Table 2. Measures of nucleotide diversities and neutrality test statistics for the cercosporin facilitator protein (cfp) and β-tubulin 1 (tub) gene regions of Cercospora associated with purple seed stain in soybeans.
| Groups | Sample size (# of haplotypes—h) | Haplotype diversity (Hd) | Nucleotide diversity (pi) | Average # of nucleotide differences (k) | Number of variable sites (S) | Tajima’s D (P-value) |
|---|---|---|---|---|---|---|
| cpf a , b | 96 (15) | 0.76 | 0.087 | 74.0 | 210 | |
| Lineage 1 b | 54 (2) | 0.33 | 0.0004 | 0.33 | 1 | 0.66 (>0.10) |
| Lineage 2 | 12 (4) | 0.56 | 0.0009 | 0.80 | 4 | -1.38 (>0.10) |
| Lineage 3 | 8 (3) | 0.46 | 0.0006 | 0.50 | 2 | -1.31 (>0.10) |
| Lineage 4 | 22 (6) | 0.54 | 0.0007 | 0.62 | 5 | -1.63 (>0.10) |
| tub a , b | 96 (28) | 0.75 | 0.012 | 15.3 | 100 | |
| Lineage 1 a | 54 (6) | 0.24 | 0.0008 | 1.03 | 26 | -2.66 (<0.001) |
| Lineage 2 | 12 (6) | 0.88 | 0.0067 | 8.04 | 19 | 1.21 (>0.10) |
| Lineage 3 | 8 (8) | 1.00 | 0.0074 | 8.82 | 24 | -0.45 (>0.10) |
| Lineage 4 b | 22 (8) | 0.79 | 0.0034 | 4.03 | 25 | -1.56 (>0.10) |
| Concatenated set a , c | 108 (44) | 0.86 | 0.045 | 91.9 | 316 | |
| Lineage 1 a | 54 (8) | 0.46 | 0.0007 | 1.36 | 27 | |
| Lineage 2 | 12 (8) | 0.92 | 0.0043 | 8.85 | 23 | |
| Lineage 3 | 8 (8) | 1.00 | 0.0046 | 9.32 | 26 | |
| Lineage 4 b | 22 (12) | 0.90 | 0.0023 | 4.65 | 30 | |
| Recombinants | 12 (8) | 0.85 | 0.0124 | 25.39 | 146 |
a with the addition of sequence data from CPC 5068, the type strain of C. kikuchii.
b excluding 12 sequences from recombinant isolates (harboring cfp from Lineage 1 and tub from Lineage 2).
c including 12 sequences from recombinant isolates (harboring cfp from Lineage 1 and tub from Lineage 2).