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MOLECULARECOLOGY RESOURCES VOLUME 14, NUMBER 3, MAY 2014
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MOLECULARECOLOGYRESOURCES
VOLUME 14NUMBER 3
MAY2014
ISSN 1755-098X
Published by Wiley Blackwell
men_14_3_oc_Layout 1 4/3/2014 9:54 AM Page 1
Characterizing DNA preservation in degraded specimens ofAmara alpina (Carabidae: Coleoptera)
PETER D. HEINTZMAN,*1 SCOTT A. ELIAS,† KAREN MOORE,‡ KONRAD PASZKIEWICZ‡ and
IAN BARNES*2
*School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK, †Department of Geography, Royal
Holloway University of London, Egham, TW20 0EX, UK, ‡Exeter Sequencing Service, Biosciences, College of Life &
Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
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. Metage-
nomic characterization 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 specimens of beetles in future genetic studies, and we see no reason why this would not be
the case for other orders of insect.
Keywords: ancient DNA, Coleoptera, DNA preservation, metagenomics, museum DNA, shotgun sequencing
Received 20 August 2013; revision received 15 November 2013; accepted 19 November 2013
Introduction
The beetles (Insecta: Coleoptera) are the most speciose
insect order (40%; >350 000 species) (Gullan & Cranston
2010) and are found in nearly all terrestrial ecosystems,
fulfilling a great variety of niches (Grove & Stork 2000;
New 2007). They are therefore a major focus of biological
investigation, in which a genetic approach is often
required. To conduct genetic studies, specimens need to
be collected. However, due to the inhospitable nature of
some regions, such as the arctic, there may be limited
access and opportunity for collecting fresh specimens.
Due to more than two centuries of collection effort,
hundreds of millions of insect specimens have been
deposited in museum collections (Arino 2010), thereby
reducing the need to sample directly from difficult
regions (Schaefer et al. 2009). In addition, these speci-
mens can add a temporal perspective, on a decadal to
centennial timescale (Rowe et al. 2011), to genetic studies
(Harper et al. 2006; Hartley et al. 2006). However, DNA
from museum specimens is highly degraded (Wandeler
et al. 2007), which has no doubt dissuaded researchers
from utilizing them. Previous genetic studies have gener-
ally been small in scale and limited in scope, with no
standardized data that characterize the DNA present in
these remains (Goldstein & Desalle 2003; Gilbert et al.
2007a; Thomsen et al. 2009; Castalanelli et al. 2010; Gib-
son et al. 2012). A large-scale assessment of the propor-
tion and preservation of endogenous DNA is therefore
required. This would inform researchers keen to exploit
these genetic resources, as well as museum curators who
may be concerned about potentially destructive genetic
analyses (Mandrioli 2008).
Ancient beetle specimens, which are routinely recov-
ered from permafrost and other environments (Elias
Correspondence: Peter D. Heintzman, Fax: 1-831-459-5353;
E-mail: [email protected] Present address: Department of Ecology and Evolutionary
Biology, University of California, Santa Cruz, 1156 High Street,
Santa Cruz, CA 95064, USA2Present address: Earth Sciences Department, Natural History
Museum, Cromwell Road, London, SW7 5BD, UK
© 2013 John Wiley & Sons Ltd
Molecular Ecology Resources (2014) 14, 606–615 doi: 10.1111/1755-0998.12205
2010), are also potential genetic resources that have the
capacity to further extend the temporal aspect of beetle
DNA studies to millennial timescales. Recent proof of
concept studies has demonstrated the presence of beetle
ancient (a)DNA from a variety of environments and ages
(Reiss 2006; Willerslev et al. 2007; King et al. 2009; Thom-
sen et al. 2009), with permafrost considered to have the
greatest potential (Reiss 2006). The next step in beetle
aDNA research is to characterize the DNA present in
permafrost-preserved remains, which would assess their
potential as a future genetic resource.
The aim of this study therefore was to characterize
DNA preservation in beetle remains from both museum
and ancient environments. In characterizing DNA pres-
ervation from these two environments, we wished to
estimate the potential for recovery of DNA from very
small samples, overall success rate of PCR amplification,
retrievable fragment length using both PCR and Illumina
shotgun sequencing, as well as using the latter to exam-
ine the extent and nature of contamination, and potential
recovery of the metagenome. Altogether, these data
provide an overview of DNA preservation in both dry-
stored museum and ancient permafrost-preserved beetle
remains. Amara alpina (Carabidae: Coleoptera) was
selected as the study taxon, as it is well represented in
permafrost deposits, especially those of Beringia (Elias
et al. 2000) from which aDNA of a multitude of taxa has
been recovered (Shapiro & Cooper 2003) and is well
represented in the museum collections of Europe and
North America. Additionally, A. alpina is the most
cold-adapted ground beetle (Bennike et al. 2000) and is
important for palaeoclimatic and palaeoenvironmental
reconstruction (Elias 2010).
Materials and methods
Specimen provenance, age and collection
Specimens were divided into three age classes: modern
(<10 years old), museum (dry-stored collections;
>10 years old) and ancient (permafrost deposits). All
specimens, including age and provenance, are listed in
Table S1 (Supporting information). Modern specimens
(n = 6) were collected from four Beringian (Chukotka,
Alaska, Yukon) localities between 2002 and 2004.
Museum specimens (n = 133), which had either been
pinned or glued to a card mount, were gathered from
the Canadian National Collection of Insects, Arachnids
and Nematodes (CNC) in April 2010 and the Swedish
Museum of Natural History (NRM) in May 2011. These
specimens were originally collected between 9 and
136 years before DNA extraction was conducted and
originated from 89 localities in Scandinavia (n = 28),
Russia (n = 29) and North America (n = 76). A single
hind leg (including femur, tibia, tarsi), which is not
informative for morphological identification, was
removed for each analysis.
Ancient specimens (n = 148), consisting of complete
or broken isolated sclerites, were collected from 15 Berin-
gian sites between 2003 and 2006 (Table S2, Supporting
information). Specimens ranged in age from >560 000 to
5900 calendar years old, based on either radiocarbon
dating of associated plant remains, relative tephra dating
of layers above or below beetle-bearing sediments, or
through rough stratigraphic correlation. Specimens were
isolated from the sediment and stored at room tempera-
ture (Elias 1994). Prior to DNA extraction, ancient speci-
mens were stored at �20 °C to reduce further
degradation (Reiss 2006).
DNA extraction
Degraded specimens (museum, ancient) were extracted,
and PCR reactions were prepared, following standard-
ized aDNA handling protocols (Cooper & Poinar 2000;
Hofreiter et al. 2001; Gilbert et al. 2005; Wandeler et al.
2007). These included using sterile, dedicated ancient
DNA laboratories (Royal Holloway, NRM) and conduct-
ing independent replication (Data S1, Supporting infor-
mation). DNA was extracted using the QIAamp DNA
Micro kit (Qiagen), with a modified version of the tissues
protocol. This included using carrier RNA and conduct-
ing the final eluting step twice (50 lL each). Overnight
lysis was conducted for 16 to 20 hours. Tween-20 was
added to DNA extracts (final concentration of 0.05%) to
prevent DNA adhering to the plastic tube surface (Fau-
lds et al. 2004). Extraction controls were used in a ratio of
one control to five samples. Specimens were not disinte-
grated prior to extraction as initial investigation indi-
cated that this did not affect the DNA recovery
likelihood. Modern DNA was extracted by Mack (2008)
using the same method, with the exception that complete
specimens were digested instead of a single hind leg
[following Gilbert et al. (2007a)]. Two specimens (one
modern, one ancient) were extracted in a previously
published study (Thomsen et al. 2009).
PCR and Sanger sequencing
Three markers were targeted: mitochondrial COI, and
multicopy nuclear 28S and ITS1. Novel overlapping
species-specific primer sets were designed using Oligo
v6.8 (Rychlik & Rychlik 2005). Primer design templates
were based on data from Gilbert et al. (2007a), Mack
(2008), Thomsen et al. (2009) and GenBank. PCR ampli-
fication conditions, primer sequences, sets and anneal-
ing temperatures are listed in Data S1 and Table S3
(Supporting information). Purification and sequencing
© 2013 John Wiley & Sons Ltd
DNA PRESERVATION IN DEGRADED BEETLE SPECIMENS 607
of PCR products followed Brace et al. (2012). Sequencing
was also conducted at the NRM using an ABI 3100
genetic analyser and BigDye Terminator chemistry
(v1.1). Sequence data were quality-checked manually in
Sequencher v4.7 (Gene Codes) and compared against the
Basic Local Alignment Search Tool (BLAST) database
and A. alpina reference sequences (GenBank: KF695187-
KF695189) to ensure that the correct target had been
amplified. To detect any potential cross-sample contami-
nation, sequence data from overlapping fragments were
compared for each specimen. Due to the small sample
size of the modern data set, data from modern and
museum specimens were combined and are hereafter
referred to as museum. All stated fragment lengths
include primer sequence.
Specimens were considered to yield mitochondrial
(mt)DNA or nuclear (nu)DNA if one or more fragments
were recovered for each data type. All specimens that
failed to yield any DNA were tested with a minimum of
three or two primer sets for mtDNA and nuDNA,
respectively. The use of species-specific primers could
impede amplification if specimens had been taxonomi-
cally misidentified prior to PCR, leading to DNA recov-
ery rates being underestimated. Therefore, to assess
primer set specificity, primers were also tested on a spec-
imen from a congeneric species (A. glacialis). One ancient
specimen that yielded mtDNA was excluded from the
analysis of DNA recovery rates, due to extract exhaus-
tion prior to testing for the presence of nuDNA.
All mtDNA PCR products were sequence verified as
A. alpina. A total of 142 nuDNA PCR products were
sequenced, with at least one nuDNA fragment being
sequence verified from 71 of the 187 specimens reported
to have yielded nuDNA (museum: 45/136, ancient: 26/
51).
Amplification success was defined as the number of
mtDNA (COI) fragments recovered from eight overlap-
ping PCR primer sets, which had products of between
124 and 196 bp. Different combinations of these primers,
which amplified longer fragments (287 to 514 bp), were
tested on the museum specimens (Table S3, Supporting
information). A combination that would have amplified
four overlapping fragments was treated as four frag-
ments retrieved. For museum specimens, age was deter-
mined using either the collection date or other data
(e.g. specimen collected on the same collecting trip as a
specimen with an explicit collection date) stated on the
specimen label (Table S1, Supporting information).
Dated museum specimens were binned into 50-year time
intervals. Ancient specimens were binned into twenty
thousand year (ka) time intervals with age determined
by calibrated dates (Table S2, Supporting information).
Specimens binned as >60 ka ranged in age from >100 to
>560 ka. To assess whether older specimens yielded
fewer DNA fragments, two-tailed Kruskal–Wallis tests
were employed in SPSS v19. Specimens that were
undated or imprecisely dated (e.g. Late Pleistocene,
‘LP’), as well as museum specimens that did not yield
mtDNA, were excluded from Kruskal–Wallis tests.
To assess the longest amplifiable mtDNA fragment,
museum specimens were initially tested for a 446 bp
fragment. Successfully amplified specimens were tested
for longer fragments and those that failed to amplify a
product were tested for sequentially shorter fragments.
A linear regression was performed in SPSS to test for a
relationship between the longest amplifiable fragment
and age. The specimens excluded from the Kruskal–Wal-
lis tests were also excluded from the regression analysis.
Illumina library preparation, shotgun sequencing andanalysis
Six samples (two from each age class), with excellent
DNA recovery based on Sanger sequencing, were used
for shotgun sequencing (Table S1, Supporting informa-
tion). DNA libraries were constructed using a modified
version of the Meyer & Kircher (2010) protocol, without
the initial DNA fragmentation step, and using QIAquick
spin columns (Qiagen) for all purification steps. These
modifications are listed in Data S1, Supporting informa-
tion. Amplified and indexed libraries were quantified
using a spectrophotometer and gel electrophoresis.
These were then diluted to equimolar concentrations,
pooled and sequenced on the Illumina HiSeq-2000
platform at the Exeter Sequencing Facility, using a
single lane of 2 9 100 cycles on a paired-end flow cell,
following the manufacturer’s instructions.
Raw HiSeq data were filtered to remove poor-quality
reads and sequencing artefacts using the standard (Blan-
kenberg et al. 2010) and FASTX toolkits (all v1.0.0 unless
otherwise stated), respectively, on the Galaxy server
(Goecks et al. 2010). Reads were binned by sample using
the FASTX Barcode Splitter, with a single base mismatch
permitted. For each data set, forward and reverse reads
were merged using SeqPrep, which combined the two
reads if overlap was detected and removed adapter
sequence. SeqPrep output consisted of the merged and
remaining unmerged reads, with between 87.2 and
99.7% of filtered reads being successfully merged. A
detailed methodology and pipeline of shotgun data qual-
ity control is available in Data S1 and Fig. S1 (Supporting
information).
To characterize the fragment length distribution of
endogenous DNA from A. alpina, merged reads were
aligned to 15 short reference sequences using Bowtie2
(Langmead & Salzberg 2012). These references included
eight mtDNA (658 to 16823 bp) and seven nuDNA (183
to 1043 bp) sequences that were either downloaded from
© 2013 John Wiley & Sons Ltd
608 P . D . HEINTZMAN ET AL .
GenBank or originated from the Sanger data of this study
(Table S4, Supporting information). At least one repre-
sentative sequence was chosen for each locus available
for Amara, as well as the three available carabid mitoge-
nomes (as of 14/09/2012). A reference genome was not
used here, as the two available Coleoptera genomes
belong to taxa [Tribolium castaneum, Dendroctonus ponder-
osae (Richards et al. 2008; Keeling et al. 2013)] that
diverged from A. alpina more than 250 million years ago
(McKenna & Farrell 2009) and were therefore deemed
insufficiently similar to act as reference sequences.
Duplicate sequences were not removed from BAM files,
due to biases observed during duplicate removal (Data
S2 and Table S5, Supporting information). To ensure the
reasonable assignment of reads to reference sequences,
BAM files were indexed and visually inspected using
Tablet v1.12.09.03 (Milne et al. 2010). Fragment length
information was extracted from aligned reads in the
BAM files and pooled into two categories for each sam-
ple (mtDNA and nuDNA). Distributions were plotted
using a five-point centred moving average to smooth
length distributions. Descriptive statistics were calcu-
lated, and comparisons of fragment length distributions
between DNA categories were performed using t-tests in
SPSS. Appropriate t-statistics were selected using the
results of Levene’s test for equality of variances.
To assess the metagenome of degraded specimens,
merged and remaining unmerged read files were concat-
enated, and the ‘Collapse’ tool in Galaxy was used to
remove PCR duplicates. Reads were assembled into con-
tigs using a de novo assembly tool (clc_novo_assemble) in
the CLC assembly cell v4.0.6-beta, with the minimum
contig size set to 40 bp. Contigs were produced in this
way to increase the likelihood of robust taxonomic
assignment (Prufer et al. 2010) and to further collapse
PCR duplicates. Contig sequences were identified taxo-
nomically using BLAST v2.2.25 (database downloaded
on 23/08/2012 and gi_taxid_nucl.bin downloaded on
03/09/2012). Resulting taxonomic assignments were
visualized in MEGAN v4.70.3 (Huson et al. 2011), with
parameters set to minScore = 50, minComplexity = 0.44,
topPercent = 10, winScore = 0 and minSupport = 5.
These parameters ensured that contigs with low-quality
BLAST hits were excluded. Taxonomic information for
each of the specimens was combined, normalized and
collapsed to the rank of Class where possible. The twelve
most abundant classes were scrutinized further by
assessing the major composite genera, which each
comprised >2% of the identifiable contigs across all
specimens.
Results and discussion
DNA recovery rate
Nearly, all museum specimens (96%) yielded both
mtDNA and nuDNA (Table 1). Previous dry-stored
museum beetle DNA studies have reported a 46 to 100%
recovery rate (Goldstein & Desalle 2003; Gilbert et al.
2007a; Thomsen et al. 2009), which demonstrates the rela-
tive effectiveness of the methods employed here. The
three specimens that did not yield DNA were all from
the CNC, collected from the same locality, in the same
year, by the same collector and represent all the tested
specimens from this locality. We speculate that DNA-
degrading substances, such as ethyl acetate, may have
been used to kill and/or temporarily store these speci-
mens (Reiss et al. 1995; Dillon et al. 1996; Gilbert et al.
2007a).
In ancient specimens, 26% yielded both mtDNA and
nuDNA, whereas 54% yielded neither, and ~10% yielded
either mtDNA or nuDNA only (Table 1). This is the first
reported recovery of nuDNA from a permafrost-pre-
served invertebrate and the second report of mtDNA
recovered from permafrost-preserved invertebrate ma-
crofossils [following Thomsen et al. (2009)]. MtDNA and
nuDNA were recovered from localities aged up to 55 000
and 41 000 radiocarbon years before present, respec-
tively, which represents the oldest ancient invertebrate
DNA recovered from macrofossils for both DNA types
(King et al. 2009; Thomsen et al. 2009). These recovery
rates are low compared with recovery rates from perma-
frost-preserved bone, which range between 22 and 80%
(Barnes et al. 2002, 2007; Shapiro et al. 2004; Campos et al.
2010a,b). This may be due to the very small size of beetle
sclerites (<0.5 mg), which are two to three orders of
Table 1 The recovery rates of mitochondrial and nuclear DNA from museum and ancient specimens of A. alpina
Age class N mt+nu Prop. (%) mt Prop. (%) nu Prop. (%) None Prop. (%)
Museum 139 134 96.40 0 0.00 2 1.44 3 2.16
Ancient 148* 38 25.85 16 10.88 13 8.84 80 54.42
All 287 172 59.93 16 5.57 15 5.23 83 28.92
mt+nu, mitochondrial and nuclear DNA recovered; mt, mitochondrial DNA only; nu, nuclear DNA only; none, no endogenous DNA;
N, quantity.
*One specimen was excluded from DNA recovery calculations.
© 2013 John Wiley & Sons Ltd
DNA PRESERVATION IN DEGRADED BEETLE SPECIMENS 609
magnitude smaller than the material used in bone-based
studies (Barnes et al. 2002, 2007; Shapiro et al. 2004; Cam-
pos et al. 2010a,b), therefore resulting in fewer template
molecules available for amplification. In addition, bones
are often ground into a fine powder to increase the DNA
yield. However, due to the potential loss of specimen
material, this was not conducted here. Alternatively,
thermal age analysis indicates that aDNA preservation
may be an order of magnitude poorer in beetle remains
when compared to bone (King et al. 2009), which may be
due to apatite reducing the fragmentation rate of DNA
in bone (Lindahl 1993).
Misidentification was not detected in ancient speci-
mens that yielded DNA (n = 68). It is unlikely that spe-
cies-specific primer sets would have prevented any
potentially misidentified specimens from yielding DNA,
as primer sets were also successfully tested on a conge-
neric species (A. glacialis). Therefore, the assertion made
by Quaternary entomologists that even single broken
sclerites can be reliably identified (Coope 2004; Elias
2010) is supported by the genetic data.
DNA preservation by age
All mtDNA fragments were successfully amplified from
80.6% of museum specimens, whereas 3.6% yielded none
(Fig. 1a). The five specimens that did not yield mtDNA
were two of the oldest specimens from the NRM and the
three CNC specimens that did not yield any DNA. The
15.8% of specimens that amplified one to seven
fragments were almost exclusively >100 years old. The
relationship between museum specimen age and amplifi-
cation success was highly significant (two-tailed
Kruskal–Wallis test: v2 = 58.995, d.f. = 2, P < 0.001). This
may indicate that the concentration of amplifiable DNA
decreases with age, due to the continuing occurrence of
strand breaks or other forms of damage (Lindahl 1993),
or the accumulation of interstrand cross-links through
time reducing amplification opportunity (Hansen et al.
2006). Decreasing amplification success with specimen
age has also been observed in other museum beetles (Gil-
bert et al. 2007a; Thomsen et al. 2009; Gibson et al. 2012),
as well as other insect orders (Watts et al. 2007; Strange
et al. 2009; van Houdt et al. 2010; Ugelvig et al. 2011;
Andersen & Mills 2012).
In the 37% of ancient A. alpina specimens that yielded
mtDNA, the majority of specimens yielded either one to
two fragments (16%) or seven to eight (15%; Fig. 1b). The
observation that around 15% of specimens yielded all, or
nearly all, of the mtDNA fragments tested demonstrates
the potential of ancient specimens for future PCR-based
studies. In contrast to the museum specimens, there was
a weak, but nonsignificant relationship between ancient
specimen age and the number of amplifiable fragments
(two-tailed Kruskal–Wallis test: v2 = 7.042, d.f. = 3,
P = 0.071). The ancient specimens originated from geo-
graphically widespread localities and could have there-
fore been subjected to differing preservation conditions,
which may explain the lack of a significant relationship
between age and amplification success. However, it
should be noted that specimens of >60 ka all failed to
yield aDNA, but the sample size of these specimens was
small (n = 5). Reduced amplification success with
increasing specimen age in nonfrozen sediment-
preserved beetles has been observed elsewhere (King
et al. 2009).
Age is a highly significant predictor of the longest
amplifiable fragment (Fig. 1c) (linear regression:
R2 = 0.441, F = 98.612, d.f. = 1.125, P < 0.001). This sug-
gests that strand breaks and/or interstrand cross-links
are still occurring for decades after the specimen has
been desiccated and stored. However, the regression
Fragments retrieved876543210
Spec
imen
s (%
)
80
60
40
20
0
Fragments retrieved876543210
Spec
imen
s (%
) 60
40
20
0
Collection year1990195019101870
Long
est f
ragm
ent (
bps) 600
400
200
0
(a) (b) (c)
Fig. 1 Amplification success of mitochondrial DNA from (a) museum and (b) ancient specimens of A. alpina based on the number of
amplifiable fragments, and (c) the longest amplifiable fragment retrieved from museum specimens by collection year. Colours indicate
specimen age: (a) collection year, blue: 1951–2004; red: 1901–1950; off-white: 1851–1900; green: no date, and (b) calibrated age, red:
1–20 ka; orange: 21–40 ka; green: 41–60 ka; blue: >61 ka; grey: no date. In (c), the trend line equation is y = 1.946x � 3410.417, and the
dotted lines illustrate 95% confidence intervals.
© 2013 John Wiley & Sons Ltd
610 P . D . HEINTZMAN ET AL .
analysis may have been affected by several limitations in
the data set, including potential differences in efficiency
between primer sets and the noncontinuous nature of
the fragment lengths targeted. Comparable relationships
between age and maximum retrievable fragment length
have been shown in specimens of other insect orders
(Strange et al. 2009; Ugelvig et al. 2011). Intriguingly,
these studies targeted microsatellites, suggesting that
this observation may be applicable to mtDNA and
nuDNA, as well as a variety of different insect orders.
The regression analysis suggests that shorter mtDNA
fragments, of length viable for both PCR and next-gener-
ation sequencing-based approaches (70 bp), may be
retrievable from museum specimens of late 18th century
age. This is earlier than the oldest recovered museum
insect mtDNA (1820) (Thomsen et al. 2009) and encom-
passes the vast majority of entomological specimens
housed in collections, indicating their potential utility as
genetic resources.
Fragment length distributions
A total of 43.3 million paired-end reads were obtained
from the HiSeq run, of which 38 million passed quality
control measures and were assigned to a sample. 64 424
reads (0.17% of filtered reads) were identified as originat-
ing from A. alpina (Table S5, Supporting information).
However, due to the use of short reference sequences,
these reads represent a tiny fraction of the total number
of reads that originated from A. alpina.
The length distributions of the identified reads indi-
cate that nuDNA mean fragment length (79 to 109 bp) is
significantly shorter than mtDNA (61 to 101 bp; Fig. 2;
t-tests: P < 0.001; Table S6, Supporting information).
These length distributions and mean length values are
similar between all samples and comparable to other
museum and ancient DNA data sets (Gilbert et al. 2007b,
2008; Miller et al. 2009; Rasmussen et al. 2011; Kircher
2012). The disparity between mtDNA and nuDNA mean
fragment length is in agreement with recent studies of
vertebrates from permafrost and sediment deposits (Sch-
warz et al. 2009; Allentoft et al. 2012), which suggest that
nuDNA degrades at a faster rate than mtDNA. This may
be due to the circular configuration of mtDNA making it
less accessible to exonucleases (Allentoft et al. 2012), the
double membrane of the mitochondrion offering addi-
tional protection (Schwarz et al. 2009) or the interaction
of nuDNA and histones facilitating strand breaks
(Binladen et al. 2006).
Metagenomic analysis
Contigs from modern and museum samples ranged in
length from 40 to 7935 bp, with N50 values of between
125 and 184 bp, of which 0.4 to 0.5% could be taxonomi-
cally identified (Table S7, Supporting information). The
taxonomic profiles of these samples are comparable
(Fig. 3), even considering the large age range of these
samples (9 to 138 years) and their independent storage
histories in separate museums (Table S1, Supporting
information). This suggests that the museum metage-
nome of historical dried beetle, and perhaps insect, speci-
mens may be fairly consistent, regardless of age or
storage collection.
0
0.01
0.02
0 50 100 150
0
0.01
0.02
Modern-1 Ancient-1Museum-1
Modern-2 Museum-2 Ancient-2
200Frag. length (bps)
Frag. length (bps)200150100500
Prop
. of r
eads
Prop
. of r
eads
Frag. length (bps)200150100500
Prop
. of r
eads
0.01
0
0.02
Frag. length (bps)200150100500
Prop
. of r
eads
0.01
0
0.02
0.03
Frag. length (bps)200150100500
Prop
. of r
eads
0
0.02
0.04
Frag. length (bps)200150100500
Prop
. of r
eads
0
0.02
0.04
Fig. 2 Fragment length distributions of DNA from three age classes (modern, museum, ancient) of A. alpina. The proportion of reads is
the number of reads for a given fragment length divided by the total number of reads in that sample. Fitted lines are based on a five-
point centred moving average. Solid line: nuclear DNA, dotted line: mitochondrial DNA.
© 2013 John Wiley & Sons Ltd
DNA PRESERVATION IN DEGRADED BEETLE SPECIMENS 611
The Insecta made up 38 to 49% of identifiable contigs
(Fig. 3; Table S7, Supporting information), which were
classified as belonging to model species in the Lepidop-
tera, Hymenoptera, Diptera, Hemiptera and Coleoptera
(Table S8, Supporting information). These model insects
have their nuclear genomes in the BLAST database and
are therefore biased towards during taxonomic assign-
ment. An exception is Abax, which does not have a refer-
ence genome, but is taxonomically close to A. alpina
(both Carabidae: Harpalinae). The number and variety of
component taxa further demonstrates the issues associ-
ated with the lack of a suitable reference genome, which,
together with the very low proportion of contigs that
could be assigned, would suggest that a substantial num-
ber of A. alpina contigs were not identified (Prufer et al.
2010). The single-leg extracted museum samples contain
comparable proportions of insect DNA to the whole-
specimen extracted modern samples, which suggests
that a single leg is sufficient for yielding museum DNA
from insects.
Parasites and commensals constitute the majority of
the bacterial contigs in the modern and museum
samples. Alphaproteobacterial contigs were mainly
composed of Wolbachia. The Wolbachia contigs for mod-
ern-1 were assigned to the wPip strain, whereas contigs
for the other modern and museum samples were
assigned to wRi. These strains belong to different
Wolbachia supergroups [wRi: A, wPip: B; (Klasson et al.
2009)], which would therefore suggest two separate
infection histories in this species. Contigs identified to
the bacterial class Mollicutes, which comprise 19% in
modern-2 and are found in very low proportions in the
museum samples, are made up of Spiroplasma. These
are arthropod commensals, which can be pathogenic
(Regassa & Gasparich 2006). As a commensal, Spiroplas-
ma are found in the arthropod gut and become patho-
genic when they enter the hemolymph (Regassa &
Gasparich 2006). Given that the modern samples had
far higher proportions of Spiroplasma compared with
the museum samples and that DNA was extracted
from whole specimens rather than legs in the former, it
is inferred that Spiroplasma detected here were com-
mensals. Another major bacterial parasite of beetles,
Rickettsia (Duron et al. 2008), was not detected in any of
the samples analysed. We see no obvious reason why
this metagenomic approach would not be applicable to
the investigation of parasitism in museum specimens of
other insect orders, as well as other arthropod groups.
The remaining identifiable contigs in the modern and
museum samples were assigned to the Mammalia (9 to
17%; Homo, Mus), Actinopterygii (Danio), Eudicotyledons
and Saccharomycetes. The origins of these contaminant
contigs are speculated to be from human handling
(Homo), the museum environment (Eudicotyledons,
InsectaArachnida
MammaliaActinopterygii SaccharomycetesEudicotyledons
AlphaproteobacteriaBetaproteobacteria GammaproteobacteriaMollicutes
ActinobacteriaFlavobacteriia
Prop
. of i
dent
ified
con
tigs (
%)
0
10
20
30
50
Modern-1
40
Modern-2 Museum-1 Museum-2 Ancient-1 Ancient-2
Fig. 3 Metagenomic composition of DNA from three age classes (modern, museum, ancient) of A. alpina. The twelve most abundant
classes and phyla across all data sets are illustrated, in descending order. Invertebrates: red, vertebrates: orange, plants and fungi: yel-
low, Proteobacteria: green, other bacteria: blue.
© 2013 John Wiley & Sons Ltd
612 P . D . HEINTZMAN ET AL .
Saccharomycetes, Mus) and potential misassignments in
the BLAST database.
The two ancient samples comprise contigs that range
in length from 40 to 11617 bp, with N50 values of
between 174 and 214 bp, of which 16 to 19% could be
taxonomically identified (Table S7, Supporting informa-
tion). These samples have profoundly different
taxonomic profiles to the modern and museum samples,
with 0.2 to 0.3% of identified contigs assigned as Insecta
(Fig. 3; Table S7, Supporting information). There were
contigs assigned to Amara in both ancient samples. Given
the large taxonomic diversity of insects and the limited
amount of genetic information available for Amara, we
would not expect any contigs to be falsely identified to
the target genus, if the insect contigs were an artefact of
background contamination. Mammalian contamination
was low in the ancient samples (0.2 to 2%).
The vast majority of identified contigs from the
ancient samples were assigned to the Proteobacteria and
Actinobacteria. The ratios of these bacterial groups differ,
with the Alpha- and Betaproteobacteria (30 to 38% of
identified contigs) and Actinobacteria (38%) dominating
in ancient-1 and ancient-2, respectively (Fig. 3). These
bacterial compositions are consistent with the prove-
nance of these samples (permafrost); the component gen-
era suggest the samples were from glacial or periglacial
soils/sediments, near aquatic sources (Table S8, Support-
ing information). This was inferred from Polaromonas
[glacial and periglacial deposits (Darcy et al. 2011)],
Caulobacter [aquatic or semi aquatic habitats (Laub et al.
2007)] and the remaining genera being typical of a soil/
sediment environment (Janssen 2006; Philippot et al.
2007; Doughari et al. 2011). This complements the locality
information for these samples (Goldbottom Creek and
Titaluk River, in permanently frozen sediment) and
opens up the possibility of identifying potentially
unknown or dubious provenance information based on
the bacterial metagenome of ancient samples. However,
the diversity and ubiquity of many environmental bacte-
ria would only allow for general inferences to be made.
Although the proportion of endogenous DNA from
A. alpina in these chitinous remains seems to be around
two orders of magnitude lower than other permafrost or
cold-preserved tissues, such as bone and hair (Poinar
et al. 2006; Gilbert et al. 2008; Miller et al. 2008; Lindqvist
et al. 2010), this is due to BLAST bias, which resulted
from the lack of a suitable reference genome. Based on
the proportion of contigs identified, modern and
museum samples have an average of 165 times more
insect DNA than ancient samples. However, based on
the proportion of all contigs, this ratio decreases from
165:1 to 4:1, with the disparity between these two ratios
being due to a far greater proportion of contigs identi-
fied in the ancient samples (Table S7, Supporting
information). This suggests that the amount of insect
DNA in permafrost-preserved remains is comparable to
the amount found in museum specimens, although
direct comparison between the museum and the ancient
samples may be problematic if insect DNA in the ancient
samples was outcompeted by environmental DNA
during shotgun sequencing.
Conclusions
Using museum and ancient specimens of the ground
beetle A. alpina, this study has explored DNA preserva-
tion in degraded beetle specimens and assessed their
potential utility for future genetic studies. Museum spec-
imens have great potential, with nearly all specimens
containing amplifiable endogenous DNA. Furthermore,
it was possible to recover parasite sequences, which indi-
cates that museum specimens could be routinely used to
study host–parasite associations over decadal to centen-
nial timescales (Tsangarasa & Greenwood 2012). Ampli-
fiable endogenous DNA could only be recovered from
45% of ancient specimens, which would suggest that
large quantities of specimens would be required for
large-scale analyses. The vast majority of extracted DNA
was identified as originating from environmental bacte-
ria, although this was probably due to BLAST bias. The
major hurdle to future degraded insect DNA research
will be the availability of appropriate reference genome
sequences for maximum exploitation of recovered
sequence data. International initiatives, such as the 5000
insect genomes project (i5k), are anticipated to provide
such reference genomes over the next 5 years.
Acknowledgements
The authors thank Svetlana Kuzmina and Philip Thomsen for
specimens and DNA extracts; Yves Bousquet, Anthony Davies
(both CNC) and Johannes Bergsten (NRM) for access to the
museum specimens; Selina Brace, Jessica Thomas, Edwin van
Leeuwen, Roland Preece, Aurelien Ginolhac, Matthias Meyer
and Martin Kircher for technical advice and assistance; and Tom
Gilbert, Stephen Rossiter and three anonymous reviewers for
comments on earlier drafts of this work. PDH acknowledges
funding from a RHUL Reid Scholarship, the RHUL Research
Strategy Fund and SYNTHESYS (SE-TAF-1185; SYNTHESYS
receives funding from the European Community–ResearchInfrastructure Action under FP7 ‘Capacities’ Specific Pro-
gramme). Details on the i5k initiative can be found at: http://
www.arthropodgenomes.org/wiki/i5K.
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P.D.H., I.B. and S.A.E. designed the research. I.B. and
S.A.E. oversaw the project. S.A.E. provided ancient
samples. P.D.H. and S.A.E. performed the research. K.M.
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Data accessibility
Representative mitochondrial and nuclear DNA
sequences have been deposited in GenBank with Acces-
sion nos. KF695187-KF695189. BAM files and metage-
nomic data sets are in the DRYAD database at doi:10.
5061/dryad.0179t. Sample data can be found in the
online supplementary material.
Supporting Information
Additional Supporting Information may be found in the online
version of this article:
Data S1 Supplementary methods.
Data S2 Duplicate removal bias.
Fig. S1 Customised workflow for analysis of Illumina paired-
end DNA sequence data.
Table S1 Data on all Amara specimens used in this study.
Table S2 Locality data for ancient specimens of A. alpina.
Table S3 Primers used in this study.
Table S4 Details of the 15 reference sequences used to retrieve
A. alpina sequences from the merged read files.
Table S5 The proportion of reads per sample (a) aligned to the
15 reference sequences listed in Table S4, and (b) affected by the
duplicate removal bias toward nuclear DNA in modern and
museum samples.
Table S6 Mean fragment length differences between mitochon-
drial and nuclear DNA.
Table S7 Details of the contigs used for metagenomic assess-
ment, and the proportion that were taxonomically assigned,
including those for the Insecta.
Table S8 Major taxonomic components of the groups identified
in Fig 3, and their inferred origin.
© 2013 John Wiley & Sons Ltd
DNA PRESERVATION IN DEGRADED BEETLE SPECIMENS 615