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.