ddRADseq Marathrum from northern South America
500 ng high-molecular DNA and purified fragments with Sera-Mag SpeedBeads prior to ligation of barcoded Illumina adapters. Libraries were size selected to 415515 bp on a Pippin prep (Sage Science) using a modified protocol where pooled samples were each run in a separate lane and size selected in reference to one lane running only the R2 marker reagent. Final library amplification used Illumina indexed primers and HF-Phusion TAQ. We determined library size distributions and concentrations on an Agilent 2200 TapeStation. Samples were sent to the QB3 sequencing facility at UC Berkeley, where qPCR was performed to determine sequenceable library concentrations prior to multiplexing equimolar amounts of each library and sequencing 150 single-end reads in two lanes of an Illumina HiSeq 4000.