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. 2017 Apr 13;8:44. doi: 10.3389/fgene.2017.00044

Table 3.

Summary statistics for all LINE clades, families and subgroups considered in this study.

Mean number of differences in polymorphic insertions Tajima’s D Number of polymorphic loci % of private insertions % of fixed differences % of shared differences Mean FST



Dataset All Florida Gulf-Atl Florida Gulf-Atl Florida Gulf-Atl
SNPs 0.21 0.22 0.36 -0.62 0.47 314575 60.25 15.85 0.19 23.72 0.12
L1 All 0.15 0.22 0.31 -1.39∗∗∗ -0.48∗∗ 2508 65.67 19.46 0 14.87 0.04∗∗
L1_AC1 to 16 FL 0.15 0.21 0.32 -1.46∗∗∗ -0.13 454 71.81 18.5 0 9.69 0.04
TR 0.18 0.25 0.30 -0.95 -0.5∗∗ 1062 59.13 15.35 0 25.52 0.04∗∗∗
L1_AC17 to 20 FL 0.11 0.17 0.28 -2.06∗∗∗ -0.78∗∗∗ 635 68.82 27.09 0 4.09 0.03
TR 0.14 0.20 0.31 -1.6∗∗∗ -0.24 357 71.71 19.33 0 8.96 0.04
L2 All 0.15 0.23 0.28 -1.27∗∗∗ -0.74∗∗∗ 11210 61.06 23.76 0 15.18 0.05∗∗
FL 0.13 0.20 0.28 -1.65∗∗∗ -0.75∗∗∗ 769 67.1 25.1 0 7.80 0.04∗∗∗
TR 0.15 0.23 0.28 -1.24∗∗∗ -0.74∗∗∗ 10440 60.61 23.66 0 15.73 0.05∗∗
CR1 All 0.15 0.22 0.31 -1.31∗∗∗ -0.29 27802 70.35 18.02 0.02 11.62 0.05
FL 0.14 0.21 0.30 -1.51∗∗∗ -0.49∗∗ 2578 68 23.27 0 8.73 0.05
TR 0.16 0.22 0.31 -1.29∗∗∗ -0.27 25224 70.59 17.48 0.02 11.91 0.05
R4 All 0.17 0.24 0.25 -1.04 -1.1∗∗∗ 1729 49.1 20.76 0 30.13 0.03∗∗∗
FL 0.16 0.23 0.25 -1.16∗∗ -1.21∗∗∗ 1017 47.79 20.94 0 31.27 0.02∗∗∗
TR 0.18 0.25 0.27 -0.87 -0.93∗∗∗ 712 50.98 20.51 0 28.51 0.04∗∗∗
RTE-1 All 0.11 0.18 0.23 -1.91∗∗∗ -1.42∗∗∗ 2853 62.57 33.16 0 4.28 0.02∗∗∗
FL 0.11 0.18 0.22 -2.00∗∗∗ -1.52∗∗∗ 1774 61.72 35.17 0 3.10 0.02∗∗∗
TR 0.12 0.19 0.24 -1.77∗∗∗ -1.23∗∗∗ 1079 63.95 29.84 0 6.21 0.02∗∗∗
RTEBovB All 0.25 0.31 0.34 -0.08+ 0.06 514 37.74 12.84 0 49.42 0.05∗∗∗
FL 0.27 0.38 0.33 0.76 -0.06 8 25 25 0 50.00 0.14
TR 0.25 0.31 0.34 -0.1 0.06 506 37.94 12.65 0 49.41 0.05

Mean pairwise divergence was computed only for loci polymorphic within a population and represents the average number of differences in polymorphic insertions or SNPs computed for all pairs of individuals (equivalent to nucleotide diversity). The number of private, shared, and fixed polymorphisms are provided as proportions of sites polymorphic in the whole sample. For each group for which coalescence simulations were performed, we provide a one-tailed p-value based on where the observed value for the statistics fell in the simulated distribution. We did not perform separate simulations for truncated and complete elements in RTEBovB due to the low number of polymorphic complete insertions. All, All elements; FL, full-length; TR, truncated; +, Tajima’s D fell in the 0.1% upper tail of the distribution. p-value < 0.05; ∗∗p-value < 0.01; ∗∗∗p-value < 0.001.