Table 1. Summary of phylogenetic analyses performed in this study.
| Dataset | #char | Analysis/Model | ML topology | (R,M)/(S,M)bootstrap |
|---|---|---|---|---|
| 314 Gene Dataset | ||||
|
| ||||
| 314G | 46,573 | ML/WAG+G, partitioned | S(R,M) | 59/37 |
| 314G | 46,573 | ML/Dayhoff+G, unpartitioned | R(S,M) | 30/70 |
| 314G | 46,573 | ML/Dayhoff+G, partitioned | R(S,M) | 32/68 |
| 314G | 46,573 | ML/GTR+G, partitioned | S(R,M) | 42/54 |
| 314G | 46,573 | ML/LG+G, partitioned | S(R,M) | 54/44 |
| 314G | 46,573 | ML/WAG+G, unpartitioned | R(S,M) | 44/56 |
| 314G | 46,573 | ML/WAG+G, partitioned, b-lengths unlinked | R(S,M) | 41/52 |
| 314G | 46,573 | ML/LG+G, partitioned, b-lengths unlinked | R(S,M) | 60/31 |
| 295G | 43,662 | ML/WAG+G, partitioned | S(R,M) | 45/55 |
| 64G | 11,622 | ML/WAG+G, partitioned | S(R,M) | 61/30 |
| 131G | 23,180 | ML/WAG+G, partitioned | S(R,M) | 71/26 |
| 209G | 34,944 | ML/WAG+G, partitioned | S(R,M) | 67/29 |
| 314G | 46,573 | Bayes/LG+G, partitioned (MrBayes) | S(R,M) | |
| 314G | 46,573 | Bayes/unpartitioned CAT-GTR (Phylobayes) | R(S,M) | |
| 314G | 46,573 | Bayes,/unpartitionedGTR+G (Phycas) | R(S,M) | 0.01/0.99 |
| 314G | NA | Astral | R(S,M) | 55/NA |
| 314G-no-Wallemia | 46,573 | ML/WAG+G, partitioned | S(R,M) | 82/18 |
| 314G-no-Wallemia | 46,573 | ML/WAG+G, unpartitioned | S(R,M) | 84/16 |
| 314G-no-Wallemia | 46,573 | ML/LG+G, partitioned | S(R,M) | 82/18 |
| 314G-no-Malassezia | 46,573 | ML/WAG+G, partitioned | R(S,M) | 27/73 |
| 314G-no-Wall./Mal. | 46,573 | ML/LG+G, partitioned | S(R,M) | 58/42 |
| 314G/c20 | 38,456 | ML/WAG+G, partitioned | S(R,M) | 55/45 |
| 314G/c19-20 | 31,234 | ML/WAG+G, partitioned | M(S,R) | 43 |
| 314G/c18-20 | 29,543 | ML/WAG+G, partitioned | NA | NA |
| 205G | 30,896 | ML/LG+G, partitioned, b-lengths unlinked | R(S,M) | 43/57 |
| 205G | 30,896 | ML/WAG+G, partitioned, b-lengths unlinked | R(S,M) | 41/59 |
| 205G | 30,896 | ML/LG+G, partitioned | R(S,M) | 27/73 |
| 205G | 30,896 | ML/WAG+G, partitioned | R(S,M) | 22/78 |
|
| ||||
| 824 Gene Dataset | ||||
|
| ||||
| 824G | 165,465 | ML/WAG+G, partitioned | R(S,M) | 5/95 |
| 824G/c20 | 137,702 | ML/WAG+G, partitioned | R(S,M) | 16/84 |
| 824G/c19-20 | 81,981 | ML/WAG+G, partitioned | NA | 20/19 |
| 824G/c18-20 | 56,149 | ML/WAG+G, partitioned | NA | 2/3 |
| 824G/c17-20 | 43,218 | ML/WAG+G, partitioned | NA | 2/0 |
| 824G | 165,465 | Bayes/model, partitioned (MrBayes) | R(S,M) | |
| 824G | NA | Astral | R(S,M) | NA/95 |
| 824G-no-Wallemia | 165,465 | ML/WAG+G, partitioned | R(S,M) | 1/99 |
| 824G | 165,465 | ML/WAG+G, partitioned + b-lengths unlinked (Iq-Tree) | R(S,M) | 1/75 |
|
| ||||
| 901 Gene Dataset | ||||
|
| ||||
| 901G | 241,004 | ML/WAG+G, partitioned | R(S,M) | 1/99 |
| 901G/c20 | 202,598 | ML/WAG+G, partitioned | R(S,M) | 2/98 |
| 901G/c19-20 | 128,347 | ML/WAG+G, partitioned | NA | 3/2 |
| 901G/c18-20 | 95,197 | ML/WAG+G, partitioned | NA | 3/2 |
| 901G/c17-20 | 80,230 | ML/WAG+G, partitioned | NA | 0/0 |
| 901G | NA | Astral | R(S,M) | 99/NA |
|
| ||||
| Other | ||||
|
| ||||
| 950G | 704,775 | ML/WAG+G, partitioned | R(S,M) | NA |
| Gene content | 50,971 | ML/Mk2 | S(R,M) | 98/2 |
Notes: The Maximum likelihood topology and support values are shown as a function of dataset name, number of characters and the methods and model employed. NA for topology means the monophyly of one of more of the subphyla broke down. Removal of the fast-evolving amino acid categories are indicated by c20 … c17-20, corresponding to the removal of the fastest, to the four fastest rate categories.