Nadja Schneller 2023-09-14
We use analysis of molecular variance (AMOVA) to test for associations between inversion genotypes and two key ecological factors structuring our samples. The first of these inshore/offshore corresponds to major differences in turbidity, salinity, temperature variability and proximity to terrestrial inputs (nutrients, agricultural chemicals etc).
We used the amova function in the poppr package to test whether
genetic variance among sites distributed across both shores
(inshore/offshore) was greater than within shore. A model with reef
nested within shore was used to account for the fact that samples were
taken in groups from 9 reefs and randtest with 999 repeats was used to
test the significance of variance components @Excoffier1992-pe through
random permutations of the data. No variance component in this analysis
was statistically stignificant (p>0.2).
| locus | statphi | pvalue |
|---|---|---|
| L1 | -0.0986722 | 0.889 |
| L2 | -0.0567917 | 0.835 |
| L3 | 0.0332071 | 0.234 |
| L4 | -0.0267604 | 0.560 |
| L5 | -0.1087607 | 0.920 |
To test whether symbiont type was associated with inversion haplotype we conducted AMOVA again but this time with the model ~symbiont/reef where symbiont was coded according to whether the colony harboured C1 or C2. All colonies with uncertain dominant symbiont were excluded.
| locus | statphi | pvalue |
|---|---|---|
| L1 | -0.0484223 | 0.725 |
| L2 | -0.0226950 | 0.428 |
| L3 | 0.0096877 | 0.560 |
| L4 | 0.0250664 | 0.300 |
| L5 | -0.1327794 | 0.856 |