The utility of formalin-fixed tissues and allozyme supernatant for
population genomics and considerations for combining capture- and
RADseq-based SNP datasets
Abstract
Until recently many historical museum specimens were largely
inaccessible to genomic inquiry, but high-throughput sequencing (HTS)
approaches have allowed researchers to successfully sequence genomic DNA
from dried and fluid-preserved museum specimens. In addition to
preserved specimens, many museums contain large series of allozyme
supernatant samples but the amenability of these samples to HTS has not
yet been assessed. Here, we compared the performance of a target-capture
approach using alternative sources of genomic DNA from ten specimens of
spring salamanders (Plethodontidae: Gyrinophilus porphyriticus)
collected 1985–1990: allozyme supernatants, allozyme homogenate
pellets, and formalin-fixed tissues. We designed capture probes based on
double-digest restriction-site associated (RADseq) sequencing derived
loci from seven of the specimens and assessed the success and
consistency of capture and RADseq technical replicates. This study
design enabled direct comparisons of data quality and potential biases
among the different datasets for phylogenomic and population genomic
analyses. We found that in phylogenetic analyses, all replicates for a
given specimen clustered together, but in principal component space,
RADseq replicates did not cluster with corresponding capture-based
replicates. SNP calls were on average 18.3% different between technical
replicates, but these discrepancies were primarily due to differences in
heterozygous/homozygous SNP calls. We demonstrate that both allozyme
supernatant and formalin-fixed samples can be successfully used for
population genomic analyses and we discuss ways to identify and reduce
biases associated with combining capture and RADseq data.