Paleogenetic investigations of hominin diversity and dispersals in Eurasian prehistory

Ancient DNA (aDNA) is able to provide genetic snapshots into the human past that can be linked together to study evolutionary processes and demographic patterns impossible to uncover with the study of modern-day DNA alone. In this thesis I make use of major methodological “game changers” in the field of aDNA in order to reconstruct complete mitochondrial DNA (mtDNA), as well as genome-wide nuclear data (nDNA) from ancient human specimens. The combination of next generation sequencing (NGS) technologies and target enrichment paired up with sampling of different anatomical elements, enabled me to expand the amount of analyzable hominin remains ranging from Pleistocene European hunter-gatherers to Holocene farmers in Remote Oceania. I first investigated the mtDNA of late Neandertals from Goyet cave in Belgium and of an archaic femur from Hohlenstein-Stadel in southwest Germany to explore the changes in genetic diversity of this extinct hominins through time and provide the temporal interval for a putative African gene flow event into Neandertal populations. In addition, I carried out two studies that explored demographic changes in European Upper Paleolithic and Mesolithic hunter-gatherers by means of both mtDNA and nDNA, and revealed population structure and unexpected genetic turnovers in Ice Age Europe. By expanding the temporal and geographical distribution of genomic data it was able to infer population movements in European prehistory and compare them to climatic and archaeological records over almost 40,000 years. While the formation of some genetic clusters tightly matches to the associated archaeological changes across Europe, other major genomic transformations seem to be more influenced by environmental fluctuations. In the last project, I contributed in producing aDNA of four individuals among the first settlers of Vanuatu and Tonga in the Southwest Pacific. Sampling the petrous portion of their temporal bones allowed me to retrieve genomic data from climatic conditions unfavorable for DNA preservation. Those genomes highlight the role of previously unknown dispersals in shaping the ancestry of present-day people in Remote Oceania. Here, I take a time trip to shed light into the genetic history of our ancestors and closest extinct relatives.Die Analyse alter DNA (aDNA) erlaubt Einblicke in die genetische Vergangenheit der Menschheit und hiermit die Möglichkeit Entwicklungsprozesse und demografische Muster zu untersuchen, welche aus Sicht der Genetik rezenter Populationen verborgen bleiben. In meiner Doktorarbeit wende ich neueste methodische Errungenschaften an, um ganze mitochondriale Genome sowie genom-weite Daten prähistorischer Individuen zu rekonstruieren. Die gezielte Anreicherung menschlicher DNA durch Hybridisierungmethoden gepaart mit Next Generation Sequenzierungs-technologie erlaubte es mir die Anzahl erfolgreich analysierter menschlicher Skelettreste um altsteinzeitliche Jaeger-Sammler sowie die der frühesten Siedler des südwestlichen Pazifiks zu erweitern. Zunächst gelang mir die erfolgreiche genetische Untersuchung von späten Neandertalern aus der Goyet Höhle in Belgien sowie eines archaischen Femur aus der Hohlenstein-Stadel Höhle, SW Deutschland. Diese beiden Studien ermöglichten einen diachronen Einblick in die genetische Diversität archaischer Homininen und lieferten zudem eine mögliche Zeitspanne für genetischen Einfluss aus Afrika in Neandertaler-Gruppen Europas. In zwei weiteren Arbeiten zu mitochondrialer sowie Kern-DNA konnte ich überraschenderweise mehrfach genetische und demografische Umwälzungen in Europas Altsteinzeit nachweisen. Eine sehr gute geographische sowie zeitliche Auflösung an Fundmaterial der frühen Besiedlungsgeschichte Europas erlaubte es mir zudem die genetischen Daten mit archäologischem Fundkontext sowie geologischen bzw. paläo-klimatischen Daten abzugleichen und hiermit die Siedlungsdynamik früher Europäer zu erfassen. Interessanterweise lassen sich genetische cluster mit archäologischen Sachkulturen bzw. deren Änderungen durch die Zeit verbinden, während andere Veränderungen eher in Einklang mit den dramatischen Klimafluktuationen der letzten 40,000 Jahre gebracht werden können. In meinem letzten Kapitel beschreibe ich meinen Beitrag zu einer Arbeit, welche die Erstbesiedlung der südpazifischen Inseln Vanuatu und Tonga untersucht hat. Uns gelang die Generierung von genomweiten Daten aus den Felsenbeinen von vier Individuen aus tropischen Regionen – ein Unterfangen, das bis dahin unmöglich schien. Die genetischen Ergebnisse werfen neues Licht auf die Besiedlungsgeschichte und die genetische Komplexität in der Genese der Bewohner der südwestpazifischen Inseln in Ozeanien. Mit dieser Arbeit gelingt mir ein zeitlich wie geographisch weit gefächerter Einblick in die genetische Herkunft unserer Vorfahren sowie eng mit uns verwandter, aber heute ausgestorbener, menschlicher Entwicklungslinien

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.This project has received funding by the European Research Council under the European Union’s Horizon 2020 research and innovation programme under grant agreements no. 803147-RESOLUTION (to S.T.), no. 771234-PALEoRIDER (to W.H.), no. 864358 (to K.M.), no. 724703 and no. 101019659 (to K.H.). K.H. is also supported by the Deutsche Forschungsgemeinschaft (DFG FOR 2237). E.A. has received funding from the Van de Kamp fonds. PACEA co-authors of this research benefited from the scientific framework of the University of Bordeaux’s IdEx Investments for the Future programme/GPR Human Past. A.G.-O. is supported by a Ramón y Cajal fellowship (RYC-2017-22558). L. Sineo, M.L. and D.C. have received funding from the Italian Ministry of University and Research (MUR) PRIN 2017 grants 20177PJ9XF and 20174BTC4R_002. H. Rougier received support from the College of Social and Behavioral Sciences of CSUN and the CSUN Competition for RSCA Awards. C.L.S. and T. Saupe received support from the European Union through the European Regional Development Fund (project no. 2014-2020.4.01.16-0030) and C.L.S. received support from the Estonian Research Council grant PUT (PRG243). S. Shnaider received support from the Russian Science Foundation (no. 19-78 10053)

The role of emerging elites in the formation and development of communities after the fall of the Roman Empire

Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups

Cueva de los Torrejones revisited. New insights on the paleoecology of inland Iberia during the Late Pleistocene

34 p.The interior of the Iberian Peninsula has orographic conditions that make this territory especially vulnerable to Quaternary climate oscillations and which actually could have made it decisive for Paleolithic human populations at critical points. For this reason, the information provided by paleontological sites is important for reconstructing climatic and environmental conditions during the Late Pleistocene and understanding how they influenced the species that inhabited them, including humans. Nevertheless, the archaeo-paleontological record is scarce in central Iberia for the Late Pleistocene. A central Iberian site that is key to addressing this issue is Cueva de los Torrejones, which was discovered and excavated during the nineties. Clues indicating the presence of Neandertal populations near the cave site were announced during prior field excavations, including Neandertal remains, Middle Paleolithic artifacts, and evidence of anthropic exploitation of faunal resources at the site. Here we report the new results from the recent excavations and research, including detailed studies on stratigraphy, micromorphology, macro and microvertebrate paleontology, physical and molecular anthropology, taphonomy and zooarchaeology, and analysis of lithic and pottery remains. Our research has led to the detection of three Prehistoric chronologies recorded at the site. The oldest episode corresponds to between MIS 5 and MIS 4 in which the cave was used by carnivores. The second episode is represented by a faunal association dated to 30.0 ka cal BP and is indicative of cooler and more arid environmental conditions and, therefore, compatible with the worsening climate detected previously for MIS 3 in this area. The last episode corresponds to the Chalcolithic, directly dated to ~5000 cal BP in which humans used the cavity for funerary purposes. The DNA analysis of the human remain was assigned to mtDNA haplogroup K, which was originated in the Near East and reached western Europe through the Neolithic expansion. Human occupation during the Paleolithic has been ruled out, including Paleolithic human remains and any kind of anthropic intervention on the Hermann’s tortoise and leopard as was previously proposed at the site.European Research CouncilJunta de Comunidades de Castilla la ManchaMinisterio de Ciencia e InnovaciónCentro Nacional de Investigación sobre la Evolución Humana (CENIEH

Neandertal Cannibalism And Neandertal Bones Used As Tools In Northern Europe

Almost 150 years after the first identification of Neandertal skeletal material, the cognitive and symbolic abilities of these populations remain a subject of intense debate. We present 99 new Neandertal remains from the Troisième caverne of Goyet (Belgium) dated to 40,500–45,500 calBP. The remains were identified through a multidisciplinary study that combines morphometrics, taphonomy, stable isotopes, radiocarbon dating and genetic analyses. The Goyet Neandertal bones show distinctive anthropogenic modifications, which provides clear evidence for butchery activities as well as four bones having been used for retouching stone tools. In addition to being the first site to have yielded multiple Neandertal bones used as retouchers, Goyet not only provides the first unambiguous evidence of Neandertal cannibalism in Northern Europe, but also highlights considerable diversity in mortuary behaviour among the region’s late Neandertal population in the period immediately preceding their disappearance.Scientific Reports 6. (2016)2045-232

The impact of human dispersals and local interactions on the genetic diversity of coastal Papua New Guinea over the past 2,500 years

The inhabitants of New Guinea and its outlying islands have played an important role in the human history of the Pacific region. Nevertheless, the genetic diversity, particularly of pre-colonial communities, is still understudied. Here we present the ancient genomes of 42 individuals from Papua New Guinea (PNG). The ancient genomic results of individuals from Watom Island (Bismarck Archipelago) and the south and northeastern coasts of PNG are contextualized with new (bio-) archaeological data. The individuals’ accelerator mass spectrometry (AMS) dates span 2,500 years of human habitation, and our results demonstrate the influences of different dispersal events on the genetic make-up of ancient PNG communities. The oldest individuals show an unadmixed Papuan-related genetic signature, whereas individuals dating from 2,100 years before present carry varying degrees of an East-Asian-related contribution. These results and the inferred admixture dates suggest a centuries-long delay in genetic mixture with local communities after the arrival of populations with Asian ancestry. Two geographically close communities on the South Coast, AMS dated to within the past 540 years, diverge in their genetic profiles, suggesting differences in their interaction spheres involving groups with distinct ancestries. The inferred split time of these communities around 650 years before present coincides with intensified settlement activity and the emergence of regional trade networks

The role of emerging elites in the formation and development of communities after the fall of the Roman Empire

Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups

Understanding 6th-century barbarian social organization and migration through paleogenomics.

Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern Italy.This work was supported by National Science Foundation award #1450606, the Anneliese Maier Research Award of the Alexander von Humboldt Foundation, the Max Planck Society, the German Federal Ministry for Education and Research, the Swedish Riksbankens Jubieleumfond, the Gerard B. Lambert Foundation, the Institute for Advanced Study Director’s Office, and the Italian Ministry for University and Research Department of Excellence Program