Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera)

• Main Authors: Heintzman, Peter D., Elias, Scott A., Moore, Karen, Paszkiewicz, Konrad, Barnes, Ian
• Format: Dataset
• Language: unknown
• Published: 2013
• Subjects: Life sciences; medicine and health care; metagenomics; Late Pleistocene; Quaternary; Coleoptera; Insecta; shotgun sequencing; Carabidae; ancient DNA; Recent; DNA preservation; Wolbachia; museum DNA; Spiroplasma; Holocene; Amara alpina; Scandinavia; North America; Russia; Canada; Sweden; archeo; museo; permafrost
• Online Access: https://doi.org/10.5061/dryad.0179t

DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, the potential of these samples as genetic resources is currently unassessed. Here, using Sanger and Illumina shotgun sequence data, we explored DNA preservation in specimens of the ground beetle Amara alpina, from both museum and ancient environments. Nearly all museum specimens had amplifiable DNA, with the maximum amplifiable fragment length decreasing with age. Amplification of DNA was only possible in 45% of ancient specimens. Preserved mitochondrial DNA fragments were significantly longer than those of nuclear DNA in both museum and ancient specimens. Metagenomic characterisation of extracted DNA demonstrated that parasite-derived sequences, including Wolbachia and Spiroplasma, are recoverable from museum beetle specimens. Ancient DNA extracts contained beetle DNA in amounts comparable to museum specimens. Overall, our data demonstrate that there is great potential for both museum and ancient beetle specimens in future genetic studies. Reference sequences for museum-1Reference sequences for sample museum-1. Use with file 'Alignment of merged reads for museum-1'.Amara_alpina.reference_list.museum1.fastaReference sequences for museum-2Reference sequences for sample museum-2. Use with file 'Alignment of merged reads for museum-2'.Amara_alpina.reference_list.museum2.fastaReference sequences for modern-1Reference sequences for sample modern-1. Use with file 'Alignment of merged reads for modern-1'.Amara_alpina.reference_list.modern1.fastaReference sequences for modern-2Reference sequences for sample modern-2. Use with file 'Alignment of merged reads for modern-2'.Amara_alpina.reference_list.modern2.fastaReference sequences for ancient-1Reference sequences for sample ancient-1. Use with file 'Alignment of merged reads ...