UCE targeted enrichment of Catharus swainsoni: MMNH 43640
For extracting DNA from tissue samples, we followed the standard Qiagen Blood and Tissue Kit (Germantown, Maryland) protocol for muscle tissue. Toepads were extracted either using a protocol developed specifically for degraded samples by Andres Cuervo (pers comm.) using the QIAamp DNA Micro Kit (Germantown, Maryland) spin columns or a Phenol-Chloroform extraction protocol followed by bead cleanup as described by Tsai et al. (2019). All toepad samples were extracted by individuals who had not handled modern tissues samples that day and in a lab in which no modern avian tissue or blood samples were processed. Extracted DNA was quantified by either qPCR with PicoGreen (Blotta et al. 2005; Eugene, Oregon) or a Qubit (Eugene, Oregon). Samples were submitted to Rapid Genomics (Gainesville, FL) for library preparation and UCE sequencing. Libraries were enriched for UCEs using either the 2.5k tetrapod probe kit (2,386 UCEs) supplemented with approximately 100 avian exons or the standard 5k tetrapod probe kit (5060 UCEs; Faircloth et al 2012). Libraries were sequenced with either 100 (2.5k kit) or 150 (5k kit) base pair, paired end reads