Table 4.
Selection scans performed on the RNA‐seq olive dataset with BayeScan and PCAdapt
| Software | Population pairwise comparisons | Parameter | Threshold | No. outlier SNPs | No. contigs with outliers | No. enriched GO terms |
|---|---|---|---|---|---|---|
| BayeScan | Oleasters vs. cultivated | 100 | FDR = 0.05 | 30 | 22 | 0 |
| 1000 | FDR = 0.05 | 7 | 7 | 0 | ||
| Eastern oleasters vs. all cultivated | 100 | FDR = 0.05 | 0 | / | / | |
| 1000 | FDR = 0.05 | 0 | / | / | ||
| Eastern oleasters vs. eastern cultivated | 100 | FDR = 0.05 | 0 | / | / | |
| 1000 | FDR = 0.05 | 0 | / | / | ||
| Eastern accession vs. western accessions | 100 | FDR = 0.05 | 1 | 1 | 0 | |
| 1000 | FDR = 0.05 | 0 | / | / | ||
| Eastern cultivars vs. western cultivars | 100 | FDR = 0.05 | 0 | / | / | |
| 1000 | FDR = 0.05 | 0 | / | / | ||
| Eastern oleasters vs. western oleasters | 100 | FDR = 0.05 | 0 | / | / | |
| 1000 | FDR = 0.05 | 0 | / | / | ||
| PCAdapt | All olives | factors 1‐2 | FDR = 0.01 | 3211 | 1119 | 298 |
| All olives | factor 2 | top 1% | 3000 | 1649 | 97 | |
| Eastern olives | factor 1 | FDR = 0.01 | 0 | / | / |
The parameter column in the case of BayeScan indicates the value set for the prior odds. For PCAdapt, it indicates the principal component used to find outlier loci.