Tamias alpinus (the Alpine chipmunks) exon capture probe design

Targeted exons were derived from 6,249 protein-coding genes with a target size totaling 4Mb, and spanned a wide range of evolutionary rates in the genome (Bi et al. 2012). In addition to the T. alpinus exons, we targeted the ~16 kb T. alpinus complete mitochondrial genome and 350 bp from the consensus Spermophilus (S. fulvus, S. major, and S. pygmaeus) SRY gene to assess empirical error rates and potential sample contamination (Bi et al. 2012). We also selected seven nuclear genes (acrosin, acp5, cmyc, rag-1, anon, zan, and zp2) previously sequenced in Tamias (6,031 bp total), which were used as positive controls in post-capture qPCR assays to determine the initial enrichment quality.