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 Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform.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.

Dataset of oxygen, carbon, and strontium isotope values from the Imperial Roman site of Velia (ca. 1st-2nd c. CE), Italy.

The oxygen (δ18Ocarbonate), strontium (87Sr/86Sr), and previously unpublished carbon (δ13Ccarbonate) isotope data presented herein from the Imperial Roman site of Velia (ca. 1st to 2nd c. CE) were obtained from the dental enamel of human permanent second molars (M2). In total, the permanent M2s of 20 individuals (10 male and 10 female) were sampled at the Museo delle Civiltà in Rome (formerly the Museo Nazionale Preistorico Etnografico "L. Pigorini") and were subsequently processed and analysed at McMaster University. A subsample of teeth (n=5) was initially subjected to Fourier transform infrared spectroscopy (FTIR) analysis to assess for diagenetic alteration through calculation of crystallinity index (CI) values. Subsequently, tooth enamel was analysed for δ13Ccarbonate and δ18Ocarbonate (VPDB) using a VG OPTIMA Isocarb isotope ratio mass spectrometer (IRMS) at McMaster Research for Stable Isotopologues (MRSI), and 87Sr/86Sr was measured by dynamic multi-collection using a thermal ionization mass spectrometer (TIMS) in the School of Geography and Earth Sciences. The dental enamel isotope data presented represent the first δ18O, δ13Ccarbonate, and 87Sr/86Sr values analysed from Imperial Roman Campania to date, providing data of use for comparative analyses of δ18O, δ13C, and 87Sr/86Sr values within the region and for assisting in documenting human mobility in archaeological contexts. Full interpretation of the δ18O and 87Sr/86Sr data presented here is provided in "Imperial Roman mobility and migration at Velia (1st to 2nd c. CE) in southern Italy" [1].

Mapping the origins of Imperial Roman workers (1st-4th century CE) at Vagnari, Southern Italy, using 87 Sr/86 Sr and δ18 O variability.

OBJECTIVES: We obtained the oxygen and strontium isotope composition of teeth from Roman period (1st to 4th century CE) inhabitants buried in the Vagnari cemetery (Southern Italy), and present the first strontium isotope variation map of the Italian peninsula using previously published data sets and new strontium data. We test the hypothesis that the Vagnari population was predominantly composed of local individuals, instead of migrants originating from abroad. MATERIALS AND METHODS: We analyzed the oxygen (18 O/16 O) and strontium (87 Sr/86 Sr) isotope composition of 43 teeth. We also report the 87 Sr/86 Sr composition of an additional 13 molars, 87 Sr/86 Sr values from fauna (n = 10), and soil (n = 5) samples local to the area around Vagnari. The 87 Sr/86 Sr variation map of Italy uses 87 Sr/86 Sr values obtained from previously published data sources from across Italy (n = 199). RESULTS: Converted tooth carbonate (δ18 ODW ) and 87 Sr/86 Sr data indicate that the majority of individuals buried at Vagnari were local to the region. ArcGIS bounded Inverse Distance Weighting (IDW) interpolation of the pan-Italian 87 Sr/86 Sr data set approximates the expected 87 Sr/86 Sr range of Italy's geological substratum, producing the first strontium map of the Italian peninsula. DISCUSSION: Results suggest that only 7% of individuals buried at Vagnari were born elsewhere and migrated to Vagnari, while the remaining individuals were either local to Vagnari (58%), or from the southern Italian peninsula (34%). Our results are consistent with the suggestion that Roman Imperial lower-class populations in southern Italy sustained their numbers through local reproduction measures, and not through large-scale immigration from outside the Italian peninsula.

17th Century Variola Virus Reveals the Recent History of Smallpox.

Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1-4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4-9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4-6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18th and 19th centuries, concomitant with the development of modern vaccination.