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Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

  1. Christopher E Laumer  Is a corresponding author
  2. Harald Gruber-Vodicka
  3. Michael G Hadfield
  4. Vicki B Pearse
  5. Ana Riesgo
  6. John C Marioni
  7. Gonzalo Giribet
  1. Wellcome Trust Sanger Institute, United Kingdom
  2. European Molecular Biology Laboratories-European Bioinformatics Institute, United Kingdom
  3. Max Planck Institute for Marine Microbiology, Germany
  4. Pacific Biosciences Research Center and the University of Hawaii-Manoa, United States
  5. University of California, United States
  6. The Natural History Museum, United Kingdom
  7. University of Cambridge, United Kingdom
  8. Harvard University, United States
Short Report
Cite this article as: eLife 2018;7:e36278 doi: 10.7554/eLife.36278
5 figures, 2 tables, 3 data sets and 1 additional file

Figures

Figure 1 with 2 supplements
Consensus phylogram showing deep metazoan interrelationships under Bayesian phylogenetic inference of the 430-orthologue amino acid matrix, using the CAT + GTR + Г4 mixture model.

All nodes received full posterior probability. Numerical annotations of given nodes represent Extended Quadripartition Internode Certainty (EQP-IC) scores, describing among-gene-tree agreement for both the monophyly of the five major metazoan clades and the given relationships between them in this reference tree. A bar chart on the right depicts the proportion of the total orthologue set each terminal taxon is represented by in the concatenated matrix. ‘Placozoa H1’ in this and all other figures refers to the GRELL isolate sequenced in Srivastava et al., 2008, which has there and elsewhere been referred to as Trichoplax adhaerens, despite the absence of type material linking this name to any modern isolate. Line drawings of clade representatives are taken from the BIODIDAC database (http://biodidac.bio.uottawa.ca/).

https://doi.org/10.7554/eLife.36278.004
Figure 1—figure supplement 1
Maximum likelihood tree under the C60 +LG + FO + R4 profile mixture model, inferred from the 430-orthologue matrix with full taxon sampling.

Nodes annotated with ultrafast bootstrap supports with NNI correction; unannotated nodes received full support.

https://doi.org/10.7554/eLife.36278.005
Figure 1—figure supplement 2
Maximum likelihood tree under a profile mixture model inferred from the 430-orthologue matrix, with only Placozoa H1 used to represent this clade.

Nodes annotated with ultrafast bootstrap supports with NNI correction; unannotated nodes received full support.

https://doi.org/10.7554/eLife.36278.006
Consensus phylogram under Bayesian phylogenetic inference under the CAT + GTR + Г4 mixture model, on the 430-orthologue concatenated amino acid matrix, recoded into 6 Dayhoff groups.

Nodes annotated with posterior probability; unannotated nodes received full support.

https://doi.org/10.7554/eLife.36278.007
Posterior consensus trees from CAT + GTR + Г4 mixture model analysis of a 94,444 amino acid supermatrix derived from the 303 single-copy conserved eukaryotic BUSCO orthologs, analysed in A.

amino acid space or (B) the Dayhoff-6 reduced alphabet space. Nodal support values comprise posterior probabilities; nodes with full support not annotated. Taxon colourings as in previous Figures. (C) Plot of z-scores (summed absolute distance between taxon-specific and global empirical frequencies) from representative posterior predictive tests of amino acid compositional bias, from both the BUSCO 303-orthologue matrix (red) and the initial 430-orthologue matrix (blue). Placozoan taxon abbreviations are shown in blue font.

https://doi.org/10.7554/eLife.36278.008
Figure 4 with 2 supplements
Schematic depiction of deep metazoan interrelationships in posterior consensus trees from CAT + GTR + Г4 mixture model analyses of matrices made from subsets of genes passing or failing a sensitive null-simulation test of compositional heterogeneity.

Panels correspond to (A) the amino acid matrix made within the failing set; (B) the amino acid matrix derived from the passing set; (C) the Dayhoff-6 recoded matrix from the failing set; (D) the Dayhoff-6 recoded matrix from the passing set. Only nodes with posterior probability less than 1.00 are annotated numerically.

https://doi.org/10.7554/eLife.36278.010
Figure 4—figure supplement 1
Maximum likelihood tree under a profile mixture model inferred from the 349-orthologue matrix composed from the subset of genes binned as failing the null-simulation compositional bias test.

Nodes annotated with ultrafast bootstrap supports with NNI correction; unannotated nodes received full support.

https://doi.org/10.7554/eLife.36278.011
Figure 4—figure supplement 2
Maximum likelihood tree under a profile mixture model inferred from the 348-orthologue matrix composed from the subset of genes binned as passing the null-simulation compositional bias test.

Nodes annotated with ultrafast bootstrap supports with NNI correction; unannotated nodes received full support.

https://doi.org/10.7554/eLife.36278.012
Author response image 1

Tables

Table 1
Summary statistics describing the contiguity and completeness of the draft host metagenome bins from the three clade A placozoan isolates utilized in this paper, presented in comparison to the reference H1 strain.
https://doi.org/10.7554/eLife.36278.003
H11H4H6H1
assembly span (Mbp)56.6383.3976.798.06
scaffold number5813533783101415
scaffold N50 (kbp)12.73825.9712.845790
GC%30.7630.8429.929.37
BUSCO2 Eukaryota
complete (of 303)
220276239294
BUSCO2 Eukaryota
complete + partial (of 303)
246282265298
Average # of hits per BUSCO1.001.041.001.00
% of BUSCOs with more
than one match
0.453.990.420.34
Table 2
Mean (and standard deviation of) z-scores from posterior predictive tests of per-site amino acid diversity and among-lineage compositional homogeneity, called for amino-acid alignments using the PhyloBayes-MPI v1.8 readpb_mpi –div and –comp options, respectively, with burn-ins selected as per the posterior consensus summaries shown elsewhere.

Except for the diversity statistic in the test-passing matrix, all tests reject (at p=0.05) the adequacy of the inferred CAT + GTR + Г4 model to describe the data.

https://doi.org/10.7554/eLife.36278.009
DiversityComposition (mean)Composition (maximum)
430 matrix1.94 (0.09)181.35 (7.50)105.04 (3.13)
BUSCO 303-gene matrix11.27 (0.73)334.98 (4.56)107.56 (6.17)
comp-failed matrix2.51 (0.19)270.16 (12.03)173.87 (9.15)
comp-passed matrix0.81 (0.18)107.67 (10.10)63.19 (6.95)

Data availability

SRA accession codes, where used, and all alternative sources for sequence data (e.g. individually hosted websites, personal communications), are listed above in the Materials and Methods section. A DataDryad accession is available at https://doi.org/10.5061/dryad.6cm1166, which makes available all helper scripts, orthogroups, multiple sequence alignments, phylogenetic program output, and raw host proteomes inputted to OrthoFinder. Metagenomic bins containing placozoan host contigs and raw RNA reads used to derive gene annotations from H4, H6 and H11 isolates are also provided in this accession. PhyloBayes. chain files, due to their large size, are separately accessioned at in Zenodo at https://doi.org/10.5281/zenodo.1197272. Raw RNA-seq data from three separate isolates of Placozoan haplotype H4 have been deposited in NCBI BioProject under accession code PRJNA505163.

The following data sets were generated
  1. 1
  2. 2
    Zenodo
    1. C Laumer
    2. H Gruber-Vodicka
    3. MG Hadfield
    4. VB Pearse
    5. A Riesgo
    6. JC Marioni
    7. G Giribet
    (2018)
    PhyloBayes chain data from: Placozoa and Cnidaria are sister taxa.
    https://doi.org/10.5281/zenodo.1197272
  3. 3

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