A river runs through it - ancient DNA data on the neolithic populations of the Great Hungarian Plain

This thesis was part of a multidisciplinary research project funded by the German Research Foundation (“Bevölkerungsgeschichte des Karpatenbeckens in der Jungsteinzeit und ihr Einfluss auf die Besiedlung Mitteleuropas”, grant no. Al 287/10-1) aimed at elucidating the population history of the Carpathian Basin during the Neolithic. The Carpathian Basin was an important waypoint on the spread of the Neolithic from southeastern to central Europe. On the Great Hungarian Plain (Alföld), the first farming communities appeared around 6000 cal BC. They belonged to the Körös culture, which derived from the Starčevo-Körös-Criş complex in the northern Balkans. Around 5600 cal BC the Alföld-Linearbandkeramik (ALBK), so called due to its stylistic similarities with the Transdanubian and central European LBK, emerged in the northwestern Alföld. Following a short “classical phase”, the ALBK split into several regional subgroups during its later stages, but did not expand beyond the Great Hungarian Plain. Marking the beginning of the late Neolithic period, the Tisza culture first appeared in the southern Alföld around 5000 cal BC and subsequently spread into the central and northern Alföld. Together with the Herpály and Csőszhalom groups it was an integral part of the late Neolithic cultural landscape of the Alföld. Up until now, the Neolithic cultural succession on the Alföld has been almost exclusively studied from an archaeological point of view, while very little is known about the population genetic processes during this time period. The aim of this thesis was to perform ancient DNA (aDNA) analyses on human samples from the Alföld Neolithic and analyse the resulting mitochondrial population data to address the following questions: is there population continuity between the Central European Mesolithic hunter-gatherer metapopulation and the first farming communities on the Alföld? Is there genetic continuity from the early to the late Neolithic? Are there genetic as well as cultural differences between the regional groups of the ALBK? Additionally, the relationships between the Alföld and the neighbouring Transdanubian Neolithic as well as other European early farming communities were evaluated to gain insights into the genetic affinities of the Alföld Neolithic in a larger geographic context. 320 individuals were analysed for this study; reproducible mitochondrial haplogroup information (HVS-I and/or SNP data) could be obtained from 242 Neolithic individuals. According to the analyses, population continuity between hunter-gatherers and the Neolithic cultures of the Alföld can be excluded at any stage of the Neolithic. In contrast, there is strong evidence for population continuity from the early to the late Neolithic. All cultural groups on the Alföld were heavily shaped by the genetic substrate introduced into the Carpathian Basin during the early Neolithic by the Körös and Starčevo cultures. Accordingly, genetic differentiation between regional groups of the ALBK is not very pronounced. The Alföld cultures are furthermore genetically highly similar to the Transdanubian Neolithic cultures, probably due to common ancestry. In the wider European context, the Alföld Neolithic cultures also highly similar to the central European LBK, while they differ markedly from contemporaneous populations of the Iberian Peninsula and the Ukraine. Thus, the Körös culture, the ALBK and the Tisza culture can be regarded as part of a “genetic continuum” that links the Neolithic Carpathian Basin to central Europe and likely has its roots in the Starčevo -Körös-Criş complex of the northern Balkans.Die vorliegende Arbeit war Bestandteil des von der Deutschen Forschungsgemeinschaft (DFG) geförderten Projektes“Bevölkerungsgeschichte des Karpatenbeckens in der Jungsteinzeit und ihr Einfluss auf die Besiedlung Mitteleuropas” (Al 287/10-1). Das Karpatenbecken spielte eine Schlüsselrolle in der Ausbreitung der neolithischen Lebensweise von Südost- nach Zentraleuropa. Die große ungarische Tiefebene (ung. Alföld) im östlichen Karpatenbecken wurde erstmals um 6000 cal BC von Ackerbau treibenden Gruppen besiedelt. Diese Gruppen gehörten der Körös-Kultur an, die dem Starčevo-Körös-Criş-Komplex des nördlichen Balkan entstammte. Um 5600 cal BC entstand im nordwestlichen Alföld die sogenannte Alföld-Linearbandkeramik (ALBK), die zur gleichen kulturellen Sphäre wie die Transdanubische und die Mitteleuropäische Linearbandkeramik gerechnet wird. Nach einer kurzen “klassischen” Phase spaltete sich die ALBK in ihrer mittleren und späten Phase in verschiedene Regionalstile auf., expandierte allerdings nicht über die Grenzen der Tiefebene hinaus. Der Beginn des Spätneolithikums im Alföld fällt mit dem Auftreten der Tisza-Kultur um 5000 cal BC zusammen. Die Tisza-Kultur breitete sich vom südlichen in das zentrale und nördliche Alföld aus und bildete gemeinsam mit den Herpály- und Csőszhalom-Gruppen einen integralen Bestandteil der kulturellen “Landschaft” des spätneolithischen Alföld. Die neolithische Kulturfolge im Alföld wurde bisher fast ausschließlich archäologisch erforscht, sodass wenig über populationsgenetische Ereignisse in dieser Zeit bekannt ist. Ziel dieser Arbeit war es, “ancient DNA” (aDNA)-Untersuchungen an menschlichen Knochen von verschiedenen früh- mittel- und spätneolithischen Fundplätzen im Alföld durchzuführen und einen diachronen Satz mitochondrialer DNA-Daten zu erstellen. Der Datensatz wurde unter Verwendung verschiedener Methoden der populationsgenetischen Statistik ausgewertet, um Antworten auf folgende Fragestellungen zu erhalten: Gibt es Populationskontinuität zwischen mesolithschen Jäger-Sammler-Gruppen in Mitteleuropa und den ersten Ackerbau treibenden Gruppen im Alföld? Besteht genetische Kontinuität von der früh- bis zur spätneolithischen Zeit? Gibt es genetische Unterschiede zwischen den Regionalstilen der mittleren und späten ALBK? Die Populationsdaten aus dem Alföld wurden außerdem mit Datensätzen aus dem benachbarten Transdanubien sowie weiteren (früh)neolithischen Gruppen aus Europa verglichen, um Informationen über genetische Affinitäten des Alföld-Neolithikums in einem breiteren geografischen Kontext zu erhalten. Im Rahmen dieser Studie wurden 320 Individuen analysiert. Reproduzierte mitochondriale HVS-I-Sequenzen bzw. SNP-Daten konnten von 242 Individuen gewonnen werden. Die Untersuchungen zeigen, dass Populationskontinuität zwischen Jäger-Sammlern und Ackerbau treibenden Gruppen im Alföld für jede Zeitphase und (Regional)gruppe ausgeschlossen werden kann. Demgegenüber steht eine deutliche Kontinuität von Früh- bis Spätneolithikum. Die neolithischen Kulturen des Alföld wurden stark und langanhaltend durch das genetische Substrat geprägt, dass schon zu Beginn der Neolithisierung mit den Körös- und Starčevo-Kulturen in das Karpatenbecken gelangte. Entsprechend ist eine genetische Differenzierung zwischen den Regionalgruppen der ALBK nur schwach ausgeprägt. Die Kulturen des Alföld sind den zeitgleichen Gruppen in Transdanubien sehr ähnlich, was vermutlich auf den gemeinsamen Ursprung zurückzuführen ist. Im überregionalen Kontext ähneln die Alföld-Kulturen genetisch auch stark der zentraleuropäischen LBK, während sie sich von den (früh)neolithischen Kulturen der Iberischen Halbinsel oder der Ukraine deutlich unterscheiden. Die Kulturabfolge Körös-ALBK-Tisza-Kultur kann daher als Teil eines “genetischen Kontinuums” betrachtet werden, welches das jungsteinzeitliche Karpatenbecken mit Mitteleuropa verbindet und seinen Ursprung im Starčevo-Körös-Criş-Komplex des nördlichen Balkan hat

A new future of forensic Y-chromosome analysis: Rapidly mutating Y-STRs for differentiating male relatives and paternal lineages

The panels of 9-17 Y-chromosomal short tandem repeats (Y-STRs) currently used in forensic genetics have adequate resolution of different paternal lineages in many human populations, but have lower abilities to separate paternal lineages in populations expressing low Y-chromosome diversity. Moreover, current Y-STR sets usually fail to differentiate between related males who belong to the same paternal lineage and, as a consequence, conclusions cannot be drawn on the individual level as is desirable for forensic interpretations. Recently, we identified a new panel of rapidly mutating (RM) Y-STRs, composed of 13 markers with mutation rates above 1 x 10(-2), whereas most Y-STRs, including all currently used in forensics, have mutation rates in the order of 1 x 10(-3) or lower. In the present study, we demonstrate in 604 unrelated males sampled from 51 worldwide populations (HGDP-CEPH) that the RM Y-STRs provide substantially higher haplotype diversity and haplotype discrimination capacity (with only 3 haplotypes shared between 8 of the 604 worldwide males), than obtained with the largest set of 17 currently used Y-STRs (Yfiler) in the same samples (33 haplotypes shared between 85 males). Hence, RM Y-STRs yield high-resolution paternal lineage differentiation and provide a considerable improvement compared to Yfiler. We also find in this worldwide dataset substantially less genetic population substructure within and between geographic regions with RM Y-STRs than with Yfiler Y-STRs. Furthermore, with the present study we provide enhanced data evidence that the RM Y-STR panel is extremely successful in differentiating between closely and distantly related males. Among 305 male relatives, paternally connected by 1-20 meiotic transfers in 127 independent pedigrees, we show that 66% were separated by mutation events with the RM Y-STR panel whereas only 15% were with Yfiler; hence, RM Y-STRs provide a statistically significant 4.4-fold increase of average male relative differentiation relative to Yfiler. The RM Y-STR panel is powerful enough to separate closely related males; nearly 50% of the father and sons, and 60% of brothers could be distinguished with RM Y-STRs, whereas only 7.7% and 8%, respectively, with Yfiler. Thus, by introducing RM Y-STRs to the forensic genetic community we provide important solutions to several of the current limitations of Y chromosome analysis in forensic genetics. (C) 2011 Elsevier Ireland Ltd. All rights reserved

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

Abstract Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's 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

Parallel paleogenomic transects reveal complex genetic history of early European farmers

Ancient DNA studies have established that Neolithic European populations were descended from Anatolian migrants1–8 who received a limited amount of admixture from resident hunter-gatherers3–5,9. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date—a total of 180 samples, 130 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000–2900 BCE, n = 100), Germany (5500–3000 BCE, n = 42), and Spain (5500–2200 BCE, n = 38)—we investigate the population dynamics of Neolithization across Europe. 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 that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions