DOI: 10.5061/dryad.31g05
title: Data from: Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA

description: Despite advances that allow DNA sequencing of old museum specimens,
 sequencing small-bodied, historical specimens can be challenging and
 unreliable as many contain only small amounts of fragmented DNA.
 Dependable methods to sequence such specimens are especially critical if
 the specimens are unique. We attempt to sequence small-bodied (3–6 mm)
 historical specimens (including nomenclatural types) of beetles that have
 been housed, dried, in museums for 58–159 years, and for which few or no
 suitable replacement specimens exist. To better understand ideal
 approaches of sample preparation and produce preparation guidelines, we
 compared different library preparation protocols using low amounts of
 input DNA (1–10 ng). We also explored low-cost optimizations designed to
 improve library preparation efficiency and sequencing success of
 historical specimens with minimal DNA, such as enzymatic repair of DNA. We
 report successful sample preparation and sequencing for all historical
 specimens despite our low-input DNA approach. We provide a list of
 guidelines related to DNA repair, bead handling, reducing adapter dimers,
 and library amplification. We present these guidelines to facilitate more
 economical use of valuable DNA, and enable more consistent results in
 projects that aim to sequence challenging, irreplaceable historical
 specimens.
description: breveGroupContextAnalysesThe NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the breve species group (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.LionephaContextAnalysesThe NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the genus Lionepha (Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.obscuripenneGroupContextAnalysesThe NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the obscuripenne species group (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.TrepanedorisContextAnalysesThe NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in subgenus Trepanedoris (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.NotaphusContextAnalysesThe NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in subgenus Notaphus (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.DNA3890 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s018-indexD712-D502-AGCGATAG-GCCTCTAT-LIB0206_S18_L006_R1_001 (paired) trimmed (paired) contig list.fasDNA3782 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane5-index05-ACAGTG-3782_ACAGTG_L005_R1_001 (paired) trimmed (paired) contig list.fasDNA4233 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s001-indexD705-D505-ATTCAGAA-CTTCGCCT-LIB0120_S1_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0217 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane2-s096-indexD711-D504-TCTCGCGC-TCAGAGCC-LIB0217_S96_L002_R1_001 (paired)-1 trimmed (paired) trimmed (paired) contig list.fasLIB0216 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane2-s095-indexD710-D505-TCCGCGAA-CTTCGCCT-LIB0216_S95_L002_R1_001 (paired)-1 trimmed (paired) trimmed (paired) contig list.fasLIB0213 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane1-s009-indexD706-D504-GAATTCGT-TCAGAGCC-LIB0213_S9_L001_R1_001 (paired) trimmed (paired) contig list.fasLIB0179 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane1-s002-indexD707-D504-CTGAAGCT-TCAGAGCC-LIB0179_S2_L001_R1_001 (paired) trimmed (paired) contig list.fasLIB0178 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s857-indexD706-D506-GAATTCGT-TAAGATTA-LIB0178_S857_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0182 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane1-s003-indexD711-D506-TCTCGCGC-TAAGATTA-LIB0182_S3_L001_R1_001 (paired) trimmed (paired) contig list.fasLIB0171 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s854-indexD710-D504-TCCGCGAA-TCAGAGCC-LIB0171_S854_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0175 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s855-indexD702-D508-TCCGGAGA-GTCAGTAC-LIB0175_S855_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0154 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s851-indexD708-D502-TAATGCGC-GCCTCTAT-LIB0154_S851_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0153 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s850-indexD704-D508-GAGATTCC-GTCAGTAC-LIB0153_S850_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0184 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s859-indexD707-D505-CTGAAGCT-CTTCGCCT-LIB0184_S859_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0147 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s840-indexD705-D506-ATTCAGAA-TAAGATTA-LIB0147_S840_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0157 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s853-indexD702-D506-TCCGGAGA-TAAGATTA-LIB0157_S853_L007_R1_001 (paired) trimmed (orphans) contig list.fasLIB0177 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s856-indexD705-D502-ATTCAGAA-GCCTCTAT-LIB0177_S856_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0181 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s858-indexD710-D503-TCCGCGAA-AGGATAGG-LIB0181_S858_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0210 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane1-s006-indexD708-D501-TAATGCGC-AGGCTATA-LIB0210_S6_L001_R1_001 (paired) trimmed (paired) contig list.fasLIB0180 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s847-indexD708-D505-TAATGCGC-CTTCGCCT-LIB0180_S847_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0183 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s848-indexD712-D501-AGCGATAG-AGGCTATA-LIB0183_S848_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0176 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s009-indexD704-D502-GAGATTCC-GCCTCTAT-LIB0176_S9_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0155 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane7-s852-indexD705-D503-ATTCAGAA-AGGATAGG-LIB0155_S852_L007_R1_001 (paired) trimmed (paired) contig list.fasLIB0164 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s843-indexD703-D508-CGCTCATT-GTCAGTAC-LIB0164_S843_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0168 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s845-indexD709-D502-CGGCTATG-GCCTCTAT-LIB0168_S845_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0167 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s844-indexD706-D501-GAATTCGT-AGGCTATA-LIB0167_S844_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0173 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s846-indexD707-D503-CTGAAGCT-AGGATAGG-LIB0173_S846_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0149 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s841-indexD701-D503-ATTACTCG-AGGATAGG-LIB0149_S841_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0186 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane1-s004-indexD704-D507-GAGATTCC-ACGTCCTG-LIB0186_S4_L001_R1_001 (paired) trimmed (paired) contig list.fasLIB0185 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s849-indexD706-D504-GAATTCGT-TCAGAGCC-LIB0185_S849_L006_R1_001 (paired) trimmed (paired) contig list.fasLIB0150 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane6-s842-indexD702-D504-TCCGGAGA-TCAGAGCC-LIB0150_S842_L006_R1_001 (paired) trimmed (paired) contig list.fasDNA3205 de novo assemblyList of contigs generated from the de novo assembly in CLC Genomics Workbenchlane4_NoIndex_L004_R1_001 (paired) trimmed (paired) contig list.fas