ddRADseq of Zonotrichia capensis
Following Poland et al. (2012) double-digest RAD-Seq libraries were constructed at the Institute for Integrative Systems Biology (IBIS; at Laval University) using the restriction enzyme pairing of SbfI and MspI. Uniquely barcoded samples were pooled into a library and then size selected for roughly 100-300 bp using a BluePippin DNA size selection system (Sage Science Inc., Beverly, MA, USA). The library was forwarded to Gnome Qubec (Gnome Qubec Innovation Centre) and assessed using a LabChip GX (Perkin-Elmer, MA, USA) instrument to determine library size quality. The library was then sequenced as single-end, 100 base-pair reads on a single Illumina HiSeq2000 lane (Illumina, San Diego, CA, USA).