Genome-Wide DNA from Degraded Petrous Bones and the Assessment of Sex and Probable Geographic Origins of Forensic Cases

Searching for alternative high DNA-yielding bone types for DNA analysis of aged skeletal remains

The petrous bone contains significantly higher amounts of DNA than any other human bone. Because of highly destructive sampling and because it is not always part of the recovered remains, the need for alternative sources of DNA is important. To identify additional optimal bone types, petrous bones were compared to femurs, tali, and calcanei sampled from 66 adult skeletons from two distinct modern-era Christian cemeteries. An extraction method employing full demineralization was used to obtain DNA, real-time PCR quantification to ascertain DNA quantity and degradation, and a commercial forensic short tandem repeats (STR) PCR amplification kit to determine genetic profiles. Statistical analysis was performed to explore the differences in DNA yield, DNA degradation, and success of STR amplification. A systematic studies exploring intra-skeletal variability in DNA preservation including various excavation sites differing by time period and geographical position are rare, and the second part of the investigation was based on a comparison of both archaeological sites, which allowed us to compare the effect of different post-mortem intervals and environmental conditions on DNA preservation. The older burial site in Črnomelj was active between the 13th and 18th century, whereas the more recent Polje burial was in use from the 16th to 19th century, creating different temporal and geographical environments. Results for the Črnomelj burial site revealed that the petrous bone outperformed all other bone types studied, except the calcaneus. At the Polje archeological site calcanei, tali, and femurs yielded the same STR typing success as petrous bones. The results obtained highlight the importance of careful bone sample selection for DNA analysis of aged skeletal remains. In addition to petrous bones, calcanei were found to be an alternative source of DNA when older burial sites are investigated. When more recent burial sites are processed, calcanei, tali, and femurs should be sampled besides petrous bones, not only because they exhibited good performance, but also because of easier sampling and easier grinding in the case of trabecular bones. This study contributes valuable insights into the potential use of various skeletal types as a source of DNA for investigation of aged skeletal remains, and it offers practical implications for forensic and archaeological investigations.

Accessory tympanic plate ossicle: a new osteological entity

The auricular cartilage, which is typically soft and flexible, can calcify or ossify because of diseases such as diabetes mellitus, trauma, radiation therapy for cancer, and more commonly from frostbite. Calcified, ossified, or hardened auricular cartilage is a rare finding in the clinical literature and appears to be absent in the physical and forensic anthropological literature. This study examines the ossified auricular cartilage and tests whether the hypothesis can be identified in postmortem skeletonized tissue and be part of the external auditory meatus. A total of 290 crania were examined for accessory ossicles. A descriptive and interpretative analysis was performed grossly, histologically, and morphometrically to document the morphology and location of the ossicles, investigate their structure, and perform hypothesis testing. Results revealed that seven females and one male crania from a total of 290 crania (2.76%) exhibit semi-ossified auricular cartilage attached to the tympanic plate of the temporal bone. The morphology and location of the ossicles at the junction of the auricle and external auditory meatus indicate they are hardened auricular cartilage that was verified with histological observations. Regression analysis indicates that addition of the ossicle to the depth of the auditory tube significantly changes coefficient of determination (R2) with respect to cranial breadth. In conclusion, results indicate that small cartilaginous structures of the external ear may ossify forming accessory tympanic plate ossicles that potentially could be identified in skeletal remains as a new osteological entity. This report highlights the types of information that can be gained using an approach that integrates forensic anthropology, gross anatomy, and histology.

Evaluation of a New DNA Extraction Method on Challenging Bone Samples Recovered from a WWII Mass Grave

Bones and teeth represent a common finding in ancient DNA studies and in forensic casework, even after a long burial. Genetic typing is the gold standard for the personal identification of skeletal remains, but there are two main factors involved in the successful DNA typing of such samples: (1) the set-up of an efficient DNA extraction method; (2) the identification of the most suitable skeletal element for the downstream genetic analyses. In this paper, a protocol based on the processing of 0.5 g of bone powder decalcified using Na2EDTA proved to be suitable for a semi-automated DNA extraction workflow using the Maxwell® FSC DNA IQ™ Casework Kit (Promega, Madison, WI, USA). The performance of this method in terms of DNA recovery and quality was compared with a full demineralisation extraction protocol based on Qiagen technology and kits. No statistically significant differences were scored according to the DNA recovery and DNA degradation index (p-values ≥ 0.176; r ≥ 0.907). This new DNA extraction protocol was applied to 88 bone samples (41 femurs, 19 petrous bones, 12 metacarpals and 16 molars) allegedly belonging to 27 World War II Italian soldiers found in a mass grave on the isle of Cres (Croatia). The results of the qPCR performed by the Quantifiler Human DNA Quantification kit showed values above the lowest Limit of Quantification (lLOQ; 23 pg/µL) for all petrous bones, whereas other bone types showed, in most cases, lower amounts of DNA. Replicate STR-CE analyses showed successful typing (that is, >12 markers) in all tests on the petrous bones, followed by the metacarpals (83.3%), femurs (52.2%) and teeth (20.0%). Full profiles (22/22 autosomal markers) were achieved mainly in the petrous bones (84.2%), followed by the metacarpals (41.7%). Stochastic amplification artefacts such as drop-outs or drop-ins occurred with a frequency of 1.9% in the petrous bones, whereas they were higher when the DNA recovered from other bone elements was amplified (up to 13.9% in the femurs). Overall, the results of this study confirm that petrous bone outperforms other bone elements in terms of the quantity and quality of the recovered DNA; for this reason, if available, it should always be preferred for genetic testing. In addition, our results highlight the need for accurate planning of the DVI operation, which should be carried out by a multi-disciplinary team, and the tricky issue of identifying other suitable skeletal elements for genetic testing. Overall, the results presented in this paper support the need to adopt preanalytical strategies positively related to the successful genetic testing of aged skeletal remains in order to reduce costs and the time of analysis.

Record-matching of STR profiles with fragmentary genomic SNP data

In many forensic settings, identity of a DNA sample is sought from poor-quality DNA, for which the typical STR loci tabulated in forensic databases are not possible to reliably genotype. Genome-wide SNPs, however, can potentially be genotyped from such samples via next-generation sequencing, so that queries can in principle compare SNP genotypes from DNA samples of interest to STR genotype profiles that represent proposed matches. We use genetic record-matching to evaluate the possibility of testing SNP profiles obtained from poor-quality DNA samples to identify exact and relatedness matches to STR profiles. Using simulations based on whole-genome sequences, we show that in some settings, similar match accuracies to those seen with full coverage of the genome are obtained by genetic record-matching for SNP data that represent 5-10% genomic coverage. Thus, if even a fraction of random genomic SNPs can be genotyped by next-generation sequencing, then the potential may exist to test the resulting genotype profiles for matches to profiles consisting exclusively of nonoverlapping STR loci. The result has implications in relation to criminal justice, mass disasters, missing-person cases, studies of ancient DNA, and genomic privacy.

A comparison between petrous bone and tooth, femur and tibia DNA analysis from degraded skeletal remains

Skeletal remains are the only biological material that remains after long periods; however, environmental conditions such as temperature, humidity, and pH affect DNA preservation, turning skeletal remains into a challenging sample for DNA laboratories. Sample selection is a key factor, and femur and tooth have been traditionally recommended as the best substrate of genetic material. Recently, petrous bone (cochlear area) has been suggested as a better option due to its DNA yield. This research aims to evaluate the efficiency of petrous bone compared to other cranium samples (tooth) and postcranial long bones (femur and tibia). A total amount of 88 samples were selected from 38 different individuals. The samples were extracted by using an organic extraction protocol, DNA quantification by Quantifiler Trio kit and amplified with GlobalFiler kit. Results show that petrous bone outperforms other bone remains in quantification data, yielding 15-30 times more DNA than the others. DNA profile data presented likeness between petrous bone and tooth regarding detected alleles; however, the amount of DNA extracted in petrous bones allowed us to obtain more informative DNA profiles with superior quality. In conclusion, petrous bone or teeth sampling is recommended if DNA typing is going to be performed with environmentally degraded skeletal remains.

More than urns: A multi-method pipeline for analyzing cremation burials

Burial rites of archaeological populations are frequently interpreted based on cremated remains of the human body and the urn they were deposited in. In comparison to inhumations, information about the deceased is much more limited and dependent on fragmentation, selection of body regions, taphonomic processes, and excavation techniques. So far, little attention has been paid to the context in which urns are buried. In this study, we combined archaeological techniques with anthropology, computed tomography, archaeobotany, zooarchaeology, geochemistry and isotopic approaches and conducted a detailed analysis on a case study of two Late Bronze Age urns from St. Pölten, Austria (c. 1430 and 1260 cal. BCE). The urns were recovered en-bloc and CT-scanned before the micro-excavation. Osteological and strontium isotope analysis revealed that the cremated remains comprised a young adult female and a child that died at the age of 10-12 years. Both individuals had been subject to physiological stress and were likely local. Animal bones burnt at different temperatures suggested different depositional pathways into the urn and pit as part of the pyre, food offerings, and unintentional settlement debris. Eight wild plant and five crop plant species appeared as part of the local landscape, as food offerings and fire accelerants. Sediment chemistry suggests that pyre remains were deposited around the urns during burial. Multi-element geochemistry, archaeobotany, and zooarchaeology provide insights into the Late Bronze Age environment, the process of cremation, the gathering of bones and final funerary deposition.

Human bony labyrinth as a sex indicator in subadults

Due to the durability and good preservation of the petrous bone in archaeological and forensic contexts, the value of the inner ear as a sex indicator has been evaluated in various studies. Previous findings suggest that the morphology of the bony labyrinth is not stable in the postnatal period. In this study, we aim to assess the sexual dimorphism of the bony labyrinth via analysis of computed tomography (CT) data obtained from 170 subadults (birth to 20 y.o.) and test whether the postnatal changes of the bony labyrinth affect the level of dimorphism in the inner ear. A set of 10 linear measurements of 3D labyrinth models as well as 10 size and shape indices were analyzed. Sexually dimorphic variables were used to produce sex estimation formulae with discriminant function analysis. The produced formulae allowed for the correct classification of up to 75.3 % of individuals aged from birth to 15 years old. Sexual dimorphism was not significant for individuals between 16 and 20 years of age. This study suggests that the morphology of the subadult bony labyrinth exhibits significant sexual dimorphism in individuals under 16 years of age, which can aid the forensic identification process. Although postnatal growth of the temporal bone seems to affect the level of sexual dimorphism present in the inner ear, the formulae created in this study could be used as an additional tool for sex estimation of subadult (<16 y.o.) remains.

Medico-Legal Issues in Cremation: Comparative Analysis of International Legislation

Cremation has seen a constant increase in popularity all around the world. Because of its extensively destructive nature, however, a series of medico-legal issues arise concerning identification, forensic autopsy, external examination, histological, toxicological and genetic exams to be performed not in the immediacy of death. The aim of this study is to compare the international legislation on cremation, seeking the response of various countries to their medico-legal issues. Several affinities but also some differences were found. Similarities include the need for a certificate by a medical examiner excluding any medico-legal issues and non-natural causes of death and the expression of consent to cremation given by the deceased when still alive otherwise by relatives. Significant differences were found in German law, which provides for a second medical examination prior to cremation and in Italian law providing for the medical examiner to collect biological samples from the body and store them for a minimum of ten years for any future purpose of justice. The Italian approach could give a plausible solution to the medico-legal issues raised by cremation with the imperative premise, however, we need to look deeply into its privacy and consent implications, cost-benefits rate, sample collection and storage protocol.

Eye and Hair Color Prediction of Ancient and Second World War Skeletal Remains Using a Forensic PCR-MPS Approach

To test the usefulness of the forensic PCR-MPS approach to eye and hair color prediction for aged skeletons, a customized version of the PCR-MPS HIrisPlex panel was used on two sets of samples. The first set contained 11 skeletons dated from the 3rd to the 18th centuries AD, and for each of them at least four bone types were analyzed (for a total of 47 samples). In the second set, 24 skeletons from the Second World War were analyzed, and only petrous bones from the skulls were tested. Good-quality libraries were achieved in 83.3% of the cases for the ancient skeletons and in all Second World War petrous bones, with 94.7% and 100% of the markers, respectively, suitable for SNP typing. Consensus typing was achieved for about 91.7% of the markers in 10 out of 11 ancient skeletons, and the HIrisPlex-S webtool was then used to generate phenotypic predictions. Full predictions were achieved for 3 (27.3%) ancient skeletons and 12 (50%) Second World War petrous bones. In the remaining cases, different levels of AUC (area under the receiver operating curve) loss were computed because of no available data (NA) for 8.3% of markers in ancient skeletons and 4.2% of markers in Second World War petrous bones. Although the PCR-based approach has been replaced with new techniques in ancient DNA studies, the results show that customized forensic technologies can be successfully applied to aged bone remains, highlighting the role of the template in the success of PCR-MPS analysis. However, because several typical errors of ancient DNA sequencing were scored, replicate tests and accurate evaluation by an expert remain indispensable tools.

DNA profiling from human bone cells in the absence of decalcification and DNA extraction

Bone cells are a suitable substrate for DNA analysis if required to identify the person from whom a sample was taken. Osteocytes, the most abundant cell type in bone, are embedded within mineralized bone matrix. To release DNA from osteocytes for subsequent analyses, either demineralization of the mineral matrix or an overnight incubation is routinely carried out. In this study, we report on a simplified and rapid approach to analyze preserved bone samples that omits this lengthy decalcification process. Nine tibial bone samples were processed to release matrix-free bone cells after fragmentation without the use of liquid nitrogen. Cell morphology was assessed by microscopy at 220× magnification following staining with Diamond^™ Nucleic Acid Dye. Based on the presence of stained nuclei, samples were processed either using a DNA extraction process or by a semi-direct PCR process. The analysis of the quantity and quality of DNA isolated by both methods was carried out by real-time PCR and STR profiling to assess inhibition of PCR and DNA degradation. All samples resulted in informative STR profiles with minimal indication of inhibitors. These results demonstrate a potential approach of STR profiling from matrix-free bone cells within 8 hours without decalcification and DNA extraction.

Costal cartilage ensures low degradation of DNA needed for genetic identification of human remains retrieved at different decomposition stages and different postmortem intervals

Introduction

The study aimed to evaluate if costal cartilage is a good source of DNA for genetic individual identification tests performed in forensic autopsies.

Materials and Methods

The study included samples of costal cartilage collected from 80 cadavers retrieved from different environments: indoors (flat/hospital), outdoors (primarily in the forest), a coal mine, a fire site, uninhabited buildings, a basement, bodies of fresh water, exhumation sites, and unknown locations. After isolation of DNA chondrocytes, T. Large autosomal chromosome (214 bp), T. Small autosomal chromosome (80 bp), and the Y chromosome (75 bp; for male cadavers), sequences were amplified using real-time PCR. Additionally, 23 autosomal short tandem repeat (STR) loci and 16 Y chromosome STR loci were amplified using multiplex PCR. Forensic DNA typing was done using capillary electrophoresis and all results were analyzed.

Results

There was no statistically significant difference in DNA concentration after T. Large, T. Small autosomal chromosome and the Y chromosome amplification between samples collected from cadavers retrieved from different environments. The DNA degradation index was the same regardless of the postmortem interval. The results show that it is possible to generate a full genetic profile from costal cartilage samples collected from cadavers retrieved from different environments and at different times elapsed after death.

Conclusions

The results suggest that costal cartilage can be routinely collected during forensic autopsies, especially from cadavers at the advanced decomposition stage.

Insights into Punic genetic signatures in the southern necropolis of Tharros (Sardinia)

BACKGROUND

Phoenician and Punic expansions have been protagonists of intense trade networks and settlements in the Mediterranean Sea.

AIMS

The maternal genetic variability of ancient Punic samples from the Sardinian necropolis of Tharros was analysed, with the aim to explore genetic interactions and signatures of past population events.

SUBJECTS AND METHODS

The mtDNA HVS-I and coding region SNPs were analysed in 14 Punic samples and 74 modern individuals from Cabras and Belvì (for which the HVS-II region was also analysed). The results were compared with 5,590 modern Euro-Mediterranean sequences and 127 ancient samples.

RESULTS

While contemporary groups fall within the genetic variability of other modern Sardinians, our Punic samples reveal proximity to present-day North-African and Iberian populations. Furthermore, Cabras and Belvì cluster mainly with pre-Phoenician groups, while samples from Tharros project with other Punic Sardinian individuals.

CONCLUSION

This study provides the first preliminary insights into the population dynamics of the Punic site of Tharros. While the number of currently available samples does not allow definitive investigation of the connection with indigenous Sardinian groups, our results seem to confirm internal migratory phenomena in the central-western Mediterranean and female participation in the Punic mobility.

Progress in forensic bone DNA analysis: Lessons learned from ancient DNA

Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.

Strontium isotope ratios related to childhood mobility: Revisiting sampling strategies of the calcined human pars petrosa ossis temporalis

RATIONALE

Strontium isotope analysis can be applied to the calcined human otic capsule in the petrous part (pars petrosa ossis temporalis; PP) to gain information on childhood mobility in archaeological and forensic contexts. However, only a thin layer of the otic capsule, the inner cortex, demonstrates virtually no remodelling. This paper proposes an improved sampling method for the accurate sampling of the inner cortex of the otic capsule to ensure that ⁸⁷ Sr/⁸⁶ Sr ratios related to early childhood are obtained.

METHODS

Calcined rib and diaphyseal fragments and PP from ten cremation deposits are sampled for strontium isotope analysis, whereby our improved sampling strategy is applied to sample the inner cortex of the otic capsule. This allows inter- and intraskeletal ⁸⁷ Sr/⁸⁶ Sr comparison within an Iron Age collection from Oss, The Netherlands.

RESULTS

Forty percent (4/10) of the calcined PP that were evaluated for this study show marked differences in ⁸⁷ Sr/⁸⁶ Sr (0.00035-0.00065) between the inner cortex and the bone sample surrounding this layer, the external cortex that has higher remodelling rates. Differences in ⁸⁷ Sr/⁸⁶ Sr between various skeletal elements also aided in the identification of the minimum number of individuals.

CONCLUSIONS

Our study demonstrates the problematic nature of the external cortex and stresses the need for a precise sampling method of the correct areas of the otic capsule. This can only be obtained by cutting the calcined PP midmodiolarly to enable adequate combustion degree assessment, and the correct identification and sampling of the inner cortex of the otic capsule.

Sexing the bony labyrinth: A morphometric investigation in a subadult and adult Belgian identified sample

In forensic anthropology, sex estimation is a fundamental step in assessing individual biological profiles when analyzing human skeletons. Yet, current methods are not reliable enough to allow an accurate sex identification of highly fragmented, burnt, or subadult remains. This paper aims to investigate sexual dimorphism of the bony labyrinth on both identified subadult and adult individuals. The bony labyrinth is of particular interest for sex estimation since it is alleged to complete size and maturation pre-pubertally and is located inside the petrous part of the temporal bone which protects it from taphonomic processes. The study was performed on 93 CT scans of identified individuals from two Belgian osteological collections (19-20th century) and from current pediatric images (Erasme hospital, Brussels). Linear and angular measurements were taken on 2D slices of right bony labyrinths. Intra- and interobservers error measurements were calculated. Statistical tests were used to unravel any morphological variations between subadult and adult bony labyrinths and to highlight differences between females and males, separately in subadults and adults. Linear discriminant functions were established by cross-validation and tested on an independent sample from Belgium. Some measurements were significantly different between subadults and adults, and between females and males within both subadult and adult samples. Univariate functions achieved 72.7% in subadults and 68.4% in adults whereas multivariate equations increased accuracy respectively up to 84.9% and 78.4%. This study entails promising results to design a sex estimation method suitable for fragmented and/or subadult remains. Further metric approaches are needed to explore bony labyrinth sexual dimorphism.

A systematic investigation of human DNA preservation in medieval skeletons

Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.

A novel method of male sex identification of human ancient skeletal remains

Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle.

Sequence conservation of mitochondrial (mt)DNA during expansion of clonal mammary epithelial populations suggests a common mtDNA template in CzechII mice

One major foundation of cancer etiology is the process of clonal expansion. The mechanisms underlying the complex process of a single cell leading to a clonal dominant tumor, are poorly understood. Our study aims to analyze mitochondrial DNA (mtDNA) for somatic single nucleotide polymorphisms (SNPs) variants, to determine if they are conserved throughout clonal expansion in mammary tissues and tumors. To test this hypothesis, we took advantage of a mouse mammary tumor virus (MMTV)-infected mouse model (CzechII). CzechII mouse mtDNA was extracted, from snap-frozen normal, hyperplastic, and tumor mammary epithelial outgrowth fragments. Next generation deep sequencing was used to determine if mtDNA “de novo” SNP variants are conserved during serial transplantation of both normal and neoplastic mammary clones. Our results support the conclusion that mtDNA “de novo” SNP variants are selected for and maintained during serial passaging of clonal phenotypically heterogeneous normal cellular populations; neoplastic cellular populations; metastatic clonal cellular populations and in individual tumor transplants, grown from the original metastatic tumor. In one case, a mammary tumor arising from a single cell, within a clonal hyperplastic outgrowth, contained only mtDNA copies, harboring a deleterious “de novo” SNP variant, suggesting that only one mtDNA template may act as a template for all mtDNA copies regardless of cell phenotype. This process has been attributed to “heteroplasmic-shifting”. A process that is thought to result from selective pressure and may be responsible for pathogenic mutated mtDNA copies becoming homogeneous in clonal dominant oncogenic tissues.