A Woman with a Sword? – Weapon Grave at Suontaka Vesitorninmäki, Finland

In 1968, a weapon grave with brooches was found at Suontaka Vesitorninmäki, Hattula, Finland. Since then, the grave has been interpreted as evidence of powerful women, even female warriors and leaders in early medieval Finland. Others have denied the possibility of a woman buried with a sword and tried to explain it as a double burial. We present the first modern analysis of the grave, including an examination of its context, a soil sample analysis for microremains, and an aDNA analysis. Based on these analyses, we suggest a new interpretation: the Suontaka grave possibly belonged to an individual with sex-chromosomal aneuploidy XXY. The overall context of the grave indicates that it was a respected person whose gender identity may well have been non-binary.

Lipid biomarker-based verification of TB infection in mother’s and daughter’s mummified human remains (Vác Mummy Collection, 18th century, CE, Hungary)

The perpetual burden of tuberculosis (TB) keeps drawing the focus of research on this disease. Among other risk factors (e.g., poor living conditions, malnutrition, smoking, HIV infection, etc.), being in close contact with a TB infected person requires special attention. For a better understanding of the disease, paleopathological investigations concerning TB have been carried out with various techniques for a long a time; nevertheless, analysis of incidence among family members is hardly possible in past populations. An exceptional group of naturally mummified individuals, the collection of the Vác mummies (Hungary, 18th century CE), is known about the large TB incidence rate, which has been revealed by aDNA analysis. Besides the high rate of TB infection, another interesting aspect of the collection is that in some cases, the family connections could be reconstructed. In this paper, we present the mycocerosic acid profiles gained by HPLC-HESI-MS measurements of two Vác mummies, who were mother and daughter according to the personal records. Earlier metagenomic analysis already revealed mixed M. tuberculosis infection with the same bacterial strains in both individuals; moreover, the same bacterial strains were recorded in both cases.

Successful extraction of insect DNA from recent copal inclusions: limits and perspectives

Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.

New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples

Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.

Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic

Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia.

Combining Ancient DNA and Radiocarbon Dating Data to Increase Chronological Precision

This paper examines how ancient DNA data can enhance radiocarbon dating. Because there is a limit to the number of years that can separate the dates of death of related individuals, the ability to identify first-, second-, and third-degree relatives through aDNA analysis can serve as a constraint on radiocarbon date range estimates. To determine the number of years that can separate related individuals, we modeled maximums derived from biological extremes of human reproduction and death ages and compiled data from historic and genealogical death records. We used these estimates to evaluate the date ranges of a global dataset of individuals that have been radiocarbon dated and for which ancient DNA analysis identified at least one relative. We found that many of these individuals could have their date ranges reduced by building in date of death separation constraints. We examined possible reasons for date discrepancies of related individuals, such as dating of different skeletal elements or wiggles in the radiocarbon curve. Our research demonstrates that when combined, radiocarbon dating and ancient DNA analysis can provide a refined and richer view of the past.

COMBINING ANCIENT DNA AND RADIOCARBON DATING DATA TO INCREASE CHRONOLOGICAL PRECISION

This paper examines how ancient DNA data can enhance radiocarbon dating. Because there is a limit to the number of years that can separate the dates of death of related individuals, the ability to identify first-, second-, and third-degree relatives through aDNA analysis can serve as a constraint on radiocarbon date range estimates. To determine the number of years that can separate related individuals, we modeled maximums derived from biological extremes of human reproduction and death ages and compiled data from historic and genealogical death records. We used these estimates to evaluate the date ranges of a global dataset of individuals that have been radiocarbon dated and for which ancient DNA analysis identified at least one relative. We found that many of these individuals could have their date ranges reduced by building in date of death separation constraints. We examined possible reasons for date discrepancies of related individuals, such as dating of different skeletal elements or wiggles in the radiocarbon curve. Our research demonstrates that when combined, radiocarbon dating and ancient DNA analysis can provide a refined and richer view of the past.

Ancient DNA Analysis of the Thulamela Remains: Deciphering the Migratory Patterns of a Southern African Population

Ancient DNA (aDNA) analysis was employed to obtain information on the population relationships of the two Thulamela individuals (AD 1400-1700) and six other skeletons from various archaeological sites of the southern African Iron Age – Tuli (Botswana), Nwanetsi, Makgope, Happy Rest and Stayt. Although sequences were short, it seems that the Thulamela female aligns somewhat more with eastern populations as opposed to the male who aligns more with western groups. This result is not surprising given that the two individuals were buried at the same site but their burials were hundreds of years apart. It was also possible to identify genetic links between the Iron Age individuals and modern southern African populations (e.g. some of the skeletons assessed showed maternal genetic similarities to present-day Sotho/Tswana groups) and to separate the samples into at least two genetic groups. Poor quality and quantity of DNA meant that only haplogroups, not subhaplogroups, of the individuals could be traced.

Ancient DNA

This chapter examines how ancient DNA (aDNA) analysis has helped reconstruct ancient history. It focuses in particular on cases investigating Roman history. History leaves traces in the human genome as well as those of pathogens and domesticates. While much can be gleaned from the genetic fossils preserved in extant genomes, genomes are palimpsests, with more recent events overwriting previous ones in part. The study of aDNA—DNA preserved in archaeological, paleontological, and museum sources—permits investigations into the genome before and after historic events and observations into how it evolves in real time. The field of aDNA also has a palimpsestic nature in which older results are not only extended and revised, but totally discarded due to rapid technological advances. The chapter briefly describes biochemistry of ancient DNA and the history of its research. Through several key case studies, it shows the potential for aDNA research to clarify the course of ancient history, and also highlights some of its weaknesses and limitations.