Table 2. Nested AMOVA for Acanthaster planci population samples, where region and sampling location nested within region are the two hierarchical factors.
| Source of Variation (contrast tests indented) | df | MS | Var Comp | Notation | Φ | P-value |
| Region | 2 | 1507.5 | 10.33 | ΦCT | 0.60 | <0.001 |
| NC vs SC & NW | 1 | 2822.4 | 10.64 | Φ1 | 0.61 | <0.001 |
| SC vs NW | 1 | 192.7 | 1.40 | Φ2 | 0.17 | <0.001 |
| Population Samples (Region) | 20 | 31.4 | 0.89 | ΦSC | 0.13 | <0.001 |
| Between Subregions | ||||||
| NW1 vs NW2-5 | 1 | 23.6 | 0.77 | Φ3 | 0.11 | 0.001 |
| NC1-10 vs NC11-14 | 1 | 86.8 | 0.37 | Φ4 | 0.06 | <0.001 |
| Outbreaks vs Non-outbreaks within Archipelagos | ||||||
| NC1-10 | 1 | 2.9 | −0.02 | Φ5 | −0.00 | 0.733 |
| NW2-5 | 1 | 16.0 | 0.25 | Φ6 | 0.04 | 0.013 |
| Outbreaks vs Non-outbreaks within Region | ||||||
| SC | 1 | 74.9 | 1.94 | Φ7 | 0.24 | 0.001 |
| Between Outbreaks within Archipelagos | ||||||
| NC2* vs NC8* | 1 | 5.6 | 0.05 | Φ8 | 0.01 | 0.207 |
| NW2* vs NW5* | 1 | 6.0 | −0.03 | Φ9 | −0.01 | 0.498 |
| Between Outbreaks within SC region | ||||||
| SC1* vs SC3* | 1 | 216.1 | 6.84 | Φ10 | 0.53 | <0.001 |
| Between Islands with Multiple Samples in NC | ||||||
| NC12-14 vs NC5-7 & NC1-4 | 1 | 125.2 | 0.74 | Φ11 | 0.11 | <0.001 |
| NC5-7 vs NC1-4 | 1 | 6.4 | 0.02 | Φ12 | 0.00 | 0.167 |
| Between Years on the Big Island of Hawai'i | ||||||
| NC1 vs NC2-4 (1982 vs 2000's) | 1 | 7.6 | 0.05 | Φ13 | 0.01 | 0.087 |
| Between Habitats within Pearl & Hermes Atoll | ||||||
| NC12 vs NC13-14 (forereef vs other hab.) | 1 | 39.5 | 0.58 | Φ14 | 0.09 | 0.001 |
| NC13 vs NC14 (lagoon vs backreef) | 1 | 8.2 | 0.09 | Φ15 | 0.01 | 0.191 |
| Within Population Sample Error | 636 | 6.001 | 6.0010 | |||
| Total | 658 |
While it is common to present an ANOVA table with pre-planned contrast tests, it is uncommon for AMOVA. To provide a bearing, we explicitly label the common tests of region and samples nested within region as ΦCT and ΦSC [50]. AMOVA estimates of genetic differentiation/fixation for each contrast are labeled sequentially Φ1–13. These thirteen a priori linear contrasts were performed to test the genetic differentiation among regions (NC = north central, NW = northwestern, SC = south central), between outbreak and non-outbreak population samples nested within regions, between pairs of outbreak populations nested within their respective regions, between the Mariana Archipelago and Yap in the western Caroline Islands (NW), between the main Hawaiian Islands (MHI; NC1-10) and the Northwestern Hawaiian Islands (NWHI; NC11-14), among the highly sampled island populations at Pearl & Hermes Atoll (PHR; NC12-14), Maui Nui (Maui, Lāna'i, and Moloka'I; NC5-7), and the Big Island of Hawai'I (NC1-4), among habitats sampled within PHR, and between the samples from 1982 (NC1) and the 2000s on the Big Island of Hawai'I (NC2-4). An * denotes an outbreak population. Statistically significant Φ values are listed in bold face type.