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).