Table 1.
Phylogenetic analyses of eight ancient chicken mtDNA sequences
| Sequences | Samples | Scored variants (np 233–558) | Haplogroup |
| CR1-F | 246 | ||
| NC_001323 | 246 | A | |
| KC456222 | WY2 | 246-446 | AB? Or B? |
| KC456221 | WY1 | 246-256-261-310-315 | ABZY? Or ABZ? |
| KC456220 | NZT3 | 246-315-362-446 | AB? Or A? |
| KC456219 | NZT2 | 246-272G-446 | AB? Or B? |
| KC456218 | NZT1 | 246-315 | AB? Or A? |
| KC456217 | JLD2 | @243-246-256-261-281-306-310-315-415 | CD |
| KC456216 | JLD1 | @243-246-256-261-281-306-310-315 | CD |
| KC456215 | CS1 | @243-246-256-261-310-315-446 | EFGHIWZ |
The np in the sequences (GenBank accession nos. KC456215–KC456222) are scored relative to the reference sequence NC_007235. These sequences are located in np 233–558 relative to NC_007235. The primers CR1-F, CR1-R, CR2-F, and CR2-R are located in np 233–253, 395–418, 385–405, and 538–559 relative to NC_007235, respectively. The haplogroup nomenclature is taken from the published chicken mtDNA haplogroup tree (2). Suspected mutations due to errors are in bold. Mutations toward a base identical-by state to the reference sequences are indicated with the prefix @.