Missing Data, Incomplete Taxa, and Phylogenetic Accuracy
Abstract
The problem of missing data is often considered to be the most important obstacle in reconstructing the phylogeny of fossil taxa and in combining data from diverse characters and taxa for phylogenetic analysis. Empirical and theoretical studies show that including highly incomplete taxa can lead to multiple equally parsimonious trees, poorly resolved consensus trees, and decreased phylogenetic accuracy. However, the mechanisms that cause incomplete taxa to be problematic have remained unclear. It has been widely assumed that incomplete taxa are problematic because of the proportion or amount of missing data that they bear. In this study, I use simulations to show that the reduced accuracy associated with including incomplete taxa is caused by these taxa bearing too few complete characters rather than too many missing data cells. This seemingly subtle distinction has a number of important implications. First, the so-called missing data problem for incomplete taxa is, paradoxically, not directly related to their amount or proportion of missing data. Thus, the level of completeness alone should not guide the exclusion of taxa (contrary to common practice), and these results may explain why empirical studies have sometimes found little relationship between the completeness of a taxon and its impact on an analysis. These results also (1) suggest a more effective strategy for dealing with incomplete taxa, (2) call into question a justification of the controversial phylogenetic supertree approach, and (3) show the potential for the accurate phylogenetic placement of highly incomplete taxa, both when combining diverse data sets and when analyzing relationships of fossil taxa.
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A potentially reduced phylogenetic and/or dating accuracy associated with missing data is primarily caused by the occurrence of too few complete characters rather than too many missing positions.
“Indeed, a potentially reduced phylogenetic (and/or dating) accuracy associated with missing data is primarily caused by the occurrence of too few complete characters rather than too many missing positions (47).”
From The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? (2004) · cites this paper as [47]
Cites
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032 · 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
AMNIOTE PHYLOGENY AND THE IMPORTANCE OF FOSSILS
Gauthier, J., Kluge, A. G., & Rowe, T. (1988) · Cladistics · doi:10.1111/j.1096-0031.1988.tb00514.x · Cited by 1,085 · see citing works
Definition, diagnosis, and origin of Mammalia
Rowe, T. (1988) · Journal of Vertebrate Paleontology · doi:10.1080/02724634.1988.10011708 · Cited by 532 · see citing works
Grande, L., & Bemis, W. E. (1998) · Journal of Vertebrate Paleontology · doi:10.1080/02724634.1998.10011114 · Cited by 509 · see citing works
The Importance Of Fossils In Phylogeny Reconstruction
Donoghue, M. J., Doyle, J. A., Gauthier, J., Kluge, A. G., & Rowe, T. B. (1989) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.20.110189.002243 · Cited by 445 · see citing works
Phylogenetic 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
Character Analysis in Morphological Phylogenetics: Problems and Solutions
Wiens, J. J. (2001) · Systematic Biology · doi:10.1080/106351501753328811 · Cited by 380 · see citing works
Self-citationDistributions of Tree Comparison Metrics--Some New Results
Steel, M., & Penny, D. (1993) · Systematic Biology · doi:10.1093/sysbio/42.2.126 · Cited by 348 · see citing works
Significance of Fossils in Determining Evolutionary Relationships
Patterson, C. (1981) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.12.110181.001211 · Cited by 302 · see citing works
The Use of Tree Comparison Metrics
Penny, D., & Hendy, M. D. (1985) · Systematic Biology · doi:10.1093/sysbio/34.1.75 · Cited by 272 · 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
Self-citationCoping 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
Molecular and Morphological Supertrees for Eutherian (Placental) Mammals
Liu, F.-G. R., Miyamoto, M. M., Freire, N. P., Ong, P. Q., Tennant, M. R., Young, T. S., & Gugel, K. F. (2001) · Science · doi:10.1126/science.1056346 · Cited by 246 · see citing works
Approaches for Assessing Phylogenetic Accuracy
Hillis, D. M. (1995) · Systematic Biology · doi:10.1093/sysbio/44.1.3 · Cited by 243 · see citing works
Taxon Sampling and the Accuracy of Large Phylogenies
Rannala, B. H., Huelsenbeck, J. P., Yang, Z., & Nielsen, R. (1998) · Systematic Biology · doi:10.1080/106351598260680 · Cited by 233 · see citing works
Fragmentary Taxa, Missing Data, and Ambiguity: Mistaken Assumptions and Conclusions
Kearney, M. (2002) · Systematic Biology · doi:10.1080/10635150252899824 · Cited by 209 · 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
Resolution of a Supertree/Supermatrix Paradox
Gatesy, J., Matthee, C. A., DeSalle, R., & Hayashi, C. Y. (2002) · Systematic Biology · doi:10.1080/10635150290102311 · Cited by 206 · see citing works
The phylogenetic system : the systematization of organisms on the basis of their phylogenesis
Ax, P. (1987) · Cited by 199 · 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
Incomplete taxa, incomplete characters, and phylogenetic accuracy: is there a missing data problem?
Wiens, J. J. (2003) · Journal of Vertebrate Paleontology · doi:10.1671/0272-4634(2003)023[0297:iticap]2.0.co;2 · Cited by 165 · see citing works
Self-citationExtinction and the origin of species
Nixon, K. C., Wheeler, Q. D., & Novacek, M. J. (1992) · Cited by 152 · see citing works
Assessment of the Accuracy of Matrix Representation with Parsimony Analysis Supertree Construction
Bininda‐Emonds, O. R. P., & Sanderson, M. J. (2001) · Systematic Biology · doi:10.1080/10635150120358 · Cited by 145 · see citing works
Anderson, J. S. (2001) · Systematic Biology · doi:10.1080/10635150119889 · Cited by 136 · see citing works
Combining Data Sets with Different Numbers of Taxa for Phylogenetic Analysis
Wiens, J. J., & Reeder, T. W. (1995) · Systematic Biology · doi:10.1093/sysbio/44.4.548 · Cited by 129 · see citing works
Self-citationGao, K., Norell, M. A., & Akademi., M. S. U. (1998) · Biodiversity Heritage Library (Smithsonian Institution) · Cited by 77 · see citing works
Missing data and rhynchosaur phylogeny
Wilkinson, M., & Benton, M. J. (1995) · Historical Biology · doi:10.1080/10292389509380517 · Cited by 69 · see citing works
Phylogeny of the Trilobite Subgenus Acanthopyge (Lobopyge)
Ebach, M. C. (2001) · Cladistics · doi:10.1006/clad.1999.0145 · Cited by 31 · see citing works
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TRY – a global database of plant traits
KATTGE, J., DÍAZ, S., LAVOREL, S., PRENTICE, I. C., LEADLEY, P., BÖNISCH, G., GARNIER, E., WESTOBY, M., REICH, P. B., WRIGHT, I. J., et al. (2011) · Global Change Biology · doi:10.1111/j.1365-2486.2011.02451.x · Cited by 2,638 · see citing works
Tunicates 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
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
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 · 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
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
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
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 · 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
Flot, J.-F., Couloux, A., & Tillier, S. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-372 · Cited by 139 · see citing works
Dececchi, T. A., Narbonne, G. M., Greentree, C., & Laflamme, M. (2017) · Paleobiology · doi:10.1017/pab.2016.54 · Cited by 40 · see citing works
- Authors
- Wiens, J. J.
- Affiliations
- Stony Brook University (US)
- Corresponding author
- Wiens, John J.
- ORCID
- Wiens, John J.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-08-01
- Volume
- 52
- Issue
- 4
- Pages
- 528-538
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2152933358
- Cited by
- 691
- References
- 29
- Citations by year
- 2026: 20 · 2025: 18 · 2024: 18 · 2023: 24 · 2022: 19 · 2021: 30 · 2020: 43 · 2019: 29 · 2018: 25 · 2017: 32 · 2016: 34 · 2015: 31 · 2014: 33 · 2013: 28 · 2012: 43
- FWCI
- 8.04
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Systematic Biology (publishedVersion)
- PubMed (publishedVersion)
- 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, phylogenetic accuracy, fossil taxon, phylogenetic supertrees, parsimony, consensus trees, data combination, phylogenetic placement
- MeSH terms
- Computer Simulation, Data Interpretation, Statistical, Fossils, Phylogeny, Research Design
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