title: Base population, generation 0
design: We created an advanced intercross outbred population (AIP) from 37 of the 205 sequenced, wild-derived, inbred Drosophila Genetic Reference Panel (DGRP) lines. These 37 lines are minimally related (polygenic relatedness < 0.08), maximally homozygous (genome-wide heterozygosity < 5%), have the standard karyotype for all common polymorphic inversions, and are not infected with Wolbachia. The lines were first crossed in a round robin design to ensure equal representation of each genotype.   We then prepared a DNA library by pooling 173 female flies from mix of base populations at generation 0 of mass selection. Flies were flash frozen on clean CO2 pads and homogenized using TIssuelyser (Qiagen, Inc.) in lysis buffer. Genomic DNA was extracted using magnetic beads and fragmented to 300-400bp using Covaris S220. Fragmented DNA was used to produce barcoded DNA libraries using NEXTflex™ DNA Barcodes (Bioo Scientific, Inc.) with an Illumina TrueSeq compatible protocol. Libraries were quantified using Qubit dsDNA HS Kits (Life Technologies, Inc.) and Bioanalyzer (Agilent Technologies, Inc.) to calculate molarity. Libraries were then diluted to equal molarity and re-quantified, and all samples were pooled together. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM. Pooled library samples were clustered on an Illumina cBot and sequenced on two Hiseq2500 high throughput lanes using 125 bp paired-end v4 chemistry.