Phylogenetic tree of great tit Mhc class I exon 3 sequences. The tree was constructed using Neighbour-Joining method and Tamura-Nei model. The sequences [GenBank: JQ034624 - JQ035485] differed at the length of exon 3 being either 221 bp, 215 bp or 212 bp. The tree was rooted with a chicken (Gallus gallus) Mhc class I sequence [Genbank: AY234770] and the reliability of the branches was tested with 1000 bootstrap replicates. Bootstrap supports for the major clades are indicated with numbers. Pseudogene alleles bearing stop codons are marked in red and putatively non-functional alleles (Group 1) are marked in blue. The rest of the alleles represent Group 2 (except the chicken Mhc class I sequence). The chicken Mhc allele is marked in grey. The sequences that are 221-basepair long are indicated by purple squares and the sequences that are 215-basepair long are indicated by green squares. The 212-basepair sequences are not marked.
Sepil et al. BMC Evolutionary Biology 2012 12:68 doi:10.1186/1471-2148-12-68