The DOI matches its Crossref record; 77 of the 77 references it cites were found in a registry or an index.
Revisiting metazoan phylogeny with genomic sampling of all phyla
Open accessAbstract
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.
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“Interestingly, some recent studies have reported Placozoa as sister to Cnidaria (sometimes paired with Ctenophora second) when minimizing compositional heterogeneity5,33, and we have also recovered some support for this (RL2 analysis of WEA15 dataset) (Fig. 3c).”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [5]
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“Furthermore, we previously showed that cnidarians and placozoans are united as sister lineages to the exclusion of bilaterians and sponges based on the mixing of genes from ALG_Ea and ALG_F found on cnidarian chromosomes and placozoan scaffolds57, consistent with recent gene trees55.”
From Ancient gene linkages support ctenophores as sister to other animals (2023) · cites this paper as [55]
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“If sponges are monophyletic (as supported by recent phylogenomic studies8,10,55), then the four fusions-with-mixing that are found in demosponges and parahoxozoans must be shared by all sponges.”
From Ancient gene linkages support ctenophores as sister to other animals (2023) · cites this paper as [55]
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“The RL2 findings also support recent efforts pairing recoding and site-heterogeneous models to resolve difficult, ancient nodes in animal phylogeny5,9,24,33, despite the erosion of data relevant to more shallow nodes.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [5]
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Citations
Cites
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Broad phylogenomic sampling improves resolution of the animal tree of life
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“If corroborated by other analyses, however, our clade may resurrect the core aspect of the Polyzoa hypothesis: that Bryozoa and Entoprocta descend from a common ancestor with asexual budding and/or coloniality [1].”
BackgroundResultSelf-citationCriscuolo, A., & Gribaldo, S. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-210 · Cited by 1,667
A 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
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
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 6×
“Our initial ML tree showed evidence of redundant and poorly placed individual taxa, as well as the presence of some clades previously shown to be driven by compositional bias (e.g. Polyzoa [26]; electronic supplementary material, figure S1).”
BackgroundInfluentialSelf-citationLartillot, N., Brinkmann, H., & Philippe, H. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s4 · Cited by 705
Rare genomic changes as a tool for phylogenetics
Rokas, A., & Holland, P. W. H. (2000) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(00)01967-4 · Cited by 693
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The new animal phylogeny: Reliability and implications
Adoutte, A., Balavoine, G., Lartillot, N., Lespinet, O., Prud'homme, B., & de Rosa, R. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.9.4453 · Cited by 512
Research works printed but not linked: 1
- Ax P, 1999, Das System der Metazoa II. Ein Lehrbuch der phylogenetischen Systematik
Cited by
Sorted by citations
NCBI Taxonomy: a comprehensive update on curation, resources and tools
Schoch, C. L., Ciufo, S., Domrachev, M., Hotton, C. L., Kannan, S., Khovanskaya, R., Leipe, D., Mcveigh, R., O’Neill, K., Robbertse, B., et al. (2020) · Database · doi:10.1093/database/baaa062 · Cited by 2,635
“These include PACMAD and BOP clades in grasses, the numerous groups and subgroups in the fly genus Drosophila and several important TaxNodes near the root of Metazoa, e.g. Eumetazoa, Bilateria, Amoebozoa or the Sar clade.”
BackgroundAncient gene linkages support ctenophores as sister to other animals
Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362
Deeply conserved synteny and the evolution of metazoan chromosomes
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PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
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Metadata
- Authors
- Laumer, C. E., Fernández, R., Lemer, S., Combosch, D., Kocot, K. M., Riesgo, A., Andrade, S. C. S., Sterrer, W., Sørensen, M. V., & Giribet, G.
- Affiliations
- European Bioinformatics Institute (GB)
- Harvard University (US)
- University of Alabama (US)
- Natural History Museum (GB)
- Universidade de São Paulo (BR)
- Bermuda Natural History Museum, PO Box FL 145, Flatts, FLBX, Bermuda
- Natural History Museum of Denmark (DK)
- Corresponding author
- Laumer, Christopher E.
- ORCID
- Venue
- Proceedings of the Royal Society B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2019-07-10
- Volume
- 286
- Issue
- 1906
- Pages
- 20190831
- ISSN
- 0080-4649 (ISSN-L)
- 0962-8452
- 1471-2954
- PMC
- PMC6650721
- OpenAlex
- W2957892651
- Semantic Scholar
- 19950757d5ee0e9f1ec51627ad75dc7ffaa31ab8
- Cited by
- 360
- References
- 77
- Citations by year
- 2026: 24 · 2025: 41 · 2024: 65 · 2023: 61 · 2022: 55 · 2021: 59 · 2020: 43 · 2019: 10
- FWCI
- 14.23
- Type
- journal article
- Language
- en
- Update notices
- correction (2019-11-06)
- Open access
- hybrid
- doi.org
- Locations
- Proceedings of the Royal Society B Biological Sciences (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by)
- Funders
- National Science Foundation (DEB-0732903, DEB-1457539)
- Faculty of Arts and Sciences (Internal core funding to GG)
- Museum of Comparative Zoology, Harvard University (Internal core funding to GG)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Marine Invertebrate Physiology and Ecology
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Keywords
- animal phylogeny, Lophophorata, Gnathifera, chaetognaths, Spiralia, Panarthropoda, Lophotrochozoa, Ctenophora, Entoprocta, Cycliophora, Placozoa, Cnidaria, matrix construction, stationarity assumption, phylogenetic incongruence
- MeSH terms
- Animals, Classification, Phylogeny, Genomics
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