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Fig. S1 Distribution and sampling locations of Berthelot’s pipits (inset) in the North Atlantic.

Fig. S2 Mean (±99% CI) number of MHC haplotypes in the pipit metapopulation as a function of the number of founders.

Fig. S3 Convergence and mean (±SE) sequence similarity between MHC haplotypes.

Fig. S4 Changes in mean amino acid p-distance between all pairwise combinations of haplotypes in populations for amino acids coded by the (a) non-PBR and (b) PBR codons.

Table S1 Frequencies of MHC class I exon 3 haplotypes across 13 island populations of Berthelot’s pipit, grouped by lineage.

Table S2 Output from a sliding window analysis created to detect gene conversion in Berthelot’s pipit MHC haplotypes (see text for details).

Table S3 Sequences obtained from amplifying and cloning duplicated MHC class I exon 3 loci from individual Berthelot’s pipits from Tenerife (TF) and Madeira (M).

Appendix S1 Mutual exclusivity of MHC haplotypes within lineages.

Appendix S2 Assessing convergence on empirical and simulated data.

Appendix S3 Assembly settings and likelihood of chimeric sequences arising in silico.

Appendix S4 Microsatellite genotypes and mitochondrial cytochrome b haplotypes in Berthelot's pipit individuals.

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