Frequency of occurrence (in %) of MHCIIB exon 2 alleles in 108 individuals, sorted from highest to lowest values.

<p>Arrows indicate the alleles found in gDNA as well as cDNA.</p

Maximum likelihood tree of exon 2 MHCIIB and MHCIIY sequences across galliform species.

<p>Different colours indicate taxa, whose neutral phylogeny is shown in small inserted figure (based on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone.0069135-Eo1" target="_blank">[91]</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone.0069135-Shen1" target="_blank">[92]</a>). The sequence of DAB1 of the barn owl (Acc. no. EF641260) was used as an outgroup. Only bootstrap values >50 are shown. For the complete list of sequences used, with GenBank accession numbers and references see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone.0069135.s002" target="_blank">File S2</a>.</p

PCR conditions and details on primers used for DAB3 sequencing.

<p>PCR conditions and details on primers used for DAB3 sequencing.</p

Review of MHC structure in galliform species.

<p>Review of MHC structure in galliform species.</p

General Linear Mixed Models explaining female mate choice decision based on three measures of mate dissimilarity.

<p>Table shows parameter estimates (with 1 standard error) for significant terms, degrees of freedom (df), test statistics (F), and significance levels (<i>P</i>). For the terms not included in the final model, the level of non-significance was obtained by entering the term into the minimal adequate model. The fixed terms included in minimal adequate models are indicated by bold typeset.</p

Putative amino acid sequence alignment.

<p>The alignment starts at the 2nd amino acid position encoded by the exon 2 in MHCIIB. Sequences of chicken (<i>Gaga</i>_BLB1-haplB19 and <i>Gaga</i>_BLB2-haplB19, GenBank accession no. AB426151), barn owl (<i>Tyal</i>_DAB1-allele02, EU442602) and little spotted kiwi (<i>Apow</i>_DAB*allele08, HQ639687) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone.0069135-Miller4" target="_blank">[90]</a> are shown for comparison. Dots represent identity to the sequence on top. Asterisks (*) indicate the amino acid positions under positive selection (based on CodeML analysis, model M8, posterior probability >0.95). Plus signs (+) mark the antigen-binding sites (ABS) in humans <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone.0069135-Brown1" target="_blank">[64]</a>. Tracts 1–7 depict codons contained in conversion tracts as given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069135#pone-0069135-t003" target="_blank">Table 3</a>. Black triangles represent the placement of two recombination breakpoints as detected by GARD.</p

Relationship between measures of mate dissimilarity and female choice.

<p>The measures of mate dissimilarity were (a) allele summation, (b) allele divergence and (c) simple contrast. Full (n = 20, left panel) and limited (n = 17, right panel) datasets were used for calculation. Female choice was measured as the number of eggs deposited by females when spawning with a particular male. Symbol size (a, b) represents the level of overlap of individual data points, with a maximum of 6 overlapping points (the largest square). The line represents the best fit of a simple linear regression. Error bars (c) represent ±1 standard error.</p

Gene conversion events among 12 nucleotide sequences of MHCIIB exon 2 in the Grey partridge.

<p>Gene conversion events among 12 nucleotide sequences of MHCIIB exon 2 in the Grey partridge.</p

The number of synonymous (dS) and non-synonymous (dN) substitutions per site for ABS, non-ABS and all sites in exon 2 of MHC class IIB (mean±SE); the value of Z-test of positive selection and probability (<i>P</i>) that positive selection acts on these sites.

<p>The number of synonymous (dS) and non-synonymous (dN) substitutions per site for ABS, non-ABS and all sites in exon 2 of MHC class IIB (mean±SE); the value of Z-test of positive selection and probability (<i>P</i>) that positive selection acts on these sites.</p