A comparison of crystal structure in fresh, burned and archaic bone - Implications for forensic sampling

Targeted enrichment of whole-genome SNPs from highly burned skeletal remains

Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality and quantity using next-generation sequencing (NGS). We present whole-genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed-effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole-genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures <350°C are the most likely sources for higher genomic DNA yields. Furthermore, we observed an inverse correlation between the number of captured SNPs and the extent to which samples were burned, as well as a significant decrease in the total number of SNPs measured for samples subjected to temperatures >350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.

Raman Spectra and Ancient Life: Vibrational ID Profiles of Fossilized (Bone) Tissues

Raman micro-spectroscopy is a non-destructive and non-contact analytical technique that combines microscopy and spectroscopy, thus providing a potential for non-invasive and in situ molecular identification, even over heterogeneous and rare samples such as fossilized tissues. Recently, chemical imaging techniques have become an increasingly popular tool for characterizing trace elements, isotopic information, and organic markers in fossils. Raman spectroscopy also shows a growing potential in understanding bone microstructure, chemical composition, and mineral assemblance affected by diagenetic processes. In our lab, we have investigated a wide range of different fossil tissues, mainly of Mesozoic vertebrates (from Jurassic through Cretaceous). Besides standard spectra of sedimentary rocks, including pigment contamination, our Raman spectra also exhibit interesting spectral features in the 1200-1800 cm-1 spectral range, where Raman bands of proteins, nucleic acids, and other organic molecules can be identified. In the present study, we discuss both a possible origin of the observed bands of ancient organic residues and difficulties with definition of the specific spectral markers in fossilized soft and hard tissues.

Physicochemical Changes in Bone Bioapatite During the Late Postmortem Interval Pre- and Post-Burning

Postmortem chemical transformation of bone bioapatite can take place during early diagenesis, resulting in a more thermodynamically stable mineral phase. This paper examines the impact of a one year postmortem interval on unburnt and burnt bone's structural and chemical alterations. This question is of importance for the reconstruction of funerary practices involving cremation in the archaeological record, as well as forensic anthropological investigations. Fleshed pig (Sus scrofa) tibiae were left exposed in a field, then collected at 14, 34, 91, 180, and 365 day intervals prior to being burnt in an outdoor fire (≤750 °C bone temperature). Fresh (fleshed) tibiae acted as unburnt and burnt controls. Also included in the study were two cremated human bone fragments from Middle-Late Neolithic (ca. 3300-2500 BCE) Ireland. Samples were analyzed for major and trace elements using an electron microprobe wavelength dispersive analyzer and molecular structures using Fourier transform infrared spectroscopy. Linear regression, principal component analysis, linear discriminant analysis, and multivariate analysis of variance were performed for statistical analysis. Results indicate that the concentrations of elements associated with extracellular fluid (K, Na, and Cl) change with the postmortem interval (PMI) and survive burning. K values under 0.07 ± 0.01 wt% in the inner and mid-cortical zones of burnt bones suggest that bones were not burnt immediately after death. Using this criterion, results from the archaeological samples would indicate a PMI of at least weeks to months prior to cremation. Ca, P, Fe, Al, Si, and Sr are not significantly altered with burning, and Fe, Al, Si, and Sr are also unaffected by the PMI. In unburnt bones increased crystallinity and carbonate loss are detectable in <1 year, but both are obscured by burning. Structurally, the carbonate to phosphate ratio (C/P), the phosphate high temperature, and cyanamide to phosphate (CN/P) are the most useful ratios for discriminating between unburnt and burnt bones.

Comparison of bone demineralisation procedures for DNA recovery from burned remains

Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.