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Table S1 Marker details relating to PCR amplification including forward and reverse primer sequences, annealing temperature, number of PCR cycles and enzyme used in amplification (HOT = HotStar; GOLD = AmpliTaqGold). Italic style loci indicate the subset of 122 markers used in the multi-species amplification effort.

Table S2 Detailed information on polymorphism and orthologogy for individual markers. #Ind = number of collared flycatcher individuals screened for polymorphisms, S(nc) = number of non-coding single nucleotide polymorphisms, S(c) = number of coding single nucleotide polymorphisms, S/NS = synonymous (S), non-synonymous (N) or nonsense (Ns) coding single nucleotide polymorphisms, Indel = number of indels, Pi = nucleotide diversity, Pi+/− = standard error of nucleotide diversity, Taj D = point estimate of Tajima's D statistic, Chr = chromosome of best BLAST hit in the chicken genome, Pos = start position of best BLAST hit, Score = BLAST hit score value, GC cf = GC content in collared flycatcher intron, GC ch = GC content in chicken intron, Intr C = intron length in chicken, Intr CF = intron length for completely sequenced introns in collared flycatcher, Ex seq = length of exonic sequence obtained in collared flycatcher, Intr seq = length of intronic sequence obtained in collared flycatcher.

Table S3 Summary of the amplification success in the multi-species screen. Successful amplification is indicated with an X. (X) means we could not get perfectly specific bands. G. gallus = chicken, A. funereus = Tengmalm's owl, F. peregrinus = peregrine falcon, F. albicollis = collared flycatcher, P. caeruleus = blue tit, A. arundinaceus = great reed warbler.

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