Additional file 1 of Rediscovering the unusual, solitary bryozoan Monobryozoon ambulans Remane, 1936: first molecular and new morphological data clarify its phylogenetic position
Creators: name: Schwaha, Thomas
name: Decker, Sebastian H.
name: Baranyi, Christian
name: Saadi, Ahmed J.
Publisher: name: figshare
Year: 2024
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Additional file 1: Table S1. Details of the specimens, collection localities, GenBank Sequence Read Archive (SRA) accession numbers and sources of publicly available sequences. Table S2. Tests of compositional homogeneity determine whether models adequately represented the compositional variation of the data for both data matrices. Table S3. Detailed results of PPA analyses related to Table 1. This table illustrates the empirical heterogeneity observed directly from the data, the average posterior predictive mean and the dispersion around the mean for the mean amino for the five PPA statistics of the complete dataset. Table S4. Detailed results of PPA analyses related to Table 1. This table illustrates the empirical heterogeneity observed directly from the data, the average posterior predictive mean and the dispersion around the mean for the mean amino for the five PPA statistics of the subsampled dataset. Table S5. Fossil calibration nodes used. Each of the nodes used in calibration have the same number in Fig. 7. The second column gives the input used in MCMCTree for the Cauchy “L”, skew normal “SN” and uniform “B” prior age distributions. Table S6. Summary statistics of the transcriptome assembly for Monobryozoon ambulans. Table S7. Number of unique and total functional annotation of the Monobryozoon ambulans transcriptome using Trinotate pipeline. Figure S1. Maximum likelihood phylogeny of Bryozoa based on the complete data matrix, including 422,961 AAs from 2,014 OGs using unpartitioned analysis with PMSF model. All nodes are supported by 100 ultrafast bootstraps. The scale bar represents 1 substitutional change per 100 AAs. Figure S2. Bayesian inference tree of Bryozoa based on the complete data matrix, including 422,961 AAs from 2,014 OGs with CAT-F81 + G4 model. Bayesian posterior probabilities are only shown for nodes that are not maximally supported. The scale bar represents 1 substitutional change per 100 AAs. Figure S3. Bayesian inference tree of Bryozoa based on the complete data matrix, including 422,961 AAs from 2,014 OGs with CAT-GTR + G4 model. Bayesian posterior probabilities are only shown for nodes that are not maximally supported. The scale bar represents 1 substitutional change per 100 AAs. Figure S4. Maximum likelihood phylogeny of Bryozoa based on the subsampled data matrix, including 310,190 AAs from 1500 OGs using partitioned analysis. Values on some nodes represent ML ultrafast bootstrap support and only shown for nodes that are not maximally supported by all analyses. The scale bar represents 1 substitutional change per 100 AAs. Figure S5. Maximum likelihood phylogeny of Bryozoa based on the subsampled data matrix, including 310,190 AAs from 1500 OGs using unpartitioned analysis with PMSF model. All nodes are supported by 100 ultrafast bootstraps. The scale bar represents 1 substitutional change per 100 AAs. Figure S6. Bayesian inference tree of Bryozoa based on the subsampled data matrix, including 310,190 AAs from 1500 OGs with CAT-F81 + G4 model. Bayesian posterior probabilities are only shown for nodes that are not maximally supported. The scale bar represents 1 substitutional change per 100 AAs. Figure S7. Bayesian inference tree of Bryozoa based on the subsampled data matrix, including 310,190 AAs from 1500 OGs with CAT-GTR + G4 model. Bayesian posterior probabilities are only shown for nodes that are not maximally supported. The scale bar represents 1 substitutional change per 100 AAs. Figure S8. Time-calibrated phylogeny of Bryozoa using MCMCTree based on the complete data matrix with posterior distributions based on the skew normal priors. A time scale in Ma is shown above the tree, with geographical periods labelled below the tree. Node bars represent 95% confidence intervals of age estimates and raw numbers for mean. Figure S9. Time-calibrated phylogeny of Bryozoa using MCMCTree based on the complete data matrix with posterior distributions based on the uniform priors. A time scale in Ma is shown above the tree, with geographical periods labelled below the tree. Node bars represent 95% confidence intervals of age estimates and raw numbers for mean. Figure S10. Ancestral state reconstruction for the lifestyles in bryozoans. The pie area indicates the likelihood of character state at each node. Figure S11. Convergence plots for the divergence time analyses showing the relationship between the posterior mean of the two runs of each calibration strategy (A Cauchy, B skew normal and C uniform). Figure S12. Top 20 species taxonomic distribution on the basis of BLASTX and BLASTP hits of Monobryozoon ambulans transcriptome against UniRef90 database. Figure S13. GO functional annotation of Monobryozoon ambulans transcriptome. Orange represents cellular component, blue represents biological process, and green represents molecular function. The Y-axis represents distribution of the top 15 GO terms of each category, the X-axis the number of transcripts. Pie-charts showing the percentage of three GO categories. Figure S14. Classification of eggNOG annotations of the Monobryozoon ambulans transcriptome. The capital letters on the Y-axis represent different eggNOG categories. X-axis shows the number of transcripts in each eggNOG category.