Table S1 General information on ecology and distribution of the twelve species of kestrels and falcons analysed.

Table S2 Indices of neutral markers diversity at: (A) microsatellite, (B) mitochondrial DNA, and C) RAG-1 for several species and populations-within-species of falcons and kestrels.

Figure S1 Phylogenetic relationships among Falco species inferred from nucleotide sequences of the cytochrome b gene. Partial neighbour-joining tree obtained from (Roulin & Wink, 2004).

Figure S2 (A) Alignment of the nucleotide sequences of intron 3 (for the MHC class I) and intron 2 plus exon 3 (for the MHC class II B). (B) Neighbour-joining tree of MHC class I and MHC class II B gene fragments.

Figure S3 Amplification of MHC loci from cDNA in the Eleonora’s falcon.

Figure S4 Alignment of the nucleotide and amino acid sequences of MHC class I and MHC class II alleles in falcons.

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