Table 2. Nested Clade Phylogeographic Analysis of the geographical distribution of Brachionus plicatilis haplotypes.
| Clade | Distribution | Inference key sequence | Biological Inference | |
| 1-9: | H13 | SA1, GAL, CHI | 1-19 NO | Allopatric fragmentation |
| H14 | Basin 1 | |||
| 1-17: | H16 | SA1, SA2, MOJ, CAP, HOS | 1-2-3-5-6-7-8 YES | Restricted gene flow / dispersal but with some long distance dispersal over intermediate areas not occupied by the species; or past gene flow followed by extinction of intermediate populations |
| H17 | FUE | |||
| H21 | ATA, HOY, CAS, MOJ, PET, SAL, SLD, CLO | |||
| 2-3: | 1-6 | TUR | 1-2-11-12 NO | Contiguous range expansion from HOS to TOS and TUR |
| 1-7 | HOS | |||
| 1-8 | HOS | |||
| 1-11 | TOS | |||
| 2-4: | 1-9 | Basin 1, SA1, GAL, CHI | 1-2-3-4 NO | Restricted gene flow with isolation by distance |
| 1-10 | CHI | |||
| 2-7: | 1-16 | HOY, SLD, PET | 1-19 NO | Allopatric fragmentation |
| 1-18 | Basin 3 | |||
| 3-2: | 2-3 | HOS, TOS, TON, TUR | 1-2-11-12-13 YES | Long distance colonization, past larger range coupled with subsequent extinction |
| 2-4 | Basin 1, SA1, GAL, CHI | |||
| 2-9 | HOS, SA1 | |||
| 3-4: | 2-6 | Basin 1, Basin 4, Basin 5, SA1, SA2, CLO, HOS | 1-2-3-4 NO | Restricted gene flow with isolation-by-distance |
| 2-7 | Basin 3, HOY, PET, SLD | |||
| Total: | 3-1 | HOS, TOS, TON | 1-2-3-5-6-7 YES | Restricted gene flow / dispersal but with some long distance dispersal |
| 3-2 | Basin 5, CHI, SA1, GAL, HOS, TOS, TUR | |||
| 3-3 | TOS, TON, TUR | |||
| 3-4 | Basin 1, 3, 4 and 5, SA1, SA2, HOS, CLO |
We show the eight clades with significant GeoDis results (all clades showed p-value<0.0001), haplotype and clade distributions (see Table 1 for pond acronyms). When we found a clade in all ponds in a basin we only refer the basin number (Figure 1). We show the sequence followed in the inference key (version 28th April 2009). See Figure 3 for the haplotype network and nested design with haplotype and clade designations.