe, H., Lopez, P., Brinkmann, H., Budin, K., Germot, A., Laurent, J., Moreira, D., Müller, M., & Guyader, H. L. (2000) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2000.1130 · Cited by 247 · see citing works
Self-citationRibosomal RNA trees misleading?
Hasegawa, M., & Hashimoto, T. (1993) · Nature · doi:10.1038/361023b0 · Cited by 230 · see citing works
Can the Cambrian explosion be inferred through molecular phylogeny?
Philippe, H., Chenuil, A., & Adoutte, A. (1994) · Development · doi:10.1242/dev.1994.supplement.15 · Cited by 226 · see citing works
Self-citationSoltis, P. S., Albert, V. A., Savolainen, V., Hilu, K. W., Qiu, Y., Chase, M. W., Farris, J. S., Stefanović, S., Rice, D. W., Palmer, J. D., et al. (2004) · Trends in Plant Science · doi:10.1016/j.tplants.2004.08.008 · Cited by 207 · see citing works
Woese, C. R., Achenbach, L. A., Rouvière, P. E., & Mandelco, L. (1991) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(11)80311-5 · Cited by 206 · see citing works
Should phylogenetic models be trying to ‘fit an elephant’?
Steel, M. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.04.001 · Cited by 163 · see citing works
Philippe, H., Sörhannus, U., Baroin‐Tourancheau, A., Perasso, R., Gasse, F., & Adoutte, A. (1994) · Journal of Evolutionary Biology · doi:10.1046/j.1420-9101.1994.7020247.x · Cited by 156 · see citing works
Self-citationTaxon Sampling, Bioinformatics, and Phylogenomics
Rosenberg, M. S., & Kumar, S. (2003) · Systematic Biology · doi:10.1080/10635150390132894 · Cited by 149 · see citing works
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
Stefanović, S., Rice, D. W., & Palmer, J. D. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-35 · Cited by 143 · see citing works
Gee, H. (2003) · Nature · doi:10.1038/425782a · Cited by 126 · see citing works
Taylor, D. J. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh156 · Cited by 94 · see citing works
Rodent monophyly: pitfalls of molecular phylogenies.
Philippe, H. (1997) · PubMed · Cited by 88 · see citing works
Self-citationThe place of Amborella within the radiation of angiosperms
Lockhart, P. J., & Penny, D. (2005) · Trends in Plant Science · doi:10.1016/j.tplants.2005.03.006 · Cited by 42 · see citing works
Improved Consensus Network Techniques for Genome-Scale Phylogeny
Holland, B. R. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj061 · Cited by 39 · see citing works
(2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh215 · Cited by 7 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Talavera, G., & Castresana, J. (2007) · Systematic Biology · doi:10.1080/10635150701472164 · Cited by 5,599 · see citing works
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901 · see citing works
Anisimova, M. O., Gil, M., Dufayard, J.-F., Dessimoz, C., & Gascuel, O. (2011) · Systematic Biology · doi:10.1093/sysbio/syr041 · Cited by 1,299 · see citing works
Resolving difficult phylogenetic questions: Why more sequences are not enough
Philippe, H., Brinkmann, H., Lavrov, D. V., Littlewood, D. T. J., Manuel, M., Wörheide, G., & Baurain, D. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000602 · Cited by 1,129 · see citing works
Self-citationThe genome of Eucalyptus grandis
Myburg, A. A., Grattapaglia, D. G., Tuskan, G. A., Hellsten, U., Hayes, R. D., Grimwood, J., Jenkins, J. W., Lindquist, E., Tice, H. N., Bauer, D., et al. (2014) · Nature · doi:10.1038/nature13308 · Cited by 916 · see citing works
Burki, F., Roger, A. J., Brown, M. W., & Simpson, A. G. B. (2020) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2019.08.008 · Cited by 913 · see citing works
Genome-Based Taxonomic Classification of the Phylum Actinobacteria
Nouioui, I., Carro, L., García-López, M., Meier‐Kolthoff, J. P., Woyke, T., Kyrpides, N. C., Pukall, R., Klenk, H., Goodfellow, M., & Göker, M. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02007 · Cited by 771 · see citing works
Lartillot, N., Brinkmann, H., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s4 · Cited by 705 · see citing works
Self-citationRibosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
Jolley, K. A., Bliss, C. M., Bennett, J. S., Bratcher, H. B., Brehony, C., Colles, F. M., Wimalarathna, H. M. L., Harrison, O. B., Sheppard, S. K., Cody, A. J., et al. (2012) · Microbiology · doi:10.1099/mic.0.055459-0 · Cited by 652 · see citing works
Inferring ancient divergences requires genes with strong phylogenetic signals
Salichos, L., & Rokas, A. (2013) · Nature · doi:10.1038/nature12130 · Cited by 616 · see citing works
Ruhfel, B. R., Gitzendanner, M. A., Soltis, P. S., Soltis, P. S., & Burleigh, J. G. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-23 · Cited by 547 · see citing works
Pattern pluralism and the Tree of Life hypothesis
Doolittle, W. F., & Bapteste, E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610699104 · Cited by 546 · see citing works
A simple, fast, and accurate method of phylogenomic inference
Wu, M., & Eisen, J. A. (2008) · Genome biology · doi:10.1186/gb-2008-9-10-r151 · Cited by 510 · see citing works
Hördt, A., López, M. G., Meier‐Kolthoff, J. P., Schleuning, M., Weinhold, L.-M., Tindall, B. J., Gronow, S., Kyrpides, N. C., Woyke, T., & Göker, M. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00468 · Cited by 492 · see citing works
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.
(2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-99 · Cited by 475 · see citing works
Wagner, C. E., Keller, I., Wittwer, S., Selz, O. M., Mwaiko, S., Greuter, L., Sivasundar, A., & D, O. S. C. (2012) · Molecular Ecology · doi:10.1111/mec.12023 · Cited by 446 · see citing works
Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics
Zhang, S., Jin, J., Chen, S., Chase, M. W., Soltis, P. S., Li, H., Yang, J., Li, D.-Z., & Yi, T. (2017) · New Phytologist · doi:10.1111/nph.14461 · Cited by 396 · see citing works
Odronitz, F., & Kollmar, M. (2007) · Genome biology · doi:10.1186/gb-2007-8-9-r196 · Cited by 391 · see citing works
Pollard, D. A., Iyer, V. N., Moses, A. M., & Eisen, M. B. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020173 · Cited by 389 · see citing works
Misof, B. Y., & Misof, K. (2009) · Systematic Biology · doi:10.1093/sysbio/syp006 · Cited by 367 · see citing works
The Eukaryotic Tree of Life from a Global Phylogenomic PerspectivePreprint
Burki, F. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a016147 · Cited by 360 · see citing works
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
Roure, B., Baurain, D., & Philippe, H. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss208 · Cited by 365 · see citing works
Self-citationError, signal, and the placement of Ctenophora sister to all other animals
Whelan, N. V., Kocot, K. M., Moroz, L. L., & Halanych, K. M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1503453112 · Cited by 331 · see citing works
Xiang, Y., Huang, C., Hu, Y., Wen, J., Li, S., Yi, T., Chen, H., Xiang, J., & Mā, H. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw242 · Cited by 351 · see citing works
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Zhu, Q.-Y., Mai, U., Pfeiffer, W., Janssen, S., Asnicar, F., Sanders, J. G., Belda-Ferre, P., Al-Ghalith, G., Kopylova, E., McDonald, D., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13443-4 · Cited by 309 · see citing works
Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
García-López, M., Meier‐Kolthoff, J. P., Tindall, B. J., Gronow, S., Woyke, T., Kyrpides, N. C., Hahnke, R. L., & Göker, M. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02083 · Cited by 351 · see citing works
Genomic data do not support comb jellies as the sister group to all other animals
Pisani, D., Pett, W., Dohrmann, M., Feuda, R., Rota-Stabelli, O., Philippe, H., Lartillot, N., & Wörheide, G. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518127112 · Cited by 319 · see citing works
Self-citationPhylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats
Simon, M., Scheuner, C., Meier‐Kolthoff, J. P., Brinkhoff, T., Wagner‐Döbler, I., Ulbrich, M., Klenk, H., Schomburg, D., Petersen, J., & Göker, M. (2017) · The ISME Journal · doi:10.1038/ismej.2016.198 · Cited by 338 · see citing works
Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships
Pick, K. S., Philippe, H., Schreiber, F., Erpenbeck, D., Jackson, D. J., Wrede, P., Wiens, M., Alie, A., Morgenstern, B., Manuel, M., et al. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq089 · Cited by 334 · see citing works
Self-citationChiari, Y., Cahais, V., Galtier, N., & Delsuc, F. (2012) · BMC Biology · doi:10.1186/1741-7007-10-65 · Cited by 340 · see citing works
Self-citationDetecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
Rodríguez-Ezpeleta, N., Brinkmann, H., Roure, B., Lartillot, N., Lang, B. F., & Philippe, H. (2007) · Systematic Biology · doi:10.1080/10635150701397643 · Cited by 323 · see citing works
Self-citationPhylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal
Sharma, P. P., Kaluziak, S. T., Pérez-Porro, A. R., González, V. L., Hormiga, G., Wheeler, W. C., & Giribet, G. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu235 · Cited by 322 · see citing works
The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates
Soubrier, J., Steel, M., Lee, M. S. Y., Sarkissian, C. S. I. D., Guindon, S., Ho, S. Y. W., & Cooper, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss140 · Cited by 316 · see citing works
Complexity of avian evolution revealed by family-level genomes
Stiller, J., Feng, S., Chowdhury, A.-A., Rivas-González, I., Duchêne, D. A., Fang, Q., Deng, Y., Kozlov, A. M., Stamatakis, A., Claramunt, S., et al. (2024) · Nature · doi:10.1038/s41586-024-07323-1 · Cited by 307 · see citing works
Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees
Salichos, L., Stamatakis, A., & Rokas, A. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu061 · Cited by 303 · see citing works
Phylotranscriptomic consolidation of the jawed vertebrate timetree
Irisarri, I., Baurain, D., Brinkmann, H., Delsuc, F., Sire, J.-Y., Kupfer, A., Petersen, J., Jarek, M., Meyer, A., Vences, M., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0240-5 · Cited by 299 · see citing works
Self-citationThe quest for orthologs: finding the corresponding gene across genomes
Kuzniar, A., van Ham, R. C. H. J., Pongor, S., & Leunissen, J. A. M. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.08.009 · Cited by 296 · see citing works
Reddy, S., Kimball, R. T., Pandey, A., Hosner, P. A., Braun, M. J., Hackett, S. J., Han, K.-L., Harshman, J. S., Huddleston, C. J., Kingston, S. E., et al. (2017) · Systematic Biology · doi:10.1093/sysbio/syx041 · Cited by 288 · see citing works
En route to a genome-based classification of Archaea and Bacteria?
Klenk, H., & Göker, M. (2010) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2010.03.003 · Cited by 271 · see citing works
Dealing with incongruence in phylogenomic analyses
Galtier, N., & Daubin, V. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2008.0144 · Cited by 272 · see citing works
A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans
Marlétaz, F., Peijnenburg, K. T. C. A., Goto, T., Satoh, N., & Rokhsar, D. S. (2019) · Current Biology · doi:10.1016/j.cub.2018.11.042 · Cited by 268 · see citing works
Deep metazoan phylogeny: When different genes tell different stories
Nosenko, T., Schreiber, F., Adamska, M., Adamski, M., Eitel, M., Hammel, J., Maldonado, M., Müller, W. E. G., Nickel, M., Schierwater, B., et al. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.01.010 · Cited by 254 · see citing works
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 · see citing works
Oakley, T. H., Wolfe, J. M., Lindgren, A. R., & Zaharoff, A. K. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss216 · Cited by 265 · see citing works
Baurain, D., Brinkmann, H., Petersen, J., Rodríguez‐Ezpeleta, N., Stechmann, A., Demoulin, V., Roger, A. J., Burger, G., Lang, B. F., & Philippe, H. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq059 · Cited by 248 · see citing works
Self-citationWeighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees
Zhang, C., & Mirarab, S. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac215 · Cited by 252 · see citing works
Ågren, J., Sundström, A., Håfström, T., & Segerman, B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039107 · Cited by 249 · see citing works
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Eme, L., Tamarit, D., Caceres, E., Stairs, C. W., Anda, V. D., Schön, M. E., Seitz, K. W., Dombrowski, N., Lewis, W. H., Homa, F., et al. (2023) · Nature · doi:10.1038/s41586-023-06186-2 · Cited by 236 · see citing works
Gordon, J., Byrne, K. P., & Wolfe, K. H. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000485 · Cited by 243 · see citing works
Ma, P.-F., Zhang, Y.-X., Zeng, C., Guo, Z., & Li, D.-Z. (2014) · Systematic Biology · doi:10.1093/sysbio/syu054 · Cited by 243 · see citing works
Phylogenomic evidence for multiple losses of flight in ratite birds
Harshman, J., Braun, E. L., Braun, M. J., Huddleston, C. J., Bowie, R. C. K., Chojnowski, J. L., Hackett, S. J., Han, K.-L., Kimball, R. T., Marks, B. D., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803242105 · Cited by 239 · see citing works
The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
Nabhan, A. R., & Sarkar, I. N. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr014 · Cited by 237 · see citing works
Genome-Based Taxonomic Classification of Bacteroidetes
Hahnke, R. L., Meier‐Kolthoff, J. P., García-López, M., Mukherjee, S., Huntemann, M., Ivanova, N., Woyke, T., Kyrpides, N. C., Klenk, H., & Göker, M. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.02003 · Cited by 234 · see citing works
Phylogenomic Insights into Animal Evolution
Telford, M. J., Budd, G. E., & Philippe, H. (2015) · Current Biology · doi:10.1016/j.cub.2015.07.060 · Cited by 213 · see citing works
Self-citationBroadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
Parfrey, L. W., Grant, J. R., Tekle, Y. I., Lasek‐Nesselquist, E., Morrison, H. G., Sogin, M. L., Patterson, D. J., & Katz, L. A. (2010) · Systematic Biology · doi:10.1093/sysbio/syq037 · Cited by 232 · see citing works
Campbell, L. I., Rota‐Stabelli, O., Edgecombe, G. D., Marchioro, T., Longhorn, S. J., Telford, M. J., Philippe, H., Rebecchi, L., Peterson, K. J., & Pisani, D. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105499108 · Cited by 230 · see citing works
Self-citationAdditional molecular support for the new chordate phylogeny
Delsuc, F., Tsagkogeorga, G., Lartillot, N., & Philippe, H. (2008) · genesis · doi:10.1002/dvg.20450 · Cited by 231 · see citing works
Self-citationEvolution and biogeography of gymnosperms
Wang, X., & Ran, J. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.02.005 · Cited by 227 · see citing works
Hsiang, A. Y., Field, D. J., Webster, T. H., Behlke, A. D., Davis, M. B., Racicot, R. A., & Gauthier, J. A. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0358-5 · Cited by 226 · see citing works
Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants
Finet, C., Timme, R., Delwiche, C. F., & Marlétaz, F. (2010) · Current Biology · doi:10.1016/j.cub.2010.11.035 · Cited by 224 · see citing works
Asgard archaea capable of anaerobic hydrocarbon cycling
Seitz, K. W., Dombrowski, N., Eme, L., Spang, A., Lombard, J., Sieber, J. R., Teske, A., Ettema, T. J. G., & Baker, B. J. (2019) · Nature Communications · doi:10.1038/s41467-019-09364-x · Cited by 225 · see citing works
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
Hime, P. M., Lemmon, A. R., Lemmon, E. C. M., Prendini, E., Brown, J. M., Thomson, R. C., Kratovil, J. D., Noonan, B. P., Pyron, R. A., Peloso, P. L. V., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa034 · Cited by 213 · see citing works
Hagman, A., Säll, T., Compagno, C., & Piskur, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068734 · Cited by 219 · see citing works
Between a Pod and a Hard Test: The Deep Evolution of Amoebae
Kang, S., Tice, A. K., Spiegel, F. W., Silberman, J. D., Pánek, T., Čepička, I., Kostka, M., Kosakyan, A., Alcântara, D. M. C., Roger, A. J., et al. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx162 · Cited by 218 · see citing works
Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics
Young, A. D., & Gillung, J. P. (2019) · Systematic Entomology · doi:10.1111/syen.12406 · Cited by 215 · see citing works
Phylogenomics of Lophotrochozoa with Consideration of Systematic Error
Kocot, K. M., Struck, T. H., Merkel, J., Waits, D. S., Todt, C., Brannock, P. M., Weese, D., Cannon, J. T., Moroz, L. L., Lieb, B., et al. (2016) · Systematic Biology · doi:10.1093/sysbio/syw079 · Cited by 204 · see citing works
Babesia Life Cycle – When Phylogeny Meets Biology
Jalovecká, M., Sojka, D., Ascencio, M., & Schnittger, L. (2019) · Trends in Parasitology · doi:10.1016/j.pt.2019.01.007 · Cited by 208 · see citing works
A fungal phylogeny based on 82 complete genomes using the composition vector method
Wang, H., Xu, Z. L., Gao, L., & Hao, B. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-195 · Cited by 196 · see citing works
Causes, consequences and solutions of phylogenetic incongruence
Som, A. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbu015 · Cited by 193 · see citing works
Plastid phylogenomic insights into the evolution of Caryophyllales
Yao, G., Jin, J., Li, H., Yang, J., Mandala, V. S., Croley, M., Mostow, R. S., Douglas, N. A., Chase, M. W., Christenhusz, M. J. M., et al. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.12.023 · Cited by 189 · see citing works
Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes
Gonçalves, D. J. P., Simpson, B. B., Ortiz, E. M., Shimizu, G. H., & Jansen, R. K. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.05.022 · Cited by 191 · see citing works
Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset
Higdon, J. W., Bininda‐Emonds, O. R. P., Beck, R. M. D., & Ferguson, S. H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-216 · Cited by 193 · see citing works
Song, F., Li, H., Jiang, P., Zhou, X. J., Liu, J., Sun, C., Vogler, A. P., & Cai, W. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw086 · Cited by 186 · see citing works
Torruella, G., Derelle, R., Paps, J., Lang, B. F., Roger, A. J., Shalchian-Tabrizi, K., & Ruiz-Trillo, I. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/msr185 · Cited by 169 · see citing works
Gomila, M., Busquets, A., Mulet, M., Garcı́a-Valdés, E., & Lalucat, J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02422 · Cited by 174 · see citing works
Pitfalls in supermatrix phylogenomics
Philippe, H., Vienne, D. M. D., Ranwez, V., Roure, B., Baurain, D., & Delsuc, F. (2017) · European Journal of Taxonomy · doi:10.5852/ejt.2017.283 · Cited by 173 · see citing works
Self-citationZeng, L., Zhang, N., Zhang, Q., Endress, P. K., Huang, J., & Mā, H. (2017) · New Phytologist · doi:10.1111/nph.14503 · Cited by 171 · see citing works
Huerta-Cepas, J., Dopazo, H., Dopazo, J., & Gabaldón, T. (2007) · Genome Biology · doi:10.1186/gb-2007-8-6-r109 · Cited by 176 · see citing works
Genomics, biogeography, and the diversification of placental mammals
Wildman, D. E., Uddin, M., Opazo, J. C., Liu, G., Lefort, V., Guindon, S., Gascuel, O., Grossman, L. I., Romero, R. J., & Goodman, M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704342104 · Cited by 170 · see citing works
treespace : Statistical exploration of landscapes of phylogenetic trees
Jombart, T., Kendall, M., Garcia, J. A., & Colijn, C. (2017) · Molecular Ecology Resources · doi:10.1111/1755-0998.12676 · Cited by 169 · see citing works
Sperling, E. A., Peterson, K. J., & Pisani, D. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp148 · Cited by 172 · see citing works
The Phylogeny and Evolution of Ants
Ward, P. S. (2014) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-120213-091824 · Cited by 172 · see citing works
Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade
Thrash, J. C., Boyd, A., Huggett, M. J., Grote, J., Carini, P., Yoder, R. J., Robbertse, B., Spatafora, J. W., Rappé, M. S., & Giovannoni, S. J. (2011) · Scientific Reports · doi:10.1038/srep00013 · Cited by 166 · see citing works
An integrated phylogenomic approach toward pinpointing the origin of mitochondria
Wang, Z., & Wu, M. (2015) · Scientific Reports · doi:10.1038/srep07949 · Cited by 165 · see citing works
Evolutionary Diversity of the Mitochondrial Calcium Uniporter
Bick, A. G., Calvo, S. E., & Mootha, V. K. (2012) · Science · doi:10.1126/science.1214977 · Cited by 158 · see citing works
Sloan, D. B., Triant, D. A., Forrester, N. J., Bergner, L. M., Wu, M., & TAYLOR, D. R. (2013) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.12.004 · Cited by 163 · see citing works
Ballesteros, J. A., & Sharma, P. P. (2019) · Systematic Biology · doi:10.1093/sysbio/syz011 · Cited by 158 · see citing works
Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study
Rota-Stabelli, O., Lartillot, N., Philippe, H., & Pisani, D. (2013) · Systematic Biology · doi:10.1093/sysbio/sys077 · Cited by 155 · see citing works
Self-citationQuattrini, A. M., Faircloth, B. C., Dueñas, L. F., Bridge, T. C. L., Brugler, M. R., Calixto-Botía, I., DeLeo, D. M., Forêt, S., Herrera, S., Lee, S. M., et al. (2017) · Molecular Ecology Resources · doi:10.1111/1755-0998.12736 · Cited by 162 · see citing works
Building the avian tree of life using a large-scale, sparse supermatrix
Burleigh, J. G., Kimball, R. T., & Braun, E. L. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.12.003 · Cited by 156 · see citing works
Kück, P., & Struck, T. H. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2013.09.011 · Cited by 143 · see citing works
Wu, C., Wang, Y., Hsu, C.-Y., Lin, C.-P., & Chaw, S. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr095 · Cited by 153 · see citing works
Meiklejohn, K. A., Faircloth, B. C., Glenn, T. C., Kimball, R. T., & Braun, E. L. (2016) · Systematic Biology · doi:10.1093/sysbio/syw014 · Cited by 153 · see citing works
Michelle, C., Vourc’h, P., Mignon, L., & Andres, C. R. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9225-6 · Cited by 153 · see citing works
The search for the fungal tree of life
McLaughlin, D. J., Hibbett, D. S., Lutzoni, F. M., Spatafora, J. W., & Vilgalys, R. J. (2009) · Trends in Microbiology · doi:10.1016/j.tim.2009.08.001 · Cited by 154 · see citing works
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Hahn, M. W. (2007) · Genome biology · doi:10.1186/gb-2007-8-7-r141 · Cited by 153 · see citing works
Wägele, J. W., & Mayer, C. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-147 · Cited by 152 · see citing works
Liu, Y., Cox, C. J., Wang, W., & Goffinet, B. (2014) · Systematic Biology · doi:10.1093/sysbio/syu049 · Cited by 149 · see citing works
DiscoVista: Interpretable visualizations of gene tree discordance
Sayyari, E., Whitfield, J. B., & Mirarab, S. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.01.019 · Cited by 149 · see citing works
Holzer, A. S., Bartošová‐Sojková, P., Born‐Torrijos, A., Lövy, A., Hartigan, A., & Fiala, I. (2018) · Molecular Ecology · doi:10.1111/mec.14558 · Cited by 150 · see citing works
- Authors
- JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H.
- Affiliations
- Canadian Institute for Advanced Research (CA)
- Corresponding author
- PHILIPPE, H
- Venue
- Trends in Genetics
- Publisher
- Elsevier BV
- Published
- 2006-04
- Volume
- 22
- Issue
- 4
- Pages
- 225-231
- ISSN
- 0168-9525 (ISSN-L)
- OpenAlex
- W2140099453
- Cited by
- 698
- References
- 39
- Citations by year
- 2026: 17 · 2025: 27 · 2024: 27 · 2023: 38 · 2022: 26 · 2021: 28 · 2020: 62 · 2019: 64 · 2018: 33 · 2017: 45 · 2016: 33 · 2015: 29 · 2014: 40 · 2013: 32 · 2012: 41
- FWCI
- 13.58
- Type
- journal article
- Language
- en
- Open access
- green
- hal.science
- Licence
- Locations
- Trends in Genetics (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Keywords
- phylogenomics, phylogenetic incongruence, single-gene phylogeny, orthologs, data selection
- MeSH terms
- Models, Biological, Nucleotides, Phylogeny, Yeasts, Genome, Fungal, Genomics
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
