Ocymyrmex_contigs

DNA was extracted destructively (either using the whole specimen or two legs, depending on the size of the specimen) or non-destructively (by soaking the whole specimen in proteinase-K and then rinsing in ethanol and remounting) from mounted museum specimens collected between 1980 and 2015, using a DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA). The standard protocol described by the manufacturer was followed except for the final elution step; 130 µL of AE buffer was added to ensure that there was enough DNA for quality checks and UCE library preparation. We ran 10 µL of each DNA extract on a 2% agarose gel to assess any degradation of DNA. The quantity of extracted genomic DNA was quantified using a Qubit 2.0 fluorometer high sensitivity kit (Life Technologies). DNA concentrations ranged between 0,06 to 20,9 ng/µL (Appendix B: Table B1). All UCE laboratory work was conducted in the Laboratories of Analytical Biology (L.A.B.) facilities of the National Museum of Natural History, Smithsonian Institution (Washington, U.S.A.).DNA was sheared to a target size of approximately 250–600 bp by sonication using a Qsonica Q800 sonicator (Qsonica LLC, Newton, CT, U.S.A.). Sheared DNA fragments were used for genomic library preparations following a modified protocol described in Faircloth et al. (2015), using a Kapa Hyper Prep Library Kit (Kapa Biosystems, Wilmington, MA, U.S.A.) and a generic SPRI substitute (Fisher et al., 2011; “speedbeads” (Faircloth et al., 2015)) for bead-based clean-up steps. We ligated dual-indexing Illumina TruSeq-style adapters (iTru i5 and i7 primers) (Faircloth and Glenn, 2012) to 15 µL DNA template during a PCR reaction consisting of 25 µL HiFi HotStart polymerase (Kapa Biosystems, Wilmington, MA, U.S.A.), 2.5 µL each of iTru i5 and i7 primers (5nM each) and 5 µL ddH20. The following thermal protocol was used: 98°C for 45 s, 13 cycles of 98°C for 15 s, 65°C for 30 s, 72°C for 60 s and final extension at 72°C for 5 min. PCR products were purified using 1.0X speedbeads and eluted with 23 mL of pH 8 elution buffer (EB; 10 mM Tris-Cl, pH 8.5; ddH2O). DNA concentration was measured using a Qubit 2.0 fluorometer. In addition, we ran 2 µL of library products on an agarose gel. We pooled libraries together at equimolar concentrations into enrichment pools, and pool concentrations were adjusted accordingly using a vacuum centrifuge.Enrichment was performed using the ‘Hymenoptera-v2-ANT-SPECIFIC’ bait set, which includes 9446 unique baits