Calculating allelic mismatch between technical replicates
We calculated the proportion of shared alleles between technical replicates for all specimens using custom scripts (see Data Accessibility) and conducted this assessment using both the probe and contig SNP datasets. We required replicates to share at least 200 biallelic SNPs (400 alleles) with no missing data and sorted allelic mismatches for a given SNP into those with different homozygous calls (two allele differences) and those related to different heterozygous/homozygous calls (one allele difference). Further, in cases of heterozygous mismatches, we identified which replicate was heterozygous and which was homozygous (e.g., supernatant vs. RADseq). The number of samples in each comparison is shown in Table 2.