Table 2.
Effects of reduced taxon and site sampling
| Supports for Great Ape parasites sister-group of: | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Number of Taxa | Genes | Rodent | Primate+Rodent | Primate | ||||||
| PP, | SH, | BS | PP, | SH, | BS | PP, | SH, | BS | ||
| CytB | 0.221, | *, | 0.306 | 0.612, | 0.29, | 0.444 | 0.166, | *, | 0.250 | |
| 8 Taxa | Cox1 | 0.152, | *, | 0.374 | 0.848, | 0.45, | 0.610 | 0.000, | *, | 0.016 |
| Cox3 | 0.922, | 0.63, | 0.659 | 0.002, | *, | 0.013 | 0.070, | *, | 0.313 | |
| Conc. | 0.971, | 0.58, | 0.655 | 0.029, | *, | 0.316 | 0.000, | *, | 0.029 | |
| CytB | 0.911, | 0.77, | 0.548 | 0.074, | *, | 0.225 | 0.013, | *, | 0.009 | |
| 33 Taxa | Cox1 | 0.022, | *, | 0.336 | 0.976, | 0.61, | 0.606 | 0.001, | *, | 0.043 |
| Cox3 | 0.985, | 0.90, | 0.801 | 0.003, | *, | 0.011 | 0.012, | *, | 0.092 | |
| Conc. | 0.999, | 0.93, | 0.821 | 0.001, | *, | 0.174 | 0.000, | *, | 0.004 | |
Dependency of clade support on a reduced (8 Taxa) or extended (33 Taxa) taxon sampling, and on individual (CytB, Cox1 and Cox3 genes) or concatenated (Conc.) gene analyses. Models GTRnt + Γ4 + I and GTRnt + Γ4 were applied to nucleotide alignments, under maximum-likelihood (ML) and Bayesian (BI) methods, respectively. Cells display support as [PP, SH, BS] with PP: posterior probability (BI), SH: Shimodaira-Hasegawa-like support (ML), and BS: bootstrap support (ML). "*": not applicable. Main lineages of mammalian parasites are defined according to their host preference: "Rodent", "Primate" and "Great Ape" (see Additional file 1, Table 1).