Table 3. Recombination detected within and between clades of Verticillium dahliae shown in Figure 1 using the program RDP3 [59].
| Clade | Lineages | Number of individualsin clade or lineage | Number of SNPsin lineage | Number of recombinationevents detecteda |
| I, II and lineage 2BR1 | All lineages | 141 (26)b | 26748 (26552)c | 443 |
| I & II | All lineages, excluding 2BR1 | 139 (25) | 26406 (26210) | 364 |
| I | 1A/1B & 2B334 | 92 (13) | 4333 (4244) | 22 |
| 1A/1B & 2B334 (excludinghaplotype VEMS481) | 91 (12) | 4126 (4037) | 0 | |
| 1A/1B | 78 | 1040 | 2 | |
| 1A/1B (excluding haplotype VEMS481) | 77 | 175 | 0 | |
| 2B334 | 14 | 62 | 0 | |
| II | II-1 & II-2 | 47 (14) | 18374 (18165) | 338 |
| II-1 | 2A & 4B | 20 | 5958 | 65 |
| 2A & 4B (excluding haplotypes395, V496 and V498) | 17 | 4492 | 0 | |
| 2A | 13 | 3290 | 22 | |
| 2A (excluding haplotypes 395,V496 and V498) | 10 | 92 | 0 | |
| 4B | 7 | 94 | 0 | |
| II-2 | 2B824, 4A & 6 | 27 | 11000 | 90 |
| 2B824 & 4A, excluding lineage 6 | 25 | 7348 | 4 | |
| 2B824 & 4A, excluding lineage 6& haplotype 320 | 24 | 7245 | 0 | |
| 2B824 | 13 | 212 | 0 | |
| 4A, including haplotype 320 | 12 | 144 | 0 |
SNP haplotypes were generated by genotyping by sequencing [52] by alignments of sequences to reference genome of isolate VdLs.17 [48].
a
Number of recombination events was determined in RDP3 using default parameters for significant events.
b
Number of haplotypes in subset used in RDP3 analysis is shown in parentheses; highly similar haplotypes were omitted because they add significantly to computation time but do not help to reveal unique recombination events.
c
Number of SNPs in the full data set, with the number for subsets used in RDP3 in parentheses.