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Table 4 Phylogenetic relationships of ectoprocts, brachiopods and phoronids according to different phylogenetic analyses (only sister group relationships with one other phylum; more complex relationships are not considered).

From: The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships

Method Data set Tree Figure Ectoprocta+Phoronida Ectoprocta+Entoprocta Ectoprocta+Annelida Ectoprocta+Gastropoda Brachiopoda+Annelida Phoronida+Nemertea Phoronida+Entoprocta
Maximum-likelihood (MtZoa+F model) Amino acid data set, with Lingula Additional file 2        <50
Maximum-likelihood (GTR model) Nucleotide data set Additional file 3     <50 86 <50  
Maximum-likelihood (GTR model) Nucleotide data set (Gblocks edited) Additional file 4      <50   
Maximum-likelihood (GTR model) Nucleotide data set (direct nucleotide alignment) Additional file 5      99   
Maximum-likelihood (MtZoa+F model) Amino acid data set Additional file 6      52   52
Maximum-likelihood (MtZoa+F model) Amino acid data set (Gblocks edited) Additional file 7     <50   <50  
Maximum-likelihood (GTR model) 1st and 2nd codon positions 5B     <50 <50 <50  
nhPhyML Nucleotide data set; starting tree GTR tree Additional file 8     x   x  
nhPhyML Nucleotide data set; starting tree CAT tree Additional file 9 x       
Bayesian (CAT model) Amino acid data set 5A    0.84     
Bayesian (CAT model) Amino acid data set; 10 taxa with the most strongly differing amino acid composition excluded Additional file 11    0.78     0.58
Maximum-likelihood (MtZoa+F model) Amino acid data set; 10 taxa with the most strongly differing amino acid composition excluded Additional file 12   <50    <50   
Bayesian (CAT model) Amino acid data set recoded using 9 minmax chi-squared bins' Additional file 14    0.92     
Maximum-likelihood (MULTIGAMMA model) Amino acid data set recoded using 9 minmax chi-squared bins Additional file 15      60   
Bayesian (CAT model) Amino acid data set recoded using 6 minmax chi-squared bins Additional file 16      0.96   
Maximum-likelihood (MULTIGAMMA model) Amino acid data set recoded 6 minmax chi-squared bins Additional file 17      <50   <50
Bayesian (CAT model) Amino acid data set recoded using Dayhoff groups Additional file 18        
Maximum-likelihood (MULTIGAMMA model) Amino acid data set recoded Dayhoff groups Additional file 19        <50
Bayesian (CAT+BP model) Amino acid data set Additional file 20    0.63     
Maximum-likelihood (GTR model) Nucleotide data set, 20% of the alignment positions with highest sitewise rates removed Additional file 21      98   
Maximum-likelihood (MtZoa+F model) Amino acid data set; 10% of the alignment positions with highest sitewise rates removed Additional file 22      <50   58
  1. Unless noted otherwise, the analyses are based on alignments edited with ALISCORE and the nucleotide alignments are derived from the amino acid alignments. If a group is monophyletic, the posterior probability respectively the bootstrap support is given.