Supplementary Table 1 Description of the Copia genomic sequences from the 12 Drosophila genome searches.
Species / Symbol / Region / PositionLTR-ULR
D. melanogaster / A1 / 3R / 15940011-15940450
A4 / U / 9085950-9086389
A5 / 3L / 2113000-2113439
A6 / X / 5825876-5826316
A7 / 3RHet / 2448871-2449311
A8 / 3LHet / 666615-667055
B1 / U / 6802618-6803031
B2 / 3L / 12954939-12955353
D. simulans / A1 / 2R / 1083313-1083753
A2 / chr2h_Mrandom_039 / 25750-26187
A3 / chrU_M_1494 / 1250-1689
B1 / chrU_M_1901 / 530-942
B2 / chr2h_Mrandom_038 / 43713-44129
C1 / chrU_M_1028 / 1205-1567
C2 / chrU_M_5031 / 789-1163
C3 / chr3h_Mrandom_003 / 48505-48879
C4 / chrU_M_2295 / 7581-7956
C5 / chr2h_Mrandom_039 / 21097-21471
C6 / 2R / 1205642-1206017
D. sechellia / C1 / scaffold_67 / 99798-100173
C2 / scaffold_479 / 3583-3958
C3 / scaffold_80 / 12906-13283
C4 / scaffold_1185 / 4664-5041
C5 / scaffold_2788 / 1600-1976
C6 / scaffold_26 / 331633-332012
C7 / scaffold_18 / 747254-747630
C8 / scaffold_10813 / 906-1282
C9 / scaffold_4520 / 1763-2139
C10 / scaffold_94 / 3841-4217
C11 / scaffold_878 / 1195-1571
C12 / scaffold_1731 / 3115-3487
C13 / scaffold_1639 / 1871-2253
C14 / scaffold_467 / 7125-7503
C15 / scaffold_351 / 1-358
Reverse transcriptase
D. melanogaster / A1 / 3R / 27159518-27159770
A4 / X / 4180135-4180387
D. simulans / A1 / chrU_M_804 / 1933-2185
A2 / chr2h_Mrandom_039 / 24207-24459
A3 / chr2h_Mrandom_038 / 50551-50803
A5 / chrU_M_2608 / 1115-1367
Supplementary Table 1, continuation.
Species / Symbol / Region / PositionReverse Transcriptase
D. simulans / A6 / chrU_M_226 / 238-490
A7 / chrU_M_2295 / 4483-4735
A8 / chrU_M_2579 / 795-1047
D. sechellia / A1 / scaffold_116 / 88475-88727
A4 / scaffold_209 / 17995-18247
A5 / scaffold_94 / 743-995
A6 / scaffold_7595 / 370-622
A7 / scaffold_7475 / 248-500
A9 / scaffold_1833 / 1943-2195
A10 / scaffold_4601 / 1027-1277
A12 / scaffold_8980 / 1204-1456
A13 / scaffold_18 / 744205-744457
A14 / scaffold_5484 / 586-838
A15 / scaffold_1731 / 133-385
A16 / scaffold_1501 / 2322-2574
A20 / scaffold_878 / 4331-4583
A21 / scaffold_479 / 8707-8959
A22 / scaffold_80 / 16133-16385
A25 / scaffold_1581 / 3005-3257
A26 / scaffold_7249 / 17-260
D. yakuba / A1 / v2_chrUn_141 / 5733-5983
Supplementary Table 2 Pairwise genetic distance between the LTR-ULR Copia regions of Zaprionus, melanogaster and repleta species calculated by the Maximum Composite Likelihood method as implemented by MEGA 4.1.
1 / 2 / 3 / 4 / 5 / 6 / 7 / 8 / 9 / 10 / 11 / 12 / 13 / 14 / 15 / 16 / 17 / 18 / 19 / 20 / 21 / 22 / 23 / 24 / 25 / 26 / 27 / 28 / 29 / 30 / 31 / 321. Dkoep / -
2. Dbuzz / ,098 / -
3. Dseri / ,075 / ,065 / -
4. Dgouv / ,022 / ,095 / ,073 / -
5. Danto / ,012 / ,090 / ,068 / ,019 / -
6. Dserm / ,022 / ,098 / ,071 / ,002 / ,019 / -
7. Dpach / ,007 / ,095 / ,076 / ,019 / ,010 / ,022 / -
8. Dmoja / ,091 / ,015 / ,057 / ,087 / ,081 / ,090 / ,087 / -
9. DmelA1 / ,600 / ,591 / ,569 / ,574 / ,584 / ,573 / ,601 / ,596 / -
10. DmelA4 / ,600 / ,591 / ,569 / ,574 / ,584 / ,573 / ,601 / ,596 / ,002 / -
11. DmelA5 / ,605 / ,596 / ,574 / ,579 / ,589 / ,577 / ,606 / ,601 / ,002 / ,005 / -
12. DmelA6 / ,602 / ,593 / ,572 / ,576 / ,587 / ,575 / ,603 / ,598 / ,000 / ,002 / ,002 / -
13. DmelA7 / ,602 / ,593 / ,576 / ,576 / ,587 / ,575 / ,603 / ,598 / ,002 / ,005 / ,005 / ,002 / -
14. DmelA8 / ,598 / ,589 / ,567 / ,572 / ,582 / ,571 / ,599 / ,594 / ,005 / ,007 / ,007 / ,005 / ,007 / -
15. DmelX02599 / ,612 / ,603 / ,581 / ,586 / ,596 / ,585 / ,613 / ,608 / ,002 / ,005 / ,000 / ,002 / ,005 / ,007 / -
16. DmelAF063873 / ,607 / ,598 / ,576 / ,581 / ,591 / ,580 / ,608 / ,603 / ,007 / ,005 / ,005 / ,007 / ,009 / ,011 / ,005 / -
17. DmelAF063874 / ,611 / ,602 / ,580 / ,585 / ,595 / ,583 / ,612 / ,607 / ,014 / ,011 / ,011 / ,014 / ,016 / ,018 / ,012 / ,007 / -
18. Dmel AF063877 / ,621 / ,612 / ,590 / ,595 / ,605 / ,593 / ,622 / ,617 / ,005 / ,007 / ,005 / ,005 / ,007 / ,009 / ,005 / ,009 / ,016 / -
19. DsimA1 / ,587 / ,584 / ,553 / ,562 / ,584 / ,561 / ,594 / ,595 / ,021 / ,018 / ,023 / ,021 / ,023 / ,023 / ,023 / ,023 / ,030 / ,026 / -
20. DsimA2 / ,587 / ,589 / ,567 / ,567 / ,588 / ,566 / ,594 / ,600 / ,021 / ,019 / ,023 / ,021 / ,023 / ,023 / ,023 / ,023 / ,031 / ,026 / ,014 / -
21. DsimA3 / ,580 / ,582 / ,552 / ,574 / ,582 / ,572 / ,587 / ,594 / ,028 / ,026 / ,030 / ,028 / ,030 / ,028 / ,030 / ,030 / ,038 / ,033 / ,009 / ,014 / -
22. DsimAF063881 / ,592 / ,589 / ,558 / ,585 / ,589 / ,583 / ,599 / ,600 / ,035 / ,032 / ,037 / ,035 / ,037 / ,035 / ,037 / ,037 / ,045 / ,040 / ,016 / ,021 / ,007 / -
23. DsimD10880 / ,581 / ,587 / ,572 / ,566 / ,587 / ,565 / ,588 / ,599 / ,021 / ,019 / ,023 / ,021 / ,023 / ,023 / ,023 / ,023 / ,030 / ,026 / ,014 / ,016 / ,016 / ,025 / -
24. DyakAF063884 / ,606 / ,597 / ,575 / ,580 / ,591 / ,579 / ,607 / ,602 / ,005 / ,002 / ,007 / ,005 / ,007 / ,009 / ,007 / ,007 / ,014 / ,009 / ,021 / ,021 / ,028 / ,035 / ,021 / -
25. DteiAF063883 / ,600 / ,591 / ,569 / ,574 / ,584 / ,573 / ,601 / ,596 / ,000 / ,002 / ,002 / ,000 / ,002 / ,005 / ,002 / ,007 / ,014 / ,005 / ,021 / ,021 / ,028 / ,035 / ,021 / ,005 / -
26. DereAF063869F / ,613 / ,604 / ,582 / ,587 / ,597 / ,586 / ,614 / ,609 / ,002 / ,005 / ,005 / ,002 / ,005 / ,007 / ,005 / ,009 / ,016 / ,007 / ,023 / ,023 / ,030 / ,037 / ,023 / ,007 / ,002 / -
27. DmelB1 / ,568 / ,559 / ,539 / ,542 / ,552 / ,540 / ,569 / ,565 / ,005 / ,002 / ,005 / ,005 / ,007 / ,007 / ,005 / ,005 / ,012 / ,005 / ,022 / ,022 / ,027 / ,035 / ,022 / ,005 / ,005 / ,007 / -
28. DmelB2 / ,591 / ,582 / ,561 / ,564 / ,575 / ,563 / ,592 / ,587 / ,012 / ,010 / ,012 / ,012 / ,015 / ,007 / ,012 / ,012 / ,020 / ,012 / ,027 / ,027 / ,032 / ,040 / ,027 / ,007 / ,012 / ,015 / ,010 / -
29. DmelAF063876 / ,578 / ,568 / ,548 / ,551 / ,561 / ,549 / ,578 / ,574 / ,002 / ,000 / ,005 / ,002 / ,005 / ,002 / ,005 / ,005 / ,012 / ,005 / ,020 / ,020 / ,025 / ,032 / ,020 / ,002 / ,002 / ,005 / ,002 / ,005 / -
30. DmelAF063875 / ,586 / ,576 / ,556 / ,559 / ,569 / ,557 / ,587 / ,582 / ,010 / ,007 / ,012 / ,010 / ,012 / ,010 / ,012 / ,012 / ,018 / ,012 / ,027 / ,027 / ,032 / ,039 / ,027 / ,010 / ,010 / ,012 / ,010 / ,012 / ,005 / -
31. DsimB1 / ,560 / ,567 / ,555 / ,539 / ,562 / ,538 / ,567 / ,584 / ,035 / ,032 / ,035 / ,035 / ,035 / ,035 / ,035 / ,035 / ,042 / ,035 / ,025 / ,020 / ,025 / ,032 / ,027 / ,035 / ,035 / ,037 / ,032 / ,037 / ,030 / ,038 / -
32. DsimB2 / ,592 / ,594 / ,575 / ,566 / ,589 / ,565 / ,599 / ,611 / ,037 / ,034 / ,037 / ,037 / ,037 / ,037 / ,037 / ,037 / ,045 / ,037 / ,027 / ,022 / ,027 / ,034 / ,032 / ,037 / ,037 / ,040 / ,035 / ,040 / ,033 / ,040 / ,017 / -
33. DsimAF063882 / ,558 / ,565 / ,535 / ,543 / ,565 / ,542 / ,565 / ,578 / ,030 / ,027 / ,030 / ,030 / ,032 / ,032 / ,030 / ,030 / ,037 / ,030 / ,012 / ,020 / ,015 / ,025 / ,017 / ,030 / ,030 / ,032 / ,030 / ,035 / ,028 / ,035 / ,030 / ,035
34. DyakAF063885 / ,597 / ,587 / ,567 / ,569 / ,580 / ,568 / ,598 / ,593 / ,007 / ,005 / ,010 / ,007 / ,010 / ,010 / ,010 / ,010 / ,017 / ,010 / ,024 / ,025 / ,030 / ,037 / ,025 / ,007 / ,007 / ,010 / ,007 / ,012 / ,005 / ,012 / ,035 / ,038
35. DereAF063870 / ,578 / ,568 / ,548 / ,550 / ,561 / ,549 / ,578 / ,573 / ,007 / ,005 / ,007 / ,007 / ,010 / ,007 / ,007 / ,007 / ,015 / ,010 / ,025 / ,025 / ,030 / ,037 / ,025 / ,007 / ,007 / ,010 / ,007 / ,010 / ,005 / ,010 / ,035 / ,038
36. DsimC1 / ,530 / ,526 / ,505 / ,510 / ,527 / ,509 / ,533 / ,539 / ,034 / ,034 / ,034 / ,034 / ,031 / ,034 / ,034 / ,037 / ,045 / ,034 / ,020 / ,022 / ,025 / ,031 / ,025 / ,037 / ,034 / ,037 / ,034 / ,040 / ,032 / ,040 / ,025 / ,028
37. DsimC2 / ,538 / ,544 / ,526 / ,524 / ,539 / ,522 / ,541 / ,562 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,041 / ,050 / ,038 / ,024 / ,024 / ,030 / ,035 / ,030 / ,041 / ,038 / ,041 / ,038 / ,044 / ,036 / ,044 / ,019 / ,022
38. DsimC3 / ,549 / ,556 / ,538 / ,535 / ,551 / ,534 / ,552 / ,574 / ,035 / ,035 / ,035 / ,035 / ,035 / ,036 / ,036 / ,038 / ,047 / ,036 / ,022 / ,022 / ,027 / ,033 / ,027 / ,038 / ,035 / ,038 / ,036 / ,041 / ,033 / ,042 / ,016 / ,019
39. DsimC4 / ,564 / ,558 / ,552 / ,550 / ,566 / ,548 / ,567 / ,576 / ,041 / ,041 / ,041 / ,041 / ,041 / ,041 / ,041 / ,044 / ,052 / ,041 / ,027 / ,027 / ,033 / ,038 / ,033 / ,044 / ,041 / ,044 / ,041 / ,047 / ,039 / ,047 / ,022 / ,024
40. DsimC5 / ,544 / ,551 / ,533 / ,530 / ,546 / ,529 / ,547 / ,569 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,041 / ,050 / ,038 / ,024 / ,024 / ,030 / ,035 / ,030 / ,041 / ,038 / ,041 / ,038 / ,044 / ,036 / ,045 / ,019 / ,022
41. DsimC6 / ,578 / ,579 / ,558 / ,564 / ,580 / ,563 / ,582 / ,596 / ,047 / ,047 / ,047 / ,047 / ,044 / ,047 / ,047 / ,050 / ,058 / ,047 / ,033 / ,033 / ,038 / ,044 / ,039 / ,050 / ,047 / ,050 / ,047 / ,053 / ,045 / ,053 / ,030 / ,033
42. DsimAF063880 / ,518 / ,517 / ,500 / ,504 / ,515 / ,502 / ,521 / ,538 / ,069 / ,066 / ,069 / ,069 / ,067 / ,070 / ,067 / ,069 / ,076 / ,067 / ,049 / ,049 / ,052 / ,057 / ,058 / ,070 / ,069 / ,070 / ,064 / ,073 / ,065 / ,074 / ,052 / ,058
43. DsecC1 / ,554 / ,561 / ,543 / ,540 / ,556 / ,539 / ,558 / ,579 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,041 / ,050 / ,038 / ,024 / ,024 / ,030 / ,035 / ,030 / ,041 / ,038 / ,041 / ,038 / ,044 / ,036 / ,044 / ,019 / ,022
44. DsecC2 / ,559 / ,566 / ,548 / ,545 / ,561 / ,544 / ,563 / ,584 / ,041 / ,041 / ,041 / ,041 / ,041 / ,041 / ,041 / ,044 / ,052 / ,041 / ,027 / ,027 / ,033 / ,038 / ,033 / ,044 / ,041 / ,044 / ,041 / ,047 / ,039 / ,047 / ,022 / ,024
45. DsecC3 / ,560 / ,562 / ,544 / ,541 / ,557 / ,539 / ,563 / ,579 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,041 / ,049 / ,038 / ,024 / ,025 / ,030 / ,035 / ,033 / ,041 / ,038 / ,041 / ,038 / ,044 / ,036 / ,044 / ,019 / ,022
46. DsecC4 / 560 / ,562 / ,544 / ,541 / ,557 / ,539 / ,563 / ,579 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,041 / ,049 / ,038 / ,024 / ,024 / ,030 / ,035 / ,033 / ,041 / ,038 / ,041 / ,038 / ,044 / ,036 / ,044 / ,019 / ,022
47. DsecC5 / ,564 / ,566 / ,547 / ,544 / ,560 / ,543 / ,567 / ,583 / ,041 / ,041 / ,041 / ,041 / ,041 / ,041 / ,041 / ,044 / .052 / ,041 / ,027 / ,027 / ,033 / ,038 / ,036 / ,044 / ,041 / ,044 / ,041 / ,047 / ,039 / ,047 / ,022 / ,024
48. DsecC6 / ,555 / ,557 / ,539 / ,536 / ,552 / ,535 / ,558 / ,574 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,038 / ,041 / ,049 / ,038 / ,024 / ,024 / ,030 / ,035 / ,033 / ,041 / ,038 / ,041 / ,038 / ,044 / ,036 / ,044 / ,019 / ,021
49. DsecC7 / ,550 / ,551 / ,539 / ,531 / ,546 / ,529 / ,553 / ,569 / ,044 / ,044 / ,044 / ,044 / ,044 / ,044 / ,044 / ,047 / ,055 / ,044 / ,030 / ,030 / ,035 / ,041 / ,038 / ,047 / ,044 / ,047 / ,044 / ,050 / ,042 / ,050 / ,019 / ,027
50. DsecC8 / ,572 / 574 / ,555 / ,544 / ,569 / ,543 / ,575 / ,591 / ,044 / ,044 / ,044 / ,044 / ,044 / ,044 / ,044 / ,047 / ,055 / ,044 / ,033 / ,033 / ,038 / ,044 / ,041 / ,047 / ,044 / ,047 / ,044 / ,050 / ,042 / ,050 / ,027 / ,030
51. DsecC10 / ,576 / ,578 / ,559 / ,557 / ,573 / ,555 / ,580 / ,596 / ,047 / ,047 / ,047 / ,047 / ,047 / ,047 / ,047 / ,049 / ,058 / ,047 / ,033 / ,033 / ,038 / ,044 / ,041 / ,049 / ,047 / ,050 / ,047 / ,052 / ,045 / ,053 / ,027 / ,030
52. DsecC11 / ,568 / ,583 / ,564 / ,549 / ,565 / ,547 / ,572 / ,600 / ,050 / ,050 / ,050 / ,050 / ,050 / ,047 / ,050 / ,052 / ,061 / ,050 / ,036 / ,036 / ,041 / ,047 / ,044 / ,053 / ,049 / ,053 / ,050 / ,053 / ,047 / ,053 / ,030 / ,033
53. DsecC12 / ,561 / ,568 / ,549 / ,546 / ,562 / ,545 / ,564 / ,585 / ,050 / ,050 / ,050 / ,050 / ,050 / ,050 / ,050 / ,053 / ,062 / ,050 / ,036 / ,036 / ,041 / ,047 / ,042 / ,053 / ,050 / ,053 / ,050 / ,056 / ,048 / ,057 / ,030 / ,033
54. DsecC13 / ,588 / ,580 / ,571 / ,562 / ,585 / ,561 / ,592 / ,592 / ,057 / ,057 / ,057 / ,057 / ,057 / ,057 / ,057 / ,060 / ,068 / ,057 / ,043 / ,043 / ,052 / ,057 / ,052 / ,060 / ,057 / ,060 / ,057 / ,063 / ,055 / ,064 / ,043 / ,046
55. DsecC14 / ,572 / ,567 / ,555 / ,552 / ,568 / ,551 / ,575 / ,585 / ,055 / ,055 / ,055 / ,055 / ,055 / ,055 / ,055 / ,058 / ,066 / ,055 / ,041 / ,041 / ,046 / ,052 / ,049 / ,058 / ,055 / ,058 / ,055 / ,061 / ,053 / ,061 / ,035 / ,038
Symbols: Dmel: D. melanogaster, Dsim: D. simulans, Dyak: D. yakuba, Dere: D. erecta, Dmau: D. mauritiana, Dsec: D. sechellia, Dtei: D. teissieri, Ztub: Z. tuberculatus, Zcam: Z. camerounensis, Zdav: Z. davidi, Zgab: Z. gabonicus, Zafr: Z. africanus, Zind: Z. indianus.
Supplementary Table 2, continuation.
56. DsecC15 / ,621 / ,630 / ,609 / ,600 / ,624 / ,599 / ,626 / ,649 / ,061 / ,061 / ,061 / ,061 / ,061 / ,061 / ,061 / ,064 / ,074 / ,061 / ,046 / ,047 / ,052 / ,058 / ,055 / ,064 / ,061 / ,064 / ,062 / ,068 / ,059 / ,068 / ,038 / ,043
57. DsecAF063879 / ,549 / ,556 / ,538 / ,535 / ,551 / ,534 / ,552 / ,573 / ,052 / ,052 / ,052 / ,052 / ,052 / ,055 / ,052 / ,055 / ,064 / ,052 / ,041 / ,041 / ,046 / ,052 / ,046 / ,055 / ,052 / ,055 / ,044 / ,050 / ,042 / ,050 / ,024 / ,027
58. DsecAF063878 / ,565 / ,546 / ,554 / ,551 / ,567 / ,549 / ,568 / ,559 / ,081 / ,078 / ,081 / ,081 / ,081 / ,084 / ,081 / ,081 / ,086 / ,081 / ,067 / ,064 / ,067 / ,072 / ,070 / ,081 / ,081 / ,084 / ,081 / ,086 / ,079 / ,087 / ,069 / ,072
59. DmauAF063872 / ,525 / ,528 / ,508 / ,505 / ,522 / ,504 / ,528 / ,547 / ,052 / ,049 / ,052 / ,052 / ,052 / ,052 / ,052 / ,052 / ,058 / ,052 / ,041 / ,033 / ,038 / ,044 / ,041 / ,052 / ,052 / ,055 / ,050 / ,055 / ,048 / ,056 / ,030 / ,030
60. DereAF063871 / ,533 / ,525 / ,505 / ,513 / ,529 / ,511 / ,536 / ,544 / ,052 / ,049 / ,052 / ,052 / ,052 / ,052 / ,052 / ,052 / ,058 / ,052 / ,041 / ,033 / ,038 / ,044 / ,041 / ,052 / ,052 / ,055 / ,050 / ,055 / ,048 / ,056 / ,030 / ,030