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. 2008 May;179(1):455–473. doi: 10.1534/genetics.107.083659

TABLE 4.

DNA polymorphism and population differentiation in Australia and the United States

Gene Chromosome Location of gene (Mb) Length of sequenced region (bp) n s FST Sig Northern π Southern π Northern θ Southern θ Tajima's D (north) Tajima's D (south) Hd (north) Hd (south)
Australian sequence data
Or22 (region 1) 2L 1.5 711 12 11 0.701 0.001 0.011 0.001 0.013 0.002 −0.057 −1.712 0.939 0.618
Or22 (region 2) 2L 1.5 1391 19 17 0.566 0.001 0.006 0.002 0.010 0.004 −1.626 −2.097 0.994 0.895
CG5470 3R 11.8 744 15 15 0.390 — 0.005 0.009 0.010 0.009 −1.910 0.070 0.895 0.829
TfIIB 3L 4.3 1063 15 12 0.364 0.001 0.017 0.003 0.015 0.005 0.329 −1.947 0.914 0.970
tefu 3R 11.1 941 17 14 0.344 0.050 0.008 0.003 0.008 0.004 −0.284 −1.350 0.949 0.824
CG13466 3L 14.9 486 14 13 0.324 Golden 0.012 0.003 0.012 0.006 −0.031 −1.594 0.956 0.423
αTub67C 3L 9.7 1113 15 12 0.322 0.001 0.024 0.004 0.018 0.004 1.390 −0.100 0.990 0.939
pnt (region 1) 3R 19.2 462 14 12 0.287 Golden 0.008 0.007 0.005 0.006 0.515 −0.830 0.857 0.628
Or59c 2R 19.0 1134 13 11 0.281 0.001 0.016 0.018 0.016 0.014 −0.049 −0.707 0.987 0.982
Gr93c 3R 17.7 395 16 16 0.280 Golden 0.015 0.012 0.010 0.010 1.000 0.110 0.892 0.683
foraging 2L 3.6 474 9 15 0.251 Golden 0.023 0.012 0.022 0.018 0.217 −1.366 0.962 0.825
chm 2L 7.4 1376 14 10 0.245 0.050 0.016 0.010 0.015 0.014 0.364 −1.568 0.989 1.000
Gr28b 2L 7.5 1310 15 13 0.221 — 0.018 0.007 0.017 0.012 0.329 −1.826 0.990 1.000
CG14356 3R 10.0 716 16 15 0.202 — 0.010 0.012 0.016 0.018 −1.524 −1.413 0.983 0.905
Mdr49 2R 8.5 841 15 13 0.180 — 0.009 0.012 0.011 0.014 −1.060 −0.652 0.962 1.000
CG2989 X 1.9 459 16 14 0.175 Golden 0.018 0.013 0.012 0.015 1.344 −0.946 0.900 0.923
CG34008 3R 16.4 1328 15 8 0.174 0.050 0.013 0.009 0.012 0.010 0.392 −0.592 0.962 1.000
Fas1 3R 12.5 459 14 10 0.169 Golden 0.001 0.002 0.001 0.002 0.842 −0.657 0.440 0.711
cher 3R 12.9 975 16 15 0.168 0.001 0.009 0.010 0.011 0.013 −0.625 −1.023 0.992 1.000
cp309 3L 15.0 459 17 15 0.165 Golden 0.006 0.007 0.004 0.008 −0.276 −1.966 0.860 0.476
spn-D 3R 23.0 423 15 13 0.164 Golden 0.013 0.018 0.014 0.016 −0.316 0.675 0.838 0.923
CG7747 2R 11.8 1205 17 15 0.156 0.001 0.007 0.013 0.009 0.012 −0.822 0.358 0.956 0.990
R2 3L 3.0 1000 11 13 0.140 R 0.011 0.008 0.013 0.010 −0.653 −0.965 0.982 0.987
dmrt93B 3R 16.9 1237 10 11 0.125 0.001 0.034 0.023 0.033 0.025 0.158 −0.340 1.000 1.000
R4 3R 14.8 900 16 13 0.122 R 0.021 0.015 0.015 0.017 1.726 −0.645 0.942 0.949
pnt (region 2) 3R 19.2 432 17 6 0.121 Golden 0.014 0.007 0.013 0.008 0.368 −0.735 0.904 0.6
intergenic-6 2R 11.2 673 11 14 0.116 — 0.009 0.012 0.012 0.011 −1.288 0.279 0.945 0.978
CG30457 2R 12.7 930 10 13 0.091 0.001 0.019 0.013 0.017 0.012 0.550 0.203 0.978 0.795
CG32606 X 13.8 298 17 15 0.090 Golden 0.010 0.001 0.012 0.003 −0.736 −1.670 0.507 0.371
mod(mdg4) 3R 17.2 1186 17 14 0.090 — 0.015 0.016 0.013 0.018 0.599 −0.418 0.968 0.923
R5 2R 8.3 965 15 15 0.063 R 0.007 0.009 0.010 0.009 −1.240 0.007 0.990 0.971
grapes 2L 16.7 1168 12 10 0.045 — 0.015 0.017 0.014 0.018 0.265 −0.470 1.000 1.000
R1 2R 10.7 1003 12 11 0.034 R 0.010 0.011 0.011 0.010 −0.057 0.476 0.985 0.982
DmsR-2 3L 2.3 1130 14 14 0.025 0.001 0.015 0.006 0.023 0.010 −1.594 −1.968 1.000 1.000
R6 2L 16.7 993 13 12 0.015 R 0.006 0.007 0.007 0.006 −0.490 0.741 0.910 0.924
CG1942 2R 3.2 1144 10 14 0.013 — 0.007 0.009 0.009 0.010 −0.902 −0.462 0.978 0.989
CG9153 3L 1.3 1369 14 13 0.012 0.001 0.008 0.010 0.009 0.011 −0.408 −0.554 0.989 1.000
R7 3R 21.5 980 15 13 0.006 R 0.012 0.013 0.013 0.014 −0.219 −0.138 0.971 0.962
mei-41 X 16.2 1049 13 8 0.000 — 0.006 0.005 0.006 0.005 0.111 −0.014 0.949 0.786
dco 3R 26.9 1192 14 8 0.000 — 0.017 0.012 0.022 0.012 −0.952 0.054 0.989 0.893
R10 X 11.6 873 10 9 0.000 R 0.004 0.003 0.006 0.004 −1.187 −1.840 0.867 0.833
Random average 0.054 0.011 0.010 0.010 0.009 −0.303 −0.338 0.950 0.944
Significant average 0.233 0.013 0.009 0.013 0.010 0.027 −0.932 0.906 0.816
U. S. sequence data
CG6947 3L 12.0 1236 14 14 0.328 — 0.002 0.006 0.005 0.006 −2.085 0.057 0.604 0.945
grapes 2L 16.7 1168 13 15 0.257 0.050 0.019 0.017 0.018 0.018 0.316 −0.470 1.000 1.000
cp309 3L 15.0 459 16 16 0.221 Golden 0.004 0.009 0.006 0.009 −1.585 −0.165 0.542 0.900
Gr93c 3R 17.7 395 16 16 0.200 Golden 0.011 0.011 0.017 0.015 −0.010 0.438 0.817 0.917
CR15280 2L 14.8 1069 11 13 0.183 0.001 0.013 0.012 0.012 0.011 0.385 0.191 0.982 0.987
star1 3L 18.5 699 13 9 0.182 0.001 0.003 0.002 0.003 0.003 0.519 −1.728 0.679 0.222
3L-1 3L 20.2 1292 13 15 0.140 — 0.004 0.002 0.005 0.004 −0.173 −1.767 0.949 0.895
pnt (region 2) 3R 19.2 432 12 12 0.134 Golden 0.014 0.012 0.016 0.012 −0.303 −0.033 0.985 0.894
R6 2L 16.7 993 8 14 0.128 R 0.008 0.007 0.009 0.007 −0.510 0.090 1.000 0.989
CG13466 3L 14.9 486 15 16 0.120 Golden 0.004 0.012 0.007 0.015 −1.582 −0.707 0.790 0.975
Mob1 3L 11.5 974 14 10 0.080 0.001 0.022 0.032 0.017 0.026 1.360 1.130 0.978 0.978
dmrt93B 3R 16.9 1237 15 16 0.080 0.001 0.024 0.034 0.025 0.025 −0.301 1.530 1.000 0.992
chm 2L 7.4 1363 20 15 0.079 0.001 0.019 0.016 0.018 0.017 0.132 −0.293 0.989 1.000
mei-41 X 16.2 1049 13 10 0.078 0.050 0.008 0.006 0.009 0.010 −0.728 −1.303 0.987 0.964
egl 2R 19.3 821 16 16 0.066 0.001 0.008 0.005 0.009 0.009 −0.343 −1.830 0.933 0.950
pnt (region 1) 3R 19.2 462 14 15 0.064 Golden 0.007 0.008 0.008 0.009 −0.598 −0.410 0.835 0.952
foi 3L 8.5 1270 15 16 0.057 — 0.006 0.009 0.010 0.010 −1.410 −0.626 0.971 1.000
R4 3R 14.8 900 13 15 0.054 R 0.015 0.022 0.020 0.021 −1.240 0.146 1.000 0.990
foraging 2L 3.6 474 13 16 0.044 Golden 0.008 0.008 0.010 0.011 −1.220 −1.130 0.889 0.905
CG32606 X 13.8 298 16 12 0.033 Golden 0.005 0.014 0.011 0.016 −2.211 −0.432 0.350 0.833
R1 2R 10.7 1003 13 8 0.032 R 0.010 0.008 0.011 0.008 −0.509 −0.156 1.000 0.964
R7 3R 21.5 981 11 11 0.027 R 0.009 0.012 0.009 0.011 0.123 0.380 0.945 0.982
Fs-scb 2R 10.8 1361 16 16 0.025 — 0.003 0.005 0.005 0.007 −1.539 −0.102 0.908 0.967
spn-D 3R 23.0 423 16 16 0.024 Golden 0.017 0.013 0.017 0.011 −0.004 0.639 0.967 0.817
CG5224 2R 14.0 1307 16 14 0.021 0.050 0.019 0.020 0.015 0.019 1.070 0.240 0.983 1.000
R5 2R 8.3 965 14 15 0.008 R 0.004 0.007 0.008 0.010 −2.186 −1.362 0.934 0.971
CG2989 X 1.9 459 12 13 0.000 Golden 0.016 0.015 0.018 0.001 0.199 1.290 0.955 0.910
Fas1 3R 12.5 457 13 12 0.000 Golden 0.003 0.002 0.004 0.004 −0.161 −1.291 0.718 0.636
CG7738 2R 6.8 818 8 11 0.000 0.001 0.025 0.020 0.020 0.019 1.163 0.084 0.964 0.982
bol 3L 9.1 1260 16 15 0.000 — 0.007 0.008 0.008 0.009 −0.313 −0.384 0.992 1.000
R10 X 11.6 873 9 13 0.000 R 0.005 0.004 0.006 0.005 −0.892 −0.967 0.944 0.718
R2 3L 3.0 1000 9 15 0.000 R 0.010 0.009 0.011 0.009 −0.416 0.079 0.917 0.981
Random average 0.036 0.009 0.010 0.011 0.010 −0.804 −0.256 0.963 0.942
Significant average 0.093 0.012 0.013 0.013 0.013 −0.195 −0.213 0.867 0.891

Summary statistics are shown for each sequenced amplicon. “Sig” indicates whether this region is a significant region at the 0.05 or 0.001 thresholds or a golden probe; “R” indicates that the locus was chosen randomly. Loci that remain significant after eliminating information from probes with q-values > 0.6 are in boldface type. Loci that are not significant or random were sequenced for other reasons and should not be considered representative of the genome. n, number of chromosomes from the northern population; s, number of chromosomes from the southern population; Hd, haplotype diversity.