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The utility of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based SNP datasets
  • +2
  • Kyle O'Connell,
  • Kevin Mulder,
  • Addison Wynn,
  • Kevin de Queiroz,
  • Rayna Bell
Kyle O'Connell
National Museum of Natural History
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Kevin Mulder
Universidade do Porto
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Addison Wynn
National Museum of Natural History
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Kevin de Queiroz
Smithsonian Institution
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Rayna Bell
California Academy of Sciences
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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.
26 Feb 2021Submitted to Molecular Ecology Resources
09 Mar 2021Submission Checks Completed
09 Mar 2021Assigned to Editor
17 Mar 2021Reviewer(s) Assigned
23 Apr 2021Review(s) Completed, Editorial Evaluation Pending
14 May 2021Editorial Decision: Revise Minor
11 Jun 2021Review(s) Completed, Editorial Evaluation Pending
11 Jun 20211st Revision Received
14 Jul 2021Editorial Decision: Accept