Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias
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Abstract
The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for Cnidaria and Bilateria as seen in most published work to date, depending on the orthologues selected to construct the matrix. We demonstrate that a majority of genes show evidence of compositional heterogeneity, and that support for the Cnidaria + Bilateria clade can be assigned to this source of systematic error. In interpreting these results, we caution against a peremptory reading of placozoans as secondarily reduced forms of little relevance to broader discussions of early animal evolution.
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The RL2 findings support recent efforts pairing recoding and site-heterogeneous models to resolve difficult, ancient nodes in animal phylogeny, despite the erosion of data relevant to more shallow nodes.
“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 [33]
The recovery of Placozoa as sister to Cnidaria in recoded WEA15 analyses is in-line with the proposal that compositional heterogeneity obscures this relationship.
“We also recovered Placozoa as sister to Cnidaria in our recoded analyses of the WEA15 dataset (RL1 UFBOOT = 54%; RL2 UFBOOT = 90%) (Supplementary Fig. 22), in-line with the proposal that compositional heterogeneity obscures this relationship33.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [33]
Some recent studies have reported Placozoa as sister to Cnidaria (sometimes paired with Ctenophora second) when minimizing compositional heterogeneity.
“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 [33]
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Revisiting metazoan phylogeny with genomic sampling of all phyla
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Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2
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The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution
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Hidden cell diversity in Placozoa: ultrastructural insights from Hoilungia hongkongensis
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The enigmatic Placozoa part 1: Exploring evolutionary controversies and poor ecological knowledge
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A taxon-rich and genome-scale phylogeny of Opisthokonta
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DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies
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A Phylogenomic Backbone for Gastropod Molluscs
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Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum
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Developmental processes in Ediacara macrofossils
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Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails
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Self-citationPlacozoan fiber cells: mediators of innate immunity and participants in wound healing
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Multiple outgroups can cause random rooting in phylogenomics
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Early eukaryotic origins and metazoan elaboration of MAPR family proteins
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Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions
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Binary fission in Trichoplax is orthogonal to the subsequent division plane
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A macroscopic free-swimming medusa from the middle Cambrian Burgess Shale
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Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny
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Inferring Ancient Relationships with Genomic Data: A Commentary on Current Practices
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An evolutionary genomics view on neuropeptide genes in Hydrozoa and Endocnidozoa (Myxozoa)
Koch, T. L., Hauser, F., & Grimmelikhuijzen, C. J. P. (2021) · BMC Genomics · doi:10.1186/s12864-021-08091-2 · Cited by 15 · see citing works
Ancient fish lineages illuminate toll-like receptor diversification in early vertebrate evolution
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Is the deuterostome clade an artifact?
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Small RNAs in Cnidaria: A review
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Разнообразие клеточных типов у гаплотипа H4 Placozoa sp.
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A renaissance of microRNAs as taxonomic and phylogenetic markers in animals
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Diversity, function and evolution of marine invertebrate genomesPreprint
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Unde venisti PGRMC? Grand-Scale Biology from Early Eukaryotes and Eumetazoan Animal Origins
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Self-citationThe evolution of complex multicellularity in animals
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Horizontal Transfer and Gene Loss Shaped the Evolution of Alpha-Amylases in Bilaterians
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BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more
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Piezo proteins, mechano reception and behaviour in Hydra
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A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergencesPreprint
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Accurate, comprehensive database of group I introns and their homing endonucleases
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Self-citationEvolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model
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Reply to: Available data do not rule out Ctenophora as the sister group to all other Metazoa
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Evolution of Neuropeptide Signaling: From a Single Cell to Mammals
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Ancient conservation of androglobin expression reveals its evolutionary link to ciliary processes
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Introduction: Young Approaches to Animal Evolution
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Long-Term Culturing of Placozoans (Trichoplax and Hoilungia)
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Apicortin, a Putative Apicomplexan-Specific Protein, Is Present in Deep-Branching Opisthokonts
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An ancient lysozyme in placozoans participates in acidic extracellular digestion
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Beyond Congruence: Evidential Integration and Inferring the Best Evolutionary ScenarioPreprint
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Early transitions in the evolution of cognition
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Self-citation
- Authors
- Laumer, C. E., Gruber-Vodicka, H., Hadfield, M. G., Pearse, V. B., Riesgo, A., Marioni, J. C., & Giribet, G.
- Affiliations
- European Bioinformatics Institute (GB)
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Hawaiʻi at Mānoa (US)
- University of California, Santa Cruz (US)
- Natural History Museum (GB)
- Harvard University (US)
- Corresponding author
- Laumer, Christopher E
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2018-10-30
- Volume
- 7
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC6277202
- OpenAlex
- W2898892386
- Cited by
- 112
- References
- 104
- Citations by year
- 2026: 5 · 2025: 11 · 2024: 9 · 2023: 13 · 2022: 13 · 2021: 27 · 2020: 18 · 2019: 14 · 2018: 2
- FWCI
- 11.22
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Max-Planck-Institut fuer Marine Microbiologie
- European Bioinformatics Institute
- Harvard University (Faculty of Arts and Sciences)
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Keywords
- Placozoa, Cnidaria, animal phylogeny, compositional heterogeneity, early animal evolution, sister group relationships
- MeSH terms
- Animals, Base Composition, Bayes Theorem, Cnidaria, Models, Genetic, Phylogeny, Bias, Likelihood Functions, Metagenome, Placozoa
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