Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas.

Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai1. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse-the 'ecocide' theory2-4. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated5-7. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670-1950 CE) and whole-genome sequenced (0.4-25.6×). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250-1430 CE.

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.

Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic.

The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities.

Reconstruction of human dispersal during Aurignacian on pan-European scale.

The Aurignacian is the first techno-complex related with certainty to Anatomically Modern Humans in Europe. Studies show that they appeared around 43-42 kyr cal BP and dispersed rapidly in Europe during the Upper Palaeolithic. However, human dispersal is a highly convoluted process which is until today not well understood. Here, we provide a reconstruction of the human dispersal during the Aurignacian on the pan-European scale using a human dispersal model, the Our Way Model, which combines archaeological with paleoclimate data and uses the human existence potential as a unifying driver of human population dynamics. Based on the reconstruction, we identify the different stages of the human dispersal and analyse how human demographic processes are influenced by climate change and topography. A chronology of the Aurignacian human groups in Europe is provided, which is verified for locations where archaeological dating records are available. Insights into highly debated hypotheses, such as human dispersal routes, are provided.

The chronology of the human colonization of the Canary Islands.

The human colonization of the Canary Islands represents the sole known expansion of Berber communities into the Atlantic Ocean and is an example of marine dispersal carried out by an African population. While this island colonization shows similarities to the populating of other islands across the world, several questions still need to be answered before this case can be included in wider debates regarding patterns of initial colonization and human settlement, human-environment interactions, and the emergence of island identities. Specifically, the chronology of the first human settlement of the Canary Islands remains disputed due to differing estimates of the timing of its first colonization. This absence of a consensus has resulted in divergent hypotheses regarding the motivations that led early settlers to migrate to the islands, e.g., ecological or demographic. Distinct motivations would imply differences in the strategies and dynamics of colonization; thus, identifying them is crucial to understanding how these populations developed in such environments. In response, the current study assembles a comprehensive dataset of the most reliable radiocarbon dates, which were used for building Bayesian models of colonization. The findings suggest that i) the Romans most likely discovered the islands around the 1st century BCE; ii) Berber groups from western North Africa first set foot on one of the islands closest to the African mainland sometime between the 1st and 3rd centuries CE; iii) Roman and Berber societies did not live simultaneously in the Canary Islands; and iv) the Berber people rapidly spread throughout the archipelago.

Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives.

The strategic location of North Africa has led to cultural and demographic shifts, shaping its genetic structure. Historical migrations brought different genetic components that are evident in present-day North African genomes, along with autochthonous components. The Imazighen (plural of Amazigh) are believed to be the descendants of autochthonous North Africans and speak various Amazigh languages, which belong to the Afro-Asiatic language family. However, the arrival of different human groups, especially during the Arab conquest, caused cultural and linguistic changes in local populations, increasing their heterogeneity. We aim to characterize the genetic structure of the region, using the largest Amazigh dataset to date and other reference samples. Our findings indicate microgeographical genetic heterogeneity among Amazigh populations, modeled by various admixture waves and different effective population sizes. A first admixture wave is detected group-wide around the twelfth century, whereas a second wave appears in some Amazigh groups around the nineteenth century. These events involved populations with higher genetic ancestry from south of the Sahara compared to the current North Africans. A plausible explanation would be the historical trans-Saharan slave trade, which lasted from the Roman times to the nineteenth century. Furthermore, our investigation shows that assortative mating in North Africa has been rare.

Environmental conditions associated with initial northern expansion of anatomically modern humans.

The ability of our ancestors to switch food sources and to migrate to more favourable environments enabled the rapid global expansion of anatomically modern humans beyond Africa as early as 120,000 years ago. Whether this versatility was largely the result of environmentally determined processes or was instead dominated by cultural drivers, social structures, and interactions among different groups, is unclear. We develop a statistical approach that combines both archaeological and genetic data to infer the more-likely initial expansion routes in northern Eurasia and the Americas. We then quantify the main differences in past environmental conditions between the more-likely routes and other potential (less-likely) routes of expansion. We establish that, even though cultural drivers remain plausible at finer scales, the emergent migration corridors were predominantly constrained by a combination of regional environmental conditions, including the presence of a forest-grassland ecotone, changes in temperature and precipitation, and proximity to rivers.

Abrupt onset of intensive human occupation 44,000 years ago on the threshold of Sahul.

Archaeological evidence attests multiple early dispersals of Homo sapiens out of Africa, but genetic evidence points to the primacy of a single dispersal 70-40 ka. Laili in Timor-Leste is on the southern dispersal route between Eurasia and Australasia and has the earliest record of human occupation in the eastern Wallacean archipelago. New evidence from the site shows that, unusually in the region, sediment accumulated in the shelter without human occupation, in the window 59-54 ka. This was followed by an abrupt onset of intensive human habitation beginning ~44 ka. The initial occupation is distinctive from overlying layers in the aquatic focus of faunal exploitation, while it has similarities in material culture to other early Homo sapiens sites in Wallacea. We suggest that the intensive early occupation at Laili represents a colonisation phase, which may have overwhelmed previous human dispersals in this part of the world.

Ancient genomes revealed the complex human interactions of the ancient western Tibetans.

The western Tibetan Plateau is the crossroad between the Tibetan Plateau, Central Asia, and South Asia, and it is a potential human migration pathway connecting these regions. However, the population history of the western Tibetan Plateau remains largely unexplored due to the lack of ancient genomes covering a long-time interval from this area. Here, we reported genome-wide data of 65 individuals dated to 3,500-300 years before present (BP) in the Ngari prefecture. The ancient western Tibetan Plateau populations share the majority of their genetic components with the southern Tibetan Plateau populations and have maintained genetic continuity since 3,500 BP while maintaining interactions with populations within and outside the Tibetan Plateau. Within the Tibetan Plateau, the ancient western Tibetan Plateau populations were influenced by the additional expansion from the south to the southwest plateau before 1,800 BP. Outside the Tibetan Plateau, the western Tibetan Plateau populations interacted with both South and Central Asian populations at least 2,000 years ago, and the South Asian-related genetic influence, despite being very limited, was from the Indus Valley Civilization (IVC) migrants in Central Asia instead of the IVC populations from the Indus Valley. In light of the new genetic data, our study revealed the complex population interconnections across and within the Tibetan Plateau.

Demographic models predict end-Pleistocene arrival and rapid expansion of pre-agropastoralist humans in Cyprus.

The antiquity of human dispersal into Mediterranean islands and ensuing coastal adaptation have remained largely unexplored due to the prevailing assumption that the sea was a barrier to movement and that islands were hostile environments to early hunter-gatherers [J. F. Cherry, T. P. Leppard, J. Isl. Coast. Archaeol. 13, 191-205 (2018), 10.1080/15564894.2016.1276489]. Using the latest archaeological data, hindcasted climate projections, and age-structured demographic models, we demonstrate evidence for early arrival (14,257 to 13,182 calendar years ago) to Cyprus and predicted that large groups of people (~1,000 to 1,375) arrived in 2 to 3 main events occurring within <100 y to ensure low extinction risk. These results indicate that the postglacial settlement of Cyprus involved only a few large-scale, organized events requiring advanced watercraft technology. Our spatially debiased and Signor-Lipps-corrected estimates indicate rapid settlement of the island within <200 y, and expansion to a median of 4,000 to 5,000 people (0.36 to 0.46 km-2) in <11 human generations (<300 y). Our results do not support the hypothesis of inaccessible and inhospitable islands in the Mediterranean for pre-agropastoralists, agreeing with analogous conclusions for other parts of the world [M. I. Bird et al., Sci. Rep. 9, 8220 (2019), 10.1038/s41598-019-42946-9]. Our results also highlight the need to revisit these questions in the Mediterranean and test their validity with new technologies, field methods, and data. By applying stochastic models to the Mediterranean region, we can place Cyprus and large islands in general as attractive and favorable destinations for paleolithic peoples.

Palaeogenomic insights into the origins of early settlers on the island of Cyprus.

Archaeological evidence supports sporadic seafaring visits to the Eastern Mediterranean island of Cyprus by Epipaleolithic hunter-gatherers over 12,000 years ago, followed by permanent settlements during the early Neolithic. The geographical origins of these early seafarers have so far remained elusive. By systematically analysing all available genomes from the late Pleistocene to early Holocene Near East (c. 14,000-7000 cal BCE), we provide a comprehensive overview of the genetic landscape of the early Neolithic Fertile Crescent and Anatolia and infer the likely origins of three recently published genomes from Kissonerga-Mylouthkia (Cypriot Late Pre-Pottery Neolithic B, c. 7600-6800 cal BCE). These appear to derive roughly 80% of their ancestry from Aceramic Neolithic Central Anatolians residing in or near the Konya plain, and the remainder from a genetically basal Levantine population. Based on genome-wide weighted ancestry covariance analysis, we infer that this admixture event took place roughly between 14,000 and 10,000 BCE, coinciding with the transition from the Cypriot late Epipaleolithic to the Pre-Pottery Neolithic A (PPNA). Additionally, we identify strong genetic affinities between the examined Cypro-LPPNB individuals and later northwestern Anatolians and the earliest European Neolithic farmers. Our results inform archaeological evidence on prehistoric demographic processes in the Eastern Mediterranean, providing important insights into early seafaring, maritime connections, and insular settlement.

Physiography, foraging mobility, and the first peopling of Sahul.

The route and speed of migration into Sahul by Homo sapiens remain a major research question in archaeology. Here, we introduce an approach which models the impact of the physical environment on human mobility by combining time-evolving landscapes with Lévy walk foraging patterns, this latter accounting for a combination of short-distance steps and occasional longer moves that hunter-gatherers likely utilised for efficient exploration of new environments. Our results suggest a wave of dispersal radiating across Sahul following riverine corridors and coastlines. Estimated migration speeds, based on archaeological sites and predicted travelled distances, fall within previously reported range from Sahul and other regions. From our mechanistic movement simulations, we then analyse the likelihood of archaeological sites and highlight areas in Australia that hold archaeological potential. Our approach complements existing methods and provides interesting perspectives on the Pleistocene archaeology of Sahul that could be applied to other regions around the world.

Adaptive foraging behaviours in the Horn of Africa during Toba supereruption.

Although modern humans left Africa multiple times over 100,000 years ago, those broadly ancestral to non-Africans dispersed less than 100,000 years ago1. Most models hold that these events occurred through green corridors created during humid periods because arid intervals constrained population movements2. Here we report an archaeological site-Shinfa-Metema 1, in the lowlands of northwest Ethiopia, with Youngest Toba Tuff cryptotephra dated to around 74,000 years ago-that provides early and rare evidence of intensive riverine-based foraging aided by the likely adoption of the bow and arrow. The diet included a wide range of terrestrial and aquatic animals. Stable oxygen isotopes from fossil mammal teeth and ostrich eggshell show that the site was occupied during a period of high seasonal aridity. The unusual abundance of fish suggests that capture occurred in the ever smaller and shallower waterholes of a seasonal river during a long dry season, revealing flexible adaptations to challenging climatic conditions during the Middle Stone Age. Adaptive foraging along dry-season waterholes would have transformed seasonal rivers into 'blue highway' corridors, potentially facilitating an out-of-Africa dispersal and suggesting that the event was not restricted to times of humid climates. The behavioural flexibility required to survive seasonally arid conditions in general, and the apparent short-term effects of the Toba supereruption in particular were probably key to the most recent dispersal and subsequent worldwide expansion of modern humans.

East-to-west human dispersal into Europe 1.4 million years ago.

Stone tools stratified in alluvium and loess at Korolevo, western Ukraine, have been studied by several research groups1-3 since the discovery of the site in the 1970s. Although Korolevo's importance to the European Palaeolithic is widely acknowledged, age constraints on the lowermost lithic artefacts have yet to be determined conclusively. Here, using two methods of burial dating with cosmogenic nuclides4,5, we report ages of 1.42 ± 0.10 million years and 1.42 ± 0.28 million years for the sedimentary unit that contains Mode-1-type lithic artefacts. Korolevo represents, to our knowledge, the earliest securely dated hominin presence in Europe, and bridges the spatial and temporal gap between the Caucasus (around 1.85-1.78 million years ago)6 and southwestern Europe (around 1.2-1.1 million years ago)7,8. Our findings advance the hypothesis that Europe was colonized from the east, and our analysis of habitat suitability9 suggests that early hominins exploited warm interglacial periods to disperse into higher latitudes and relatively continental sites-such as Korolevo-well before the Middle Pleistocene Transition.

Reconstruct recent multi-population migration history by using identical-by-descent sharing.

Identical-by-descent (IBD) is a fundamental genomic characteristic in population genetics and has been widely used for population history reconstruction. However, limited by the nature of IBD, which could only capture the relationship between two individuals/haplotypes, existing IBD-based history inference is constrained to two populations. In this study, we propose a framework by leveraging IBD sharing in multi-population and develop a method, MatrixIBD, to reconstruct recent multi-population migration history. Specifically, we employ the structured coalescent theory to precisely model the genealogical process and then estimate the IBD sharing across multiple populations. Within our model, we establish a theoretical connection between migration history and IBD sharing. Our method is rigorously evaluated through simulations, revealing its remarkable accuracy and robustness. Furthermore, we apply MatrixIBD to Central and South Asia in the Human Genome Diversity Project and successfully reconstruct the recent migration history of three closely related populations in South Asia. By taking into account the IBD sharing across multiple populations simultaneously, MatrixIBD enables us to attain clearer and more comprehensive insights into the history of regions characterized by complex migration dynamics, providing a holistic perspective on intricate patterns embedded within the recent population migration history.

Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations.

Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.

Homo sapiens reached the higher latitudes of Europe by 45,000 years ago.

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Late Neanderthals persisted in western Europe several millennia after the occurrence of H. sapiens in eastern Europe1. Local hybridization between the two groups occurred2, but not on all occasions3. Archaeological evidence also indicates the presence of several technocomplexes during this transition, complicating our understanding and the association of behavioural adaptations with specific hominin groups4. One such technocomplex for which the makers are unknown is the Lincombian-Ranisian-Jerzmanowician (LRJ), which has been described in northwestern and central Europe5-8. Here we present the morphological and proteomic taxonomic identification, mitochondrial DNA analysis and direct radiocarbon dating of human remains directly associated with an LRJ assemblage at the site Ilsenhöhle in Ranis (Germany). These human remains are among the earliest directly dated Upper Palaeolithic H. sapiens remains in Eurasia. We show that early H. sapiens associated with the LRJ were present in central and northwestern Europe long before the extinction of late Neanderthals in southwestern Europe. Our results strengthen the notion of a patchwork of distinct human populations and technocomplexes present in Europe during this transitional period.

100 ancient genomes show repeated population turnovers in Neolithic Denmark.

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.

Population genomics of post-glacial western Eurasia.

Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

Genetic continuity and change among the Indigenous peoples of California.

Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity1. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico2-4. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions1,5. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.