Table 2 List of putative loci under incomplete selective sweeps in D. melanogaster Rwanda population detected by the CLR method
Chr. armCluster start to endaMax T1eSite of max T1fEmbedded ImageSample DAFgRank by option A (B)hiHSinSLClosest gene
2L1,517,366–1,529,788b1.711,527,3028,00013/1911 (12)−0.662−0.42halo
5,803,333–5,815,486b,c,d2.045,805,0018,0009/225 (3)−1.87−1.44CG11034
6,650,567–6,657,389b,d1.926,652,0118,00017/227 (13)−0.577−0.46Tango1
7,409,201–7,413,1321.817,409,8252,82811/229 (6)−0.577−1.96CG5181
14,094,223–14,102,937b1.7214,100,1588,00011/2110 (9)−1.81−2.29nAChRalpha5
16,001,993–16,020,004c2.0516,005,36916,0008/214 (5)−2.52−1.88Beat-Ic
17,221,968–17,339,080c,d6.6617,271,94564,0008/211 (1)−2.23−1.58CG6380
17,602,170–17,624,875c,d2.2817,616,35111,31311/213 (4)−1.42−1.69Sytalpha
18,446,487–18,454,5191.5518,453,14511,3138/2012 (11)−0.892−1.30bsf
18,993,669–18,999,6011.9318,996,65711,31313/206 (10)−1.23−0.97CG10650
19,480,924–19,546,7201.9119,493,56322,6278/218 (8)−1.32−0.94swm
19,729,511–19,790,297c,d3.1319,756,19722,6279/212 (2)−2.14−1.08CG10631
2R3,058,650–3,079,356d2.673,073,70145,2558/204 (5)−2.88−2.06didum
5,269,193–5,278,4632.125,271,74111,31311/206 (6)−2.38−2.14CG13954
5,756,581–5,788,3113.455,769,22332,0009/213 (3)−0.44−0.95Sec24AB
7,126,724–7,131,721c,d2.277,127,2815,65611/225 (4)−3.87−2.40CG13215
7,882,689–8,178,854c,d9.248,157,97911,3139/221 (1)−3.88−2.08otk
12,727,369–12,759,779b,c,d4.4312,737,42322,6278/222 (2)−2.40−1.81IntS8
20,061,659–20,075,219b1.5320,073,0165,65617/227 ()−1.11−0.48Nop60B
3L3,173,086–3,190,811b2.013,175,9088,00015/225 (5)−1.48−0.97Girdin
4,478,135–4,479,071b,c1.384,478,1352,82811/228 (8)−2.44−2.91CG7465
6,100,579–6,157,140b,c,d2.096,146,67911,31311/213 (3)−0.179−0.62Lcp65Ag2
6,550,102–6,557,978b,c,d1.816,551,8378,0009/216 (4)−3.92−3.52CG18769
11,825,913–11,831,926b,d1.3511,829,6152,00017/229 (9)−2.11−2.38CG43064
13,425,802–13,431,380b,d1.7013,430,1865,65611/227 (7)−2.72−3.18CG10713
16,084,427–16,136,825c,d2.8616,106,54216,00017/222 (2)−1.79−2.45Taf4
17,733,967–17,741,1722.0417,735,4338,00016/224 (6)0.0795−0.49CG7460
19,211,270–19,237,070c,d2.8919,220,33822,6278/221 (1)−1.85−2.74fz2
3R3,697,516–3,769,8862.903,727,63145,2559/195 (7)−0.1470.08mRpS9
4,155,075–4,182,5352.684,158,51864,00011/207 (9)−1.06−1.03CG9601
5,530,419–5,688,2023.915,548,75190,5108/202 (5)−1.15−1.36CG8478
8,486,190–8,497,5163.328,497,51632,00011/193 (4)1.630.53CG14395
9,040,956–9,111,809c7.039,057,70464,0008/191 (1)−2.87−1.53Ace
10,380,467–10,391,240c,d2.7310,386,8398,00010/216 (3)−2.99−2.56Pde6
12,060,488–12,066,143c,d2.4812,066,09016,00017/228 (10)−3.09−3.01tara
16,575,106–16,577,277b,d2.1016,575,11311,31316/229 (14)−1.91−2.34CG42322
17,406,332–17,432,203b3.0317,414,53216,00015/224 (2)−1.67−0.54InR
18,232,347–18,251,667b2.0918,245,93811,31312/2210 (6)−1.33−1.58lqfR
X525,809–1,798,033c2.751,350,18232,00017/221 (1)−1.06−0.97MED18
2,817,759–2,835,897c,d1.732,828,0335,65610/222 (2)−4.89−4.64kirre
14,156,405–14,160,294b,d1.2114,157,5132,82816/214 (4)−3.86−4.50CG1461
15,607,843–15,628,927b1.4315,620,3515,65614/213 (3)−1.40−1.90CG8184
  • a Positions of the first (start) and last (end) sites of significant CLR (P < 0.001) within the cluster.

  • b Overlap with a candidate region of complete selective sweep.

  • c Overlap with a cluster detected by the iHS test.

  • d Overlap with a cluster detected by the nSL test.

  • e Maximum CLR (T1) within the cluster.

  • f The location of maximum T1 or the putative nucleotide site under selection within the cluster.

  • g The derived allele frequency (DAF) in the data at the putative site under selection.

  • h The rank within the chromosome arm of the maximum T1 when option A (B) is used for calculating composite likelihoods.

  • i The value of iHS and nSL calculated at the putative site under selection detected by the CLR method.