Table 2.
Genes/loci used in the phylogenetic analyses. Information on the primers, included bases pairs, PCR protocols, and models of nucleotide substitution are indicated.
| Locus | Primers used (reference) | PCR protocol: Annealing temp. & cycles | Nucleotide substitution models | Included sites (# of excluded sites) | Phylogenetically informative sites (%) | Uninformative polymorphic sites | Invariable sites |
|---|---|---|---|---|---|---|---|
| ITS | ITS5, ITS4 (White et al. 1990) | 53 °C, 1 min, 35′ | GTR+G | 670 (136) | 230 (34 %) | 95 | 345 |
| LSU | LR5, LROR (Vilgalys n.d.) | 53 °C, 1 min, 35′ | TIM+I+G | 915 (0) | 142 (16 %) | 44 | 729 |
| Tef1 | tef1-728, tef1-986 (Carbone & Kohn 1999) | 66 °C, 55 s, 9′ | GTR+I+G | 707 (524) | 200 (20 %) | 39 | 468 |
| 56 °C, 55 s, 35′ | |||||||
| Tub | Btub-T1, Btub-T2 (O'Donnell & Cigelnik 1997) | 55 °C, 30 s, 35′ | HKY+I+G | 535 (127) | 260 (26 %) | 49 | 226 |
| Act | Tact1, Tact2 (Samuels et al. 2006) | 65 °C, 30 s, 15′ | GTR+I+G | 635 (0) | 149 (15 %) | 37 | 4498 |
| 48 °C, 30 s, 30′ | |||||||
|
Rpb1 |
crpb1a, rpb1c (Castlebury et al. 2004)
|
50 °C, 2 min, 40′
|
GTR+I+G
|
722 (52)
|
378 (52 %)
|
61
|
283
|
| Total | 4184 | 1359 (33 %) | 325 | 2500 |