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Figure S1 Comparison of coverage and sequence divergence.

Figure S2 Comparison of coverage and probe length.

Figure S3 Mitochondrial Capture Specificity.

Table S1 Locus information for passerine project.

Table S2 Locus information for Draco project.

Table S3 Average coverage per locus for the passerine project (with flanking regions).

Table S4 Average coverage per locus for the Enyalius project (with flanking regions).

Table S5 Average coverage per locus for the Draco project (with flanking regions).

Table S6 Average coverage per locus for the passerine project (without flanking regions).

Table S7 Cost comparisons of SCPP and commercial probe kits.

Table S8 SCPP Reagent Costs – Probe Generation & Hybridization.

Table S9 SCPP Reagent Costs – Oligos.

Table S10 Capture Assessment – qPCR.

Appendix S1 Bioinformatics of read processing and phylogenetic methods for passerine tree.

men12249-sup-0002-ProtocolS1.pdfapplication/PDF221KAppendix S2 Detailed protocol for SCPP.

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