title: UCE sequences of Steganomus junodi
design: We followed a standard phenol/chloroform protocol (from Saghai-Maroof et al. 1984, modified) to extract DNA from the specimens hind legs or from wholly ground specimens. Extracted DNA was quantified with a Qubit 3.0 fluormeter (Thermo Fisher Scientific, Inc.) and 2 l of extract were run out on 1.5% sodium borate gels to assess fragmentation. Based on the degree of fragmentation, samples were sheared from 0-60 seconds with a Q800R sonicator (Qsonica, LLC.), to obtain a targeted fragment size of 500-600 bp. We sheared an average of 200 ng DNA per sample and prepared dual-indexed libraries with TruSeq adapters (Faircloth and Glenn 2012), following the protocol of Faircloth et al. (2015) and the modifications from Blaimer et al. (2016a, 2016b). We used KAPA Hyper prep kits (Kapa Biosystems, Inc.), Speedbeads (SPRI beads) for cleanup (see Fisher et al. 2011), and utilized a Apollo 324 (WaferGen, Inc) liquid-handling robot. Target enrichment for 29 samples was conducted with the enhanced HymV2-ant UCE probe-set (Branstetter et al. 2017),  following Blaimer et al. (2016a, 2016b). The biotinylated RNA baits were manufactured by MYcroarray, Inc. Hybridization-reactions were conducted on a PCR-block at 65C for 24h, following washing steps (following Blumenstiel et al. 2010), and post-enrichment PCRs as in Blaimer et al. (2016a, 2016b).Enrichment success was assessed using a ViiA7 qPCR system (Thermo Fisher Scientific, Inc.), with samples being pooled at equimolar concentrations. We used a KAPA Sybr Fast qPCR kit (Kapa Biosystems, Inc.) and set up a total of four dilutions as in Blaimer et al., (2016a). The initial input concentrations were calculated by assuming 600 bp as the average fragment length. After inferring the concentrations for the separate reactions, they were finally pooled at equimolar concentrations into a single tube. We then size-selected the products for fragments between 250 and 800 bp using a BluePippin device (Sage Science, Inc.). The sequencing of the libraries was conducted on an Illumina HiSeq 2500 device with 150 bp paired end reads, at the Cornell Biotechnology Resource Center (Cornell BRC).Raw reads obtained from the Cornell BRC were trimmed with the Trimmomatic (Bolger et al. 2014) wrapper Illumiprocessor (Faircloth 2013)