Additional file 3: of A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

Phylogenies inferred from 47 individual proteins. Consensus alignments of orthologous sequences of 47 proteins retrieved from 14 amoebozoan genomes were determined using M-coffee, with eight alignment algorithms. Regions with poor consensus alignment or with long insertions in only few proteins were deleted. Phylogenies were inferred by Bayesian inference using a mixed amino-acid substitution models with rate variation between sites estimated by a gamma distribution with a proportion of invariable sites. Analysis were run for one million generations. Trees were rooted at midpoint using Figtree ( http://tree.bio.ed.ac.uk/software/figtree/ ), with posterior probabilities shown at the nodes. Panel A: proteins a-h; Panel B: proteins m-x. The consensus phylogeny of all 47 concatenated proteins (see also Fig. 2) is shown top left in Panel A. (PDF 156 kb

Additional file 4: of A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group

Tree error compensation by concatenation. Concatenated alignments of two or three proteins that individually yielded trees with a single non-consensual node at different positions were subjected to Bayesian inference as described for Additional file 3. Four out of five concatenated alignments (B-E) yielded the consensus tree (A). Only aco1 required two additional proteins to correct its topology errors. (PDF 122 kb

Additional file 1: Table S1. of A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

Gene set: The genes identified and additional information on orthology, detection method, and expression peak. (XLSX 97 kb

Additional file 2: Table S3. of A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

Oligonucleotides primer sequences for knock out studies. (DOC 56 kb

Additional file 3: of A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

Supplementary Figures 1-6. (DOCX 3657 kb

Additional file 4: Table S2. of A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae

Upregulated mutants upregulated mutant list and ko phenotype description. (XLSX 22 kb

MOESM1 of Phylogeny-wide conservation and change in developmental expression, cell-type specificity and functional domains of the transcriptional regulators of social amoebas

Additional file 1: Figure S1-S18. Annotated phylogenetic trees of transcription factor families

MOESM3 of Phylogeny-wide conservation and change in developmental expression, cell-type specificity and functional domains of the transcriptional regulators of social amoebas

Additional file 3: Table S2. Transcription factor conservation. Conservation and change in the presence, developmental expression and functional domain architecture in transcription factors across five Dictyostelid genomes

Additional file 2: Figure S3. of Improved annotation with de novo transcriptome assembly in four social amoeba species

Annotated domain diagrams for 16 D. discoideum developmentally relevant proteins which have had their protein sequence altered. (PDF 367 kb

MOESM4 of Phylogeny-wide conservation and change in developmental expression, cell-type specificity and functional domains of the transcriptional regulators of social amoebas

Additional file 4: Table S3. Transcription factors grouped by cell-type and stage specificity. The data of Additional file 3: Table S2 were compiled and sorted to generate sets that were expressed in the same cell type or at the same developmental stage, or that shared a combination of the same stage and cell type specificity