Additional file 2: of Phylogenomic analysis of Apoidea sheds new light on the sister group of bees
Creators: name: Sann, Manuela
name: Niehuis, Oliver
name: Peters, Ralph
name: Mayer, Christoph
name: Kozlov, Alexey
name: Podsiadlowski, Lars
name: Bank, Sarah
name: Meusemann, Karen
name: Misof, Bernhard
name: Bleidorn, Christoph
name: Ohl, Michael
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: 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 &gt; 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)