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. 2018 Oct 3;13(10):e0205024. doi: 10.1371/journal.pone.0205024

Table 2. Genes that show significant and nominal evidence of recent selection in D. melanogaster and in D. simulans.

D. melanogaster
Gene ID Gene name Function θw TajD TajD pval TajD pval corrected nFWH nFWH pval nFWH pval corrected EW EW pval EW pval corrected DHEW pval DHEW pval corrected TajD rank TajD rank against null nFWH rank nFWH rank against null
FBgn0039636 Atg14 Autophagy: Nucleation 9.1430 -1.9260 0.0036 0.0479 -1.8983 0.0416 0.4079 0.0599 0.0063 0.0134 0.0020 0.0781 1.47 0.41 4.41 3.27
FBgn0260858 Ykt6 Autophagy/Phagocytosis: Phagosome internalization; autophagosome expansion/fusion with lysosome 2.8690 -2.1510 0.0012 0.0271 -0.6169 0.1664 0.4079 0.5516 0.0003 0.0013 0.0270 0.0782 5.88 6.94 45.59 51.02
FBgn0039705 Atg16 Autophagy/Phagocytosis: Phagosome maturation; autophagosome expansion 5.9160 -1.2470 0.0814 0.1579 -1.7148 0.0552 0.4079 0.1303 0.0000 0.0000 0.0100 0.0781 80.88 77.96 7.35 4.90
FBgn0010435 emp Phagocytosis: Recognition—receptor 4.4820 -1.1770 0.1058 0.1811 -1.5438 0.0656 0.4079 0.2024 0.0132 0.0241 0.0160 0.0781 92.65 89.39 5.88 3.67
FBgn0014011 Rac2 Phagocytosis: Internalization 5.3780 -0.8280 0.2168 0.2634 -1.5064 0.0666 0.4079 0.0452 0.0435 0.0662 0.0280 0.0782 60.29 60.41 8.82 5.71
FBgn0031969 pes Phagocytosis: Recognition—receptor 15.4180 -1.2590 0.0820 0.1584 -0.1963 0.2664 0.4152 0.0143 0.0019 0.0051 0.0300 0.0782 4.41 5.71 76.47 76.33
D. simulans
Gene ID Gene name Function θw TajD TajD pval TajD pval corrected nFWH nFWH pval nFWH pval corrected EW EW pval EW pval corrected DHEW pval DHEW pval corrected TajD rank TajD rank against null nFWH rank nFWH rank against null
FBgn0191479 Rab1 Autophagy/Phagocytosis: Fusion with lysosome 1.5723 -1.4054 0.0766 0.2167 -0.8680 0.1365 0.7198 0.3673 0.0922 1.0000 0.0078 0.8734 12.31 11.64 6.15 3.02
FBgn0191695 Atg8b Autophagy/Phagocytosis: Phagocytosis internalization; autophagosome expansion 2.8301 -1.6322 0.0405 0.2167 -0.8833 0.1246 0.7198 0.2857 0.0183 1.0000 0.0117 0.8734 10.77 11.64 1.54 2.16
FBgn0181823 Vamp7 Autophagy/Phagocytosis: Fusion with lysosome 1.8867 -1.9589 0.0222 0.2167 -0.7603 0.1454 0.7198 0.4388 0.0242 1.0000 0.0197 0.8734 1.54 0.86 7.69 3.02
FBgn0185198 Rac1 Phagocytosis: Internalization 2.8301 -1.9303 0.0186 0.2167 -0.3022 0.2352 0.7198 0.2347 0.0930 1.0000 0.0450 0.8734 6.15 6.47 26.15 22.41

θw, Watterson’s θ; TajD, Tajima’s D; nFWH, normalized Fay and Wu’s H; EW, Ewens-Watterson statistic; DHEW, DHEW compound statistic P-value; TajD/nFWH/EW/DHEW pval corrected, P-values with multiple testing correction. For each focal-control pair, comparison score was calculated for Tajima’s D and Fay and Wu’s H and the scores were ranked from largest to smallest in the ‘rank’ column. Random assignment of a control gene to be “focal” and re-calculating the ranks of comparison scores created a distribution of ranks. The ranks of comparison scores from true coupling of focal and control genes compared to this distribution are listed in the ‘rank against null’ column.