Cited by 162Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic StudiesEvolution and Paleontology Studies

Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha

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Kapli, Paschalia, Telford, Maximilian J.·2020·Science Advances

Abstract

A data simulation approach shows that the contested origins of Ctenophora and Xenacoelomorpha are obscured by systematic errors.

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Crossref · 10.1126/sciadv.abc5162

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  • Whelan and Halanych's simulations questioning the reliability of the CAT model's inference of large numbers of site categories (and its placement of Porifera as sister to other animals) were found to be flawed, and improved simulations are instead consistent with Ctenophora sister deriving from LBA.

    “In-line with this Whelan and Halanych’s simulations questioning the reliability of the CAT model’s inference of large numbers of site categories (and its placement of Porifera as sister to other animals)34 were found to be flawed41, and improved simulations are instead consistent with Ctenophora sister deriving from LBA79.”

    From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [79]

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Research works printed but not linked: 15

  1. [14]Kapli P., Yang Z., Telford M. J., Phylogenetic tree building in the genomic age. Nat. Rev. Genet. 21, 428– 444 (2020). 32424311
  2. [16]Nguyen L. T., Schmidt H. A., Von Haeseler A., Minh B. Q., IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268– 274 (2015). 25371430 PMC4271533
  3. [17]Le S. Q., Gascuel O., Lartillot N., Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 24, 2317– 2323 (2008). 18718941
  4. [18]Aguinaldo A. M. A., Turbeville J. M., Linford L. S., Rivera M. C., Garey J. R., Raff R. A., Lake J. A., Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 489– 493 (1997). 9168109
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  7. [26]Bourlat S. J., Juliusdottir T., Lowe C. J., Freeman R., Aronowicz J., Kirschner M., Lander E. S., Thorndyke M., Nakano H., Kohn A. B., Heyland A., Moroz L. L., Copley R. R., Telford M. J., Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature 444, 85– 88 (2006). 17051155
  8. [27]Philippe H., Brinkmann H., Copley R. R., Moroz L. L., Nakano H., Poustka A. J., Wallberg A., Peterson K. J., Telford M. J., Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470, 255– 258 (2011). 21307940 PMC4025995
  9. [28]King N., Rokas A., Embracing uncertainty in reconstructing early animal evolution. Curr. Biol. 27, R1081– R1088 (2017). 29017048 PMC5679448
  10. [29]Siddall M. E., Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris zone. Cladistics 14, 209– 220 (1998). 34905829
  11. [30]Swofford D. L., Waddell P. J., Huelsenbeck J. P., Foster P. G., Lewis P. O., Rogers J. S., Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50, 525– 539 (2001). 12116651
  12. [32]Wang H. C., Li K., Susko E., Roger A. J., A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evol. Biol. 8, 331 (2008). 19087270 PMC2628903
  13. [33]Wang H. C., Minh B. Q., Susko E., Roger A. J., Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol. 67, 216– 235 (2018). 28950365
  14. [34]Hoang D. T., Chernomor O., Von Haeseler A., Minh B. Q., Vinh L. S., UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518– 522 (2018). 29077904 PMC5850222
  15. [35]Stamatakis A., RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312– 1313 (2014). 24451623 PMC3998144

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Authors
Kapli, P., & Telford, M. J.
Affiliations
University College London (GB)
Corresponding author
Telford, Maximilian J.
Venue
Science Advances
Published
2020-12-11
Volume
6
Issue
50
ISSN
2375-2548 (ISSN-L)
OpenAlex
W3112831972
Cited by
162
References
15
Citations by year
2026: 16 · 2025: 33 · 2024: 19 · 2023: 21 · 2022: 28 · 2021: 45
FWCI
13.46
Type
journal article
Language
en
Open access
Locations
  • Science Advances (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • UCL Discovery (University College London) (submittedVersion)
Funders
Biotechnology and Biological Sciences Research Council (BB/R016240/1)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Keywords
Ctenophora, Xenacoelomorpha, animal phylogeny, systematic errors, phylogenetic tree topology

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