Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates

Table 1.

Copy number, divergence, and age of L1 families based on their 3′ extremity

Lineage
Family
Genomic copy number
Number of sequences aligned
Length of sequences aligned (bp)
Average pairwise divergence (% ± S.E.)a
Average divergence from consensus (% ± S.E.)a
Age (Myr)b
Chimpanzee 6Myr
Baboon 25Myr
Lemur 63Myr
L1PA L1PA1 1028 198 532 0.98 ± 0.16 0.59 ± 0.13 3.1 (2.3–3.9) – – –
L1PA2 4067 199 520 2.40 ± 0.17 1.24 ± 0.10 7.6 (5.6–9.6) + – –
L1PA3 8712 200 521 3.96 ± 0.28 2.21 ± 0.20 12.5 (9.2–15.8 + – –
L1PA4 9936 165 515 5.69 ± 0.28 3.02 ± 0.19 18.0 (13.2–22.8) + – –
L1PA5 9446 195 515 6.47 ± 0.25 3.39 ± 0.18 20.4 (15.0–25.9) + – –
L1PA6 4798 195 510 8.49 ± 0.31 4.44 ± 0.21 26.8 (19.7–34.0) + ? –
L1PA7 9863 174 495 9.95 ± 0.32 5.16 ± 0.20 31.4 (23.0–39.8) + +/– –
L1PA8 6672 196 530 12.96 ± 0.45 6.92 ± 0.31 40.9 (30.0–51.8) + + –
L1PA8A 1474 184 520 13.20 ± 0.44 6.87 ± 0.26 41.7 (30.6–52.8) + + –
L1PA10 4827 181 455 14.68 ± 0.54 7.65 ± 0.31 46.4 (34.0–58.7) + + –
L1PA11 3047 189 480 16.88 ± 0.49 8.82 ± 0.30 53.3 (39.1–67.5) + + –
L1PA13B 3114 63 579 18.93 ± 0.58 9.78 ± 0.32 59.8 (43.8–75.7) + + –
L1PA12 892 78 518 18.90 ± 0.62 9.82 ± 0.35 59.7 (43.7–75.6) + + –
L1PA13A 4671 94 579 18.98 ± 0.64 10.07 ± 0.39 59.9 (43.9–75.9) + + –
L1PA14 2818 161 500 19.19 ± 0.60 10.14 ± 0.34 60.6 (44.4–76.8) + + –
L1PA15 5951 153 470 22.33 ± 0.70 11.74 ± 0.39 70.5 (51.7–89.3) + + +
L1PA16 9430 87 520 25.23 ± 0.67 13.27 ± 0.39 79.7 (58.4–100.9) + + +
L1PA17 3309 39 490 32.01 ± 1.18 17.17 ± 0.70 101.1 (74.1–128.0) + + +
L1PB L1PB1 7412 124 540 14.80 ± 0.54 8.07 ± 0.38 46.7 (34.3–59.2) + + –
L1PB2 1759 118 541 18.43 ± 0.62 9.63 ± 0.36 58.2 (42.7–73.7) + + –
L1PB3 2073 110 631 23.29 ± 0.75 12.39 ± 0.45 73.5 (53.9–93.2) + + +
L1PB4 5454 35 398 30.39 ± 1.11 16.50 ± 0.68 96.0 (70.3–121.6) + + +
L1MA L1MA1 2528 55 530 19.52 ± 0.56 10.04 ± 0.30 61.6 (45.2–78.1) + + –
L1MA2 4237 70 542 20.85 ± 0.61 10.88 ± 0.35 65.8 (48.3–83.4) + + +/–
L1MA3 5129 70 524 21.56 ± 0.73 11.39 ± 0.43 68.1 (49.9–86.2) + + +
L1MA4 6859 41 511 32.41 ± 1.02 17.85 ± 0.63 102.3 (75.0–129.6) + + +
L1MA5
2886
40
390
31.23 ± 1.17
16.78 ± 0.65
98.6 (72.3–124.9)
+
+
+

  • ↵a Divergence was calculated using the Kimura 2-parameters correction

  • ↵b Age derived from the pairwise divergence and a substitution rate of 0.17%/Myr. The numbers in parentheses correspond to the age using a calibration of 0.216% per Myr and 0.125% per Myr, respectively (see Methods)

This Article

  1. Published in Advance December 12, 2005, doi: 10.1101/gr.4001406 Genome Res. 16: 78-87

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