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Revisiting metazoan phylogeny with genomic sampling of all phyla
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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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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
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.
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