The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
Open accessAbstract
Although multiple gene sequences are becoming increasingly available for molecular phylogenetic inference, the analysis of such data has largely relied on inference methods designed for single genes. One of the common approaches to analyzing data from multiple genes is concatenation of the individual gene data to form a single supergene to which traditional phylogenetic inference procedures - e.g., maximum parsimony (MP) or maximum likelihood (ML) - are applied. Recent empirical studies have demonstrated that concatenation of sequences from multiple genes prior to phylogenetic analysis often results in inference of a single, well-supported phylogeny. Theoretical work, however, has shown that the coalescent can produce substantial variation in single-gene histories. Using simulation, we combine these ideas to examine the performance of the concatenation approach under conditions in which the coalescent produces a high level of discord among individual gene trees and show that it leads to statistically inconsistent estimation in this setting. Furthermore, use of the bootstrap to measure support for the inferred phylogeny can result in moderate to strong support for an incorrect tree under these conditions. These results highlight the importance of incorporating variation in gene histories into multilocus phylogenetics.
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.
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
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
Cited by
Bayesian inference of species trees from multilocus data
Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453
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
StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates
Ogilvie, H. A., Bouckaert, R. R., & Drummond, A. J. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx126 · Cited by 469
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
Statistical binning enables an accurate coalescent-based estimation of the avian tree
Mirarab, S., Bayzid, M. S., Boussau, B., & Warnow, T. (2014) · Science · doi:10.1126/science.1250463 · Cited by 257
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
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
Gene tree discordance causes apparent substitution rate variation
Mendes, F. K., & Hahn, M. W. (2016) · Systematic Biology · doi:10.1093/sysbio/syw018 · Cited by 189
Cloutier, A., Sackton, T. B., Grayson, P., Clamp, M., Baker, A. J., & Edwards, S. V. (2019) · Systematic Biology · doi:10.1093/sysbio/syz019 · Cited by 124
Chakrabarty, P., Faircloth, B. C., Alda, F., Ludt, W. B., Mcmahan, C. D., Near, T. J., Dornburg, A., Albert, J. S., Arroyave, J., Stiassny, M. L. J., et al. (2017) · Systematic Biology · doi:10.1093/sysbio/syx038 · Cited by 103
Angelis, K., & Dos Reis, M. (2015) · Current Zoology · doi:10.1093/czoolo/61.5.874 · Cited by 91
ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization
Yin, J., Zhang, C., & Mirarab, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz211 · Cited by 80
Wu, Y.-C., Rasmussen, M. D., Bansal, M. S., & Kellis, M. (2014) · Genome Research · doi:10.1101/gr.161968.113 · Cited by 77
Duchêne, D. A., Tong, K. J., Foster, C. S. P., Duchêne, S., Lanfear, R., & Ho, S. Y. W. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msz291 · Cited by 53
Petzold, A., & Hassanin, A. (2020) · PLOS ONE · doi:10.1371/journal.pone.0217956 · Cited by 60
Hernandez, A. M., & Ryan, J. F. (2019) · doi:10.1101/729103 · Cited by 52
The perils of intralocus recombination for inferences of molecular convergence
Mendes, F. K., Livera, A. P., & Hahn, M. W. (2019) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2018.0244 · Cited by 42
Hruska, J. P., Holmes, J., Oliveros, C., Shakya, S., Lavretsky, P., McCracken, K. G., Sheldon, F. H., & Moyle, R. G. (2023) · Ornithology · doi:10.1093/ornithology/ukad005 · Cited by 37
Sianta, S. A., & Kay, K. M. (2022) · Evolution · doi:10.1111/evo.14484 · Cited by 7
Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies
Mulhair, P. O., Pennati, A., Herrera-Ubeda, C., & Holland, P. W. H. (2025) · Current Biology · doi:10.1016/j.cub.2025.09.051 · Cited by 2
Metadata
- Authors
- Kubatko, L. S., & Degnan, J. H.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-02-01
- Volume
- 56
- Issue
- 1
- Pages
- 17-24
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- OpenAlex
- W2127713506
- Cited by
- 1,034
- References
- 1
- FWCI
- 13.77
- Type
- journal article
- Language
- en
- Open access
- bronze
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
