Characterization of class II β chain major histocompatibility complex genes in a family of Hawaiian honeycreepers: ‘Amakihi (Hemignathus virens) (VET1P.1124)

Abstract

Abstract The objective of this study was to estimate the number and degree of variation of Mhc class II β chain genes and alleles in a family of Hawaiian honeycreepers (`Amakihi, Hemignathus virens). The parents were bred in captivity and produced eight progeny. Partial antigen binding region (173 bp) fragments were produced via PCR+1 cloning and sequenced on a Beckman CEQ system, and two Roche 454 platform pyrosequencing runs. A total of 302 sequences were obtained via cloning. After quality filtering and removal of chimeras, a total of 2762 sequences were retained from 454 run 1 and 3958 sequences from 454 run 2. Unique sequences detected <3 times within an individual were discarded. All sequences were used to generate a neighbor-joining tree in MEGA v. 5.2 to evaluate sequences across family members. Singlet sequences were discarded. The remaining sequences were used to evaluate segregation and relationships of loci. A total of 19 putative loci were detected in this family. Allelic segregation was not observed among any of these loci thus they appear to be independent, but linkage was observed among four loci suggesting segregation of a haplotype among 5 progeny. The finding of 37 sequences in one individual also suggests a minimum of 19 Mhc class II loci in `Amakihi. Of these, 17 loci are classical Mhc loci thus designated as DAB, but mean diversity and evolutionary divergence values among groups suggest that two loci are non-classical and thus should be designated as DBB.