Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.

OBJECTIVE: We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS: We conducted ancient DNA studies from populations associated with Zlota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS: The maternal genetic composition found in Zlota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Zlota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION: The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Zlota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Zlota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.

AmtDB: a database of ancient human mitochondrial genomes.

Ancient mitochondrial DNA is used for tracing human past demographic events due to its population-level variability. The number of published ancient mitochondrial genomes has increased in recent years, alongside with the development of high-throughput sequencing and capture enrichment methods. Here, we present AmtDB, the first database of ancient human mitochondrial genomes. Release version contains 1107 hand-curated ancient samples, freely accessible for download, together with the individual descriptors, including geographic location, radiocarbon dating, and archaeological culture affiliation. The database also features an interactive map for sample location visualization. AmtDB is a key platform for ancient population genetic studies and is available at https://amtdb.org.

Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia.

BACKGROUND: Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death. RESULTS: In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria. CONCLUSIONS: In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome.

Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations.

OBJECTIVE: In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes. MATERIALS AND METHODS: We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyzow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS 14 C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples. RESULTS: Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyzów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study. DISCUSSION: Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyzów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.

The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.

The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24× coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.

Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC.

BACKGROUND: Recent aDNA studies are progressively focusing on various Neolithic and Hunter - Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities. RESULTS: Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK. CONCLUSIONS: We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities.

Genetic history of East-Central Europe in the first millennium CE.

BACKGROUND: The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no earlier than the sixth century CE; the second postulates that they already inhabited this region in the Iron Age (IA). Testing either hypothesis is not trivial given that cremation of the dead was the prevailing custom in Central Europe from the late Bronze Age until the Middle Ages (MA). RESULTS: To address this problem, we determined the genetic makeup of representatives of the IA Wielbark- and MA Slav-associated cultures from the territory of present-day Poland. The study involved 474 individuals buried in 27 cemeteries. For 197 of them, genome-wide data were obtained. We found close genetic affinities between the IA Wielbark culture-associated individuals and contemporary to them and older northern European populations. Further, we observed that the IA individuals had genetic components which were indispensable to model the MA population. CONCLUSIONS: The collected data suggest that the Wielbark culture-associated IA population was formed by immigrants from the north who entered the region of contemporary Poland most likely at the beginning of the first millennium CE and mixed with autochthons. The presented results are in line with the hypothesis that assumes the genetic continuation between IA and MA periods in East-Central Europe.

Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe.

The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.

Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age.

The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.

Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.

The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Asikli Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Asikli Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcin, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,3-5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.