Table 6. Inversion localization task.

We evaluated the two association-testing methods (PC-SNP and Cluster-SNP association tests) on the inversion localization task (what region is spanned by an inversion?) using two benchmark test cases (positive from a single population and positive from multiple populations). Note that the two PCA scatter plot method is not able to localize inversions. For each chromosome arm used, we indicated known inversions, the expected ranges, and the ranged identified be each method. The D. melanogaster 3R chromosome arm has three mutually-exclusive inversions, which we list separately.

Test Case	Chrom.	Inversion	Exp. Range (Mb)	PC-SNP Obs. Range (Mb)	Cluster-SNP Obs. Range (Mb)
Single	D. mel. 2L	In(2L)t	2.2–13.2	start–16.0 (PC1)	start–16.0
Single	D. mel. 2R	In(2R)NS	11.3–16.2	10.0–17.5 (PC1)	10.0–18.0
Single	D. mel. 3R	In(3R)Mo	12.6–20.6	14.0–end* (PC1)	14.0–end*
Single		In(3R)p	7.6–22.0 Mb	14.0–end* (PC1)	14.0–end*
Single		In(3R)K	17.2–24.9 Mb	14.0–end* (PC1)	14.0–end*
Multiple	150 An. gam. and col. 2L	2La	20.0–45.0	20.0–43.0 (PC2)	start–end†
Multiple	81 An. gam. 2L	2La	20.0–45.0	20.0–43.0 (PC1)	20.0–43.0
Multiple	34 An. gam. and col. 2L	2La	20.0–45.0	20.0–43.0 (PC1)	20.0–43.0

We evaluated the PC-SNP and Cluster-SNP association test methods on localizing inversions. We compared the range of inversions observed in the Manhattan plots created from these two methods with the coordinates described for these inversions in prior work [37–39, 45, 46].

*Could not resolve multiple, mutually-exclusive inversions

^†Could not resolve 2La