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. 2019 Apr 30;7:e6727. doi: 10.7717/peerj.6727

Table 2. Overview of massively parallel DNA sequencing methods applied to insect museum specimens.

Publication Taxon group Samples analyzed Sequencing approach and platform Output
Staats et al. (2013) Flies and beetles Number: three specimens;
Age: 1992–1995;
Tissue: one to three legs, thorax, whole specimen (destructive protocol)		 Shotgun whole genome skimming;
Illumina HiSeq™ 2000		 Read depth: 3.5×–146.1× (mt genome);
% Mapping: 0.002–0.82 (mt genome);
Contamination: one specimen extensive bacteriophage & fungal DNA
Tin, Economo & Mikheyev (2014) Flies and ants Number: 11 specimens;
Age: 1910–1976;
Tissue: whole specimen (non-destructive protocol)		 Shotgun whole genome skimming;
RAD-tag;
Illumina MiSeq™ & HiSeq™ 2500		 Read depth: 0.08×–1.0× (whole genome);
% Mapping: 19–76 (whole genome);
Contamination: not reported
Heintzman et al. (2014) Beetles Number: four specimens;
Age: Late Pleistocene (C14), 1875–1950 (museum);
Tissue: one hind leg, pronotum, elytron (destructive protocol)		 Shotgun whole genome skimming;
Illumina HiSeq™ 2000		 Reads aligned to reference: 0.009%–0.225× (mt genome & five nuclear loci);
% Insect contigs: 0.25–46.5;
Contamination: up to ca. 20% mammalian sequences in contigs
Maddison & Cooper (2014) Beetles Number: one specimen;
Age: 1968;
Tissue: whole specimen (non-destructive protocol)		 Shotgun whole genome skimming;
Illumina HiSeq™ 2000		 Read depth: not reported (eight gene targets);
% Gene length coverage: 95–100 (eight gene targets);
Contamination: not reported
Kanda et al. (2015) Beetles Number: 13 specimens;
Age: 1929–2010;
Tissue: whole specimen (non-destructive protocol)		 Shotgun whole genome skimming;
Illumina HiSeq™ 2000 (two lanes)		 Read depth: 0.44×–4.64× (67 gene targets);
N50: 280–700 (67 gene targets);
Contamination: possible in some specimens but not quantified
Timmermans et al. (2016) Butterflies Number: 35 specimens;
Age: 1980–2005;
Tissue: one leg (destructive protocol)		 Shotgun whole genome skimming;
Illumina MiSeq™ (1/3 flow cell)		 % Coverage: 0–100 (mt coding loci);
Contamination: not reported;
Failure rate: four out of 35 specimens any reads matching mt genomes
Suchan et al. (2016) Butterflies and grasshoppers Number: 60 specimens;
Age: 1908–1997;
Tissue: legs (destructive protocol)		 Target capture of RAD probes;
Illumina MiSeq™ & HiSeq™ (one lane each)		 Median depth: 10× (for each SNP);
% Matrix fullness: 52–72.5 (RAD loci);
Contamination: ca. 9% of contigs were of exogenous origin
Blaimer et al. (2016) Carpenter bees Number: 51 specimens;
Age: 1894–2013;
Tissue: one leg (destructive protocol)		 Target capture of Hymenopteran UCEs;
Illumina MiSeq™		 Average coverage: 7.4×–182.4× (UCE loci);
Recovered loci: 6–972 (UCE per sample);
Contamination: not reported
Pitteloud et al. (2017) Butterflies Number: 32 specimens;
Age: 1929–2012;
Tissue: legs (destructive protocol)		 PCR Multiplex & Shotgun sequencing;
Illumina MiSeq™		 Length sequences (bp): 109–7,297 (mt and rDNA loci);
Contamination: not reported

Note:

This is a selection of studies covering a variety of taxonomic groups, sampling strategies and sequencing approaches.