Patterns of Variation in MHC Class II b Loci of the Little Greenbul (Andropadus virens) with Comments on MHC Evolution in Birds
چکیده
We have isolated major histocompatibility complex (MHC) class II b loci from the little greenbul (Andropadus virens), an African songbird. We utilized preexisting information about conserved regions of the avian MHC to design primers to amplify a pool of sequences representing multiple loci. From this pool, a unique locus spanning 1109 bp that we designate as AnviDAB1 was cloned and sequenced. We designed locus-specific primers based on this sequence information and amplified six alleles from seven individuals. Compared to other A. virens MHC sequences obtained from genomic DNA or cDNA, the variability of sequences fromAnvi-DAB1 was low and the ratio of nonsynonymous to synonymous substitution was much less than one, suggesting thatAnvi-DAB1 may either be a pseudogene or a nonclassical MHC locus. Phylogenetic analysis revealed that theAnvi-DAB1 locus was highly divergent when compared with other passerine orA. virens genomic or transcribed MHC sequences. The use of conserved MHC primers followed by analysis of cloned sequences allows rapid isolation of MHC loci from exotic species and avoids laborious large-scale cloning and sequencing. The major histocompatibility complex (MHC) is a 0.1to 4-Mb segment of DNA in vertebrates and can contain over 80 genes arranged in three functional classes (Kaufman et al. 1999; Klein 1986; Trowsdale 1995). Class I genes present endogenous antigens, whereas class II MHC genes are responsible for the presentation of exogenous antigens to the immune system. This presentation of antigens to the immune system is integral to cell-mediated immune response (Klein 1986). The MHC has received considerable attention from evolutionary biologists as natural selection is widely thought to operate on MHC genes (Edwards and Hedrick 1998; Hedrick 1994). Evidence suggesting that these genes are under selection include (1) high allelic diversity (Robinson et al. 2000), (2) levels of heterozygosity that often exceed those predicted by neutrality (Black and Salzano 1981), (3) relatively long coalescent times compared to neutral expectations (Klein et al. 1993; Takahata 1990), and (4) increased nonsynonymous to synonymous substitution ratios for active portions of genes (Hughes and Nei 1988, 1989). A growing body of research has revealed that concerted evolution is common in the avian MHC (Edwards et al. 1995b; Miller and Lambert 2004; Wittzell et al. 1999) and that genomic organization differs among avian taxa (Hess et al. 2000; Kaufman et al. 1999; Shiina et al. 1999). The entire MHC of the chicken is less than 100 kb and has a relatively simple organization with small introns and few pseudogenes (Kaufman et al. 1999). This organization has been designated the minimal essential MHC (Kaufman et al. 1995) and refers to a gene family that is highly reduced in physical size, gene copy number, and expression and contains few nonfunctional loci. Observations on the chicken MHC have led to suggestions that the avian MHC differs dramatically from the mammalian MHC as the latter is often large (4 Mb), can vary in gene copy number, and possesses many pseudogenes (MHC Sequencing Consortium 1999; Milner and Campbell 1992; Trowsdale 1995). However, limited research on songbirds indicates that the minimal essential MHC may not apply to this group as many transcribed and genomic Journal of Heredity 2006:97(2):133–142 doi:10.1093/jhered/esj013 Advance Access publication February 17, 2006 a The American Genetic Association. 2006. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.