Table 1 Description of alternative model partitioning strategies tested for fit to the combined nucleotide data
Model name | # of partitions | # of free model parameters | Description of model partitions |
|---|---|---|---|
MB1 | 1 | 10 | Single model for concatenated dataset |
MB2 | 2 | 13 | 16S; All protein coding gene fragments (dnaJ; rpoB; tuf) |
MB3 | 4 | 29 | Independent partition for each gene fragment (16S; dnaJ; rpoB; tuf) |
MB4 | 7 | 48 | 16S; two partitions for each gene fragment (codon positions 1 and 2; codon position 3) |
MB5 | 8 | 62 | 16S, stems; 16S, loops; two partitions for each gene fragment (codon positions 1 and 2; codon position 3) |
MB6 | 10 | 78 | 16S; three partitions for each gene fragment (codon positions 1, 2, and 3, separately) |
MB7 | 11 | 92 | 16S, stems; 16S, loops; three partitions for each gene fragment (codon positions 1, 2 and 3, separately) |
MB8 | 3 | 26 | 16S, stems; 16S, loops; All protein coding gene fragments (dnaJ; rpoB; tuf) |
MB9 | 5 | 43 | 16S, stems; 16S, loops; Independent partition for each protein coding gene fragment (dnaJ; rpoB; tuf) |