Table 3.
Amplification success, phylogenetic data and the substitution models used in the phylogenetic and haplotype analysis, per locus.
| Locus/Region | ARF | H-anti | OLE | ITS | MLSA | |
|---|---|---|---|---|---|---|
| Amplification success (%) | 97.11 | 99.03 | 98.07 | 99.03 | – | |
| Histoplasma isolates | This study (n) | 101 | 103 | 102 | 103 | 101 |
| GenBank (n) | 116 | 92 | 91 | 116 | 77 | |
| Total (n) | 217 | 195 | 193 | 219 | 178 | |
| Best model | K2+G | K2+G | K2 | T92+G | K2+G+I | |
| MP–consistency index | 0,814815 | 0,704918 | 0,750000 | 0,661765 | 0,500000 | |
| MP–retention index | 0,960317 | 0,920000 | 0,921986 | 0,910156 | 0,901961 | |
| MP–composite index (for all sites) | 0,837200 | 0,749278 | 0,786761 | 0,714515 | 0,572341 | |
| MP–Tree length | 78 | 97 | 75 | 107 | 301 | |
| MP–No. of tress | 9 | 2 | 1 | 5 | 2 | |
| N. of sequences | 211 | 188 | 192 | 215 | 179 | |
| N. of sites | 453 | 385 | 399 | 582 | 1237 | |
| Total number of sites (excluding sites with gaps / missing data): | 430 | 369 | 390 | 550 | 1192 | |
| Conserved characters | 392 | 309 | 336 | 497 | 1053 | |
| Variable characters | 60 | 71 | 62 | 81 | 176 | |
| Parsimony-informative characters | 40 | 38 | 48 | 51 | 98 | |
| Singletons | 20 | 33 | 14 | 30 | 78 | |
| Nucleotide diversity (pi) | 0,01397 | 0,01665 | 0,01305 | 0,01080 | 0,01346 | |
| Number of haplotypes (h) | 55 | 52 | 44 | 63 | 88 | |
| Haplotype diversity (Hd) | 0,9101 | 0,9165 | 0,8360 | 0,9146 | 0,9746 | |
| Recombination phi test (Φ) (P-value) | No (P = 0.3754) | No (P = 0.1068) | No (P = 0.6897) | No (P = 0.3) | Yes (P = 1.539e-7) | |
ARF: ADP-ribosylation factor; H-anti: H antigen precursor; OLE: Delta-9 fatty acid desaturase; ITS: Internal transcribed spacers + rRNA genes; MLSA: Multi-locus sequence analysis; MP: maximum parsimony.