MiSeq data
PCR primers for loci of interest were designed using Primer3.  Adaptors were included in the primers for a second PCR reaction to add the Illumina library sequences (ACACGACGCTCTTCCGATCT forward primer and GACGTGTGCTCTTCCGAT reverse primer).  Regions of interest were amplified via PCR and purified.  A second PCR reaction was then performed to add sample specific sequence barcodes.  PCR libraries were purified and samples run according to manufacturers instructions on an  an Illumina NextSeq 500 using a mid output 300 cycle kit.  Forward and reverse reads were merged with SeqPrep.  Reads were then demultiplexed followed by application of quality and amplicon filters.