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The distributions of the number of positively selected sites detected using the MEME test performed on subsets of 100 alleles randomly subsampled from alleles with no deletions (a) and alleles containing a 6 bp deletion (b). (DOCX 273 kb)

Primers used to amplify MHC class I in sedge warbler. (DOCX 16 kb)

Alignment of sedge warbler MHC class I amino acid sequences, covering the α1, α2 and α3 regions (species-specific nomenclature and GenBank accession numbers are used, Acsc-UA), in comparison with great reed warblers (Acar cN3, AJ 005503), white-throated sparrows Zonotrichia albicollis (XM005497294), Atlantic canaries Serinus canaria (XM009100025), golden-collared Manakins Manacus vitellinus (XM008930636), medium ground-finches Geospiza fortis (xm014311325), zebra finches Taeniopygia guttata (XM002186531), hooded crows Corvus cornix cornix (XM010392747), numbered according to full-length chicken MHC class I. Identity with sequence Acar cN3 is indicated with dots, codons corresponding to the PBR with (P). (PDF 189 kb)

Schematic overview of the primer design approach. PaDo primers, marked with red arrows, used for amplification and cloning of cDNA from 4 sedge warblers Acrocephalus schoenobaenus individuals. Hn primers (Westerdahl et al. 2004), designed for great reed warblers A. arundinaceus, used for obtaining whole exon 3 sequences in 4 individuals for both gDNA and cDNA. Subsequently sequences obtained for cDNA were used for designing specific sedge warbler primers (HnallaN and Hn46N) that amplify whole range of exon 3 MHC class I in sedge warblers, excluding a range of pseudogenes. (PDF 1364 kb)