Detail on top of L1Md4 lineage.

          
            |
|--------------------------|
|              h c6955 T/C |            
dom.                       |----------L1Md17
A2               6762 G/A  |
                 6803 T/G  |
                           |----------SD
                ~6704 C/A  |
                 6739 G/C  |
                           |----------Mustc
               ~c7224 T/C  |
                           |-----------------------------|
                 5639 T/C  |                    6820 A/T |
                *5563 A/G  |                             | 
                           |----------MusL1O1         Z lineage(s)
               c*5950 C/T  |
                 5980 T/   |
                 6059 T/C  |
                 6080 A/C  |
                *6226 C/G  |
                 6424 G/A  |
                 6492 G/A  |
                c6721 A/C  |
                 6837 G/A  |
               c*6920 C/T  |
                *6954 T/C  |
               hc6955 C/T  |
                *7102 G/T  |
                           |----------SAF
                *6626 G/A  |
                 7146 G/T  |
                           |--------------------------------|
                 5954 A/T  |                       6873 G/A |
                 5980  /C  |                       6169 C/  |
                h6271 T/A  |                                |----S4 
                *6652 T/A  |                       6793 +C  |
                 6697 T/C  |                                |----Spr48,49,68,SC2
                 7228 A/G  |                       6936 T/C |
                 7234 A/G  |                                |----D13SH1,SCH6L,S20
                 7236 A/G  |                       7265 A/G |
                 7243 A/G  |                       6169  /T |
                 7268 A/G  |                  ------------------------ SK1 et al.
                 7269 A/G  |          6825 A/G|            6755 T/C |
                 7309 T/A  |                  |--SK3 et al 6810 C/A |
           ---------------------     ~7285 -22|            7200 C/A |
  6845 T/A |        c*6920 T/C |              |--SC7       6855 G/C |
  6913 A/T |         *6954 C/T |     *7024 T/C|                     |-PL3 et al.
         TF1 grp.   hc6955 T/C |      6290  /a|            6852 T/C |
        ------------  6938 C/T |      6220 a/c|            6981 T/A | 
        |    |     |           |              |                     |-EL8
3397 A/G| *7277  *6226         |           Ms7024          6889 C/A |
3617 T/C|  +G     G/C.         |----- |    group           5980  /a |
3622 A/G|  grp.   grp.         |      |                          Ms475
4501 C/T|             3430 T/C |      AF081112                   group
        |                TF2 group    et al.
    AF081105          3526 C/A |
    AF081104         *5563 G/A |
                      6865 T/G |
                     *7102 T/G |
                     *7277 +G  |
                               |
                            L1spa group

Notable homoplasies (*)

• 7024 T/C is the namesake substitution of the Ms7024 family, but also is shared by L1MdZ and L1Bg.
• 7227 +G defines a subgroup of TF1, but also the L1spa subgroup of TF2
• 7102 G/T occurs prior to the domesticus/spretus split, but reverts in the L1spa subgroup.
• 6920, 6954, 6955 are altered above the spretus/domesticus split, then reverted in TF2, apparently en masse by a gene conversion. These are also involved in changes elsewhere on the tree.
• 5563 A/G occurs high on the lineage, but reverts in l1spa subgroup.
• 6226 G/C occurs on a subgroup of TF1, but also on L1Md4 in TF2. It's a reversion of a substitution higher on the L1Md4 lineage.
• 6652 T/A is a reversion of a substitution not far above the L1Md4/A2 split.
• 6626 G/A occurs in parallel on the spretus A2 lineage.
• 5563 A/G occurs high in lineage, then reverts on L1spa subgroup.
• 5950 C/T (CG->TG) occurs in parallel on A2 lineage.