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-1
Reference sequences for sample museum-1. Use with file 'Alignment of merged reads for museum-1'.
Amara_alpina.reference_list.museum1.fasta
Reference sequences for museum-2
Reference sequences for sample museum-2. Use with file 'Alignment of merged reads for museum-2'.
Amara_alpina.reference_list.museum2.fasta
Reference sequences for modern-1
Reference sequences for sample modern-1. Use with file 'Alignment of merged reads for modern-1'.
Amara_alpina.reference_list.modern1.fasta
Reference sequences for modern-2
Reference sequences for sample modern-2. Use with file 'Alignment of merged reads for modern-2'.
Amara_alpina.reference_list.modern2.fasta
Reference sequences for ancient-1
Reference sequences for sample ancient-1. Use with file 'Alignment of merged reads for ancient-1'.
Amara_alpina.reference_list.ancient1.fasta
Reference sequences for ancient-2
Reference sequences for sample ancient-2. Use with file 'Alignment of merged reads for ancient-2'.
Amara_alpina.reference_list.ancient2.fasta
Partial COI sequence for Amara alpina
Example partial sequence of the cytochrome oxidase subunit 1 (COI) gene for Amara alpina
Partial 28S sequence for Amara alpina
Example partial sequence of the 28S ribosomal RNA (28S) gene for Amara alpina
Partial ITS1 sequence for Amara alpina
Example partial sequence of the internal transcribed spacer 1 (ITS1) for Amara alpina
Alignment of merged reads for museum-1
Merged reads that aligned to the reference sequences for sample museum-1. Use with file 'Reference sequences for museum-1'.
Amara_alpina.merged_alignment.museum1.sam
Alignment of merged reads for museum-2
Merged reads that aligned to the reference sequences for sample museum-2. Use with file 'Reference sequences for museum-2'.
Amara_alpina.merged_alignment.museum2.sam
Alignment of merged reads for modern-2
Merged reads that aligned to the reference sequences for sample modern-2. Use with file 'Reference sequences for modern-2'.
Amara_alpina.merged_alignment.modern2.sam
Alignment of merged reads for modern-1
Merged reads that aligned to the reference sequences for sample modern-1. Use with file 'Reference sequences for modern-1'.
Amara_alpina.merged_alignment.modern1.sam
Alignment of merged reads for ancient-1
Merged reads that aligned to the reference sequences for sample ancient-1. Use with file 'Reference sequences for ancient-1'.
Amara_alpina.merged_alignment.ancient1.sam
Alignment of merged reads for ancient-2
Merged reads that aligned to the reference sequences for sample ancient-2. Use with file 'Reference sequences for ancient-2'.
Amara_alpina.merged_alignment.ancient2.sam
Contig data for modern-1
FASTA 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.fasta
Contig data for modern-2
FASTA 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.fasta
Contig data for museum-1
FASTA 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.fasta
Contig data for museum-2
FASTA 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.fasta
Contig data for ancient-1
FASTA 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.fasta
Contig data for ancient-2
FASTA 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.fasta
BLAST assignment data for modern-1
Unfiltered 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.BLAST
BLAST assignment data for modern-2
Unfiltered 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.BLAST
BLAST assignment data for museum-1
Unfiltered 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.BLAST
BLAST assignment data for museum-2
Unfiltered 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.BLAST
BLAST assignment data for ancient-1
Unfiltered 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.BLAST
BLAST assignment data for ancient-2
Unfiltered 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