Table 2.
Data characteristics and estimated evolutionary parameters from phylogenetic analyses. (The number and resolution of trees, tree length (MP); CI (ensemble consistency index), and RI (ensemble retention index) values are derived from equally weighted parsimony analysis of the data. The tree length (BI), and parameters πi, rij, piv, α, and c are derived from simultaneous Bayesian analysis of the partitioned (RAG-1 and RAG-2) and unpartitioned (combined) data (see Electronic Appendix).)
| RAG-1 | RAG-2 | combined | |
|---|---|---|---|
| length of alignment | 2965 | 1152 | 4117 |
| number of variable characters | 1439 | 654 | 2093 |
| number of informative characters | 1084 | 476 | 1560 |
| number of trees (number of nodes) | 7330 (85) | >50 000 (80) | 481 (94) |
| tree length (MP) | 5531 | 2632 | 8215 |
| CI, RI | 0.386, 0.462 | 0.387, 0.525 | 0.384, 0.478 |
| −ln(L) | 51 135.7 (51 116.9–51 157.6) | ←joint estimate | 51 177.1 (51 158.3–51 199.5) |
| tree length (BI) | 2.99 (2.91–3.08) | ←joint estimate | 3.03 (2.92–3.14) |
| πA | 0.33 (0.31–0.34) | 0.32 (0.30–0.34) | 0.33 (0.32–0.34) |
| πC | 0.21 (0.20–0.22) | 0.20 (0.18–0.22) | 0.20 (0.20–0.21) |
| πG | 0.23 (0.22–0.24) | 0.20 (0.18–0.21) | 0.22 (0.21–0.22) |
| πT | 0.24 (0.23–0.25) | 0.29 (0.27–0.30) | 0.26 (0.25–0.263) |
| rAC | 1.69 (1.45–1.99) | 0.80 (0.61–1.01) | 1.29 (1.13–1.43) |
| rAG | 5.95 (5.28–6.67) | 5.18 (4.17–6.15) | 5.50 (4.98–6.01) |
| rAT | 0.81 (0.69–0.93) | 0.48 (0.38–0.60) | 0.64 (0.56–0.71) |
| rCG | 1.71 (1.45–1.98) | 1.58 (1.23–1.95) | 1.66 (1.48–1.89) |
| rCT | 11.53 (10.18–13.13) | 5.69 (4.67–6.75) | 8.91 (7.98–9.69) |
| piv | 0.39 (0.36–0.41) | 0.29 (0.24–0.33) | 0.36 (0.34–0.38) |
| α | 1.20 (1.06–1.35) | 0.90 (0.75–1.06) | 1.05 (0.95–1.16) |
| c | 0.92 (0.89–0.95) | 1.21 (1.14–1.30) | NA |