RAxML concatenation

Concatenated alignment of 547 loci (input file for RAxML

ASTRAL gene trees

499 gene trees (input file 2 for ASTRAL-II

Readme file

Detailed information on the data packag

StarBEAST2 alignment

Alignment of 106 loci (input file for StarBEAST2

ASTRAL bootstrap trees

499 bootstrap trees (input file 1 for ASTRAL-II

Additional file 1: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Table S1. Assembly statistics and number of identified single-copy genes in the analyzed enriched data set. Table S2. Assembly statistics and number of identified single-copy genes in the analyzed transcriptomes. Table S3. Taxa with unstable phylogenetic position (a.k.a. rogue taxa) when analyzing the amino acid and the nucleotide supermatrices. Table S4. Families, subfamilies and tribes included in this study. Table S5. Detailed species list used for target DNA enrichment, including information on identity, sex and concentration of extracted genomic DNA. Table S6. Published transcriptomes of apoid wasps and bees included in the present investigation. Table S7. Official gene sets exploited to identify orthologous transcripts and enriched DNA of target single-copy protein-coding genes. Table S8. Information on required taxa when removing data blocks with poor taxonomic coverage. Table S9. Description, origin, phylogenetic position and age of fossils used to calibrate divergence times. Table S10. Four-cluster Likelihood (FcLM) results on amino acid and nucleotide level when testing the phylogenetic placement of Ammoplanina and Mellininae. Proportions of quartets, that map to specific areas in the 2D-simplex graph. (PDF 230 kb

Additional file 4: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Figure 2. Results from the Four-cluster Likelihood Mapping showing the support for the possible relationship of Ammoplanina (two species), Psenini (four species) + Odontosphecini (one species), Anthophila (42 species) and all remaining species including outgroup species to each other (58050 quartets). Original amino acid supermatrix (94,869 amino acid sites) based on a protein domain-based partitioning scheme and analyzed with partition-specific substitution models (a), permutation scheme I with supermatrix as in a, but amino acids are permuted within partitions while retaining the specific distribution of missing data (b), permutation scheme II with supermatrix as in b, but replacing amino acids in each partition with randomly selected amino acids, using amino acid frequencies as given by the LG substitution matrix, while retaining the specific distribution of missing data (c) and permutation scheme III supermatrix as given in c, but with missing data being randomly permuted (d). Figure 3. Results from the Four-cluster Likelihood Mapping showing the support for the possible relationship of Mellininae (one species), Sphecidae (19 species), Crabroninae (39 species) + Dinetinae (one species), and all remaining species including bees and outgroup species to each other (103320 quartets). Original amino acid supermatrix (94,869 amino acid sites) based on a protein domain-based partitioning scheme and analyzed with partition-specific substitution models (a), permutation scheme I with supermatrix as in a, but amino acids are permuted within partitions while retaining the specific distribution of missing data (b), permutation scheme II with supermatrix as in b, but replacing amino acids in each partition with randomly selected amino acids, using amino acid frequencies as given by the LG substitution matrix, while retaining the specific distribution of missing data (c) and permutation scheme III supermatrix as given in c, but with missing data being randomly permuted (d). Figure 4. Results from the Four-cluster Likelihood Mapping showing the support for the possible relationship of Ammoplanina (two species), Psenini (four species) + Odontosphecini (one species), Anthophila (42 species) and all remaining species including outgroup species to each other (58050 quartets). Original nucleotide supermatrix (284.607 nucleotide sites) partitioned based on applying a combination of protein domain – and codon-based partitioning scheme by modelling the 1st, 2nd and 3rd codon position separately. Each partition was analyzed with partition-specific model parameters under the nucleotide substitution model GTR+G (a), permutation scheme I with supermatrix as in a, but nucleotides are permuted within partitions while retaining the specific distribution of missing data (b), permutation scheme II with supermatrix as in b, but replacing nucleotides in each partition with randomly selected nucleotides, while retaining the specific distribution of missing data (c) and permutation scheme III supermatrix as given in c, but with missing data being randomly permuted (d). Figure 5. Results from the Four-cluster Likelihood Mapping showing the support for the possible relationship of Mellininae (one species), Sphecidae (19 species), Crabroninae (39 species) + Dinetinae (one species), and all remaining species including bees and outgroup species to each other (103320 quartets). Original nucleotide supermatrix (284.607 nucleotide sites) partitioned based on applying a combination of protein domain – and codon-based partitioning scheme by modelling the 1st, 2nd and 3rd codon position separately. Each partition was analyzed with partition-specific model parameters under the nucleotide substitution model GTR+G (a), permutation scheme I with supermatrix as in a, but nucleotides are permuted within partitions while retaining the specific distribution of missing data (b), permutation scheme II with supermatrix as in b, but replacing nucleotides in each partition with randomly selected nucleotides, while retaining the specific distribution of missing data (c) and permutation scheme III supermatrix as given in c, but with missing data being randomly permuted (d). (DOC 1269 kb

Additional file 3: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Table 1. Information on grouping of species in a given quartet when assessing the phylogenetic position of Ammoplanina (two species) and Mellininae (one species) from analyzing the amino acid supermatrix and nucleotide supermatrix including all three codon positions via Four-cluster Likelihood Mapping (FcLM). (PDF 652 kb

Additional file 2: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees

Figure S1. Ultrametric and time-calibrated tree of Apoidea estimated using a relaxed molecular clock approach as implemented in MCMCtree. The estimates are based on the analysis of 284,607 nucleotide sites and applying a combination of protein domain – and codon-based partitioning scheme by modelling 1st, 2nd and 3rd codon positions separately. Figure S2. Phylogenetic relationships of Apoidea. The phylogenetic tree was inferred from analyzing 94,869 amino acid sites under the maximum likelihood (ML) optimality criterion. The data matrix was partitioned based on a protein domain-based partitioning scheme and analyzed with partition-specific substitution models. Node labels indicate bootstrap branch support values derived from 150 bootstrap replicates. Figure S2.1. Phylogenetic relationships of Apoidea. The phylogenetic tree was inferred with ExaBayes, by analyzing 94,869 amino acid sites. The data matrix was partitioned based on a protein domain-based partitioning scheme and analyzed with partition-specific substitution models automatically selected by ExaBayes. Posterior probability values were inferred from a total of 13,500 sampled trees. Figure S3. Phylogenetic relationships of Apoidea. The phylogenetic tree was inferred from analyzing 284.607 nucleotide sites under the maximum likelihood (ML) optimality criterion. The data matrix was partitioned based on applying a combination of protein domain – and codon-based partitioning scheme by modelling 1st and 2nd codon positions separately and excluding the 3rd codon positions. Each partition was analyzed with the partition-specific model parameters under the nucleotide substitution model GTR + G. Node labels indicate bootstrap branch support values derived from 150 bootstrap replicates. Figure S3.1. Phylogenetic relationships of Apoidea. The phylogenetic tree was inferred with ExaBayes, by analyzing 284.607 nucleotide sites. The data matrix was partitioned based on applying a combination of protein domain – and codon-based partitioning scheme by modelling 1st and 2nd codon positions separately and excluding the 3rd codon positions. Each partition was analyzed with the partition-specific model parameters under the nucleotide substitution model GTR + G. Posterior probability values were inferred from a total of 13,500 sampled trees. Figure S4. Phylogenetic relationships of Apoidea. The phylogenetic tree inferred from analyzing 284.607 nucleotide sites under the maximum likelihood (ML) optimality criterion. The data matrix was partitioned based on applying a combination of protein domain – and codon-based partitioning scheme by modelling the 1st, 2nd and 3rd codon position separately. Each partition was analyzed with partition-specific model parameters under the nucleotide substitution model GTR + G. Node labels indicate bootstrap branch support values derived from 100 bootstrap replicates. Figure S4.1. Phylogenetic relationships of Apoidea. The phylogenetic tree was inferred with ExaBayes, by analyzing 284.607 nucleotide sites. The data matrix was partitioned based on applying a combination of protein domain– and codon-based partitioning scheme by modelling the 1st, 2nd and 3rd codon position separately. Each partition was analyzed with partition-specific model parameters under the nucleotide substitution model GTR + G. Posterior probability values were inferred from a total of 13,500 sampled trees. Figure S5. Comparison of divergence times and confidence intervals from four independent dating analyses conducted from with MCMCtree. Differences in the results hint at differences in the convergence of the MCMC method. The closer the dots are to the angle bisector, the more similar the estimates are for the two runs that are compared. Figure S6. Results from Bowker’s matched-pairs test of symmetry. Heat maps showing the results from pairwise comparison of aligned a) amino acid dataset and b) nucleotide dataset with all three codon positions included (PF-NT-1,2,3). White cells specify p-values > 0.05, indicating that corresponding pairs of nucleotide or amino acid sequences do not violate the assumption of global stationary, reversibility, and homogeneity (SRH) conditions. (PDF 1011 kb

BPP3_Analyses_Gehyra_nana

Input and results files for BPP3 analyses run on four different subsets of Gehyra nana taxa, to test for independence of lineages. Analyses were run twice for each subset of lineages. See Table S2 for lineage subset details