Kurt W. Alt

Ancient DNA from the first European farmers in 7500-year-old Neolithic sites

The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans.

Genome-wide patterns of selection in 230 ancient Eurasians

Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe’s first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

The importance of commensal microbes for human health is increasingly recognized, yet the impacts of evolutionary changes in human diet and culture on commensal microbiota remain almost unknown. Two of the greatest dietary shifts in human evolution involved the adoption of carbohydrate-rich Neolithic (farming) diets (beginning ∼10,000 years before the present) and the more recent advent of industrially processed flour and sugar (in ∼1850). Here, we show that calcified dental plaque (dental calculus) on ancient teeth preserves a detailed genetic record throughout this period. Data from 34 early European skeletons indicate that the transition from hunter-gatherer to farming shifted the oral microbial community to a disease-associated configuration. The composition of oral microbiota remained unexpectedly constant between Neolithic and medieval times, after which (the now ubiquitous) cariogenic bacteria became dominant, apparently during the Industrial Revolution. Modern oral microbiotic ecosystems are markedly less diverse than historic populations, which might be contributing to chronic oral (and other) disease in postindustrial lifestyles.

Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age

In 2005 four outstanding multiple burials were discovered near Eulau, Germany. The 4,600-year-old graves contained groups of adults and children buried facing each other. Skeletal and artifactual evidence and the simultaneous interment of the individuals suggest the supposed families fell victim to a violent event. In a multidisciplinary approach, archaeological, anthropological, geochemical (radiogenic isotopes), and molecular genetic (ancient DNA) methods were applied to these unique burials. Using autosomal, mitochondrial, and Y-chromosomal markers, we identified genetic kinship among the individuals. A direct child-parent relationship was detected in one burial, providing the oldest molecular genetic evidence of a nuclear family. Strontium isotope analyses point to different origins for males and children versus females. By this approach, we gain insight into a Late Stone Age society, which appears to have been exogamous and patrilocal, and in which genetic kinship seems to be a focal point of social organization.

Tracing the genetic origin of Europe's first farmers reveals insights into their social organization.

Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in todays Hungary. However, the genetic background of the LBK genesis is yet unclear. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (seventh/sixth millennia BC) from the Carpathian Basin and southeastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early southeastern European and Carpathian Basin farming cultures on Central European populations of the sixth–fourth millennia BC. Comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through southeastern Europe and the Carpathian Basin into Central Europe. However, our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting a system of patrilineal descent and patrilocal residential rules among the early farmers.

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)—the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

Human paleogenetics of Europe – The known knowns and the known unknowns

The number of ancient human DNA studies has drastically increased in recent years. This results in a substantial record of mitochondrial sequences available from many prehistoric sites across Western Eurasia, but also growing Y-chromosome and autosomal sequence data. We review the current state of research with specific emphasis on the Holocene population events that likely have shaped the present-day genetic variation in Europe. We reconcile observations from the genetic data with hypotheses about the peopling and settlement history from anthropology and archaeology for various key regions, and also discuss the data in light of evidence from related disciplines, such as modern human genetics, climatology and linguistics.

The massacre mass grave of Schöneck-Kilianstädten reveals new insights into collective violence in Early Neolithic Central Europe

Significance The Early Neolithic massacre-related mass grave of Schöneck-Kilianstädten presented here provides new data and insights for the ongoing discussions of prehistoric warfare in Central Europe. Although several characteristics gleaned from the analysis of the human skeletal remains support and strengthen previous hypotheses based on the few known massacre sites of this time, a pattern of intentional mutilation of violence victims identified here is of special significance. Adding another key site to the evidence for Early Neolithic warfare generally allows more robust and reliable reconstructions of the possible reasons for the extent and frequency of outbreaks of lethal mass violence and the general impact these events had on shaping the further development of the Central European Neolithic. Conflict and warfare are central but also disputed themes in discussions about the European Neolithic. Although a few recent population studies provide broad overviews, only a very limited number of currently known key sites provide precise insights into moments of extreme and mass violence and their impact on Neolithic societies. The massacre sites of Talheim, Germany, and Asparn/Schletz, Austria, have long been the focal points around which hypotheses concerning a final lethal crisis of the first Central European farmers of the Early Neolithic Linearbandkeramik Culture (LBK) have concentrated. With the recently examined LBK mass grave site of Schöneck-Kilianstädten, Germany, we present new conclusive and indisputable evidence for another massacre, adding new data to the discussion of LBK violence patterns. At least 26 individuals were violently killed by blunt force and arrow injuries before being deposited in a commingled mass grave. Although the absence and possible abduction of younger females has been suggested for other sites previously, a new violence-related pattern was identified here: the intentional and systematic breaking of lower limbs. The abundance of the identified perimortem fractures clearly indicates torture and/or mutilation of the victims. The new evidence presented here for unequivocal lethal violence on a large scale is put into perspective for the Early Neolithic of Central Europe and, in conjunction with previous results, indicates that massacres of entire communities were not isolated occurrences but rather were frequent features of the last phases of the LBK.

Parallel palaeogenomic transects reveal complex genetic history of early European farmers

Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 bc, n = 100), Germany (5500–3000 bc, n = 42) and Spain (5500–2200 bc, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.

Lombards on the Move – An Integrative Study of the Migration Period Cemetery at Szólád, Hungary

In 2005 to 2007 45 skeletons of adults and subadults were excavated at the Lombard period cemetery at Szólád (6th century A.D.), Hungary. Embedded into the well-recorded historical context, the article presents the results obtained by an integrative investigation including anthropological, molecular genetic and isotopic (δ15N, δ13C, 87Sr/86Sr) analyses. Skeletal stress markers as well as traces of interpersonal violence were found to occur frequently. The mitochondrial DNA profiles revealed a heterogeneous spectrum of lineages that belong to the haplogroups H, U, J, HV, T2, I, and K, which are common in present-day Europe and in the Near East, while N1a and N1b are today quite rare. Evidence of possible direct maternal kinship was identified in only three pairs of individuals. According to enamel strontium isotope ratios, at least 31% of the individuals died at a location other than their birthplace and/or had moved during childhood. Based on the peculiar 87Sr/86Sr ratio distribution between females, males, and subadults in comparison to local vegetation and soil samples, we propose a three-phase model of group movement. An initial patrilocal group with narrower male but wider female Sr isotope distribution settled at Szólád, whilst the majority of subadults represented in the cemetery yielded a distinct Sr isotope signature. Owing to the virtual absence of Szólád-born adults in the cemetery, we may conclude that the settlement was abandoned after approx. one generation. Population heterogeneity is furthermore supported by the carbon and nitrogen isotope data. They indicate that a group of high-ranking men had access to larger shares of animal-derived food whilst a few individuals consumed remarkable amounts of millet. The inferred dynamics of the burial community are in agreement with hypotheses of a highly mobile lifestyle during the Migration Period and a short-term occupation of Pannonia by Lombard settlers as conveyed by written sources.