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The remarkable archaeological record of Neolithic Orkney has ensured that these islands play a prominent role in narratives of European late prehistory, yet knowledge of the subsequent Bronze Age is comparatively poor. The Bronze Age settlement and cemetery at the Links of Noltland, on the island of Westray, offers new evidence, including aDNA, that points to a substantial population replacement between the Late Neolithic and Bronze Age. Focusing on funerary practice, the authors argue for interconnecting identities centred on household and community, patrilocality and inheritance. The findings prompt a reconsideration of the Orcadian Bronze Age, with wider implications for population movement and the uptake of cultural innovations more widely across prehistoric north-western Europe.

The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2–4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans—including 278 individuals from England—alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France

Raw sequencing reads of ancient samples produced for this study have been deposited in the European Nucleotide Archive under accession no. PRJEB46830. Modern mitochondrial genomes generated as part of this study have been deposited in GenBank, accession nos. MZ846240 to MZ848095., Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From ∼3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By ∼2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC. We tested this by comparing new genomic evidence from 22 Bronze Age and 3 Iron Age burials in northwest Orkney with Neolithic burials from across the archipelago. We identified signals of inward migration on a scale unsuspected from the archaeological record: As elsewhere in Bronze Age Britain, much of the population displayed significant genome-wide ancestry deriving ultimately from the Pontic-Caspian Steppe. However, uniquely in northern and central Europe, most of the male lineages were inherited from the local Neolithic. This suggests that some male descendants of Neolithic Orkney may have remained distinct well into the Bronze Age, although there are signs that this had dwindled by the Iron Age. Furthermore, although the majority of mitochondrial DNA lineages evidently arrived afresh with the Bronze Age, we also find evidence for continuity in the female line of descent from Mesolithic Britain into the Bronze Age and even to the present day., We thank Steve Birch, Jenny Murray, and Sue Black for help with samples; Harald Ringbauer for advice on hapROH; and Joyce Richards for comments on an early draft. Excavations at LoN and KoS are directed by H.M. and G.W., EASE (Environment and Archaeology Services), grant funded by Historic Environment Scotland. M. Ni Challanain, M. McCormick, and D. Gooney undertook osteological identifications and sample selection. K.D., M.G.B.F, P.J., M.S., G.O.-G, A.F., and S.R. were supported by a Leverhulme Trust Doctoral Scholarship program awarded to M.B.R. and M.P. DNA sequencing was also supported by the UK Natural Environment Research Council Biomolecular Analysis Facility (NBAF) at the University of Liverpool, under NBAF Pilot Scheme NBAF685, awarded to C.J.E. whilst at the University of Oxford. P.S., M.P., and M.B.R. acknowledge FCT (Fundação para a Ciência e a Tecnologia) support through project PTDC/EPH-ARQ/4164/2014, partially funded by FEDER (Fundo Europeu de Desenvolvimento Regional) funds (COMPETE 2020 project 016899). PS was supported by FCT, European Social Fund, Programa Operacional Potencial Humano, and the FCT Investigator Programme and acknowledges FCT/MEC (Ministério da Educação e Ciência) for support to CBMA through Portuguese funds (PIDDAC: Programa de Investimentos e Despesas de Desenvolvimento da Administração Central)—PEst-OE/BIA/UI4050/2014. V.M. and D.G.B. acknowledge the Science Foundation Ireland/Health Research Board/Wellcome Trust Biomedical Research Partnership Investigator Award No. 205072 to D.G.B., “Ancient Genomics and the Atlantic Burden.” The ORCADES was supported by the Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710), a Royal Society University Research Fellowship to J.F.W., the MRC (Medical Research Council) Human Genetics Unit quinquennial programme “QTL in Health and Disease,” Arthritis Research UK, and the EU FP6 EUROSPAN project (contract no. LSHG-CT-2006-018947). The Edinburgh Clinical Research Facility, University of Edinburgh, performed DNA extractions and the Sanger Institute performed whole-genome sequencing. The Viking Health Study–Shetland (VIKING) was supported by the MRC Human Genetics Unit quinquennial programme grant “QTL in Health and Disease.” DNA extractions were performed at the Edinburgh Clinical Research Facility, University of Edinburgh. Whole genome sequencing was supported by the Scottish Genomes Partnership award from the Chief Scientist Office of the Scottish Government and the MRC (grant reference SGP/1) and the MRC Whole Genome Sequencing for Health and Wealth Initiative (MC/PC/15080). We acknowledge Wellcome Trust funding (098051) for the ORCADES whole-genome sequencing. J.F.W. acknowledges support from the MRC Human Genetics Unit programme grant, “Quantitative traits in health and disease” (U. MC_UU_00007/10). We also acknowledge the invaluable contributions of the research nurses in Orkney and Shetland, the administrative team in Edinburgh, and the people of Orkney and Shetland.

Supplementary Information: The online version contains supplementary material available at https://doi.org/ 10.1038/s41598-021-95996-3., Sequence data for UE2298/MS060 can be downloaded from the European Nucleotide Archive (accession number: PRJEB47085). Newly reported present-day mtDNA sequences are deposited into GenBank (MZ920249 - MZ921390). Additional requests should be addressed to: marina.silva@crick.ac.uk; gonzalo.oteo-garcia@hud. ac.uk; m.b.richards@hud.ac.uk., Historical records document medieval immigration from North Africa to Iberia to create Islamic al-Andalus. Here, we present a low-coverage genome of an eleventh century CE man buried in an Islamic necropolis in Segorbe, near Valencia, Spain. Uniparental lineages indicate North African ancestry, but at the autosomal level he displays a mosaic of North African and European-like ancestries, distinct from any present-day population. Altogether, the genome-wide evidence, stable isotope results and the age of the burial indicate that his ancestry was ultimately a result of admixture between recently arrived Amazigh people (Berbers) and the population inhabiting the Peninsula prior to the Islamic conquest. We detect differences between our sample and a previously published group of contemporary individuals from Valencia, exemplifying how detailed, small-scale aDNA studies can illuminate fine-grained regional and temporal differences. His genome demonstrates how ancient DNA studies can capture portraits of past genetic variation that have been erased by later demographic shifts-in this case, most likely the seventeenth century CE expulsion of formerly Islamic communities as tolerance dissipated following the Reconquista by the Catholic kingdoms of the north., We thank the Museo Municipal de Arqueologia y Etnologia de Segorbe for granting access to their collections and the Conselleria d'Educacio, Investigacio, Cultura i Esport de la Generalitat Valenciana for granting the permissions for the study. We thank Lara Cassidy, Valeria Mattiangeli and Dan Bradley for valuable advice and technical support. Part of this work was delivered via the BBSRC National Capability in Genomics and Single Cell Analysis (BBS/E/T/000PR9816) at Earlham Institute by members of the Genomics Pipelines and Core Bioinformatics Groups. We wish to acknowledge the use of the Orion High Performance Computing cluster at the School of Applied Sciences, University of Huddersfield. M.S., G.O.G., A.Fi., P.J., M.G.B.F., K.D., B.Y. were supported by a Leverhulme Doctoral Scholarship awarded to M.B.R. and M.P. P.S., M.B.R., and M.P. acknowledge FCT (Fundacao para a Ciencia e a Tecnologia) support through project PTDC/EPH-ARQ/4164/2014, partially funded by FEDER funds (COMPETE 2020 project 016899). P.S., A.Br., A.R. and T.R. acknowledge FCT support through project PTDC/SOC-ANT/30316/2017. P.S. acknowledges the "Contrato-Programa" UIDB/04050/2020 and contract CEECINST/0007772018 funded by FCT I.P. A.A., A.O., and A.T. acknowledge the support of the Italian Ministry of Education, University and Research for the projects "Dipartimenti di Eccellenza" Program (2018-2022) -Department of Biology and Biotechnology "L. Spallanzani," University of Pavia and PRIN2017 20174BTC4R. The KORA research platform (KORA, Cooperative Research in the Region of Augsburg) was initiated and financed by the Helmholtz Zentrum Munchen -German Research Center for Environmental Health, which is funded by the German Federal Ministry of Education and Research and by the State of Bavaria. Furthermore, KORA research was supported within the Munich Center of Health Sciences (MC Health), LudwigMaximilians-Universitat, as part of LMUinnovativ.

Two key moments shaped the extant South Asian gene pool within the last 10 thousand years (ka): the Neolithic period, with the advent of agriculture and the rise of the Harappan/Indus Valley Civilisation; and Late Bronze Age events that witnessed the abrupt fall of the Harappan Civilisation and the arrival of Indo-European speakers. This study focuses on the phylogeographic patterns of mitochondrial haplogroups H2 and H13 in the Indian Subcontinent and incorporates evidence from recently released ancient genomes from Central and South Asia. It found signals of Neolithic arrivals from Iran and later movements in the Bronze Age from Central Asia that derived ultimately from the Steppe. This study shows how a detailed mtDNA phylogeographic approach, combining both modern and ancient variation, can provide evidence of population movements, even in a scenario of strong male bias such as in the case of the Bronze Age Steppe dispersals., M.S., P.J., S.R., G.O.-G., K.D., G.F., A.F., B.Y., M.P., and M.B.R. received support from the Leverhulme Trust Doctoral Scholarship programme. This work was partially supported by the Portuguese Foundation for Science and Technology (FCT), through the project PTDC/EPH-ARQ/4164/2014 partially funded by European Regional Development Fund (FEDER) (COMPETE 2020 project 016899). P.S. was supported by FCT, ESF and POPH through the FCT Investigator Programme (IF/01641/2013) and acknowledges FCT IP and ERDF (COMPETE2020 -POCI) for the CBMA strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569). T.R. is supported by an FCT grant (SFRH/BPD/108126/2015) and acknowledges the project [NORTE-01-0145-FEDER-000013], supported by NORTE 2020-Portugal 2020, through FEDER.

Human remains from the Iron Age in Atlantic Scotland are rare, which makes the assemblage of an adult female and numerous foetal bones at High Pasture Cave, on the Isle of Skye, particularly noteworthy. Archaeological evidence suggests that the female had been deposited as an articulated skeleton when the cave entrance was blocked off, marking the end of use of the site. Particularly intriguing is the deposition of disarticulated remains from a foetus and perinate close to the adult female, which opens the possibility that the female might have been the mother of both of the infants. We used shotgun genome sequencing in order to analyse the mitochondria) genomes of all three individuals and investigate their maternal relationship, and we report here, for the first time, complete ancient mitogenomes from foetal-aged bone fragments. While we could not exclude the possibility that the female was the mother of, or maternally related to, the foetus, we could definitely say that she was not the mother of the perinate buried alongside her. This finding is contrary to the standard archaeological interpretation, that women in such burials most likely died in childbirth and were buried together with their foetuses., KD is supported by a Leverhulme Doctoral Scholarship awarded to MBR and MP. P.S., M.B.R. and M.P. acknowledge FCT support through project PTDC/EPH-ARQ/4164/2014, partially funded by FEDER funds (COMPETE 2020 project 016899). P.S. is supported by FCT, European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme and acknowledges FCT/MEC for support to CBMA through Portuguese funds (PIDDAC)-PEst-OE/BIA/UI4050/2014. The genetic research was supported by the UK Natural Environment Research Council (NERC) Biomolecular Analysis Facility at the University of Liverpool, under NBAF Pilot Scheme NBAF685, awarded to CJE whilst at the University of Oxford.