Skeleton tree showing apomorphies in main mouse LINE-1 lineage from
~ 7 Mya to ~ 1 Mya.
bt. = boostrap score.
ancestral/descendant states listed.
ambiguous states are left blank or in lower case.
~ before entry means position is known hypervariable
(eg. a CG column) or known to be involved in homoplasy
with respect to other segments of the tree.
Coordinate system is from Loeb et al., 1985.
Coordinates used to construct tree were limited to 5387..7277.
|------- Ratlin3a &RATTRAN
|
|------- R8
6683 t/C 6865 a/T 7116 A/G |
6694 c/A 6939 G/A 7153 c/ |
6712 a/G ~6958 C/ 7230 g/C | bt.=99
6848 a/G ~7017 C/T 7263 g/C |
6859 g/A 7115 a/T |
|--------IL6A
|
5542 t/ 6037 c/T 6804 G/T 7033 t/G|
5548 c/ 6094 T/C 6815 T/C 7046 a/T|
5560 g/ ~6415 c/T 6874 C/T 7092 g/A|
5688 t/ ~6765 G/ 6885 C/A 7098 g/ |
5746 a/ 6783 T/C 6886 C/T 7153 g/ | bt.= 98 (99 w/o rat outgroup)
5750 c/ 6788 C/T ~6921 c/G 7174 G/T|
5755 g/ 6789 A/G ~6938 T/C 7200 t/g|
5968 g/ 6791 T/C 6941 C/T 7204 G/A|
5949 a/ 6795 c/T |
|--------L1Md16
6929 T/C|
5542 /C ~6385 a/g 6628 T/C ~6958 /A|
5548 /T 6439 t/G 6677 C/T 6988 G/ |
5746 /T 6583 C/G ~6765 /T ~6996 A/G| bt. = 96 (99 w/o rat outgroup)
5750 /G 6602 T/C 6914 A/T 7003 G/A|
5755 /A 6619 T/C 6923 A/T ~7255 T/C|
|
|--------MmL1FTE
| See ftenode
|
|
5494 t/ 6427 T/ 6713 A/G 7153 g/T|
5506 g/ ~6433 T/ 6741 A/T 6966 T/A 7156 T/ |
~5697 G/ ~6649 C/ 6854 A/ 6988 /A 7177 G/A| bt. = 96 (99 w/o rat outgroup)
5935 T/ 6660 A/ 6888 C/T 6998 T/G 7200 g/C|
6100 G/A 6670 T/ 6900 T/ 7098 /A 7221 T/A|
6139 T/A 6671 G/ 6913 C/T ~7146 -C 7267 G/A|
| L1Md2 clade
|----------------------------|
| 6649 /A 6787 T/G |
| 6745 /T 6900 /C |
5697 /T| ~6746 A/G 7156 /A |
6031 T/C| 6854 /T 7224 T/C |
6103 A/G| 7225 G/A |
bt. = unresolved 6426 T/C| bt.= 95 7270 G/A |
6427 /C| 7276 G/A |
7271 T/G| |---------|
| |Mmb2x1 L1Md2
|
|
|----------------------------|
5494 /A ~5626 T/C 6060 C/T 6854 /A| 6850 G/A |
5506 /T ~5704 A/G 6318 A/G 6857 C/T| 6851 C/G |
5560 /A ~5722 T/C 6550 T/C 6873 C/G| ~6385 g/a 6854 /T |
5656 A/ 5730 T/A 6649 /A 6900 /C| 6403 C/T 6877 A/T |
5776 C/T 6652 A/T 6913 /A| ~6649 /C 6880 C/T |
~5830 C/T ~6704 A/C 6953 G/A| bt. = 6667 A/T 6893 G/A |
5914 C/A 6704 +G 6954 C/T| 100 6745 /A 6900 /T |
5917 A/G 6709 T/C 6970 A/G| 6750 G/T 6906 A/G |
bt. = 100 5921 T/C 6772 C/T 7037 T/A| ~6765 t/C ~6996 G/A |
5929 C/T 6773 A/G ~7055 C/T| 6804 T/A 7040 G/A |
5935 /C 6787 T/A ~7125 A/T| 6807 G/A 7046 T/C |
~5950 C/T 6795 T/C 7156 /A| 6843 G/A 7068 G/A |
| ~~~~~~~~~ |
|~~~~~~~ | | |
L1MdA2 |L1md17 L1Md1 DAC
lineage & TF lineage Y lineage