Table 3.
Comparison of alignment properties of genes and nucleotide substitution models used in Pleosporineae phylogenetic analyses.
| LSU1 | SSU2 | ITS3 | tef14 | Combined LSU, SSU, ITS and tef1 | |
|---|---|---|---|---|---|
| Alignment strategy (MAFFT v. 7) | L-INS-i + manually | L-INS-i | E-INS-i | E-INS-i + manually | – |
| Number of characters included in analysis (including gaps) | 857 | 982 | 667 | 955 | 3461 |
| Number of constant characters | 671 | 877 | 358 | 677 | 2583 |
| Number of parsimony informative characters (%) | 158 (18%) | 75 (8%) | 286 (43%) | 226 (24%) | 745 (22%) |
| Number of uninformative and variable characters | 28 | 30 | 23 | 52 | 133 |
| Nucleotide substitution model | GTR + I + G | GTR + I + G | GTR + I + G | GTR + I + G | GTR + I + G |
1
LSU: partial 28S nrDNA.
2
SSU: partial 18S nrDNA.
3
ITS: Internal transcribed spacers.
4
tef1: translation elongation factor 1-alpha gene.