Table 2.
Locus-Specific Information for 52 L1 Loci Retrieved from the Anolis Genome and Their Frequencies in Five Green Anole Populations
| Locus | Coordinates | Length (bp) | FL or TR | % Divergence from Consensus | North Carolina | Suwannee | Central Florida | Everglades | Gulf–Atlantic |
|---|---|---|---|---|---|---|---|---|---|
| L1AC20_684 | chr4:68403974–68404330 | 357 | TR | 3.80 | 0.50 | 0.57 | 0.84 | 0.44 | 0.90 |
| L1AC12s_4:12 | chr4:126979289–126979702 | 414 | TR | 2.50 | 1.00 | 0.96 | 1.00 | 1.00 | 1.00 |
| L1AC12s_GL3 | chrUn_GL343596:105315–105733 | 419 | TR | 3.70 | 1.00 | 0.75 | 0.59 | 0.00 | 1.00 |
| L1AC11s_6:33 | chr6:33204599–33205038 | 440 | TR | 0.00 | 0.25 | 0.07 | 0.03 | 0.00 | 0.28 |
| L1AC20_150 | chr1:150575039–150575547 | 509 | TR | 7.30 | 1.00 | 0.97 | 1.00 | 0.94 | 0.88 |
| L1AC16s_GL3 | chrUn_GL343395:465703–466212 | 510 | TR | 4.30 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC16s_GL4 | chrUn_GL343471:34099–34667 | 569 | TR | 1.80 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC16s_GL5 | chrUn_GL344110:24189–24796 | 608 | TR | 1.50 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC20_257 | chr1:257099845–257100469 | 625 | TR | 12.20 | 1.00 | 1.00 | 1.00 | 0.63 | 1.00 |
| L1AC20_227 | chr5:22764139–22764850 | 712 | TR | 11.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC18_223 | chr1:223912127–223912841 | 715 | TR | 3.90 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| TE_3 | chr1:214783982–214784696 | 715 | TR | 1.40 | 0.04 | 0.00 | 0.00 | 0.00 | 0.21 |
| L1AC13s_4:27 | chr4:27512892–27513664 | 773 | TR | 3.00 | 0.40 | 0.00 | 0.00 | 0.00 | 0.91 |
| L1AC18_128 | chr1:128475510–128476320 | 811 | TR | 3.60 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC18_543 | chr5:54332386–54333253 | 868 | TR | 5.20 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC20_660 | chr5:66011824–66012703 | 880 | TR | 4.70 | 0.38 | 0.27 | 0.33 | 0.13 | 0.71 |
| L1AC17s_1:544 | chr1:54502268–54503155 | 888 | TR | 2.70 | 0.82 | 0.67 | 0.71 | 1.00 | 1.00 |
| L1AC17s_Gly | chrUn_GL343200:1968310–1969771 | 916 | TR | 1.40 | 0.27 | 0.00 | 0.03 | 0.00 | 0.00 |
| L1AC19_139 | chr3:139851678–139852602 | 925 | TR | 1.90 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC19_2:144 | chr2:144963722–144964741 | 1,020 | TR | 1.70 | 0.88 | 0.45 | 0.45 | 0.00 | 0.25 |
| L1AC18_107 | chr1:107831209–107832288 | 1,080 | TR | 1.20 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC2.26 | chrUn_GL343239:906018–907246 | 1,229 | TR | 1.10 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
| L1AC15s_1:87 | chr1:87962249–87963655 | 1,407 | TR | 0.42 | 0.10 | 0.00 | 0.00 | 0.00 | 0.03 |
| L1AC3.25 | chr2:172762715–172767090 | 4,376 | TR | 0.45 | 1.00 | 0.94 | 1.00 | 1.00 | 0.97 |
| L1AC3.24 | scaffold_24:516031–520,687a | 4,657 | TR | 0.53 | 1.00 | 0.71 | 1.00 | 0.83 | 0.81 |
| L1AC3.21 | chrUn_GL343497:464966–469686 | 4,721 | TR | 0.45 | 0.50 | 0.03 | 0.00 | 0.00 | 0.07 |
| L1AC4.17 | scaffold_125:1567058–1571933a | 4,876 | TR | 0.54 | 1.00 | 1.00 | 1.00 | 0.93 | 1.00 |
| L1AC4.18 | scaffold_43:3503254–3508180a | 4,927 | TR | 0.54 | 1.00 | 0.00 | 0.05 | 0.07 | 0.25 |
| L1AC4.15 | chr3:96424624–96429616 | 4,993 | TR | 0.50 | n/a | 0.70 | 0.77 | 1.00 | 0.96 |
| L1AC3.18 | chrUn_GL343280:1636141–1641248 | 5,108 | TR | 0.57 | 1.00 | n/a | n/a | 1.00 | 1.00 |
| L1AC4.8 | chr5:19962314–19967530 | 5,217 | FL | 0.39 | n/a | 0.00 | n/a | 0.00 | n/a |
| L1AC4.19 | chrUn_GL343243:1081190–1086410 | 5,221 | FL | 0.52 | 1.00 | 0.50 | 0.41 | 1.00 | 0.93 |
| L1AC4.22 | chr2:90589288–90594512 | 5,225 | FL | 0.46 | n/a | n/a | n/a | 0.00 | 0.31 |
| L1AC4.20 | scaffold_527:549438–554665a | 5,228 | FL | 0.85 | 0.90 | 0.13 | 0.69 | 0.13 | 0.88 |
| L1AC4.11 | chr3:178322659–178327899 | 5,241 | FL | 0.91 | n/a | 0.56 | n/a | 0.00 | 0.83 |
| L1AC4.2 | scaffold_85:3499711–3504951a | 5,241 | FL | 0.35 | 0.31 | 0.03 | 0.00 | 0.00 | 0.54 |
| L1AC4.25 | chr3:170477780–170483021 | 5,242 | FL | 0.46 | 1.00 | 0.00 | 0.00 | 0.00 | 0.24 |
| L1AC4.26 | chr3:159015596–159020837 | 5,242 | FL | 0.50 | 0.80 | 0.17 | 0.18 | 0.40 | 0.65 |
| L1AC20_3:170 | chr3:170477780–170483022 | 5,243 | FL | 0.31 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| L1AC4.21 | chr3:32972264–32977686 | 5,243 | FL | 0.66 | 0.63 | 0.00 | 0.00 | 0.25 | 0.68 |
| L1AC4.4 | scaffold_30:3968578–3973822a | 5,245 | FL | 0.52 | 0.00 | 0.18 | 0.10 | 0.50 | 0.23 |
| L1AC4.1 | chr2:172917348–172922593 | 5,246 | FL | 0.35 | 0.00 | 0.00 | 0.03 | 0.00 | 0.00 |
| L1AC8_1:108 | chr1:108322088–108328343 | 5,334 | FL | 1.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| L1AC3.4 | chr6:54998113–55004259 | 6,147 | FL | 0.47 | 0.00 | 0.13 | 0.03 | 0.00 | 0.38 |
| L1AC3.10 | chrUn_GL343295:80571–86721 | 6,151 | FL | 0.36 | 1.00 | 0.06 | 0.23 | 0.00 | 0.78 |
| L1AC15_5:14 | chr5:142569373–142575532 | 6,160 | FL | 0.10 | 0.80 | 0.22 | 0.56 | 0.00 | 0.69 |
| L1AC3.8 | Chr3:168587085–168593244 | 6,160 | FL | 0.31 | 1.00 | 0.18 | 0.10 | 0.00 | 0.61 |
| L1AC15_2:15 | chr2:153639275–153645435 | 6,161 | FL | 0.31 | 0.70 | 0.56 | 0.87 | 0.00 | 1.00 |
| L1AC3.3 | scaffold_57:1761641–1767805a | 6,165 | FL | 0.39 | 0.27 | 0.28 | 0.03 | 0.20 | 0.23 |
| L1AC11_2:10 | chr2:107077315–107083913 | 6,599 | FL | 0.06 | 0.42 | 0.11 | 0.28 | 0.00 | 0.05 |
| L1AC14_GL | chrUn_GL343255:672694–679409 | 6,716 | FL | 0.70 | 0.92 | 0.00 | 0.23 | n/a | 0.85 |
| L1AC10.2 | chr3:172235202–172242019 | 6,818 | FL | 0.73 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
Note.—n/a, not applicable.
aAn insert collected from the February 2007 version that we were not able to map onto the May 2010 version.