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DNA Isolation Genomic DNA was isolated as described (Tsai et al., 2011). DNA was quantified using SYBR green1 dye fluorescence, and standardized.   PCR amplification of targets and library preparation We followed the methods described by Tsai et al. (Tsai et al., 2011). We used 5-base barcoded adapters so that 24 libraries with different barcodes could be pooled into one 100-base paired-read sequencing lane. The name and sequence of the adapters were adA2_nnnn: P-nnnnnAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG and adB2_nnnnn: ACACTCTTTCCCTACACGACGCTCTTCCGATCTuuuuuT, where nnnnn is the 5 nucleotide barcode, u is the complementary base, and P represents 5' phosphorylation. The expected coverage per individual was calculated as follows: lane yield/(library ratio x input DNA x pooling ratio).