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Eimes JA, Townsend AK, Sepil I, Nishiumi I, Satta Y. (2015) Patterns of evolution of MHC Class II genes of crows (Corvus) suggest trans-species polymorphism. PeerJ PrePrints3:e621v2https://doi.org/10.7287/peerj.preprints.621v2
A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC) is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP), in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis) American crows (C. brachyrhynchos) and carrion crows (C. corone orientalis). Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While clustering of positively selected amino acids by supertyping revealed a single supertype shared by only jungle and carrion crows, a pattern consistent with convergence, the overall phylogenetic patterns we observed suggest that TSP, rather than convergence, explains the interspecific allelic similarity of MHC IIB genes in these species of crows.
This is a highly revised version of our initial submission.
Map of Collection Sites in Japan
Map of collection sites in Japan with the number of samples from each location: carrion crows = orange; jungle crows = green.
. MHC IIB exon 2 (246 bp) amino acid alignment of common alleles (occurring in ≥ 4 birds) of three species of crows (Coma: Corvus macrorhynchos, Coco: C. corone, Cobr: C. brachyrhynchos) with three other species of Passeriformes (Apco: Aphelocoma coerulescens, Getr: Geothlypis trichas, Tumi: Turdus migratorius) and one representative of Falconiformes (Fati: Falco tinnunculus). Accession numbers for crows are [TBA]. Accession numbers for other species are listed after label.
Neighbor joining trees (Jukes Cantor, 500 bootstrap replicates) of all MHC IIB variants in this study using a 246 bp fragment of exon 2. Branches with bootstrap support are indicated: light red ≥ 50%; dark red ≥ 70. Coco (orange) = carrion crow; Cobr (blue) = American crow; Coma (green) = jungle crow. Fig. S3A: Tree constructed by comparing non-synonymous substitutions/ nonsynonymous site from codon positions identified as variable from a Wu-Kabot Plot (11 codons). Red shading indicates supported interspecific clades. Fig. S3B: Tree constructed by comparing synonymous substitutions/synonymous site at remaining (non-Wu-Kabot) sites (71 codons). Blue shading indicates supported interspecific clades.
Neighbor joining trees (Jukes Cantor, 500 bootstrap replicates) of all MHC IIB variants in this study using a 246 bp fragment of exon 2. Branches with bootstrap support are indicated: light red ≥ 50%; dark red ≥ 70. Coco (orange) = carrion crow; Cobr (blue) = American crow; Coma (green) = jungle crow. Fig. S4A: Tree constructed by comparing non-synonymous substitutions/ nonsynonymous site from codon positions identified as the peptide binding region (PBR) in HLA (Brown et al. 1993) (22 codons). Red shading indicates supported interspecific clades. Fig. S3B: Tree constructed by comparing synonymous substitutions/synonymous site at remaining (non-PBR) sites (60 codons). Blue shading indicates supported interspecific clades.
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