Table 2. The SNP allele state profiles of genetic subgroups targeted for agarose MAMA design where the Derived SNP state is shaded and Ancestral state is unshaded.
| Major Groupa | Subgroupa | Tier 1b | Tier 2 b | Tier 2 b | Tier 2 b | Tier 3 b | Tier 4 b | Tier 5 b | Tier 6 b | Tier 7 b | Tier 2 b | Tier 3 b | Tier 4 b | Tier 5 b | Tier 6 b | Tier 7 b | Tier 2 b | Tier 2 b | Tier 3 b |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| *Mad-05c C→ | Mad-12 c G→ | Mad-08 c C→ | Mad-58 c A→ | Mad-62 c G→ | Mad-64 c T→ | Mad-65 c C→ | Mad-74 c G→ | Mad-78 c C→ | Mad-30 c G→ | Mad-32 c T→ | Mad-35 c G→ | Mad-36 c C→ | Mad-37 c G→ | Mad-38 c A→ | Mad-42 c T→ |
Mad-43 c C→ |
Mad-46 c T→ |
||
| I | kd | T | G | C | A | G | T | C | G | C | G | T | G | C | G | A | T | C | T |
| I | I1 | T | A | C | A | G | T | C | G | C | G | T | G | C | G | A | T | C | T |
| I | j | T | G | T | A | G | T | C | G | C | G | T | G | C | G | A | T | C | T |
| I | s2 | T | G | C | G | G | T | C | G | C | G | T | G | C | G | A | T | C | T |
| I | s3 | T | G | C | G | A | T | C | G | C | G | T | G | C | G | A | T | C | T |
| I | s4 | T | G | C | G | A | C | C | G | C | G | T | G | C | G | A | T | C | T |
| I | s5 | T | G | C | G | A | C | T | G | C | G | T | G | C | G | A | T | C | T |
| I | s8 | T | G | C | G | A | C | T | T | C | G | T | G | C | G | A | T | C | T |
| I | s9 | T | G | C | G | A | C | T | T | T | G | T | G | C | G | A | T | C | T |
| I | q1 | T | G | C | A | G | T | C | G | C | A | T | G | C | G | A | T | C | T |
| I | q2 | T | G | C | A | G | T | C | G | C | A | A | G | C | G | A | T | C | T |
| I | q3 | T | G | C | A | G | T | C | G | C | A | A | A | C | G | A | T | C | T |
| I | q4 | T | G | C | A | G | T | C | G | C | A | A | A | T | G | A | T | C | T |
| I | q5 | T | G | C | A | G | T | C | G | C | A | A | A | T | A | A | T | C | T |
| I | q6 | T | G | C | A | G | T | C | G | C | A | A | A | T | A | G | T | C | T |
| I | r | T | G | C | A | G | T | C | G | C | G | T | G | C | G | A | C | C | T |
| II | d | T | G | C | A | G | T | C | G | C | G | T | G | C | G | A | T | T | C |
| II | h1 | T | G | C | A | G | T | C | G | C | G | T | G | C | G | A | T | T | T |
aDescribed in Vogler et al 2011 and Vogler et al 2017
bCorresponds to levels indicated in Fig 2 in this study.
ccanSNP that define Malagasy subgroups.
dCollapsed node containing many subgroups.