Genomic utility of allozyme supernatant samples
Allozyme supernatant replicates performed well across analyses and recovered similar amounts of data compared with the pellet replicates. The one exception was USNM 525251, for which the supernatant replicate recovered only 13% of SNPs, compared to 96% of SNPs for the pellet replicate and 82% of SNPs for the formalin-fixed replicate of the same sample. This replicate also received only 2x mean sequence coverage, compared to an average of 21x across the other supernatant samples, which we hypothesize was due to poor capture efficiency as the replicate had high extraction yield and low amounts of exogenous DNA.
Allozyme supernatant and tissue pellet samples had the lowest proportion of allelic differences between technical replicates (with the exception of USNM 525251). Correspondingly, these replicates clustered together in the phylogeny and PCA and generated similar estimates of nucleotide diversity. These results suggest that allozyme supernatant samples are amenable to sequence capture approaches and that data derived from them can be combined with data derived from typical frozen tissue samples without suffering many of the biases documented for formalin-fixed samples (Williams et al. 1999; Tang, 2006). Some museum collections house large series of allozyme supernatants (Table 1) that serve as valuable records of biodiversity but have not been fully leveraged in the genomic age. These collections may serve similar purposes as other hDNA samples, such as filling sampling gaps, or evaluating genomic variation through time (Wandeler, Hoeck, & Keller, 2007; Lopez, Turner, Bellis, & Lasky, 2020).