SUPPLEMENTARY MATERIAL

Online Resource 1: Results of cross-species amplification of the 25 conserved loci on 8 individuals

For each species (Black-whiskered Vireo (VI), Caribbean Elaenia (EL), Purple-throated Carib (CA), Bananaquit (BA), Lesser Antillean Saltator (SA), Lesser Antillean Bullfinch (BU), Scaly-breasted Thrasher (TH), Plumbeous Warbler (WA)), the number of alleles observed in 8 individuals– the optimal hybridization temperature – the optimal concentration of MgCl2 are reported in this order. For example, a locus with 3 observed alleles, with an optimal hybridization temperature of 51°C and an optimal concentration of 1mM of MgCl2 is indicated by 3-T51-1mM. “No” and “Mono” respectively indicate a locus that failed to amplify and a monomorphic locus.

Locus / Primer sequences / Ref / VI / EL / CA / BA / SA / TH / WA
CAM-01 / F: AAAGGCCAAGRCCAGTATG / a / Mono / Mono / No / Mono / 4-T54-2mM / Mono / No
R: CTCTCATCCACCCTGTTAGC
CAM-02 / F: GAATTAAAGAYAGCAGATGCAGG / a / Mono / No / Mono / 8-T51-1mM / Mono / Mono / 3-T51-1mM
R: AGCTGATGAAATGAGAATGCAG
CAM-05 / F: TTACACAGACTGCAAACCGC / a / No / Mono / No / No / 4-T51-2mM / No / Mono
R: CTGTTKCTCTAGTAATGAGATCCTG
CAM-06 / F: GTGATGGTCCAGGTCTTGC / a / 6-T57-1mM / 3-T57-1mM / No / No / No / No / No
R: CAAGAGGAACAGATGAGGGTC
CAM-10 / F: TATCCMGAGAATGGGCATC / a / 10-T51-1mM / No / No / Mono / 2-T51-2mM / 5-T51-2mM / 6-T51-1mM
R: KGCTCTCATTGTCATGCTG
CAM-13 / F: TCAAATACAGCAGCAGGCAG / a / 2 -T54-1mM / Mono / Mono / Mono / Mono / Mono / Mono
R: TTCATTACCAAACAGCATCCAG
CAM-15 / F: SGACGACTCCTTTATTTCCC / a / 7-T51-1mM / Mono / No / 3-T51-2mM / Mono / No / 7-T51-1mM
R: TTCTGACTTCCYCAGGTAACAC
CAM-17 / F: CGGGTTGTAATCAAGAAGATGC / a / 3-T51-1mM / Mono / 2-T51-2mM / 2-T54-2mM / Mono / Mono / Mono
R: CTGCGGAGCAATTAACGC
CAM-18 / F: TTAAGAAGTTTACACCCAGCG / a / Mono / Mono / No / No / 2-T57-2mM / 5-T54-2mM / 3-T54-1mM
R: GCTAAATAACAGAGCCAGGAAG
CAM-19 / F: TCTTGGAGGCAGATARGAAGTG / a / 2-T51-1mM / 4-T54-2.5mM / Mono / 5-T54-1mM / 5-T51-2mM / Mono / 4-T51-1mM
R: GAGCAAGCAAAGATCACAAGC
CAM-20 / F: TAACAGGCAGGAATGCAGG / a / No / 2-T51-2.5mM / Mono / No / Mono / 2-T51-2mM / 2-T51-1mM
R: TCAGCCAGTGTTGGAGGTC
CAM-24 / F: CCCACTTCAGTCTTCAGAGC / a / 2-T54-1mM / 5-T57-2.5mM / Mono / 2-T51-1mM / Mono / Mono / 2-T51-1mM
R: TGGAGTATTTGGGATTGGAG
TG01-086 / F: CCCAGCTTTAAATCCTTCCTG / b / 2-T51-1mM / No / Mono / 2-T51-1mM / 2-T57-2.5mM / 4-T54-2.5mM / Mono
R: TACTGCCTCCAAGGCACAG
TG01-147 / F: TGAGCCACTACAGAGTGGAAA / b / Mono / 2-T57-2.5mM / 3-T51-2.5mM / 2-T54-1mM / 3-T51-2.5mM / Mono / 2-T57-1mM
R: GCCACTACAATGAAGAAAATATTACAG
TG03-002 / F: TCTTGCCTTTTTGGTATGAGTATAG / b / 2-T54-1mM / 3-T57-2.5mM / Mono / 2-T51-1mM / Mono / Mono / 3-T54-1mM
R: TACAAAGCACTGTGGAGCAG
TG03-098 / F: TTTGCCTTAATTCTTACCTCATTTG / b / 3-T54-1mM / 2-T57-2.5mM / Mono / Mono / Mono / 3-T51-2.5mM / 3-T54-1mM
R: TTGCAACCTCTGTGGAAGC
TG04-004 / F: CTGGAGCAGTATTTATATTGATCTTCC / b / 2-T51-1mM / No / 2-T51-2.5mM / Mono / Mono / 4-T51-2.5mM / 2-T51-1mM
R: GAAGATGTGTTTCACAGCATAACTG
TG04-012 / F: TGAATTTAGATCCTCTGTTCTAGTGTC / b / Mono / 5-T57-2.5mM / Mono / 4-T54-1mM / Mono / 4-T51-2.5mM / 5-T51-1mM
R: TTACATGTTTACGGTATTTCTCTGG
TG05-046 / F: AAAACATGGCTTACAAACTGG / b / Mono / Mono / Mono / Mono / 2-T51-2mM / Mono / 3-T54-1mM
R: GCTCAGATAAGGGAGAAAACAG
TG05-053 / F: GCATCATCTGGTTGAACTCTC / b / 3-T51-1mM / Mono / 2-T51-2.5mM / Mono / Mono / Mono / Mono
R: ACCCTGTTTACAGTGAGGTGTT
TG07-022 / F: CAGAAGACTGTGTTCCTTTTGTTC / b / 3-T57-2mM / Mono / 2-T57-2.5mM / No / Mono / Mono / Mono
R: TTCTAATGTAGTCAGCTTTGGACAC
TG11-011 / F: ACAAACTAAGTACATCTATATCTGAAG / b / 3-T51-1mM / Mono / 2-T51-2.5mM / 3-T51-1mM / 2-T51-2mM / 3-T51-2.5mM / 3-T54-1mM
R: TAAATACAGGCAACATTGG
TG12-015 / F: ACAACAGTGGCTTTACTGTGTGA / b / 4-T51-1mM / Mono / 4-T54-2.5mM / Mono / Mono / 2-T54-2.5mM / 5-T54-1mM
R: TACAGCAGCTGCAGCAAAGT
TG13-017 / F: GCTTTGCATCTTGCCTTAAA / b / 4-T51-1mM / 2-T57-2.5mM / 3-T51-2.5mM / 4-T54-1mM / 2-T51-2mM / Mono / Mono
R: GGTAACTACAACATTCCAACTCCT
TG22-001 / F: TTGGATTTCAGAACATGTAGC / b / Mono / Mono / 2-T51-2.5mM / No / 5-T54-2mM / 3-T51-2.5mM / 6-T51-1mM
R: TCTGATGCAAGCAAACAA

a: (Dawson et al. 2013); b: (Dawson et al. 2010)