Table 8. Inversion detection task.
We evaluated three methods (PCA with clustering, PC-SNP association testing, and Cluster-SNP association testing) on the inversion detection task (is an inversion present?) using our three benchmark test cases (negative, positive from a single population, and positive from multiple populations). For each chromosome arm used, we indicated known inversions and whether the inversion was detected by a given method. The D. melanogaster 3R chromosome arm has three mutually-exclusive inversions, which we list separately.
| Test Case | Chrom. | Inversion | Clusters | PC-SNP | Cluster-SNP |
|---|---|---|---|---|---|
| Negative | D. mel. 3L | None | 1 | No | No |
| Negative | 34 An gam. and col. 3L | None | 4 | No | No |
| Negative | 150 An gam. and col. 3L | None | 2 | No | No |
| Single | D. mel. 2L | In(2L)t | 3 | Yes (PC 1) | Yes |
| Single | D. mel. 2R | In(2R)NS | 3 | Yes (PC 1) | Yes |
| Single | D. mel. 3R | In(3R)Mo | 3 | Yes (PC 1)* | Yes* |
| Single | In(3R)p | 3 | Yes (PC 1)* | Yes* | |
| Single | In(3R)K | 3 | Yes (PC 1)* | Yes* | |
| Multiple | 150 An. gam. and col. 2L | 2La | 3 | Yes (PC 2) | No |
| Multiple | 81 An. gam. 2L | 2La | 2 | Yes (PC 1) | Yes |
| Multiple | 34 An. gam. and col. 2L | 2La | 4 | Yes (PC 1) | Yes |
We compared inversions detected by the three methods to the known inversion karyotypes for these data sets taken from the original papers describing the data [17, 37–39]. If an inversion was present with no population structure, three clusters corresponding to three possible genotypes (which may not all be present) would be expected.
*Multiple, mutually-exclusive inversions were detected as a single inversion by our methods.