Table 3.
Samples Containing Association Groups A, B, and C[Note]
|
Results from Association Group |
||||||
|
A |
B |
C |
||||
| Sample (Region) | C→T, A→G | G→A, T→C | C→T, G→A | A→G, T→C | C→T, T→C | A→G, G→A |
| DinornisCR (16733–00441) | 1 | 1 | 1j | 2 | 2j | |
| DinornisCOII (COII) | 1 | |||||
| Dinornis (11120–11958) | 1 | 1 | ||||
| Emeus16s (16s) | 1 | |||||
| EmeusCOI (COI) | 1 | |||||
| EmeusCOIII (COIII) | 1 | 1 | ||||
| EmeusND4/5 (ND4/ND5) | 1 | 1, 1j | ||||
| EmeusCOII (COII) | 1 | |||||
| EmeusCytb (cytb) | 1 | 2 | ||||
| Ursus221a | 1 | |||||
| Ursus222 | 1 | |||||
| Ursus223a | 1 | 1 | ||||
| Ursus147 | 1 | 1 | ||||
| Ursus221b | 1 | |||||
| Ursus3500 | 2 | |||||
| Ursus117001 | 1 | |||||
| Ursus151a | 1 | 1j | ||||
| Tg233 (HVRI) | 1 | |||||
| Tg232 (HVRI) | 1 | 1j | ||||
| Tg116 (HVRI) | 2j | 1j | ||||
| Tg114 (HVRI) | 1j | 1j | 1j | 1j | ||
| Tg103 (HVRI) | 2 | 2j | ||||
| Tg54 (HVRI) | 1j | |||||
| Tg145 (HVRI) | 1 | |||||
| Tg44 (HVRI) | 1 | |||||
| Tg149 (HVRI) | 3j, 2 | 2j | 3j, 3 | 2j, 1 | ||
| Tg137a (HVRI) | 1 | |||||
| Tg112 (HVRI) | 1 | |||||
| Tg105 (COIII) | 1 | |||||
| Tg63 (COIII) | 1 | 1 | ||||
| Tg148 (HVRI) | 1 | 1 | 1 | |||
| Tg136a (HVRI) | 1j | 1 | ||||
| Tg147 (HVRI) | 1j, 2 | |||||
| Tg85 (HVRI) | 1 | 1j | ||||
| Tg93 (HVRI) | 1, 1j | |||||
| Tg148 (COIII) | 1 | 1j | ||||
| Tg143 (HVRI) | 1 | |||||
| Tg129 (HVRI) | 1j | |||||
| Tg123 (HVRI) | 2j | |||||
|
Results from Association Group |
||||||
|
A |
B |
C |
||||
| Individual Totals | C→T, A→G | G→A, T→C | C→T, G→A | A→G, T→C | C→T, T→C | A→G, G→A |
| Identified jumps | 7 | 0 | 7 | 5 | 9 | 6 |
| Nonidentified jumps | 22 | 6 | 7 | 2 | 16 | 2 |
|
Results from Association Group |
||||||
| Group Totals | A | B | C | |||
|
Results from Association Group |
||||||
| Group Totals | A | B | C | |||
| Associations per group | 35 | 21 | 33 | |||
| Jumps | 7 | 12 | 15 | |||
| Nonjumps | 28 | 9 | 18 | |||
| Nonjump:jump ratio | 4 | .75 | 1.2 | |||
Note.— The three association groups are each divided into two subgroups named according to the two different base modifications observed together on same cloned sequence. A “j” after the numeral denotes direct evidence of jumping as identified following the conventional method (e.g., Pääbo 1989), in which different cloned sequences sharing a proportion of damaged sites are deemed to have arisen because of jumping PCR. These are termed here as “identified jumps”; nonidentified jumps are those that cannot be identified following the conventional methods.