DOI: 10.5061/dryad.0179t
title: Data from: Characterizing DNA preservation in degraded specimens of Amara alpina (Carabidae: Coleoptera)

description: 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.
description: 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 for ancient-1'.Amara_alpina.reference_list.ancient1.fastaReference sequences for ancient-2Reference sequences for sample ancient-2. Use with file 'Alignment of merged reads for ancient-2'.Amara_alpina.reference_list.ancient2.fastaPartial COI sequence for Amara alpinaExample partial sequence of the cytochrome oxidase subunit 1 (COI) gene for Amara alpinaPartial 28S sequence for Amara alpinaExample partial sequence of the 28S ribosomal RNA (28S) gene for Amara alpinaPartial ITS1 sequence for Amara alpinaExample partial sequence of the internal transcribed spacer 1 (ITS1) for Amara alpinaAlignment of merged reads for museum-1Merged reads that aligned to the reference sequences for sample museum-1. Use with file 'Reference sequences for museum-1'.Amara_alpina.merged_alignment.museum1.samAlignment of merged reads for museum-2Merged reads that aligned to the reference sequences for sample museum-2. Use with file 'Reference sequences for museum-2'.Amara_alpina.merged_alignment.museum2.samAlignment of merged reads for modern-2Merged reads that aligned to the reference sequences for sample modern-2. Use with file 'Reference sequences for modern-2'.Amara_alpina.merged_alignment.modern2.samAlignment of merged reads for modern-1Merged reads that aligned to the reference sequences for sample modern-1. Use with file 'Reference sequences for modern-1'.Amara_alpina.merged_alignment.modern1.samAlignment of merged reads for ancient-1Merged reads that aligned to the reference sequences for sample ancient-1. Use with file 'Reference sequences for ancient-1'.Amara_alpina.merged_alignment.ancient1.samAlignment of merged reads for ancient-2Merged reads that aligned to the reference sequences for sample ancient-2. Use with file 'Reference sequences for ancient-2'.Amara_alpina.merged_alignment.ancient2.samContig data for modern-1FASTA file of all contigs considered during the metagenomic analysis of sample modern-1. Use with 'BLAST assignment data for modern-1' in MEGAN v4.70.Amara_alpina.contigs.modern-1.fastaContig data for modern-2FASTA file of all contigs considered during the metagenomic analysis of sample modern-2. Use with 'BLAST assignment data for modern-2' in MEGAN v4.70.Amara_alpina.contigs.modern-2.fastaContig data for museum-1FASTA file of all contigs considered during the metagenomic analysis of sample museum-1. Use with 'BLAST assignment data for museum-1' in MEGAN v4.70.Amara_alpina.contigs.museum-1.fastaContig data for museum-2FASTA file of all contigs considered during the metagenomic analysis of sample museum-2. Use with 'BLAST assignment data for museum-2' in MEGAN v4.70.Amara_alpina.contigs.museum-2.fastaContig data for ancient-1FASTA file of all contigs considered during the metagenomic analysis of sample ancient-1. Use with 'BLAST assignment data for ancient-1' in MEGAN v4.70.Amara_alpina.contigs.ancient-1.fastaContig data for ancient-2FASTA file of all contigs considered during the metagenomic analysis of sample ancient-2. Use with 'BLAST assignment data for ancient-2' in MEGAN v4.70.Amara_alpina.contigs.ancient-2.fastaBLAST assignment data for modern-1Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample modern-1. Use with 'Contig data for modern-1' in MEGAN v4.70. See attached readme file for column headers.Amara_alpina.assignments.modern-1.BLASTBLAST assignment data for modern-2Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample modern-2. Use with 'Contig data for modern-2' in MEGAN v4.70. See attached readme file for column headers.Amara_alpina.assignments.modern-2.BLASTBLAST assignment data for museum-1Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample museum-1. Use with 'Contig data for museum-1' in MEGAN v4.70. See attached readme file for column headers.Amara_alpina.assignments.museum-1.BLASTBLAST assignment data for museum-2Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample museum-2. Use with 'Contig data for museum-2' in MEGAN v4.70. See attached readme file for column headers.Amara_alpina.assignments.museum-2.BLASTBLAST assignment data for ancient-1Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample ancient-1. Use with 'Contig data for ancient-1' in MEGAN v4.70. See attached readme file for column headers.Amara_alpina.assignments.ancient-1.BLASTBLAST assignment data for ancient-2Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample ancient-2. Use with 'Contig data for ancient-2' in MEGAN v4.70. See attached readme file for column headers.Amara_alpina.assignments.ancient-2.BLAST