"Maternal lineages from Iron Age to present in Eastern Fennoscandia S. Översti
Introduction: aDNA has revealed that the Neolithization involved a turnover of maternal lineages in Europe: haplogroup (hg) U, dominating in hunter-gatherers, was widely replaced by the farmer-associated hgs such as H. As a result, modern European populations show different proportions of these hgs. In Finland, mtDNA diversity resembles that observed in other populations, but holds relatively high frequency of U and shows internal substructure: U is more common in the north-east (NE) Finland and farmer-associated hgs in the south-west (SW). This pattern has been interpreted to reflect the arrival of agriculture from the south-west, most likely associated to the spread of the Corded Ware Culture c. 4,500 ya. Objectives: To provide insight into the past of Eastern Fennoscandia, complete mtDNA genomes from Iron Age to Medieval Era were obtained from Finland. These derived from five burial grounds, of which Levänluhta (300-800 AD, N=13), Luistari (600- 1130 AD, N=10) and Kirkkailanmäki (1100-1200 AD, N=16) are located in SW Finland, and Kylälahti (1200-1400 AD, N=14) and Tuukkala (1200-1400 AD, N=19) sites in south-eastern (SE) Finland. Methods: Extraction of aDNA was performed as in Meyer et al. 2010 and mtDNA capture as in Dabney et al. 2013. Raw sequence data processing was performed with EAGER and Schmutzi. Statistical analyses were calculated in Arlequin 3.5.2.2. Results: The 72 haplotypes obtained belong to hgs observed in modern Finns, but the frequencies differ both from the modern population and between studied sites: the SW sites showed higher frequency of U (60%) than the SE sites (19%) or the modern data (23 %). H showed an opposite trend: 52% in SE and 27% in SW. On sequence level, SW sites have higher affinity to the modern NE, while SE sites cluster with modern SW. Furthermore, within the SW sites the distribution of U subhaplogroups is uneven: Levänluhta has high frequency of U5a and Saami-related hg U5b1b1a whereas other SW sites show relatively high frequencies of U4. Conclusion: Our results suggest an interpretation that among the studied sites and modern Finns, there are varying levels of admixture of three ancestries: Saami (U5b1b1), possible non-Saami hunter-gatherers (U4, U5a) and farmers (H, J, T, K). The high prevalence of H in the eastern sites might reflect bidirectional arrival of the farming-associated populations into Finland, challenging the traditional assumption of the spread of agriculture from the south-west."
"Paleogenetic study of ancient archaeological finds related to Kazakh ethnogenesis N. Nurzhibek
Ethnic history of the Kazakh people is rooted in the ancient period of settling the territory of modern Kazakhstan. The 1st archaeological finds in the territory of Kazakhstan belong to the Paleolithic period. According to archaeological and paleoanthropological data, the ancient tribes spread on the territory of Kazakhstan since the Bronze Age. We studied the genetic structure of the modern Kazakhs population based on the information about pedigree analysis (shezhire) and Y-chromosome (875 persons) and mtDNA characteristics (130 persons). The DNA-analysis of two important archaeological finds, which can provide the information about ancient Human migrations and Kazakh ethnogenesis, was conducted: 1) bone remains belonging to the object of Hun elite from Hungarian Natural History Museum, dated to the middle third of the V century CE; 2) a cranium of Eneolithic period human from Botai settlement dated IV-III millennium BC. To the paleo-DNAs analysis the historical data were studied, the archaeological and anthropological evidences were obtained. It was revealed that Hun period bone remains from Hungary are characterized by R1a haplotype of Y-chromosome and D4j12 haplotype of mtDNA, that testifies the Asian origin of ancient object"s paternal and maternal lines. The phylogenetic and bioinformation analysis determines the genetic proximity of the ancient Hun with ancient and modern populations from Asia and suggests the possibility of ancient people migrations from the Asia Minor to Central and East Asia via Tibet. Comparison of ancient object"s DNA with DNAs of modern descendants of the historically mixed protopopulation Argyn, considering intratribal clans, does not reject the genetic affinity of paternal lines between ancient object and the descendants of ArgynMeiram (Suindyk and Karakesek) clan, and ancient maternal line with maternal lines of Argyn-Momyn-Sarzhetim clan descendants. Our results show that Eneolithic period man from settlement Botai, characterizes by Y-chromosome haplotype R1b1a1 and mtDNA haplotype K1b2 and the female individual is Z1mtDNA haplotype. The Eneolithic Botai individuals are closest to each other in the PC space than to any other ancient or present-day individual, and are in proximity to the upper Paleolithic Siberians from the Mal"ta or Afontova Gora archaeological sites. Botai represents a separate group that has genetic similarity with both European and Asian populations."
"Genetic diversity and social stratification in prehistoric Balkans – genomes, culture and the rise of complex societies S. Freilich1 , R. Pinhasi1 1 University of Vienna, Anthropology, Vienna, Austria
New whole genomes from Neolithic and Bronze Age Balkan specimens have been sequenced in order to assess intrapopulation genetic signatures and reconstruct ancestry in the context of social stratification as indicated in the archaeological record. The Balkan Peninsula was an important corridor for the first migrating farmers into Europe, and is a key region for understanding what impact the arrival of Neolithic migrants had on both social organisation and genetic composition in early settlements. A paucity of Balkan specimens means questions remain regarding hunter-gatherer and farmer interactions, and how social stratification developed following the Neolithic transition. Do genetic substructures correlate with intra-cemetery inequalities visible in the funerary record, and how was social status conceived? Almost forty Starčevo inhumations from the Neolithic site of Beli Manastir-Popova Zemlja are found in contracted position with ceramic vessels placed by their head, while a minority are deposited atypically in a channel. In addition, the nearby site of Bronze Age Jagodnjak-Krčevine contains inhumations accompanied by varying numbers and types of grave goods. Aims include identification of SNPs to investigate biogeographic origins, phenotype, admixture, and sex-specific mobility patterns. Furthermore, relationships to other ancient and modern Eurasian samples are investigated, as well as demographic patterns of migration and impacts on human genomic diversity. Petrous bones of 28 specimens were sampled for aDNA and extracts built into libraries. Whole genome shotgun sequencing was performed to above 1X coverage, followed by strict quality control measures and bioinformatic analyses to identify SNPs and perform tests of genomic variation and ancestry. Preliminary results from principal components analysis for nuclear SNP data show Bronze Age samples plotting uniformly, while two Neolithic specimens plot slightly out of expected range. Further measures of genetic diversity including admixture analysis, together with results of haplogroup assignment will be presented to clarify their origin and intra-population genetic substructures. Carbon, nitrogen and strontium stable isotope analysis from the same individuals will complement these results to further investigate dietary status and mobility patterns in relation to the development of social organisation in this understudied area."
"Characterizing the mesolthic to neolthic transition in central and southern Italy using genome-wide data from 10,000 to 6,000-year-old individuals A. Fromentier1
The Mesolithic period in Italy stretches from ~9,000 BC to ~6,200 BC and consists of two main phases, both characterized by different technologies: Mesolithic I (Sauveterrian, ~9,000 BC to ~6,800 BC ) and Mesolithic II (Castelnovian, ~6,800 BC to ~6,200 BC). While the archaeological record in northern Italy is abundant and follows a standard transition from Mesolithic I to II, the record from Central/Southern Italy is much more scarce. Additionally, many Mesolithic sites found in the Center/South still display Paleolithic features, and are immediately followed by the Neolithic originating in the Fertile Crescent, which reached the Adriatic coast around 6,200 BC before spreading quickly in the Italian peninsula. Overall, the Paleolithic/Mesolithic/Neolithic transitions within Central/Southern Italy remains poorly understood. In particular, the existence of both possible contacts between Mesolithic hunter-gatherers and Neolithic farmers and possible exchanges between Sicily and Tunisia, as suggested from cultural evidence, remain unclear. In order to answer these questions, we have developed a project aimed at collecting genome-wide sequence data from multiple individuals of the Mesolithic and Neolithic archaeological sites in Central/Southern Italy and Tunisia."
"Investigation of mitochondrial genomes of medieval populations (6-12th centuries AD) lived in the Ural and Volga-Kama region in context with early Hungarian
Different scientific theories exist about the origin of early Hungarians and their migration from North-Central Asia to Central Europe in the 8-9th centuries. The Hungarian conquerors arrived in the Carpathian Basin 895 AD. Until their arrival they migrated with attached folk elements that joint along the way westwards from the Ural region through the Middle-Volga region on the East-European steppe. The first relics from archaeological cultures that are most probably connected with Hungarian ancestors – the Kusnarenkovo and Karajakupovo cultures – were found in the regions of the Central and Southern Urals. The exact origin, route and chronology of the migration is still unclear and intensively debated by historians, linguists and archaeologists. In our research, we are approaching these issues with archeogenetic methods. We investigate Medieval (6-12th century) populations from the Ural region, the Carpathian Basin and principal sites of the supposed migration route, which territories had archaeological connections to each other and to early Hungarians. Our test object is the mitochondrial genome (mtDNA), which makes possible to determine the maternal descent line due to its special inheritance. We compare our complete mitochondrial genome sequences with modern and ancient populations, thereby we aim to explore the migration of Hungarian Conquerors. We examined samples from east side of the Central-Ural, from its west side and from Volga-Kama region. We sequenced the whole mitochondrial DNA of more than 65 samples, and determined mitochondrial DNA haplogroups. Based on our preliminary results, the populations are heterogeneous, in all of them appear both European and Asian haplogroups, but in different proportions. The Uralian populations show Central and Northeast Asian mtDNA composition, whereas the WestUralian population has more connections to Eastern Europe and to the Caucasus. Certain haplotypes connect the investigated Central Eurasian communities to the first Hungarians in the Carpathian Basin, although the Asian lineages were diluted along the way of migration and during the conquest of the new homeland. With these new information, we can get closer to understand the migration of Hungarian Conquerors and the maternal genetic composition of the Medieval populations of Central Eurasia."
"Population dynamics at Late Chalcolithic and Early Bronze Age Arslantepe, Anatolia E. Skourtanioti1
While Anatolia was highlighted as the genetic origin of early Neolithic European farmers, the genetic substructure in Anatolia itself as well as the demographic and cultural changes remain unclear. In eastern Anatolia, the archaeological record reflects influences from North-Central Anatolia, the northeastern sectors of Fertile Crescent and the Caucasus, and suggests that some of these were brought along with the movement of people. Central to this question is the archaeological site of Arslantepe (6th-1st millennium BC), strategically located at the Upper Euphrates, the nexus of all three regions. Arslantepe also developed one of the first state societies of Anatolia along with advanced metal-technologies. Archaeological research suggests that conflicts with surrounding groups of pastoralists affiliated to the Caucasus might have contributed to the collapse of its palatial system at the end of the Chalcolithic period (4th millennium BC). To test if these developments were accompanied by genetic changes, we generated genome-wide data from 18 ancient individuals spanning from the Late Chalcolithic period to the Early Bronze Age of Arslantepe. Our results show no evidence for a major genetic shift between the two time periods. However, we observe that individuals from Arslantepe are very heterogeneous and differentiated from other ancient western and central Anatolians in that they have more Iran/Caucasus related ancestry. Our data also show evidence for an ongoing but also recent confluence of Anatolian/Levantine and Caucasus/Iranian ancestries, highlighting the complexity of the Chalcolithic and Bronze Age periods in this region."
After the early Neolithic, there was genetic admixture.
"Paleogenomics of populations in France, from the Neolithic to the Bronze Age S. Brunel
Expanding from Anatolia into Europe about 7,500 years ago, the Neolithic culture based on agriculture followed two different routes, through the Balkans along the Danube northwards to the Hungarian plain and from there westwards to arrive in the Parisian Basin, and along the coastline of the Mediterranean basin to arrive in Southern France and Spain. Both migration waves eventually reached the territory of present-day France, where the Neolithic culture further evolved and was later replaced by the Bronze Age culture, over the course of the third and second millennia BC. While France is a geographic crossroads that provided multiple opportunities for interaction between populations of different origins, as is well documented by the archaeological record, the underlying demographic processes were not yet explored at a territory-wide scale . Here we present the complete mitochondrial genomes, Y chromosome markers and genotypes on a number of nuclear loci of interest obtained through a DNA enrichment approach of 163 Mesolithic, Neolithic and Bronze Age individuals sampled from three regions of present-day France, the North, the East, and the South. This study provides, for the first time, a highresolution 4000-year transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes associated with known phenotypes. This transect that comprises two major cultural transitions (Mesolithic-Neolithic and Neolithic-Bronze Age), reveals contrasting population dynamics between northern and southern France. The study of 120 nuclear SNPs, covering both physical and physiological traits, allowed us to follow the evolution of the allelic frequency over time of several phenotypes that characterize modern Europeans. This study fills a large gap in the understanding of the peopling of western Europe from the Mesolithic to the Bronze Age, completing the knowledge of the global process of the Neolithization of Europe."
"After the plague – genetic history of the human population of Medieval Cambridge T. Kivisild
"After the plague" is a collaborative project that combines methods of archaeology, history, osteoarchaeology, isotopes and ancient DNA of both humans and pathogens for the study of the people of Medieval Cambridge. Low coverage shotgun sequence data has been generated from more than 80 individual samples from an urban cemetery of the Hospital of St John the Evangelist, contextualized with similar data produced from other contemporary local cemeteries, including individuals of various social background, and a time transect of Cambridgeshire, with an aim to understand the effects of the Black Death epidemic(s) of 1347-1351 on the health status and genetic composition of a Medieval town population. Analyses focused on the reads mapping to the human reference genome aimed to explore how the epidemic influenced genetic diversity of the population at the scale of the entire genome and whether individual genes, those associated with immunity in particular, have shown more change than other genes. Genome-wide data has also been used to assess the diversity of urban Medieval Cambridge after the establishment of the university and the level of immigration from continental Europe among various social groups of the town."
This Zink group is as slow as molasses. Are they just skiing all the time?
"Genomic diversity of ancient individuals from the Iceman´s territory in the Eastern Italian Alps V. Coia
"Since the prehistory, the Eastern Italian Alps have been a meeting point for people with different origin. Various cultural material as well as funerary rituals documented in this region during the Copper Age (~3700-2200 a.C), suggests several contacts with non-local cultures from east and west Europe during that time. The Tyrolean Iceman (3360-3100 cal. BC) is the best representative of the Copper Age in the Eastern Alps. So far, besides the Tyrolean Iceman, only one Mesolithic sample (Veneto Dolomites) has been genetically analysed from this area. Therefore, there is a lack of regional ancient genomic data to better understand the genomic diversity of prehistoric alpine groups. Comparison with ancient and modern samples, have shown that the Iceman clusters with Early Neolithic farmers from different parts of Europe and with Neolithic individuals from Anatolia. In addition, European individuals contemporary of the Iceman cluster together. These Copper Age individuals also differ from the Iceman in their ancestry and admixture patterns, showing different proportions of Neolithic, hunter gatherers and Eastern (Yamnaya) ancestry components. Since the Iceman alone cannot be considered as representative of the genomic diversity of this alpine area, we are analyzing in this study seven additional prehistoric individuals from the Iceman´s territory. Two samples have approximately the same dating of the Iceman while the other are dating to the Middle Neolithic and to the Copper-Early Bronze Age. The new data will give us the opportunity to better understand the genomic diversity of Eastern Italian Alps and the Iceman´s genetic history. Furthermore, with additional genomic data from this crucial South-eastern European area, we will contribute to know more about the main demographic events that occurred in prehistoric Europe. First shotgun analyses of four pars petrosa samples indicate high percentage of endogenous content (from ~9% to 52%) and low mitochondrial contamination rates. All individual will be now further subjected to deeper sequencing aiming to perform genome-wide comparative analyses with the Iceman and a dataset of European and Near Eastern ancient individuals."
"Ancient Yersinia pestis genomes from Britain, France, Germany and Spain reveal extensive strain diversity during the First Plague Pandemic (541-750 CE) M. Keller
The first historically reported pandemic unambiguously assigned to Yersinia pestis is the Justinianic Plague (541-544). It was later followed by numerous outbreaks in Europe, North Africa and the Middle East until the mid-8th century, often referred to as the "First Pandemic". Despite the lack of historical records in southern Germany, the identification and characterization of the causative lineage has thus far been based solely on ancient genomes found in two early Medieval cemeteries in this region. These two genomes, that are identical, occupy a distinct phylogenetic position in the modern diversity of Y. pestis on a now extinct or undocumented branch. We aim to elucidate the evolutionary history of Y. pestis during the "First Pandemic" by sampling on a broader spatial and temporal scale, including the Mediterranean basin that is known to have been heavily affected by plague as well as more questionable regions such as Britain. After screening of more than 150 samples and performing targeted DNA enrichment of positive candidates, we recovered three new genomes from Germany, and one from each of Britain, France and Spain with 5 to 10-fold mean coverage. Only two of the genomes were identical to those previously published, having stemmed from relatively nearby cemeteries. The newly sequenced strains reveal a rapid diversification of strains during the Justinianic Plague, similar to the radiation events described in association with the "Second" (14th to 18th c.) and "Third" (19th to 20th c.) Pandemics. At least four independent strains seem to have emerged during this event, two of which were found in southern Germany. The British genome substantiates the bacterium"s presence in this region already at, likely, the onset of the "First Pandemic". However, the genomes recovered from Spain and France appear phylogenetically distinct, reflecting historical records that testify that Y. pestis affected the western Mediterranean basin multiple times during the late 6th and 7th centuries. In addition, the French genome falls in the most derived position on this branch, and seems to lack a genomic region that includes two previously identified virulence genes. Overall, the genomes we present substantially contribute to the understanding of the "First Pandemic" which remains, to, date comparatively understudied by the field of archaeogenetics."
"16th-century Yersinia pestis genome from Logroño, Spain underlines plague persistence in Europe during the Second Pandemic G. U. Neumann1
The Black Death caused by Yersinia pestis ravaged Europe between 1346-1353 AD and was followed in numerous places by further major outbreaks until the 18th century. It is still under discussion whether these were due to reintroductions of the pathogen from Asia or its persistence in local reservoirs within Europe. Here, we analyzed 55 teeth from individuals buried in the necropolis of La Inquisición at Logroño, Spain, an important station along one of the main pilgrim routes of the Camino de Santiago. From the 13th century until 1512 this site was a pilgrim hospital (Hospital de Santa María de Rocamador) and included a cemetery that probably maintained its funerary function in the following decades. In 1564, the city of Logroño was struck by a mass mortality event that is referred to as pestilencia in written historical records. During this event a great number of corpses were buried in the cemetery of the abandoned hospital. Through a qPCR based assay specific to the Yersinia pestis pla gene, located on the pPCP1 plasmid, ten of these teeth showed possible preservation of this pathogen"s DNA. Subsequently, UDG-treated DNA libraries from these extracts were prepared and were whole-genome captured for Yersinia pestis DNA. After high throughput sequencing, the data were mapped against the Yersinia pestis CO92 reference genome for authentication, as well as SNP and phylogenetic analyses. We present here a post-Black Death genome retrieved from the Iberian pensinsula and are able to show that the 1564 outbreak of pestilencia at Logroño was caused by Yersinia pestis. Phylogenetic analysis shows that the Logroño genome occupies a position within the European Yersinia pestis cluster in close relation to the previously published genomes of Ellwangen, Germany and Marseilles, France. Our data provide further support for the hypothesis of a western Eurasian focus of post-Black Death plague instead of a re-introduction from Asia and provide insights into the local diversification of Yersinia pestis during the second pandemic."
"Population transformations in the 6000-2000 BC period of the Carpathian Basin A. Szécsényi-Nagy
Here we present the population versus cultural dynamics of Neolithization and later prehistoric times in the region of today"s Hungary. We use a high-resolution genome-wide ancient DNA dataset with over 100 samples from the Neolithic, Chalcolithic and Bronze Age periods (ca. 6000–2000 BC), carefully selecting from a series of succeeding archaeological cultures. We find that Neolithic genetic diversity was shaped predominantly by local processes, with slightly different sources and proportions of hunter-gatherer ancestry compared to other regions of Europe. The most probable scenario for a Neolithic population transformation in the Carpathian Basin was an initial (small-scale) admixture pulse between the farmer and hunter-gatherer populations that was followed by continuous gene flow over many centuries. The admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. At the end of the Chalcolithic period new migration waves reached the Carpathian Basin from East (Yamnaya) and Northwest (Bell Beaker). The Early Bonze Age newcomer individuals lived in the Beaker culture complex began to admix with the descendant of the Neolithic farmers, and the new steppe type genetic ancestry reformed the genomic structure of the successor Bronze Age populations. Our results published in Lipson & Szécsényi-Nagy et al. 2017 and Olalde et al. 2018 Nature papers demonstrate the potential of time-series-based sampling and modelling approaches that clarify multiple dimensions of historical population interactions."