Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera)
Data files
Nov 27, 2013 version files 886.16 MB
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Amara_alpina.assignments.ancient-1.BLAST
96.10 MB
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Amara_alpina.assignments.ancient-2.BLAST
113.34 MB
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Amara_alpina.assignments.modern-1.BLAST
9.69 MB
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Amara_alpina.assignments.modern-2.BLAST
33.31 MB
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Amara_alpina.assignments.museum-1.BLAST
25.34 MB
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Amara_alpina.assignments.museum-2.BLAST
17.36 MB
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Amara_alpina.contigs.ancient-1.fasta
59.22 MB
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Amara_alpina.contigs.ancient-2.fasta
50.55 MB
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Amara_alpina.contigs.modern-1.fasta
114.09 MB
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Amara_alpina.contigs.modern-2.fasta
172.35 MB
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Amara_alpina.contigs.museum-1.fasta
110.55 MB
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Amara_alpina.contigs.museum-2.fasta
63.04 MB
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Amara_alpina.merged_alignment.ancient1.sam
173.02 KB
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Amara_alpina.merged_alignment.ancient2.sam
113.90 KB
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Amara_alpina.merged_alignment.modern1.sam
5.41 MB
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Amara_alpina.merged_alignment.modern2.sam
4.83 MB
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Amara_alpina.merged_alignment.museum1.sam
6.22 MB
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Amara_alpina.merged_alignment.museum2.sam
4.14 MB
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Amara_alpina.reference_list.ancient1.fasta
54.13 KB
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Amara_alpina.reference_list.ancient2.fasta
54.13 KB
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Amara_alpina.reference_list.modern1.fasta
54.13 KB
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Amara_alpina.reference_list.modern2.fasta
54.13 KB
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Amara_alpina.reference_list.museum1.fasta
54.13 KB
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Amara_alpina.reference_list.museum2.fasta
54.14 KB
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README_for_Amara_alpina.assignments.ancient-1.txt
315 B
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README_for_Amara_alpina.assignments.ancient-2.txt
315 B
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README_for_Amara_alpina.assignments.modern-1.txt
315 B
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README_for_Amara_alpina.assignments.modern-2.txt
315 B
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README_for_Amara_alpina.assignments.museum-1.txt
315 B
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README_for_Amara_alpina.assignments.museum-2.txt
315 B
Abstract
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.