Supplemental Material for Fritz et al., 2020

Figures S1 and S2 contain the permutation test resampling distributions used to identify statistically significant differences between nucleotide diversity estimates for amplicons of cad-86C 1b and 2b primer pairs. Figure S3 is a gel image showing the 5,539 bp cad-86C cDNA amplicons from the H. zea larval midguts. Table S1 contains the cad-86C 1b and 2b primer sequences. Table S2 contains the qRT-PCR primers for cad-86C and the α-Tubulin control. Table S3 contains the barcodes used for identification of cad-86C sequences from each individual. Table S4 contains a summary of the number of Illumina reads produced per individual, that remained after filtering, and coverage depth. Table S5 contains a summary of the genomic regions with low heterozygosity in GA-R and high genetic divergence between GA and GA-R. Table S6 contains a percent identity matrix for the H. zea CAD-86C with other cadherin proteins known to be involved in Bt resistance. Table S7 contains a summary of the PacBio sequencing reads produced for each H. zea individual, and the number of reads remaining after filtering. Table S8 contains haplotype frequency information for cad-86C cDNA sequences. File S1 describes the methods used to run msms. File S2 contains our ExoAP clean protocol. File S3 contains the cadherin sequences used for phylogenetic analysis. File S4 shows the cadherin protein sequences aligned by T-Coffee.