Download as pdf or txt
Download as pdf or txt
You are on page 1of 8

Forensic Science International 353 (2023) 111882

Contents lists available at ScienceDirect

Forensic Science International


journal homepage: www.elsevier.com/locate/forsciint

Comparative analysis of DNA preservation in permanent and deciduous


teeth of adults and non-adults: Implications for archaeological and
forensic research
Tamara Leskovar a, 1, Irena Zupanič Pajnič b, *, 2
a
Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
b
Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia

A R T I C L E I N F O A B S T R A C T

Keywords: This study investigates the preservation of DNA in different categories of teeth, including permanent and de­
DNA preservation ciduous, fully developed and not fully developed, in both adults and non-adults. Teeth were sampled from a
Tooth type modern-era cemetery in Ljubljana, Slovenia. DNA extraction was performed using a full demineralisation pro­
Permanent teeth
tocol. DNA quantity and quality were assessed using qPCR analyses, and autosomal STR typing was conducted to
Deciduous teeth
Skeletonized remains
verify genetic profiles. Results revealed significant differences in DNA preservation among various tooth cate­
gories. Fully developed permanent teeth of adults exhibited the highest DNA yields, attributed to their fully
developed roots and thicker cementum, which is rich in DNA. Deciduous teeth, with thinner enamel and
cementum, showed lower DNA preservation regardless of developmental stage. Non-adult teeth generally yielded
less DNA compared to adults, even when considering only fully developed permanent teeth, indicating factors
beyond developmental stage. These findings suggest that, in archaeological and forensic contexts, researchers
should prioritize fully developed permanent teeth for DNA analysis due to their superior preservation. Addi­
tionally, this study underscores the importance of considering tooth type and developmental stage when
selecting samples for genetic analysis in cases where petrous bone is unavailable, expanding our understanding of
DNA preservation in human remains.

1. Introduction Deciduous teeth are further divided into incisors, canines and molars,
while permanent teeth also have premolars [18]. Deciduous teeth start
Recovery and analyses of DNA have become an effective and rela­ to form at approximately 30 weeks in-utero and finish their develop­
tively accessible way to extract information from human skeletonized ment with all the roots closed at the age 3.5 years ± 1 year. Permanent
remains in archaeological and forensic cases. Nowadays, even analyses teeth start to develop at the age of 4.5 months ± 3 months and finish
of DNA from highly degraded skeletal tissues are possible, allowing re­ their development with the third molars roots closed at around the age
searchers to extract unique genetic information. Though research shows of 23 years [19]. As teeth differ in developmental stage or serve different
that petrous bone is optimal skeletal element to use for DNA analyses functions, different teeth have different structural properties. Incisors
[1–8], it is not always available for sampling. Other bones of the skel­ are flat and have one root, canine are more conical, with one root, which
eton do show great potential [9–12], yet teeth, if available, seem to be is longer in comparison to other teeth, premolars are round with two
the second choice [7,8,13,14]. Teeth are preferred due to their hard cusps and are usually single rooted, but can have two roots, while molars
mineral composition and low porosity, which makes them less prone to are larger, squarer and have more cusps and roots than other teeth [18].
taphonomy and contamination when compared to bones [15–17]. Deciduous teeth have thinner and shorter roots and thinner dentine
Human teeth can be separated into different categories. Based on layer and enamel when compared to permanent teeth. On the other
development, teeth can be deciduous (milk teeth) or permanent. hand, deciduous teeth have larger pulp chamber with blood vessels and

* Corresponding author.
E-mail address: irena.zupanic@mf.uni-lj.si (I.Z. Pajnič).
1
Orcid ID: 0000-0002-4585-4726
2
Orcid ID: 0000-0002-6704-015X

https://doi.org/10.1016/j.forsciint.2023.111882
Received 6 October 2023; Received in revised form 30 October 2023; Accepted 7 November 2023
Available online 10 November 2023
0379-0738/© 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
T. Leskovar and I.Z. Pajnič Forensic Science International 353 (2023) 111882

nerves, than permanent teeth [18]. Furthermore, due to posteruptive of the homogenizer and teeth were cooled with liquid nitrogen to
maturation, enamel becomes more mineralized with age and thus less prevent overheating. Before use, metal vials and metal balls were
prone to decay, especially shortly after eruption [20], but likely loses cleaned with 6% sodium hypochlorite, sterile bi-distillated water, and
this advantage with aging. Studies indicate that properties such as 80% ethanol, followed by sterilization in a Europa B xp sterilizer
dental elasticity, durability, and fracture resistance decrease with age (Tecno-Gaz, Parma, Italy), and 30 min of UV irradiation using
[21–23], making teeth more prone to deterioration [24]. BLX-Multichannel BioLink DNA Crosslinker (Vilber). From each tooth,
When sampling teeth for DNA analyses, is it advised to choose least 0.5 g of tooth powder was used for extraction. To prevent and follow
damaged teeth with intact root systems, as in such cases DNA has highest possible contamination with modern DNA, special measures [42,43]
rate of survival [14,25]. Additionally, molars are recommended, as they were followed, extraction-negative controls (ENC) were added to each
are multi-rooted with large pulp chamber [26–29]. However, molars are batch of samples [44], and all persons involved in analyses were
not always available and Heathfield et al. [30] showed that there are no include in an elimination database (their saliva was collected with
significant differences in the preservation of DNA in the four types of cotton swabs, and extracted DNA was used for STR typing). Tooth
teeth (incisors, canine, premolars and molars), indicating that sampling sample purification was carried out with the EZ1 Advanced XL ma­
could be broadened to other tooth types. In general, DNA analyses chine (Qiagen). Instructions provided by the manufacturer [45] were
performed on teeth focus on pulp tissue, which degrades relatively followed for using the EZ1&EZ2 DNA Investigator kit (Qiagen) for
quickly and is thus not necessarily the best source in case of tapho­ processing buccal swabs, and this was also in line with the previously
nomically altered skeletonized remains [31,32]. Consequently, sam­ published protocol [41] for processing tooth samples.
pling cementum presents an alternative for DNA analyses, as it is more
resistant to degradation [14,31,33].
Despite being included in various archaeological and forensic 2.3. DNA quantification
research [25,34–39], there is no specific data or guidelines on the DNA
analyses performed on teeth of non-adults or on deciduous teeth. To determine the concentration of DNA and its degradation in teeth
Though for DNA analyses sampling tooth cementum, preferably of fully extracts, qPCR analyses were performed amplifying short (Auto target)
developed teeth with closed, undamaged roots is advised, this is not and long (Deg target) autosomal targets using the PowerQuant System
always an option. In case of non-adults, permanent teeth might still be (Promega). DNA quantity was determined from Auto target measures,
developing or are not even present. Thus, deciduous teeth or partially and the degradation index was calculated from the Auto/Deg ratio. We
developed teeth are the only option. Furthermore, focusing on one part used an internal PCR control (IPC shift) to detect any possible presence of
of the tooth might also not be possible as deciduous and still developing PCR inhibitors. The Y-chromosomal target included in the same kit was
teeth are usually small and light, and the whole tooth needs to be used used to detect the presence of male DNA. Analyses were performed
for the analysis. The aim of this study is to start filing these gaps in following the technical manual [46] with the QuantStudio 5 Real-Time
knowledge by comparing DNA preservation of permanent and decidu­ PCR system, the PowerQuant Analysis Tool (https://worldwide.prom­
ous, fully developed and not fully developed teeth of adults and ega.com/resources/tools/powerquant-analysis-tool/), and Quant-Studio
non-adults. Design and Analysis Software 1. 5. 1 (Applied Biosystems, AB, Foster
City, CA, USA).
2. Materials and methods The threshold for the Auto/Deg ratio was set at 2 and the IPC shift
value was set at 0.30, as recommended by the manufacturer [46].
2.1. Sample selection Laboratory plastic and reagent cleanliness was verified through analysis
of negative template controls and extraction-negative controls. Tooth
An archaeological excavation of a modern-era cemetery that was extracts, positive controls, and negative controls were quantified in
active between the early 16th and late 19th centuries in Ljubljana – Polje duplicate, following the manufacturer’s recommendations [46]). For all
took place in 2020, and 216 graves with one third of adult and two thirds of the tooth samples, the DNA quantity obtained from 1 g of tooth was
of non-adult skeletons were uncovered [40]. For the analysis, 52 teeth calculated on the basis of the Auto target, and this was expressed in ng
from 15 non-adults and 11 adults were sampled and one to three (mostly DNA/g of tooth.
two) teeth were sampled per skeleton (Supplementary material Table 1).
From non-adults, 16 deciduous (11 molars and 5 premolars) and 17
permanent teeth (12 molars and 5 canines) were collected, and from 2.4. Autosomal STR typing
adults 19 permanent teeth (8 molars, 2 premolars and 9 canines) were
collected. Out of 36 permanent teeth, 14 were not fully developed The autosomal STR typing kit PowerPlex ESI 17 Fast System
(partially developed rooted or open apex). Pathology was observed on (Promega) was used for STR typing. PCR was performed following the
11 teeth, in one case the crown had a malformation and in ten cases mild recommendations of the manufacturer [47], using the Nexus Master­
carious lesions were observed. Cycler (Eppendorf, Hamburg, Germany). Amplification included both
positive and negative PCR controls. Variation in the final volume of
2.2. DNA extraction tooth extracts used in the PCR reaction was based on the quantification
results of the PowerQuant Auto target. If the quantification was 0.058 ng
DNA extraction was performed according to the protocol of Zupanič per μl of extract or higher, 1 ng of DNA was used as a template. The
Pajnič [41]. Because extraction method is optimized for 0.5 g of maximum DNA extract volume (17.5 μl) was used if the quantification
bone/tooth powder and deciduous and still developing teeth are small was lower than 0.058 ng per μl of extract. Maximum volume was also
and light, whole teeth were grounded for non-adults. Whole teeth were used for amplification of ENCs. Genetic profiles for the samples were
used for the analysis from adults as well so that comparison between acquired using the SeqStudio Genetic Analyzer for HID (Thermo Fisher
adult and non-adult teeth was possible. Each tooth was chemically Scientific, TFS) combined with the WEN Internal Lane Standard 500
cleaned (5% Alconox detergent (Sigma-Aldrich, St. Louis, MO, USA), (Promega), SeqStudio Data Collection Software v 1.2.1 (TFS), and
water and 80% ethanol) and UV irradiated for 30 min using GeneMapper ID-X Software v 1.6 (TFS). All ENC samples employed to
BLX-Multichannel BioLink DNA Crosslinker (Vilber, Collégien, France) monitor possible contamination with modern DNA were also typed, and
to remove surface contamination and grounded into a fine powder STR typing of elimination database samples was performed to check the
using a Bead Beater MillMix 20 homogenizer (Tehtnica, Domel, authenticity of isolated DNA and to exclude modern DNA contamination
Železniki, Slovenia) for 1 min at a frequency of 30 Hz. The metal vials of extracts.

2
T. Leskovar and I.Z. Pajnič Forensic Science International 353 (2023) 111882

2.5. Statistical analysis 3.2. STR typing

According to the research problem, comparisons were made between All samples were typed for autosomal STRs, and only 17 of them
different classes of teeth: produced useful genetic profiles, among them only four tooth samples
originated from non-adults (see Supplementary material Table 2).
– between the teeth of adults and non-adults, Thirteen samples produced STR profiles with 12 or more STRs amplified
– between deciduous and permanent teeth, and four of them generated profiles with 7–11 successfully amplified
– between full developed and not fully developed permanent teeth, STRs. For all the skeletons used in this study, petrous bones, tali,
– between fully developed and not fully developed deciduous teeth, calcanei and femurs were analyzed in our previous study and consensus
– between one rooted or more rooted permanent teeth, profiles were generated [40]. DNA profiles obtained from tooth extracts
– between one rooted or more rooted deciduous teeth. matched consensus profiles of corresponding skeletons, indicating
endogenous tooth DNA and together with clean ENCs (ENC samples did
According to the obtained results and in search of their interpreta­ not produce profiles), and no match with elimination database, elimi­
tion, additional comparisons were made accordingly. In each case, the nates contamination issue. For the most of teeth from non-adult skele­
amount of DNA (expressed in ng DNA/g of tooth), the degradation ratio tons, no DNA or low-quantity DNA was extracted and consequently,
(Auto/Deg ratio of the DNA) and STR typing results were compared. autosomal STR typing failed, showing less DNA yield in teeth sampled
The normality and homogeneity of variance was tested using the from non-adult skeletons than from adult skeletons.
Kolmogorov–Smirnov test (with Lilliefors significance correction). SM Table 1–6 show genetic profiles obtained from different amounts
Following the recommendations for statistical analyses in medical of DNA and from DNA samples with different degradation rates. SM
studies [48–50], the research hypotheses were tested using the 95% Figs. 1–3 show genetic profiles of tooth samples from which higher DNA
confidence intervals for means or medians. For the analyses, computer yields were obtained and one ng (SM Figs. 1 and 2) and 452 pg of DNA
program IBM SPSS Statistics for Windows, version 25.0 (Statistical were amplified (SM Fig. 3). Because samples with different degradation
Package for the Social Sciences Inc., Chicago, IL, USA) was used. As indexes were amplified, full profile was obtained only from sample 238
sample sizes are relatively small, confidence intervals can have limited (SM Fig. 1) with degradation index of 10.94. In sample 209 (SM Fig. 2)
power to detect significant differences [48]. Thus, formulated hypoth­ partial profile with one locus drop-out was obtained even if 1 ng of DNA
eses were also tested using p values. Significance was set as p ≤ 0.05. was used for PCR because of higher degradation of sample 209 (degra­
Data was obtained from teeth of 15 non-adults and 11 adults, dation index of 92.25 was measured). Sample 171 produced partial
together from 52 teeth. In seven cases no data was obtained for neither profile with several loci and allelic drop-outs (see SM Fig. 3) indicating
amount of DNA (expressed in ng DNA/g of tooth) and Auto/Deg ratio. In high DNA degradation (degradation index of 168.84 was calculated).
all seven cases the teeth were from non-adults. Since there was not SM Fig. 4–6 show genetic profiles of tooth samples from which lower
enough data for these seven cases, they were omitted from the com­ DNA yields were obtained and 47 pg (SM Fig. 4), 54 pg (SM Fig. 5) and
parisons. There were also 13 cases in which the amount of DNA was 39 pg of DNA were amplified (SM Fig. 6). Because samples with different
obtained while the value for the Auto/Deg ratio was not possible to degradation indexes were amplified, full profile was obtained only from
calculate because no Deg targets were amplified. The Auto/Deg ratio for sample 262 (SM Fig. 4) where degradation index was very low (3.09). In
these 13 cases was calculated using the following formula: value = Max sample 228 (SM Fig. 5) and sample 123 (SM Fig. 6) only partial profiles
+ SD. Missing values of the degradation ratio were set to 558.64, as max with several loci and allelic drop-outs were generated according to
value was 472.94 and SD was 85.70. STR typing was successful in 17 higher degradation of DNA (for sample 228 degradation index was 8.58,
cases, in each case on a permanent tooth. Thus, comparisons were only and for sample 123 it was 12.32). However, degradation was not so high
possible between not fully developed and fully developed permanent as in samples 209 and 171 and partial profiles were generated despite
teeth of adults and non-adults. very low DNA input.
The normality of the distribution of amount of DNA, Auto/Deg ratio
and STR typing was checked, using the Kolmogorov-Smirnov test 3.3. Statistics
(Supplementary material Statistics). DNA and Auto/Deg ratio were not
normally distributed (sig. < 0.05), thus non-parametric tests and me­ There were no significant differences in case of degradation ratio
dians were used to test the formulated research hypotheses. STR typing when comparing different classes of teeth. Significant differences were
was normally distributed, thus parametric tests and means were used for obtained when comparing the amount of DNA in the teeth of adults and
additional comparisons. non-adults, in deciduous and permanent teeth, and in fully developed
and not fully developed deciduous teeth. There were no significant
3. Results differences between deciduous or permanent one rooted or more rooted
teeth (Supplementary material Statistics).
Results are gathered in Supplementary material Table 2. Results suggest significant differences (p = 0.002) among non-adults
and adults in the amount of the DNA extracted from teeth. There is more
3.1. DNA quantification DNA extracted from the teeth of adults (Me=1.3, SE=0.47) than of non-
adults (Me=0.18, SE=0.10) (Fig. 1).
Supplementary material Table 2 presents tooth sample characteris­ Significant differences (p = 0.011) were also observed among de­
tics and summarizes the PowerQuant (Promega) results for DNA quan­ ciduous and permanent teeth in the amount of the DNA. There is more
tity and quality (Auto and Deg in ng DNA/μl of extract, Auto/Deg ratio DNA extracted from the permanent teeth (Me=0.89, SE=0.30) than
and the amount of DNA obtained from 1 g of tooth in ng of DNA. No DNA from deciduous teeth (Me=0.06, SE=0.12) (Fig. 2).
was obtained from seven teeth (all were from non-adults) and less than The difference in the amount of the DNA in not fully developed and
0.5 pg of human DNA per μl of extract was detected in 15 tooth samples fully developed permanent teeth is statistically significant (p = 0.008).
(12 from non-adults and three from adults). It was not possible to There is more DNA extracted from the fully developed permanent teeth
determine the Auto/Deg ratio for 20 samples (18 non-adult and 2 adult (Me=1.14, SE=0.41) than from the not fully developed permanent teeth
teeth). Extracted tooth DNA was slightly to severely degraded with (Me=0.34, SE=0.25). However, the confidence interval shows over­
degradation index ranged between 1 and 473. An IPC shift value was lapping and statistical significance is only seen in p-value (Fig. 3; Sup­
lower than 0.3 in all extracts and no amplicons were detected for ENC plementary material Statistics).
samples (data not shown). Results suggest significant differences (p = 0.030) among non-adults

3
T. Leskovar and I.Z. Pajnič Forensic Science International 353 (2023) 111882

Fig. 1. 95% confidence intervals for medians for the amount of the DNA extracted from teeth (for non-adults and adults, separately).

Fig. 2. 95% confidence intervals for medians for the amount of the DNA extracted from teeth (for permanent and deciduous teeth, separately).

and adults in the STR typing. More STRs were amplified from teeth of observed in permanent teeth, while not in deciduous. The reason could
adults (Me=13.5, SE=0.54) than of non-adults (Me=10.5, SE=1.4). be low number of not fully developed deciduous teeth (only two).
However, the confidence interval shows overlapping and statistical Another explanation is the also observed difference in permanent and
significance is only seen in p-value (Fig. 4; Supplementary material deciduous teeth, as the former presented significantly higher amounts of
Statistics). DNA. In comparison to permanent teeth, deciduous teeth are more prone
to degradation regardless of their developmental stage, as they have less
4. Discussion mineralized, thinner enamel and thinner cementum [18,51], leading to
faster degradation. This can be observed in degradation ratio, though
Significant differences in the amount of DNA were observed between not significant, double in deciduous teeth (310,9 ± 267.7) when
teeth of adults and non-adults, between deciduous and permanent teeth compared to permanent teeth (144.9 ± 216.1). The logic conclusions
and between fully developed and not fully developed permanent teeth. would thus be, that teeth of non-adults presented lower quantity of DNA
Permanent, fully developed teeth of adults presented highest amounts of because there are deciduous teeth present in the non-adult group.
DNA. As previous research has shown that damaged or open roots fasten However, when only comparing permanent, fully developed teeth of
the degradation of DNA [14,25], better preservation of DNA in fully adults and non-adults, the difference remained significant (p = 0.016),
developed teeth is completely understandable. Though, this was only with average amount of DNA/g of tooth 0.13 ± 0.09 in non-adult teeth

4
T. Leskovar and I.Z. Pajnič Forensic Science International 353 (2023) 111882

Fig. 3. 95% confidence intervals for medians for the amount of the DNA extracted from permanent teeth (for not fully developed and fully developed
teeth, separately).

Fig. 4. 95% confidence intervals for STRs (for teeth of adults and non-adults, separately).

and 1.45 ± 2.03 in adult teeth. The significant difference remained to adults (114.9 ± 189.1). One possibility is differences in enamel
present even when comparing only permanent molars, as adult molars mineralization, as highly mineralized enamel offers protection for DNA
presented on average 3.06 ± 2.7 amount of DNA/g of tooth, while non [16,52]. Studies suggest enamel mineralization is highest in first couple
adult molars 0.13 ± 0.09 amount of DNA/g of tooth. Caution is advised of years after eruption and decreases with old age [20]. Analysed fully
as with such data fragmentation sample number is low, yet it indicates developed first permanent molars of non-adults in this study originate
there is some other reason for the better preservation of DNA in teeth of from children aged 11.5 – 13.5 years. As first permanent molars erupt
adults than developmental stage or type of tooth. STR typing results around the age of 6 years, the enamel should already be highly miner­
further confirm this, as the only significant differences were observed alized. Thus, enamel maturity might also not be influencing DNA pres­
between the teeth of adults and non-adults (p = 0.030), while non be­ ervation in our case. A more thorough analysis revealed either an
tween fully developed and not fully developed teeth (see Supplementary enamel malformation or presence of carious lesions on all the analysed
Material Statistics, Appendixes 7 and 8). Degradation ratio presented no non-adult permanent, fully developed teeth. Comparison of amount of
significant differences between the fully developed permanent teeth of DNA in all the permanent teeth with (ngDNA/g tooth = 1.13 ± 1.84) or
adults and non-adults, but it should be highlighted that on average, the without pathology (ngDNA/g tooth = 1.26 ± 1.95) presented no sig­
ratio was almost double in non-adults (209.2 ± 248.4) when compared nificant differences, which agrees with other studies [53]. Thus,

5
T. Leskovar and I.Z. Pajnič Forensic Science International 353 (2023) 111882

pathology is also not a tangible reason for the differences. Especially, as Funding
observed carious lesions were relatively small and superficial, not
affecting the pulp, and the degradation ratio was lower in teeth with The work was supported by Slovenian Research and Innovation
pathology (68.5 ± 163.7) when compared to teeth without pathology Agency: project J3-3080 and Research Group Archaeology, 0581-012).
(182.88 ± 216.40). As the whole teeth were used for the analysis,
including DNA rich tooth cementum, this is the most likely reason for the CRediT authorship contribution statement
observed differences between adult and non-adult fully developed teeth.
Tooth cementum is rich in mtDNA and nuclear DNA [14,16,54–57] and Tamara Leskovar: Funding acquisition, Investigation, Methodol­
contrary to enamel, cementum apposition continues throughout life ogy, Software, Visualization, Writing – original draft. Irena Zupanič
[58]. Thus, the thickness of cementum increases with age [59] and could Pajnič: Conceptualization, Formal analysis, Funding acquisition,
cause differences between non-adult and adult permanent teeth. This Methodology, Supervision, Validation, Writing – review & editing.
would also further support the differences between permanent and de­
ciduous teeth, and fully- and not-fully developed teeth. Though these Declarations
differences could be attributed to taphonomy with deciduous/not-fully
developed teeth being more susceptive to taphonomic factors, they Research involving human participants and/or animals Research
also have shorter/not yet fully developed roots and thinner cementum involves ancient skeletons and genetic profiles of persons included in
[18,51,60], which could result in lower quantities of DNA. A reliable elimination database and from them informed consents were obtained
answer could be obtained through a direct comparison of tooth and submitted to the Medical Ethics Committee of the Republic of
cementum of teeth of adults and non-adults. However, some of the Slovenia. After submission, the Medical Ethics Committee of the Re­
analysed teeth of non-adults were not fully developed, having incom­ public of Slovenia approved the research (number of approval is 0120-
plete roots. As cementum forms on the roots, these not fully developed 526/2021/7.
teeth could distort the comparisons. To avoid this, whole tooth was used
for the DNA analyses in this study. Informed consent

5. Conclusions This research project was approved by the Medical Ethics Committee
of the Republic of Slovenia (0120-526/2021/7) and informed consents
1. Tooth Type Matters: This study highlights the significance of tooth of persons included in elimination database were submitted to the
type in DNA preservation. Permanent teeth, with their thicker Medical Ethics Committee of the Republic of Slovenia.
cementum and fully developed roots, consistently outperformed decid­
uous teeth in terms of DNA yield. Researchers should prioritize the use of Declaration of Competing Interest
permanent teeth when available for genetic analysis, as they offer a
more reliable source of DNA, especially in challenging archaeological The authors declare no conflict of interest.
and forensic cases.
2. Age-Related Variations: The study demonstrates that non-adult Data availability
teeth generally yielded lower quantities of DNA compared to adult
teeth. Even when considering only fully developed permanent teeth, The authors declare that all the data are available upon reasonable
adults consistently provided higher DNA yields. This suggests that age- request.
related factors, beyond tooth developmental stage, influence DNA
preservation. Further research is needed to explore these factors and Acknowledgements
their impact on DNA preservation in non-adult individuals.
3. Cementum as a DNA Source: Tooth cementum emerges as a This study was financially supported by the Slovenian Research
valuable alternative for DNA analysis, given its resistance to degrada­ Agency (the project “Inferring ancestry from DNA for human identifi­
tion. The thickness of cementum increases with age, potentially cation” J3-3080). The authors would like to thank The Ljubljana
contributing to higher DNA yields in adult teeth. Researchers should Museum and Galleries (MGML) and the responsible curator Martin
consider tooth cementum as a viable source of genetic material, espe­ Horvat for including the archaeological human remains from the
cially in cases where other tooth components may be compromised. museum into our study. Authors are grateful to Teo Mlinšek and Tadej
4. Implications for Archaeological and Forensic Research: These Počivavšek for DNA extraction.
findings have practical implications for both archaeological and forensic
investigations. Selecting the most suitable teeth for DNA analysis can Appendix A. Supporting information
enhance the chances of obtaining reliable genetic information from
skeletonized remains. Understanding the factors that influence DNA Supplementary data associated with this article can be found in the
preservation in teeth can lead to more informed sampling strategies and online version at doi:10.1016/j.forsciint.2023.111882.
improved success rates in genetic analyses.
This study contributes valuable insights into DNA preservation in
References
different categories of teeth and emphasizes the importance of tooth
type and age in genetic analyses of archaeological and forensic samples. [1] T. Frisch, M.S. Sørensen, S. Overgaard, M. Lind, P. Bretlau, Volume-referent bone
These findings offer guidance for researchers in optimizing their sam­ turnover estimated from the interlabel area fraction after sequential labeling, Bone
22 (1998) 677–682, https://doi.org/10.1016/S8756-3282(98)00050-7.
pling strategies and maximizing the success of DNA extraction from
[2] S.M. Edson, A.F. Christensen, S.M. Barritt, A. Meehan, M.D. Leney, L.N. Finelli,
human skeletal remains. Sampling of the cranium for mitochondrial DNA analysis of human skeletal
remains, Forensic Sci. Int. Genet. Suppl. Ser. 2 (2009) 269–270, https://doi.org/
Ethical approval 10.1016/j.fsigss.2009.09.029.
[3] C. Gamba, E.R. Jones, M.D. Teasdale, R.L. McLaughlin, G. Gonzalez-Fortes,
V. Mattiangeli, L. Domboróczki, I. Kővári, I. Pap, A. Anders, A. Whittle, J. Dani,
This research project was approved by the Medical Ethics Committee P. Raczky, T.F.G. Higham, M. Hofreiter, D.G. Bradley, R. Pinhasi, Genome flux and
of the Republic of Slovenia (0120-526/2021/7). stasis in a five millennium transect of European prehistory, Nat. Commun. 5
(2014), 5257, https://doi.org/10.1038/ncomms6257.
[4] M. Rasmussen, S.L. Anzick, M.R. Waters, P. Skoglund, M. DeGiorgio, T.W. Stafford,
S. Rasmussen, I. Moltke, A. Albrechtsen, S.M. Doyle, G.D. Poznik,

6
T. Leskovar and I.Z. Pajnič Forensic Science International 353 (2023) 111882

V. Gudmundsdottir, R. Yadav, A.-S. Malaspinas, S.S. White, M.E. Allentoft, O. [27] M. Prinz, A. Carracedo, W.R. Mayr, N. Morling, T.J. Parsons, A. Sajantila,
E. Cornejo, K. Tambets, A. Eriksson, P.D. Heintzman, M. Karmin, T.S. Korneliussen, R. Scheithauer, H. Schmitter, P.M. Schneider, DNA Commission of the
D.J. Meltzer, T.L. Pierre, J. Stenderup, L. Saag, V. Warmuth, M.C. Lopes, R. International Society for Forensic Genetics (ISFG): recommendations regarding the
S. Malhi, S. Brunak, T. Sicheritz-Ponten, I. Barnes, M. Collins, L. Orlando, role of forensic genetics for disaster victim identification (DVI), Forensic Sci. Int.
F. Balloux, A. Manica, R. Gupta, M. Metspalu, C.D. Bustamante, M. Jakobsson, Genet. 1 (2007) 3–12, https://doi.org/10.1016/j.fsigen.2006.10.003.
R. Nielsen, E. Willerslev, The genome of a late Pleistocene human from a Clovis [28] L. Rubio, L.J. Martinez, E. Martinez, S.M. De Las Heras, Study of short- and long-
burial site in western Montana, Nature 506 (2014) 225–229, https://doi.org/ term storage of teeth and its influence on DNA, J. Forensic Sci. 54 (2009)
10.1038/nature13025. 1411–1413, https://doi.org/10.1111/j.1556-4029.2009.01159.x.
[5] R. Pinhasi, D. Fernandes, K. Sirak, M. Novak, S. Connell, S. Alpaslan-Roodenberg, [29] Interpol, Best Practice Principles: Recommendations on the Use of DNA for the
F. Gerritsen, V. Moiseyev, A. Gromov, P. Raczky, A. Anders, M. Pietrusewsky, Identification of Missing Persons and Unidentified Human Remains, 2015. 〈https
G. Rollefson, M. Jovanovic, H. Trinhhoang, G. Bar-Oz, M. Oxenham, ://www.interpol.int/Media/Files/INTERPOL-Expertise/DNA/INTERPOL-Best-
H. Matsumura, M. Hofreiter, Optimal ancient DNA yields from the inner ear part of practice-principles-Recommendations-on-the-Use-of-DNA-for-the-Identification-of-
the human petrous bone, PLoS One 10 (2015), e0129102. Missing-Persons-and-Unidentified-Human-Remains〉.
[6] G. Kulstein, T. Hadrys, P. Wiegand, As solid as a rock—comparison of CE- and MPS- [30] L.J. Heathfield, T.E. Haikney, C.G. Mole, C. Finaughty, A.M. Zachou, V.E. Gibbon,
based analyses of the petrosal bone as a source of DNA for forensic identification of Forensic human identification: investigation into tooth morphotype and DNA
challenging cranial bones, Int. J. Leg. Med. 132 (2018) 13–24, https://doi.org/ extraction methods from teeth, Sci. Justice 61 (2021) 339–344, https://doi.org/
10.1007/s00414-017-1653-z. 10.1016/j.scijus.2021.05.005.
[7] E. Pilli, S. Vai, M.G. Caruso, G. D’Errico, A. Berti, D. Caramelli, Neither femur nor [31] D. Higgins, J. Kaidonis, J. Austin, G. Townsend, H. James, T. Hughes, Dentine and
tooth: petrous bone for identifying archaeological bone samples via forensic cementum as sources of nuclear DNA for use in human identification, Aust. J.
approach, Forensic Sci. Int. 283 (2018) 144–149, https://doi.org/10.1016/j. Forensic Sci. 43 (2011) 287–295, https://doi.org/10.1080/
forsciint.2017.12.023. 00450618.2011.583278.
[8] C. Parker, A.B. Rohrlach, S. Friederich, S. Nagel, M. Meyer, J. Krause, K.I. Bos, [32] J.B. Duffy, M.F. Skinner, J.D. Waterfield, Rates of putrefaction of dental pulp in the
W. Haak, A systematic investigation of human DNA preservation in medieval Northwest coast environment, J. Forensic Sci. 36 (1991) 1492–1502.
skeletons, Sci. Rep. 10 (2020), 18225, https://doi.org/10.1038/s41598-020- [33] H. Mansour, O. Krebs, J.P. Sperhake, C. Augustin, T. Koehne, M. Amling,
75163-w. K. Püschel, Cementum as a source of DNA in challenging forensic cases, J. Forensic
[9] A.Z. Mundorff, E.J. Bartelink, E. Mar-Cash, DNA preservation in skeletal elements Leg. Med. 54 (2018) 76–81, https://doi.org/10.1016/j.jflm.2017.12.015.
from the World Trade Center disaster: recommendations for mass fatality [34] L. Rudbeck, M.T.P. Gilbert, E. Willerslev, A.J. Hansen, N. Lynnerup, T. Christensen,
management*, J. Forensic Sci. 54 (2009) 739–745, https://doi.org/10.1111/ J. Dissing, mtDNA analysis of human remains from an early Danish Christian
j.1556-4029.2009.01045.x. cemetery, Am. J. Phys. Anthropol. 128 (2005) 424–429, https://doi.org/10.1002/
[10] M. Meyer, M. Kircher, M.-T. Gansauge, H. Li, F. Racimo, S. Mallick, J.G. Schraiber, ajpa.20294.
F. Jay, K. Prüfer, C. de Filippo, P.H. Sudmant, C. Alkan, Q. Fu, R. Do, N. Rohland, [35] M. Vaňharová, E. Drozdová, Sex determination of skeletal remains of 4000 year old
A. Tandon, M. Siebauer, R.E. Green, K. Bryc, A.W. Briggs, U. Stenzel, J. Dabney, children and juveniles from Hoštice 1 za Hanou (Czech Republic) by ancient DNA
J. Shendure, J. Kitzman, M.F. Hammer, M.V. Shunkov, A.P. Derevianko, analysis, Anthropol. Rev. 71 (2008) 63–70, https://doi.org/10.2478/v10044-008-
N. Patterson, A.M. Andrés, E.E. Eichler, M. Slatkin, D. Reich, J. Kelso, S. Pääbo, 0011-7.
A high-coverage genome sequence from an archaic Denisovan individual, Science [36] M. Xavier, A. Bento, A. Costa, A. Corte-Real, C. Veloso, L. Sampaio, M. Anjos,
338 (2012) 222–226, https://doi.org/10.1126/science.1224344. V. Bogas, F. Corte-Real, Primary teeth as DNA reference sample in disaster victim
[11] A.L. Emmons, J. Davoren, J.M. DeBruyn, A.Z. Mundorff, Inter and intra-individual identification (DVI), Forensic Sci. Int. Genet. Suppl. Ser. 3 (2011) e381–e382,
variation in skeletal DNA preservation in buried remains, Forensic Sci. Int. Genet. https://doi.org/10.1016/j.fsigss.2011.09.052.
44 (2020), 102193, https://doi.org/10.1016/j.fsigen.2019.102193. [37] M. Sikora, V.V. Pitulko, V.C. Sousa, M.E. Allentoft, L. Vinner, S. Rasmussen,
[12] I.Z. Pajnič, J. Inkret, T. Zupanc, E. Podovšovnik, Comparison of nuclear DNA yield A. Margaryan, P. de Barros Damgaard, C. de la Fuente, G. Renaud, M.A. Yang,
and STR typing success in second world war petrous bones and metacarpals III, Q. Fu, I. Dupanloup, K. Giampoudakis, D. Nogués-Bravo, C. Rahbek, G. Kroonen,
Forensic Sci. Int. Genet. 55 (2021), https://doi.org/10.1016/j.fsigen.2021.102578. M. Peyrot, H. McColl, S.V. Vasilyev, E. Veselovskaya, M. Gerasimova, E.Y. Pavlova,
[13] P.F. Campos, O.E. Craig, G. Turner-Walker, E. Peacock, E. Willerslev, M.T. V.G. Chasnyk, P.A. Nikolskiy, A.V. Gromov, V.I. Khartanovich, V. Moiseyev, P.
P. Gilbert, DNA in ancient bone – where is it located and how should we extract it, S. Grebenyuk, A.Y. Fedorchenko, A.I. Lebedintsev, S.B. Slobodin, B.A. Malyarchuk,
Ann. Anat. Anat. Anz. 194 (2012) 7–16, https://doi.org/10.1016/j. R. Martiniano, M. Meldgaard, L. Arppe, J.U. Palo, T. Sundell, K. Mannermaa,
aanat.2011.07.003. M. Putkonen, V. Alexandersen, C. Primeau, N. Baimukhanov, R.S. Malhi, K.-
[14] H.B. Hansen, P.B. Damgaard, A. Margaryan, J. Stenderup, N. Lynnerup, G. Sjögren, K. Kristiansen, A. Wessman, A. Sajantila, M.M. Lahr, R. Durbin,
E. Willerslev, M.E. Allentoft, Comparing ancient DNA preservation in petrous bone R. Nielsen, D.J. Meltzer, L. Excoffier, E. Willerslev, The population history of
and tooth cementum, PLoS One 12 (2017), e0170940. northeastern Siberia since the Pleistocene, Nature 570 (2019) 182–188, https://
[15] E. Meyer, M. Wiese, H. Bruchhaus, M. Claussen, A. Klein, Extraction and doi.org/10.1038/s41586-019-1279-z.
amplification of authentic DNA from ancient human remains, Forensic Sci. Int. 113 [38] W.P. Te Rijdt, R.H.P. Mieremet, T. Kraaijenbrink, J.J. Regieli, H.H. Lemmink, S.
(2000) 87–90, https://doi.org/10.1016/S0379-0738(00)00220-6. Z. Jan, P. de Knijff, Y.M. Hoedemaekers, Deciduous teeth as an alternative DNA
[16] C.J. Adler, W. Haak, D. Donlon, A. Cooper, Survival and recovery of DNA from source for postmortem genetic testing, Circ. Genom. Precis. Med. 13 (2020),
ancient teeth and bones, J. Archaeol. Sci. 38 (2011) 956–964, https://doi.org/ e002674, https://doi.org/10.1161/CIRCGEN.119.002674.
10.1016/j.jas.2010.11.010. [39] R. Manju, M.S. Ravi, Use of pulp tissue of deciduous teeth for gender determination
[17] C. Cafiero, A. Re, E. Stigliano, E. Bassotti, R. Moroni, C. Grippaudo, Optimization of - a comparative molecular analysis study, Indian J. Dent. Res. 33 (2022) 158–163,
DNA extraction from dental remains, Electrophoresis 40 (2019) 1820–1823, https://doi.org/10.4103/ijdr.ijdr_507_21.
https://doi.org/10.1002/elps.201900142. [40] A. Šuligoj, S. Mesesnel, T. Leskovar, E. Podovšovnik, I. Zupanič Pajnič, Comparison
[18] T.D. White, P.A. Folkens, The Human Bone Manual, Elsevier, Oxford, 2005. of DNA preservation between adult and non-adult ancient skeletons, Int. J. Leg.
[19] S.J. AlQahtani, M. Hector, H.M. Liversidge, Brief communication: the London atlas Med. 136 (2022) 1521–1539, https://doi.org/10.1007/s00414-022-02881-3.
of human tooth development and eruption, Am. J. Phys. Anthropol. 142 (2010) [41] I.Z. Pajnič, Extraction of DNA from human skeletal material, Methods Mol. Biol.
481–490, https://doi.org/10.1002/ajpa.21258. 1420 (2016) 89–108, https://doi.org/10.1007/978-1-4939-3597-0_7.
[20] N. Kotsanos, A.I. Darling, Influence of posteruptive age of enamel on its [42] N. Rohland, M. Hofreiter, Ancient DNA extraction from bones and teeth, Nat.
susceptibility to artificial caries, Caries Res 25 (1991) 241–250, https://doi.org/ Protoc. 2 (2007) 1756.
10.1159/000261371. [43] S. Pääbo, H. Poinar, D. Serre, V. Jaenicke-Després, J. Hebler, N. Rohland, M. Kuch,
[21] J.H. Kinney, R.K. Nalla, J.A. Pople, T.M. Breunig, R.O. Ritchie, Age-related J. Krause, L. Vigilant, M. Hofreiter, Genetic analyses from ancient DNA, Annu. Rev.
transparent root dentin: mineral concentration, crystallite size, and mechanical Genet. 38 (2004) 645–679, https://doi.org/10.1146/annurev.
properties, Biomaterials 26 (2005) 3363–3376, https://doi.org/10.1016/j. genet.37.110801.143214.
biomaterials.2004.09.004. [44] W. Parson, L. Gusmão, D.R. Hares, J.A. Irwin, W.R. Mayr, N. Morling, E. Pokorak,
[22] L. Zheng, M. Nakajima, T. Higashi, R.M. Foxton, J. Tagami, Hardness and young’s M. Prinz, A. Salas, P.M. Schneider, T.J. Parsons, DNA Commission of the
modulus of transparent dentin associated with aging and carious disease, Dent. International Society for Forensic Genetics: revised and extended guidelines for
Mater. J. 24 (2005) 648–653, https://doi.org/10.4012/dmj.24.648. mitochondrial DNA typing, Forensic Sci. Int. Genet. 13 (2014) 134–142, https://
[23] A. Nazari, D. Bajaj, D. Zhang, E. Romberg, D. Arola, Aging and the reduction in doi.org/10.1016/j.fsigen.2014.07.010.
fracture toughness of human dentin, J. Mech. Behav. Biomed. Mater. 2 (2009) [45] Qiagen Companies, Qiagen Companies. EZ1&2 DNA Investigator Handbook,
550–559, https://doi.org/10.1016/j.jmbbm.2009.01.008. Hilden, 2021.
[24] R.D. Barreto de Oliveira, F.B. de Sousa, A.A. Algarni, G.J. Eckert, A.T. Hara, [46] Promega Corporation, Promega Corporation. PowerQuant System Technical
Susceptibility of dental enamel of different ages to caries-like lesion development, Manual, Madison, WI, 2022.
Caries Res 54 (2020) 475–482, https://doi.org/10.1159/000509461. [47] Promega Corporation, PowerPlex ESI 17 Fast System for use on the Applied
[25] S.N. Tierney, J.M. Bird, Molecular sex identification of juvenile skeletal remains Biosystems Genetic Analyzers, Madison, WI, 2017.
from an Irish medieval population using ancient DNA analysis, J. Archaeol. Sci. 62 [48] M.J. Gardner, D.G. Altman, Confidence intervals rather than P values: estimation
(2015) 27–38, https://doi.org/10.1016/j.jas.2015.06.016. rather than hypothesis testing, Br. Med. J. Clin. Res. Ed. 292 (1986) 746–750.
[26] D. De Leo, S. Turrina, M. Marigo, Effects of individual dental factors on genomic [49] J. Carpenter, J. Bithell, Bootstrap confidence intervals: when, which, what? A
DNA analysis, Am. J. Forensic Med. Pathol. 21 (2000). 〈https://journals.lww.co practical guide for medical statisticians, Stat. Med. 19 (2000) 1141–1164.
m/amjforensicmedicine/Fulltext/2000/12000/Effects_of_Individual_Dental_Facto [50] T.J. DiCiccio, B. Efron, Bootstrap confidence intervals, Stat. Sci. 11 (1996)
rs_on_Genomic.23.aspx〉. 189–228, https://doi.org/10.1214/ss/1032280214.

7
T. Leskovar and I.Z. Pajnič Forensic Science International 353 (2023) 111882

[51] R. Furseth, A microradiographic and electron microscopic study of the cementum S. Popovici, P. Raczky, A. Simalcsik, T. Szeniczey, S. Vasilyev, C. Virag, N. Rohland,
of human deciduous teeth, Acta Odontol. Scand. 25 (1967) 613–645, https://doi. D. Reich, R. Pinhasi, A minimally destructive protocol for DNA extraction from
org/10.3109/00016356709019780. ancient teeth, Genome Res. 31 (2021) 472–483, https://doi.org/10.1101/
[52] D. Higgins, J.J. Austin, Teeth as a source of DNA for forensic identification of gr.267534.120.
human remains: a review, Sci. Justice 53 (2013) 433–441, https://doi.org/ [56] R.A. Rahmat, M.A. Humphries, N.A. Saedon, P.G. Self, A.M.T. Linacre, Diagnostic
10.1016/j.scijus.2013.06.001. models to predict nuclear DNA and mitochondrial DNA recovery from incinerated
[53] E. Alia-García, D. Parra-Pecharromán, A. Sánchez-Díaz, S. Mendez, A. Royuela, teeth, Int. J. Leg. Med. 137 (2023) 1353–1360, https://doi.org/10.1007/s00414-
L. Gil-Alberdi, J. López-Palafox, R. del Campo, Forensic identification in teeth with 023-03017-x.
caries, Forensic Sci. Int. 257 (2015) 236–241, https://doi.org/10.1016/j. [57] E. Chierto, G. Cena, R.W. Mann, G. Mattutino, E. Nuzzolese, C. Robino, Sweet
forsciint.2015.08.021. tooth: DNA profiling of a cranium from an isolated retained root fragment,
[54] D. Higgins, J. Kaidonis, G. Townsend, T. Hughes, J.J. Austin, Targeted sampling of J. Forensic Sci. 66 (2021) 1973–1979, https://doi.org/10.1111/1556-4029.14748.
cementum for recovery of nuclear DNA from human teeth and the impact of [58] H.A. Zander, B. Hürzeler, Continuous cementum apposition, J. Dent. Res. 37
common decontamination measures, Investig. Genet. 4 (2013) 18, https://doi.org/ (1958) 1035–1044, https://doi.org/10.1177/00220345580370060301.
10.1186/2041-2223-4-18. [59] D.W. Nitzan, Y. Michaeli, M. Weinreb, B. Azaz, The effect of aging on tooth
[55] É. Harney, O. Cheronet, D.M. Fernandes, K. Sirak, M. Mah, R. Bernardos, morphology: a study on impacted teeth, Oral. Surg. Oral. Med. Oral. Pathol. 61
N. Adamski, N. Broomandkhoshbacht, K. Callan, A.M. Lawson, J. Oppenheimer, (1986) 54–60, https://doi.org/10.1016/0030-4220(86)90203-3.
K. Stewardson, F. Zalzala, A. Anders, F. Candilio, M. Constantinescu, A. Coppa, [60] S. Kreiborg, B.L. Jensen, Tooth formation and eruption – lessons learnt from
I. Ciobanu, J. Dani, Z. Gallina, F. Genchi, E.G. Nagy, T. Hajdu, M. Hellebrandt, cleidocranial dysplasia, Eur. J. Oral. Sci. 126 (2018) 72–80, https://doi.org/
A. Horváth, Á. Király, K. Kiss, B. Kolozsi, P. Kovács, K. Köhler, M. Lucci, I. Pap, 10.1111/eos.12418.

You might also like