Table 3. Model parameters optimized during the global RAxML tree search of the 4,098-species supermatrix.
| Patterns | α | Rates | Frequencies | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Partition | A/C | A/G | A/T | C/G | C/T | G/T | A | C | G | T | ||
| nDNA, pos1 | 9,345 | 0.40 | 1.69 | 4.54 | 0.86 | 1.07 | 4.02 | 1.00 | 0.28 | 0.23 | 0.28 | 0.21 |
| nDNA, pos2 | 8,806 | 0.38 | 1.27 | 5.34 | 0.76 | 1.50 | 4.44 | 1.00 | 0.29 | 0.24 | 0.21 | 0.26 |
| nDNA, pos3 | 10,685 | 1.19 | 1.22 | 5.42 | 0.90 | 1.08 | 5.88 | 1.00 | 0.24 | 0.26 | 0.25 | 0.25 |
| mtDNA, pos1 | 1,253 | 0.52 | 1.08 | 6.67 | 1.70 | 0.17 | 16.01 | 1.00 | 0.30 | 0.25 | 0.22 | 0.23 |
| mtDNA, pos2 | 1,213 | 0.39 | 3.38 | 18.08 | 2.25 | 3.84 | 14.26 | 1.00 | 0.19 | 0.27 | 0.13 | 0.42 |
| mtDNA, pos3 | 1,292 | 0.05 | 0.36 | 9.53 | 0.52 | 0.46 | 6.04 | 1.00 | 0.42 | 0.32 | 0.04 | 0.22 |
| APP, CREM, FBN1 | 1,558 | 0.34 | 1.32 | 3.39 | 0.39 | 0.93 | 3.40 | 1.00 | 0.27 | 0.22 | 0.22 | 0.29 |
| BMI1 | 244 | 0.24 | 1.65 | 4.33 | 1.04 | 0.78 | 5.00 | 1.00 | 0.26 | 0.23 | 0.22 | 0.29 |
| PLCB4 | 287 | 0.49 | 1.03 | 3.67 | 0.52 | 0.78 | 3.08 | 1.00 | 0.32 | 0.24 | 0.19 | 0.25 |
Summarized per partition are the number of distinct alignment patterns, estimated alpha-shape parameter (α) of the gamma distribution, two-way rates of the GTR model of nucleotide evolution, and empirical base frequencies.
Abbreviations: GTR, general time-reversible; mtDNA, mitochondrial DNA; nDNA, nuclear DNA; pos., codon position; RAxML, Randomized Axelerated Maximum Likelihood