UCE target enrichment of Peremicus_FCR176_13
We extracted ancient DNA from historical museum specimens using a DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, US) following the manufacturers protocol and a standard phenol-chloroform protocol (Pbo et al., 2004; Willerslev and Cooper, 2005; McDonough et al., 2018) in an ancient DNA facility. We prepared dual-indexed libraries for Illumina sequencing using Kapa LTP Library Preparation kit (Kapa Biosystems, Boston, MA, US) following the manufacturers protocol (Kapa Biosystems V6.17), with 1/4 reactions. We performed dual indexing PCR with Nextera-style indices (Faircloth and Glenn, 2012) using Kapa HiFi Hotstart Ready Mix (Kapa Biosystems) according to the manufacturers protocols. We performed enrichment for UCEs using an in-solution DNA hybridization with synthetic RNA baits. We used the myBaits UCE Tetrapods 5Kv1 kit (Arbor Biosciences) following the myBaits protocol v3. Following enrichment and 18 cycles of PCR using universal Illumina primers (see myBaits protocol v3) and Kapa HiFi Hotstart Ready Mix (Kapa Biosystems) according to the manufacturers protocol, we sequenced the enriched libraries on a MiSeq (Illumina, Inc., San Diego, Ca, US) using two 600-cycle Reagent Kits v3 (2x300 bp) at Center for Conservation Genomics (CCG), Smithsonian Conservation Biology Institute, Washington, DC.