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Before the end of the Last Glacial Maximum (LGM, ∼16.5 ka ago) set in motion major shifts in human culture and population structure, a consistent change in lithic technology, material culture, settlement pattern, and adaptive strategies is recorded in Southern Europe at ∼18–17 ka ago. In this time frame, the landscape of Northeastern Italy changed considerably, and the retreat of glaciers allowed hunter-gatherers to gradually recolonize the Alps. Change within this renewed cultural frame (i.e., during the Late Epigravettian phase) is currently associated with migrations favored by warmer climate linked to the Bølling-Allerød onset (14.7 ka ago), which replaced earlier genetic lineages with ancestry found in an individual who lived ∼14 ka ago at Riparo Villabruna, Italy, and shared among different contexts (Villabruna Cluster). Nevertheless, these dynamics and their chronology are still far from being disentangled due to fragmentary evidence for long-distance interactions across Europe. Here, we generate new genomic data from a human mandible uncovered at Riparo Tagliente (Veneto, Italy), which we directly dated to 16,980–16,510 cal BP (2σ). This individual, affected by focal osseous dysplasia, is genetically affine to the Villabruna Cluster. Our results therefore backdate by at least 3 ka the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bølling/Allerød event. In light of the new genetic evidence, this population replacement chronologically coincides with the very emergence of major cultural transitions in Southern and Western Europe., The research was supported by the European Union through the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 724046 – Success awarded to S.B., http://www.erc-success.eu; grant agreement no. 803147 Resolution awarded to S.T., https://site.unibo.it/resolution-erc/en) as well as through the European Regional Development Fund (project no. 2014–2020.4.01.16–0030 to C.L.S. and T.S.) and projects no. 2014-2020.4.01.16-0024 and MOBTT53 (L.P.), by the Estonian Research Council personal research grant (PRG243; C.L.S.), and by UniPd PRID 2019 (L.P.).

The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.

How and when the Americas were populated remains contentious. Using ancient and modern genome wide data we found that the ancestors of all present day Native Americans including Athabascans and Amerindians entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000 year isolation period in Beringia. After their arrival to the Americas ancestral Native Americans diversified into two basal genetic branches around 13 ka one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present day East Asians (including Siberians) and more distantly Australo Melanesians. Putative “Paleoamerican” relict populations including the historical Mexican Pericúes and South American Fuego Patagonians are not directly related to modern Australo Melanesians as suggested by the Paleoamerican Model. INTRODUCTION The consensus view on the peopling of the Americas is that ancestors of modern Native Americans entered the Americas from Siberia via the Bering Land Bridge and that this occurred at least {\textasciitilde}14.6 thousand years ago (ka). However the number and timing of migrations into the Americas remain controversial with conflicting interpretations based on anatomical and genetic evidence. RATIONALE In this study we address four major unresolved issues regarding the Pleistocene and recent population history of Native Americans: (i) the timing of their divergence from their ancestral group (ii) the number of migrations into the Americas (iii) whether there was {\textasciitilde}15000 years of isolation of ancestral Native Americans in Beringia (Beringian Incubation Model) and (iv) whether there was post Pleistocene survival of relict populations in the Americas related to Australo Melanesians as suggested by apparent differences in cranial morphologies between some early (“Paleoamerican”) remains and those of more recent Native Americans. We generated 31 high coverage modern genomes from the Americas Siberia and Oceania; 23 ancient genomic sequences from the Americas dating between {\textasciitilde}0.2 and 6 ka; and SNP chip genotype data from 79 present day individuals belonging to 28 populations from the Americas and Siberia. The above data sets were analyzed together with published modern and ancient genomic data from worldwide populations after masking some present day Native Americans for recent European admixture. RESULTS Using three different methods we determined the divergence time for all Native Americans (Athabascans and Amerindians) from their Siberian ancestors to be {\textasciitilde}20 ka and no earlier than {\textasciitilde}23 ka. Furthermore we dated the divergence between Athabascans (northern Native American branch together with northern North American Amerindians) and southern North Americans and South and Central Americans (southern Native American branch) to be {\textasciitilde}13 ka. Similar divergence times from East Asian populations and a divergence time between the two branches that is close in age to the earliest well established archaeological sites in the Americas suggest that the split between the branches occurred within the Americas. We additionally found that several sequenced Holocene individuals from the Americas are related to present day populations from the same geographical regions implying genetic continuity of ancient and modern populations in some parts of the Americas over at least the past 8500 years. Moreover our results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo Melanesians the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders. Last using both genomic and morphometric analyses we found that historical Native American groups such as the Pericúes and Fuego Patagonians were not “relicts” of Paleoamericans and hence our results do not support an early migration of populations directly related to Australo Melanesians into the Americas. CONCLUSION Our results provide an upper bound of {\textasciitilde}23 ka on the initial divergence of ancestral Native Americans from their East Asian ancestors followed by a short isolation period of no more than {\textasciitilde}8000 years and subsequent entrance and spread across the Americas. The data presented are consistent with a single migration model for all Native Americans with later gene flow from sources related to East Asians and indirectly Australo Melanesians. The single wave diversified {\textasciitilde}13 ka likely within the Americas giving rise to the northern and southern branches of present day Native Americans. View larger version: In this page In a new window Download PowerPoint Slide for Teaching Population history of present day Native Americans.The ancestors of all Native Americans entered the Americas as a single migration wave from Siberia (purple) no earlier than {\textasciitilde}23 ka separate from the Inuit (green) and diversified into “northern” and “southern” Native American branches {\textasciitilde}13 ka. There is evidence of post divergence gene flow between some Native Americans and groups related to East Asians/Inuit and Australo Melanesians (yellow). Genetic history of Native Americans Several theories have been put forth as to the origin and timing of when Native American ancestors entered the Americas. To clarify this controversy Raghavan et al. examined the genomic variation among ancient and modern individuals from Asia and the Americas. There is no evidence for multiple waves of entry or recurrent gene flow with Asians in northern populations. The earliest migrations occurred no earlier than 23000 years ago from Siberian ancestors. Amerindians and Athabascans originated from a single population splitting approximately 13000 years ago. Science this issue 10.1126/science.aab3884