Table 2.
MC1R sequence polymorphism data for 23 L. coronata individuals. Asterisks indicate agreement with the consensus sequence. All variation among the four L. coronata alleles is synonymous with respect to the amino acid sequence. Heterozygous sites are denoted with standard IUPAC one-letter codes (W=A/T). Genotype refers to allelic combinations. Sites highlighted in grey are putatively functional nucleotide sites in other avian taxa. Substitutions at site 253 are associated with plumage polymorphism in snow geese (A. caerulescens) (Mundy et al. 2004). Substitutions at site 274 are associated with plumage polymorphism in bananaquits (Coereba flaveola) (Theron et al. 2001). Substitutions at site 689 are associated with plumage polymorphism in Arctic skuas (S. parasiticus; Mundy et al. 2004). All L. coronata individuals are monomorphic at these three sites. Nucleotide sites are numbered with reference to the chicken MC1R sequence. Lepidothrix serena is included as an outgroup.
| nucleotide site | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | 2 | 2 | 3 | 4 | 6 | 6 | ||||||
| 7 | 9 | 0 | 5 | 7 | 5 | 1 | 7 | 8 | ||||
| voucher number | 8 | 1 | 4 | 3 | 4 | 4 | 1 | 8 | 9 | plumage | genotype | genbank accession number |
| consensus | C | G | C | G | G | C | A | C | A | |||
| B-28461 | T | * | T | * | * | * | * | * | * | black | 1/1 | DQ388308 |
| B-16077 | T | * | T | * | * | * | * | * | * | black | 1/1 | DQ388309 |
| RWD17053 | * | * | * | * | * | * | * | * | * | black | 2/2 | DQ388310 |
| B-3105 | * | * | * | * | * | * | * | * | * | black | 2/2 | DQ388313 |
| B-4657 | * | * | * | * | * | * | * | * | * | black | 2/2 | DQ388314 |
| B-4545 | * | * | * | * | * | * | * | * | * | black | 2/2 | DQ388315 |
| B-10492 | * | * | * | * | * | * | * | * | * | intermediate | 2/2 | DQ388316 |
| B-27578 | * | * | * | * | * | * | * | * | * | intermediate | 2/2 | DQ388318 |
| B-27832 | * | * | * | * | * | * | * | * | * | intermediate | 2/2 | DQ388319 |
| B-5394 | * | * | * | * | * | * | * | * | * | green | 2/2 | DQ388311 |
| B-5487 | * | * | * | * | * | * | * | * | * | green | 2/2 | DQ388312 |
| B-40543 | * | * | * | * | * | * | * | * | * | green | 2/2 | DQ388317 |
| B-901 | * | * | * | * | * | * | * | * | * | green | 2/2 | DQ388320 |
| B-433693 | * | * | * | * | * | * | * | * | * | green | 2/2 | DQ388321 |
| B-433692 | * | * | * | * | * | * | * | * | * | green | 2/2 | DQ388322 |
| B-433689 | * | * | * | * | * | * | * | * | * | green | 2/2 | DQ388323 |
| B-433691 | * | * | * | * | * | * | W | * | * | green | 2/3 | DQ388324 |
| B-433694 | * | * | * | * | * | * | W | * | * | green | 2/3 | DQ388325 |
| B-9269 | * | * | * | * | * | * | W | * | * | green | 2/3 | DQ388326 |
| B-9306 | * | * | * | * | * | T | T | * | * | green | 4/4 | DQ388327 |
| B-31333 | * | * | * | * | * | * | T | * | * | green | 3/3 | DQ388328 |
| B-9125 | * | * | * | * | * | * | T | * | * | green | 3/3 | DQ388329 |
| B-9177 | * | * | * | * | * | * | T | * | * | green | 3/3 | DQ388330 |
| L. serena | T | A | * | * | * | * | * | T | * | n.a | n.a | DQ388331 |