Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
Abstract
Progress in sequencing technology allows researchers to assemble ever-larger supermatrices for phylogenomic inference. However, current phylogenomic studies often rest on patchy data sets, with some having 80% missing (or ambiguous) data or more. Though early simulations had suggested that missing data per se do not harm phylogenetic inference when using sufficiently large data sets, Lemmon et al. (Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol. 58:130-145.) have recently cast doubt on this consensus in a study based on the introduction of parsimony-uninformative incomplete characters. In this work, we empirically reassess the issue of missing data in phylogenomics while exploring possible interactions with the model of sequence evolution. First, we note that parsimony-uninformative incomplete characters are actually informative in a probabilistic framework. A reanalysis of Lemmon's data set with this in mind gives a very different interpretation of their results and shows that some of their conclusions may be unfounded. Second, we investigate the effect of the progressive introduction of missing data in a complete supermatrix (126 genes × 39 species) capable of resolving animal relationships. These analyses demonstrate that missing data perturb phylogenetic inference slightly beyond the expected decrease in resolving power. In particular, they exacerbate systematic errors by reducing the number of species effectively available for the detection of multiple substitutions. Consequently, large sparse supermatrices are more sensitive to phylogenetic artifacts than smaller but less incomplete data sets, which argue for experimental designs aimed at collecting a modest number (~50) of highly covered genes. Our results further confirm that including incomplete yet short-branch taxa (i.e., slowly evolving species or close outgroups) can help to eschew artifacts, as predicted by simulations. Finally, it appears that selecting an adequate model of sequence evolution (e.g., the site-heterogeneous CAT model instead of the site-homogeneous WAG model) is more beneficial to phylogenetic accuracy than reducing the level of missing data.
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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 [16]
Cites
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · see citing works
MrBayes 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
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582 · 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 10,429 · 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
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
Whelan, S., & Goldman, N. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003851 · Cited by 2,849 · see citing works
Comparison of phylogenetic trees
Robinson, D. F., & Foulds, L. R. (1981) · Mathematical Biosciences · doi:10.1016/0025-5564(81)90043-2 · Cited by 2,647 · 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
Broad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921 · cited 18× · see citing works
“This data set is an update of the one of Dunn et al. (2008) but with 19 additional species (12 sponges, 5 cnidarians, 1 ctenophore, and 1 placozoan) and less missing data for the remaining 64 species.”
BackgroundMethodResultInfluentialTunicates and not cephalochordates are the closest living relatives of vertebrates
Delsuc, F., Brinkmann, H., Chourrout, D., & Philippe, H. (2006) · Nature · doi:10.1038/nature04336 · Cited by 1,651 · see citing works
Self-citationA Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
Lartillot, N., & Philippe, H. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh112 · Cited by 1,516 · see citing works
Self-citationPhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
Lartillot, N., Lepage, T., & Blanquart, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp368 · Cited by 1,297 · see citing works
Saurischian monophyly and the origin of birds
Gauthier, J. (1986) · The Academy · doi:10.5281/zenodo.16171435 · Cited by 1,294 · 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-citationResolving 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-citationArthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
Regier, J. C., Shultz, J. W., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin, J. W., & Cunningham, C. (2010) · Nature · doi:10.1038/nature08742 · Cited by 1,018 · see citing works
Increased Taxon Sampling Greatly Reduces Phylogenetic Error
Zwickl, D. J., & Hillis, D. M. (2002) · Systematic Biology · doi:10.1080/10635150290102339 · Cited by 939 · see citing works
A Framework for the Quantitative Study of Evolutionary Trees
Hendy, M. D., & Penny, D. (1989) · Systematic Zoology · doi:10.2307/2992396 · Cited by 842 · see citing works
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
Lemmon, A. R., Emme, S. A., & Lemmon, E. M. (2012) · Systematic Biology · doi:10.1093/sysbio/sys049 · Cited by 837 · see citing works
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 · cited 15× · see citing works
“Nonetheless, it is difficult to extrapolate these observations to the original phylogeny of Hejnol et al. (2009), as it was based on a much larger supermatrix (270,580 positions and 94 species).”
BackgroundMethodResultInfluentialLartillot, N., Brinkmann, H., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s4 · Cited by 705 · see citing works
Self-citationPhylogenomics: The beginning of incongruence?
JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.003 · Cited by 698 · see citing works
Self-citationPhylogenomics Revives Traditional Views on Deep Animal Relationships
Philippe, H., Derelle, R., Lopez, P., Pick, K., Borchiellini, C., Boury-Esnault, N., Vacelet, J., Renard, E., Houliston, E., Quéinnec, E., et al. (2009) · Current Biology · doi:10.1016/j.cub.2009.02.052 · Cited by 695 · see citing works
Self-citationMissing Data, Incomplete Taxa, and Phylogenetic Accuracy
Wiens, J. J. (2003) · Systematic Biology · doi:10.1080/10635150390218330 · Cited by 691 · see citing works
Parallel adaptive radiations in two major clades of placental mammals
Madsen, O., Scally, M., Douady, C. J., Kao, D. J., DeBry, R. W., Adkins, R., Amrine, H. M., Stanhope, M. J., de Jong, W. W., & Springer, M. S. (2001) · Nature · doi:10.1038/35054544 · Cited by 653 · see citing works
MUST, 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-citationDeuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida
Bourlat, S. J., Juliusdottir, T., Lowe, C. J., Freeman, R. M., Aronowicz, J., Kirschner, M., Lander, E. S., Thorndyke, M. C., Nakano, H., Kohn, A. B., et al. (2006) · Nature · doi:10.1038/nature05241 · Cited by 568 · see citing works
Pagel, M. D., & Meade, A. (2004) · Systematic Biology · doi:10.1080/10635150490468675 · Cited by 553 · see citing works
Philippe, H., Lartillot, N., & Brinkmann, H. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi111 · Cited by 551 · see citing works
Self-citationMissing data and the design of phylogenetic analyses
Wiens, J. J. (2005) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2005.04.001 · Cited by 491 · see citing works
The New View of Animal Phylogeny
Halanych, K. M. (2004) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130124 · Cited by 489 · see citing works
Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data
Wiens, J. J., & Morrill, M. C. (2011) · Systematic Biology · doi:10.1093/sysbio/syr025 · Cited by 457 · 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
Acoelomorph flatworms are deuterostomes related to Xenoturbella
Philippe, H., Brinkmann, H., Copley, R. R., Moroz, L. L., Nakano, H., Poustka, A. J., Wållberg, A., Peterson, K. J., & Telford, M. J. (2011) · Nature · doi:10.1038/nature09676 · Cited by 432 · see citing works
Self-citationPhylogenetic supertrees: Assembling the trees of life
Sanderson, M. J., Purvis, A., & Henze, C. (1998) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(97)01242-1 · Cited by 429 · see citing works
Lemmon, A. R., Brown, J. M., Stanger‐Hall, K. F., & Lemmon, E. M. (2009) · Systematic Biology · doi:10.1093/sysbio/syp017 · Cited by 422 · see citing works
Maximum-likelihood models for combined analyses of multiple sequence data
Yang, Z. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02352289 · Cited by 409 · see citing works
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
Philippe, H., Snell, E. A., Bapteste, E. P., Lopez, P., Holland, P. W. H., & Casañe, D. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh182 · Cited by 398 · see citing works
Self-citationBapteste, E. P., Brinkmann, H., Lee, J. A., Moore, D. V., Sensen, C. W., Gordon, P. M. K., Duruflé, L., Gaasterland, T., Lopez, P., Müller, M., et al. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032662799 · Cited by 376 · see citing works
Self-citationImproved 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-citationThe Origin of Birds and the Evolution of Flight
Gauthier, J. A., & Padian, K. (1989) · Short Courses in Paleontology · doi:10.1017/s247526300000091x · Cited by 332 · see citing works
Inferring Phylogenies from RAD Sequence Data
Rubin, B. E., Ree, R. H., & Moreau, C. S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033394 · Cited by 315 · see citing works
Philippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130205 · Cited by 306 · see citing works
Self-citationCan Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?
Wiens, J. J. (2005) · Systematic Biology · doi:10.1080/10635150500234583 · Cited by 299 · see citing works
Does Adding Characters with Missing Data Increase or Decrease Phylogenetic Accuracy?
Wiens, J. J. (1998) · Systematic Biology · doi:10.1080/106351598260635 · Cited by 265 · see citing works
Rota‐Stabelli, O., Campbell, L. I., Brinkmann, H., Edgecombe, G. D., Longhorn, S. J., Peterson, K. J., Pisani, D., Philippe, H., & Telford, M. J. (2010) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2010.0590 · Cited by 264 · see citing works
Self-citationSchierwater, B., Eitel, M., Jakob, W., Osigus, H.-J., Hadrys, H., Dellaporta, S. L., Kolokotronis, S.-O., & DeSalle, R. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000020 · Cited by 260 · see citing works
The (Super)Tree of Life: Procedures, Problems, and Prospects
Bininda‐Emonds, O. R. P., Gittleman, J. L., & Steel, M. (2002) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.33.010802.150511 · Cited by 259 · see citing works
Prospects for Building the Tree of Life from Large Sequence Databases
Driskell, A. C., Ané, C., Burleigh, J. G., McMahon, M. M., O’Meara, B. C., & Sanderson, M. J. (2004) · Science · doi:10.1126/science.1102036 · Cited by 258 · see citing works
Coping with Abundant Missing Entries in Phylogenetic Inference Using Parsimony
Wilkinson, M. (1995) · Systematic Biology · doi:10.1093/sysbio/44.4.501 · Cited by 254 · see citing works
Multigene analyses identify the three earliest lineages of extant flowering plants
Parkinson, C. L., Adams, K. L., & Palmer, J. D. (1999) · Current Biology · doi:10.1016/s0960-9822(00)80119-0 · Cited by 240 · see citing works
When are Fossils Better than Extant Taxa in Phylogenetic Analysis?
Huelsenbeck, J. P. (1991) · Systematic Biology · doi:10.1093/sysbio/40.4.458 · Cited by 207 · see citing works
Soltis, 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
Fossils, Topologies, Missing Data, and the Higher Level Phylogeny of Eutherian Mammals
Novacek, M. J. (1992) · Systematic Biology · doi:10.2307/2992506 · Cited by 198 · see citing works
SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
Roure, B., Rodríguez‐Ezpeleta, N., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s2 · Cited by 187 · see citing works
Self-citationImprovement of molecular phylogenetic inference and the phylogeny of Bilateria
Lartillot, N., & Philippe, H. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2007.2236 · Cited by 178 · see citing works
Self-citationLarge-scale sequencing and the new animal phylogeny
Philippe, H., & Telford, M. J. (2006) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.08.004 · Cited by 176 · see citing works
Self-citationSperling, E. A., Peterson, K. J., & Pisani, D. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp148 · Cited by 172 · cited 4× · see citing works
“To further test this idea, we reinvestigated another difficult question pertaining to deep animal relationships (Dunn et al. 2008; Hejnol et al. 2009; Philippe et al. 2009; Sperling et al. 2009; Pick et al. 2010; Philippe, Brinkmann, Lavrov, et al. 2011) by introducing missing data in the 150 genes of Pick et al.”
BackgroundResultInfluentialMissing data and the accuracy of Bayesian phylogenetics
Wiens, J. J., & Moen, D. S. (2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08040 · Cited by 171 · see citing works
Wiens, J. J., & Tiu, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042925 · Cited by 169 · see citing works
When are Fossils better than Extant Taxa in Phylogenetic Analysis?
Huelsenbeck, J. P. (1991) · Systematic Zoology · doi:10.2307/2992240 · Cited by 153 · see citing works
Rodrigue, N., Philippe, H., & Lartillot, N. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910915107 · Cited by 151 · see citing works
Self-citationAcoel Flatworms Are Not Platyhelminthes: Evidence from Phylogenomics
Philippe, H., Brinkmann, H., Martı́nez, P., Riutort, M., & Baguñà, J. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000717 · Cited by 148 · see citing works
Self-citationTerraces in phylogenetic tree space
Sanderson, M. J., McMahon, M. M., & Steel, M. (2011) · Science · doi:10.1126/science.1206357 · Cited by 144 · cited 1× · see citing works
“This is due to 1) the need of integrating over all possible character states during the pruning algorithm when a character state is unknown and 2) a flattened likelihood surface, owing to the decrease in phylogenetic signal, that lengthens the search for the global maximum (Sanderson et al. 2011).”
BackgroundLong 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
Origin of land plants revisited in the light of sequence contamination and missing data
Laurin-Lemay, S., Brinkmann, H., & Philippe, H. (2012) · Current Biology · doi:10.1016/j.cub.2012.06.013 · Cited by 132 · see citing works
Self-citationSoria‐Carrasco, V., Talavera, G., Igea, J., & Castresana, J. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm466 · Cited by 107 · see citing works
Barley, A. J., Spinks, P. Q., Thomson, R. C., et al. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.11.005 · Cited by 95 · see citing works
Evans, N., Holder, M. T., Barbeitos, M. S., Okamura, B., & Cartwright, P. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq159 · Cited by 78 · see citing works
SDM: A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics
Criscuolo, A., Berry, V., Douzery, E., & Gascuel, O. (2006) · Systematic Biology · doi:10.1080/10635150600969872 · Cited by 78 · see citing works
Improving animal phylogenies with genomic data
Telford, M. J., & Copley, R. R. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.02.003 · Cited by 75 · see citing works
A Phylogenomic Approach to Resolve the Basal Pterygote Divergence
Simon, S., Strauss, S., von Haeseler, A., & Hadrys, H. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp191 · Cited by 69 · see citing works
Roure, B., & Philippe, H. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-17 · Cited by 64 · see citing works
Self-citationAccuracy of phylogeny reconstruction methods combining overlapping gene data sets
Kupczok, A., Schmidt, H. A., & von Haeseler, A. (2010) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-5-37 · Cited by 56 · see citing works
Fast NJ-like algorithms to deal with incomplete distance matrices
Criscuolo, A., & Gascuel, O. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-166 · Cited by 49 · see citing works
BIO::Phylo-phyloinformatic analysis using perl
Vos, R. A., Caravas, J., Hartmann, K., et al. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-63 · Cited by 46 · see citing works
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Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323926111 · Cited by 1,252 · see citing works
Self-citationSimion, P., Philippe, H., Baurain, D., Jager, M., Richter, D. J., Di Franco, A., Roure, B., Satoh, N., Quéinnec, É., Ereskovsky, A., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.02.031 · Cited by 518 · see citing works
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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
“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).”
BackgroundIntegrative modeling of gene and genome evolution roots the archaeal tree of life
Williams, T. A., Szöllősi, G. J., Spang, A., Foster, P. G., Heaps, S. E., Boussau, B., Ettema, T. J. G., & Embley, T. M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1618463114 · Cited by 233 · see citing works
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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
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Jákely, G., Paps, J., & Nielsen, C. (2015) · EvoDevo · doi:10.1186/2041-9139-6-1 · Cited by 189 · see citing works
Borowiec, M. L., Lee, E. K., Chiu, J. C., & Plachetzki, D. C. (2015) · doi:10.1101/013946 · Cited by 172 · see citing works
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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-citationWhelan, N. V., & Halanych, K. M. (2016) · Systematic Biology · doi:10.1093/sysbio/syw084 · Cited by 96 · see citing works
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- Authors
- Roure, B., Baurain, D., & Philippe, H.
- Affiliations
- Université de Montréal (CA)
- University of Liège (BE)
- Corresponding author
- Philippe, Hervé
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-08-28
- Volume
- 30
- Issue
- 1
- Pages
- 197-214
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2125070329
- Cited by
- 365
- References
- 78
- Citations by year
- 2026: 19 · 2025: 19 · 2024: 21 · 2023: 15 · 2022: 17 · 2021: 22 · 2020: 33 · 2019: 20 · 2018: 38 · 2017: 22 · 2016: 33 · 2015: 45 · 2014: 47 · 2013: 14
- FWCI
- 13.54
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- ORBi (University of Liège) (submittedVersion)
- Funders
- Canada Research Chairs
- Université de Montréal
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- missing data, phylogenomics, supermatrices, phylogenetic inference, cat model, outgroup taxa, multiple substitutions, animal phylogeny
- MeSH terms
- Amphibians, Animals, Bayes Theorem, Computer Simulation, Models, Genetic, Phylogeny, Sequence Alignment, Sequence Analysis, Evolution, Molecular, Genomics, Databases, Genetic
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