Kinship in Aegean Prehistory? Ancient DNA in Human Bones from Mainland Greece and Crete

Attempts were made to detect ancient DNA (aDNA) in samples of 89 human skeletons from Neolithic and Bronze Age sites in Greece and Crete. Ancient DNA was absent in specimens from Nea Nicomedia, Lerna, Kato Zakro: Karaviádena, and Mycenae Grave Circle A. For each of three skeletons sampled from Antron Grave Circle B, polymerase chain reactions (PCRs) gave products for nuclear but not mitochondrial DNA, but the yield of DNA was low and inconsistent, with replicate PCRs failing to give reproducible results. At Kouphovouno evidence for mitochondrial and/or nuclear aDNA was obtained from eight of the 20 skeletons that were examined, while at Mycenae Grave Circle B evidence for mitochondrial aDNA was obtained for four of the 22 skeletons that were studied, and in two cases confirmed the evidence of close kinship that had already been suggested by facial reconstruction: this in turn raises interesting questions of social relationships and the role of high-status women in MBA/LBA society. We conclude that, although aDNA might be present in some Eastern Mediterranean skeletons from later centuries of the Bronze Age, it is not commonly found in material from this period and is likely to be absent from older material.Στη μελέτη αυτή έγιναν προσπάθειες να αναγνωριστεί αρχαίο DNA (aDNA) σε δείγματα ογδόντα εννέα ανθρώπινων σκελετών προερχομένων από θέσεις της Νεολιθικής περιόδου και της Εποχής του Χαλκού στην Ελλάδα και την Κρήτη. Αρχαίο DNA δεν εντοπίστηκε σε δείγματα από τη Νέα Νικομήδεια, τη Λέρνα, την Κάτω Ζάκρο (Καραβιάδενα) και τον Ταφικό Κύκλο Α των Μυκηνών. Για κάθε έναν από τους τρεις σκελετούς, οι οποίοι εξετάστηκαν από τον Ταφικό Κύκλο Β της Αντρώνας, οι αλυσιδωτές αντιδράσεις πολυμεράσης (PCRs) απέφεραν αποτελέσματα για πυρηνικό αλλά όχι μιτοχονδριακό DNA. Η παραγωγή DNA ήταν χαμηλή και αντιφατική, με τα αντίγραφα πολυμεράσης να αποτυγχάνουν να αποφέρουν αναπαραγώγιμα αποτελέσματα. Στο Κουφόβουνο οκτώ από τους είκοσι σκελετούς, που εξετάστηκαν, έδωσαν στοιχεία για μιτοχονδρνακό ή/και πυρηνικό DNA, ενώ στον Ταφικό Κύκλο Β των Μυκηνών ενδείξεις για μιτοχονδριακό DNA έδωσαν τέσσερεις από τους είκοσι δύο σκελετούς, που μελετήθηκαν. Σε δύο περιπτώσεις επιβεβαιώθηκε η ένδειξη στενής συγγένειας, κάτι το οποίο είχε ήδη προταθεί με την αποκατάσταση των προσώπων: το γεγονός αυτό εγείρει ενδιαφέροντα ερωτήματα σχετικά με τις κοινωνικές σχέσεις και το ρόλο γυναικών υψηλής κοινωνικής στάθμης στην κοινωνία της Μέσης και της Ύστερης Εποχής του Χαλκού. Συμπεραίνουμε ότι, αν και μπορεί να αναγνωριστεί DNA σε ορισμένους σκελετούς της Ανατολικής Μεσογείου των τελευταίων αιώνων της Εποχής του Χαλκού, δεν εντοπίζεται συχνά σε υλικό αυτής της εποχής και ενδεχομένως απουσιάζει από παλαιότερο υλνκό.</jats:p

Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine

This study provides direct evidence of the dependency on relief food in Ireland around the time of the Great Famine (1845 to 1852) through dental calculus analysis of archaeological human remains. The findings show a dominance of corn (maize) and milk from the identified foodstuffs and corroborate the contemporaneous historical accounts of diet and subsistence. It shows that microparticle and proteomic analyses, even when based on small archaeological samples, can provide a valid snapshot of dietary patterns and food consumption. The occurrence of egg protein, generally only included in the diet for the better-off social classes, also highlights how these analytical techniques can provide unanticipated insights into the variability of diet in historical populations.Food and diet were class markers in 19th-century Ireland, which became evident as nearly 1 million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845 to 1852. Famine took hold after a blight (Phytophthora infestans) destroyed virtually the only means of subsistence—}the potato crop{—}for a significant proportion of the population. This study seeks to elucidate the variability of diet in mid{–}19th-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the famine. The samples derive from remains of people who died between August 1847 and March 1851 while receiving poor relief as inmates in the union workhouse in the city of Kilkenny (52{°}39' N, -7{°}15' W). The results corroborate the historical accounts of food provisions before and during the famine, with evidence of corn (maize), potato, and cereal starch granules from the microparticle analysis and milk protein from the proteomic analysis. Unexpectedly, there is also evidence of egg protein{—}a food source generally reserved only for export and the better-off social classes{—which highlights the variability of the prefamine experience for those who died. Through historical contextualization, this study shows how the notoriously monotonous potato diet of the poor was opportunistically supplemented by other foodstuffs. While the Great Irish Famine was one of the worst subsistence crises in history, it was foremost a social disaster induced by the lack of access to food and not the lack of food availability

Metagenomic analysis of Ancient Egyptian canopic jars

Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation—liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts. Objectives In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past. Methods We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR). Results Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome. Discussion In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material – and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts

Genomic palaeoparasitology traced the occurrence of Taenia asiatica in ancient Iran (Sassanid Empire, 2th cent. CE-6th cent. CE)

Palaeoparasitology investigates parasitological infections in animals and humans of past distance by examining biological remains. Palaeofaeces (or coprolites) are biological remains that provide valuable information on the disease, diet, and population movements in ancient times. Today, advances in detecting ancient DNA have cast light on dark corners that microscopy could never reach. The archaeological site of the Chehrabad salt mine of Achaemenid (550-330 BC) and Sassanid (third-seventh century AD) provides remains of various biotic and abiotic samples, including animal coprolites, for multidisciplinary studies. In the present work, we investigated coprolites for helminth eggs and larvae by microscopy and traced their biological agents' DNA by Next Generation Sequencing. Our results revealed various helminths, including Taenia asiatica, the species introduced in the 1990s. Implementing advanced modern molecular techniques like NGS gives a paramount view of pathogenic agents in space and time

Proteomic evidence of dietary sources in ancient dental calculus.

Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300-2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380-975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707