{"entity": "researcher", "timestamp": "2026-07-15T07:19:11.952Z", "family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "affiliations": ["Department Organismal Biology, EBC, Uppsala University, Uppsala, Sweden.", "Ancient DNA, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.", "Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71"}}, "publications": [{"entity": "publication", "iuid": "0ac29334eda645a1a6d1edc626fc0f09", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0ac29334eda645a1a6d1edc626fc0f09.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0ac29334eda645a1a6d1edc626fc0f09"}}, "title": "Ancestry, admixture, and pathogens in contemporaneous Neolithic farmers and foragers on the Island of Gotland.", "authors": [{"family": "Fraser", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-4714-088X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8d9acba81e4da4a1efc097e53aa4f3.json"}}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F", "orcid": "0000-0002-0201-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/c554aeb35ee04ee1ac43c5291a8d7f3c.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Ausmees", "given": "Kristiina", "initials": "K"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Correa-Mendoza", "given": "Leonardo", "initials": "L"}, {"family": "Le Meur", "given": "Adrien", "initials": "A"}, {"family": "Blanchet", "given": "Antonio", "initials": "A"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "Arrieta-Donato", "given": "Eduardo", "initials": "E", "orcid": "0009-0004-1606-1737", "researcher": {"href": "https://publications.scilifelab.se/researcher/50765f72fec044248910b7ce013ac045.json"}}, {"family": "Escobar-Rodr\u00edguez", "given": "Mariana", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Lozano-Gonzalez", "given": "Karla", "initials": "K", "orcid": "0000-0003-0329-4668", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc7c2e4b742f47688c4d48833d173778.json"}}, {"family": "Aguilar-Ordo\u00f1ez", "given": "Israel", "initials": "I"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Knutsson", "given": "Kjel", "initials": "K"}, {"family": "Wallin", "given": "Paul", "initials": "P"}, {"family": "Rascovan", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-2129-5878", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7c1c0695dbe44d78d81ecf41265d331.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2026-07-13", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642"}, "abstract": "Two archaeological cultural complexes; the Neolithic Funnelbeaker culture (FBC) and the Pitted ware culture (PWC), coexisted on Gotland for over 500 years, between ~3300 and 2800 calBCE. The ancestry of the FBC farmers and PWC marine foragers largely aligns with European Neolithic Farmers and European Mesolithic foragers, respectively, but the direct interactions between the groups on Gotland is not understood. We present a Middle Neolithic (MN) high-coverage genome and a Late Neolithic (LN) low-coverage genome from the Ansarve FBC dolmen. We investigate ancestry, admixture, and pathogens among these MN farmers (n = 6), foragers (n = 19), and the LN individual. We find that recent gene-flow between farmers and foragers could have taken place, although most gene-flow happened prior to their coexistence on the island. We also find evidence of different Yersinia pestis strains in the three cultural groups, showing that the pestis was widespread among groups with different subsistence strategies.", "doi": "10.1038/s42003-026-10498-0", "pmid": "42443543", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s42003-026-10498-0"}], "notes": [], "created": "2026-07-14T17:36:10.476Z", "modified": "2026-07-14T17:36:11.138Z"}, {"entity": "publication", "iuid": "817f65055c534d8196be40bc8a8e308c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/817f65055c534d8196be40bc8a8e308c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/817f65055c534d8196be40bc8a8e308c"}}, "title": "Equal in death: Ancient genomic analysis of children's early Christian burials.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0001-8964-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3a47cc07e9d4b8592dba430785681b5.json"}}, {"family": "Yaka", "given": "Reyhan", "initials": "R", "orcid": "0000-0002-9359-4391", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f685d3d3cac4dc6bfd4571041786add.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R", "orcid": "0000-0002-4173-8648", "researcher": {"href": "https://publications.scilifelab.se/researcher/b4cefc4ed580469ba97e32c95477d485.json"}}, {"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications.scilifelab.se/researcher/d7355501dddb4508bf453c7c1ad9f107.json"}}, {"family": "Kempe Lagerholm", "given": "Vendela", "initials": "V"}, {"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-2250-0463", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ed3c5d3aa804b7085c4f8a4036c09e1.json"}}, {"family": "Zachrisson", "given": "Torun", "initials": "T", "orcid": "0000-0001-7755-4982", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bdaee9400b347088474cc8a9147026b.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Sobrado", "given": "Ver\u00f3nica", "initials": "V"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T", "orcid": "0009-0009-3553-0718", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a32a4e171454874a03920c915d3265f.json"}}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB", "orcid": "0000-0003-3964-3065", "researcher": {"href": "https://publications.scilifelab.se/researcher/c48d3f195bbd4998b69ca678f1ff9fb7.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}], "type": "journal article", "published": "2026-07-10", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "12", "issue": "28", "pages": "eaeb8588", "issn-l": "2375-2548"}, "abstract": "Sexing the skeletal remains of young individuals is crucial yet notoriously difficult in archaeology. Children, who cannot be reliably sexed morphologically, are often excluded from gender-related research, limiting our understanding of past childhood. This issue is compounded in contexts lacking grave goods, such as early Christian burials. We conducted genomic screening of 142 individuals from Sweden dating from the late Viking Age to the Medieval period, including 68 subadults and 74 adults from 27 single and 50 multiple burials. To investigate the treatment of children in death and the role of collective graves, we applied genomic sexing and kinship analyses to individuals from three sites. Contrary to the assumption that collective burials reflect close kinship, our results show that children interred with adults rarely shared close biological ties. Burial patterns indicate that gender roles were established early, with both boys and most girls mirroring adult spatial patterns. However, flexibility existed, and extended kinship likely played a central role in structuring these communities.", "doi": "10.1126/sciadv.aeb8588", "pmid": "42430491", "labels": {"NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13353417"}], "notes": [], "created": "2026-07-14T17:36:38.635Z", "modified": "2026-07-14T17:36:39.114Z"}, {"entity": "publication", "iuid": "5f52c18408484928a5bdac12a356745d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f52c18408484928a5bdac12a356745d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f52c18408484928a5bdac12a356745d"}}, "title": "Genetic relatedness mattered in the co-burial ritual of Neolithic hunter-gatherers.", "authors": [{"family": "Mattila", "given": "Tiina Maria", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Fraser", "given": "Magdalena", "initials": "M", "orcid": "0000-0003-4714-088X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de8d9acba81e4da4a1efc097e53aa4f3.json"}}, {"family": "Koelman", "given": "Julian", "initials": "J"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Ivarsson-Aalders", "given": "Marieke", "initials": "M", "orcid": "0009-0001-5174-1840", "researcher": {"href": "https://publications.scilifelab.se/researcher/4df153464673466faa2249a0ef253d82.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Wallin", "given": "Paul", "initials": "P", "orcid": "0000-0002-0916-6264", "researcher": {"href": "https://publications.scilifelab.se/researcher/aac2463e759342bdba70ea7e40caebe2.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}], "type": "journal article", "published": "2026-02-18", "journal": {"title": "Proc. Biol. Sci.", "issn": "1471-2954", "volume": "293", "issue": "2065", "issn-l": "0962-8452"}, "abstract": "Kin relations among past societies can offer valuable information about the social dynamics of the population. Genetic data from prehistoric human remains can reveal genetic relatedness, and when combined with archaeological information, shed light on social factors shaping ancient communities. However, accessing such information on ancient hunter-gatherer societies has been challenging owing to the scarcity of temporally overlapping multi-burial sites. Here, we focused on the Pitted Ware Culture (PWC) cemetery from Ajvide (Gotland, Sweden), one of Stone Age Europe's largest and best-preserved hunter-gatherer burial grounds of the European Stone Age. We generated new genomic data from 10 individuals, primarily from co-burial contexts, and combined these with published genomes from 24 individuals across four PWC sites on Gotland. The genetic analyses revealed dual ancestry of the Gotlandic PWC, showing approximately 80% ancestry associated with earlier Mesolithic hunter-gatherer groups and 20% with farmer groups. We also identified close genetic relatives between the different studied PWC sites on Gotland, indicating mixing of the groups. All individuals buried together were closely related to one another, including first-, second- and third-degree relatives, and showed significantly elevated genetic relatedness. This demonstrates that genetic relatedness played a defining role in the co-burial ritual and extended beyond first-degree relatives.", "doi": "10.1098/rspb.2025.0813", "pmid": "41705298", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "480372"}], "notes": [], "created": "2026-06-01T08:42:52.357Z", "modified": "2026-06-01T08:42:52.890Z"}, {"entity": "publication", "iuid": "b8ca2a2dba2049ec8de7192c162898c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8ca2a2dba2049ec8de7192c162898c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8ca2a2dba2049ec8de7192c162898c4"}}, "title": "Homo sapiens-specific evolution unveiled by ancient southern African genomes.", "authors": [{"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C", "orcid": "0000-0002-3258-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fce67de4e14fa68c0edadfec0de085.json"}}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Hollfelder", "given": "Nina", "initials": "N", "orcid": "0000-0002-1567-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f81a63833c146999d73fa38f588ea06.json"}}, {"family": "Vicente", "given": "Mario", "initials": "M"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Brink", "given": "James", "initials": "J"}, {"family": "Zipfel", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-4251-884X", "researcher": {"href": "https://publications.scilifelab.se/researcher/74d1041d932a49c9bc2baca44273d4a4.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2025-12-03", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": null, "issue": null, "pages": null}, "abstract": "Homo sapiens evolved hundreds of thousands of years ago in Africa, later spreading across the globe1, but the early evolutionary process is debated2-6. Here we present whole-genome sequencing data for 28 ancient southern African individuals, including six individuals with 25\u00d7 to 7.2\u00d7 genome coverage, dated to between 10,200 and 150 calibrated years before present (cal. BP). All ancient southern Africans dated to more than 1,400 cal. BP show a genetic make-up that is outside the range of genetic variation in modern-day humans (including southern African Khoe-San people, although some retain up to 80% ancient southern African ancestry), manifesting in a large fraction of Homo sapiens-specific variants that are unique to ancient southern Africans. Homo sapiens-specific variants at amino acid-altering sites fixed for all humans-which are likely to have evolved rapidly on the Homo sapiens branch-were enriched for genes associated with kidney function. Some Homo sapiens-specific variants fixed in ancient southern Africans-which are likely to have adapted rapidly on the southern African branch-were enriched for genes associated with protection against ultraviolet light. The ancient southern Africans show little spatiotemporal stratification for 9,000 years, consistent with a large, stable Holocene population transcending archaeological phases. While southern Africa served as a long-standing geographical refugium, there is outward gene flow over 8,000 years ago; however, inward gene flow manifests only after around 1,400 years ago. The ancient genomes reported here are therefore key to the evolution of Homo sapiens, and are important for advancing our understanding of human genomic variation.", "doi": "10.1038/s41586-025-09811-4", "pmid": "41339558", "labels": {"National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-025-09811-4"}], "notes": [], "created": "2025-12-04T08:12:48.745Z", "modified": "2025-12-05T10:16:26.469Z"}, {"entity": "publication", "iuid": "e25c443cc2a84c89b1642a768afa88b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e25c443cc2a84c89b1642a768afa88b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e25c443cc2a84c89b1642a768afa88b0"}}, "title": "BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups.", "authors": [{"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "Barham", "given": "Lawrence", "initials": "L"}, {"family": "Mudenda", "given": "George", "initials": "G"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2024-08-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "7307", "issn-l": "2041-1723"}, "abstract": "Sub-equatorial Africa is today inhabited predominantly by Bantu-speaking groups of Western African descent who brought agriculture to the Luangwa valley in eastern Zambia ~2000 years ago. Before their arrival the area was inhabited by hunter-gatherers, who in many cases were subsequently replaced, displaced or assimilated. In Zambia, we know little about the genetic affinities of these hunter-gatherers. We examine ancestry of two isolated communities in Zambia, known as BaTwa and possible descendants of recent hunter-gatherers. We genotype over two million genome-wide SNPs from two BaTwa populations (total of 80 individuals) and from three comparative farming populations to: (i) determine if the BaTwa carry genetic links to past hunter-gatherer-groups, and (ii) characterise the genetic affinities of past Zambian hunter-gatherer-groups. The BaTwa populations do harbour a hunter-gatherer-like genetic ancestry and Western African ancestry. The hunter-gatherer component is a unique local signature, intermediate between current-day Khoe-San ancestry from southern Africa and central African rainforest hunter-gatherer ancestry.", "doi": "10.1038/s41467-024-50733-y", "pmid": "39181874", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI SNP genotyping": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Gothenburg": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11344834"}, {"db": "pii", "key": "10.1038/s41467-024-50733-y"}], "notes": [], "created": "2024-10-21T11:15:04.878Z", "modified": "2024-11-25T10:17:25.391Z"}, {"entity": "publication", "iuid": "c033e6d550b3493f91cfc42d9b9ebccd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c033e6d550b3493f91cfc42d9b9ebccd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c033e6d550b3493f91cfc42d9b9ebccd"}}, "title": "Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France.", "authors": [{"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG", "orcid": "0000-0002-6119-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/eea5b7ccd8f84d44b2e0be03f5c4e762.json"}}, {"family": "Peyroteo-Stjerna", "given": "Rita", "initials": "R", "orcid": "0000-0002-3309-474X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6a9ae2a39e94beba21b461ef827ce17.json"}}, {"family": "Marchand", "given": "Gr\u00e9gor", "initials": "G"}, {"family": "Bernhardsson", "given": "Carolina", "initials": "C", "orcid": "0000-0002-3258-275X", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8fce67de4e14fa68c0edadfec0de085.json"}}, {"family": "Vialet", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Chetty", "given": "Darshan", "initials": "D", "orcid": "0000-0003-4668-1182", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a9c8096ccbc4b4e943373d9a3acd5b1.json"}}, {"family": "Ala\u00e7aml\u0131", "given": "Erkin", "initials": "E", "orcid": "0009-0009-0702-3313", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fb8084ce6634c9c8e33cc29e98f8252.json"}}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Bouquin", "given": "Denis", "initials": "D"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "Garmond", "given": "Nicolas", "initials": "N"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2024-03-05", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "121", "issue": "10", "pages": "e2310545121", "issn-l": "0027-8424"}, "abstract": "Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic fa\u00e7ade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and T\u00e9viec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, T\u00e9viec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.", "doi": "10.1073/pnas.2310545121", "pmid": "38408241", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10927518"}], "notes": [], "created": "2024-02-27T13:17:58.460Z", "modified": "2024-11-25T10:22:31.622Z"}, {"entity": "publication", "iuid": "3bc1aebcc63f41edbfce850538cda6c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3bc1aebcc63f41edbfce850538cda6c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3bc1aebcc63f41edbfce850538cda6c4"}}, "title": "Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe.", "authors": [{"family": "Mattila", "given": "Tiina M", "initials": "TM", "orcid": "0000-0002-1298-7370", "researcher": {"href": "https://publications.scilifelab.se/researcher/0dbb4f417ab0440fb02a305aaf81b3d5.json"}}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Ala-Hulkko", "given": "Terhi", "initials": "T", "orcid": "0000-0002-0884-2152", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f4036f2bc54136a489b22aaba390d7.json"}}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Constantinescu", "given": "Mihai", "initials": "M"}, {"family": "Rotea", "given": "Mihai", "initials": "M"}, {"family": "Palinca\u0219", "given": "Nona", "initials": "N", "orcid": "0000-0001-5308-4349", "researcher": {"href": "https://publications.scilifelab.se/researcher/f4275405ad5045da8909e05ac7fb9dd9.json"}}, {"family": "Wilk", "given": "Stanis\u0142aw", "initials": "S"}, {"family": "Czerniak", "given": "Lech", "initials": "L", "orcid": "0000-0002-0352-5385", "researcher": {"href": "https://publications.scilifelab.se/researcher/73f2691cdc7f424784c4a7d1dbb2957e.json"}}, {"family": "Kruk", "given": "Janusz", "initials": "J"}, {"family": "\u0141apo", "given": "Jerzy", "initials": "J"}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P", "orcid": "0000-0003-4452-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/035ae0d32cf649f6a82c6e4df78cc122.json"}}, {"family": "Potekhina", "given": "Inna", "initials": "I"}, {"family": "Soficaru", "given": "Andrei", "initials": "A"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Netea", "given": "Mihai G", "initials": "MG", "orcid": "0000-0003-2421-6052", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0b25efbd9ee43e7a873baaaec4cf34c.json"}}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG", "orcid": "0000-0002-3897-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f103c7d36c24ac981fbd8291fea853c.json"}}, {"family": "Persson", "given": "Per", "initials": "P", "orcid": "0009-0007-4490-2494", "researcher": {"href": "https://publications.scilifelab.se/researcher/178194b694e04e8d9520328ddda9bd11.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2023-08-09", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "793", "issn-l": "2399-3642"}, "abstract": "The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.", "doi": "10.1038/s42003-023-05131-3", "pmid": "37558731", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10412644"}, {"db": "pii", "key": "10.1038/s42003-023-05131-3"}], "notes": [], "created": "2023-08-14T06:19:02.423Z", "modified": "2024-01-16T13:48:32.510Z"}, {"entity": "publication", "iuid": "cac2b2a5dca44746b91a68788dce04df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cac2b2a5dca44746b91a68788dce04df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cac2b2a5dca44746b91a68788dce04df"}}, "title": "Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age.", "authors": [{"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P", "orcid": "0000-0003-4452-7704", "researcher": {"href": "https://publications.scilifelab.se/researcher/035ae0d32cf649f6a82c6e4df78cc122.json"}}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Ehler", "given": "Edvard", "initials": "E", "orcid": "0000-0003-1774-0091", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d5e30a4e46e47d8b800d5242e23d7de.json"}}, {"family": "Breszka", "given": "Agnieszka", "initials": "A"}, {"family": "G\u00f3rski", "given": "Jacek", "initials": "J"}, {"family": "Taras", "given": "Halina", "initials": "H"}, {"family": "Szczepanek", "given": "Anita", "initials": "A"}, {"family": "Pola\u0144ska", "given": "Marta", "initials": "M"}, {"family": "W\u0142odarczak", "given": "Piotr", "initials": "P", "orcid": "0000-0003-0359-7386", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4581e4213be44969693180b26b3f263.json"}}, {"family": "Lasota-Ku\u015b", "given": "Anna", "initials": "A", "orcid": "0000-0002-0603-846X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8716e836f3894e28bee1bcacffb7245a.json"}}, {"family": "W\u00f3jcik", "given": "Irena", "initials": "I"}, {"family": "Romaniszyn", "given": "Jan", "initials": "J"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Ko\u015bko", "given": "Aleksander", "initials": "A"}, {"family": "Ignaczak", "given": "Marcin", "initials": "M"}, {"family": "Sadowski", "given": "Sylwester", "initials": "S"}, {"family": "Matoga", "given": "Andrzej", "initials": "A"}, {"family": "Grossman", "given": "Anna", "initials": "A"}, {"family": "Ilchyshyn", "given": "Vasyl", "initials": "V"}, {"family": "Yahodinska", "given": "Maryna O", "initials": "MO"}, {"family": "Roma\u0144ska", "given": "Adriana", "initials": "A"}, {"family": "Tunia", "given": "Krzysztof", "initials": "K"}, {"family": "Przyby\u0142a", "given": "Marcin", "initials": "M"}, {"family": "Grygiel", "given": "Ryszard", "initials": "R"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}], "type": "historical article", "published": "2023-08-01", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "14", "issue": "1", "pages": "4395"}, "abstract": "The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.", "doi": "10.1038/s41467-023-40072-9", "pmid": "37528090", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10393988"}, {"db": "pii", "key": "10.1038/s41467-023-40072-9"}], "notes": [], "created": "2023-10-19T12:43:53.699Z", "modified": "2024-01-16T13:48:32.641Z"}, {"entity": "publication", "iuid": "2aed043e07494edeb8d66c6047ca7cfd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2aed043e07494edeb8d66c6047ca7cfd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2aed043e07494edeb8d66c6047ca7cfd"}}, "title": "Northwest African Neolithic initiated by migrants from Iberia and Levant.", "authors": [{"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG", "orcid": "0000-0002-6119-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/eea5b7ccd8f84d44b2e0be03f5c4e762.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Mart\u00ednez-S\u00e1nchez", "given": "Rafael M", "initials": "RM"}, {"family": "Vera-Rodr\u00edguez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Iriarte", "given": "Eneko", "initials": "E", "orcid": "0000-0001-8365-5616", "researcher": {"href": "https://publications.scilifelab.se/researcher/112f0c5761e84deea89b2b7cb68521ce.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Bokbot", "given": "Youssef", "initials": "Y"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "comparative study", "published": "2023-06-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "618", "issue": "7965", "pages": "550-556"}, "abstract": "In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1-3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.", "doi": "10.1038/s41586-023-06166-6", "pmid": "37286608", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10266975"}, {"db": "pii", "key": "10.1038/s41586-023-06166-6"}], "notes": [], "created": "2023-11-29T10:51:14.891Z", "modified": "2024-01-16T13:48:33.294Z"}, {"entity": "publication", "iuid": "07fe9e3eec8b4340aa05343a657ea24d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/07fe9e3eec8b4340aa05343a657ea24d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/07fe9e3eec8b4340aa05343a657ea24d"}}, "title": "Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.", "authors": [{"family": "Rifkin", "given": "Riaan F", "initials": "RF", "orcid": "0000-0003-1791-3706", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b6691b2d64749e197ef0ddd36fd5af1.json"}}, {"family": "Vikram", "given": "Surendra", "initials": "S", "orcid": "0000-0002-4721-2890", "researcher": {"href": "https://publications.scilifelab.se/researcher/9171a14995cc47de9fb4d70bf4fe9aa9.json"}}, {"family": "Alcorta", "given": "Jaime", "initials": "J"}, {"family": "Ramond", "given": "Jean-Baptiste", "initials": "JB", "orcid": "0000-0003-4790-6232", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f9b3ec176bd489daeeb78e1ef0a1acf.json"}}, {"family": "Cowan", "given": "Don A", "initials": "DA", "orcid": "0000-0001-8059-861X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc756e07160f4c888fbdc7612936db03.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "240", "issn-l": "2399-3642"}, "abstract": "The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.", "doi": "10.1038/s42003-023-04582-y", "pmid": "36869137", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9984395"}, {"db": "pii", "key": "10.1038/s42003-023-04582-y"}], "notes": [], "created": "2023-11-29T11:28:26.513Z", "modified": "2023-11-29T11:28:26.659Z"}, {"entity": "publication", "iuid": "1263db35dcf5464c8840a71f59c535e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1263db35dcf5464c8840a71f59c535e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1263db35dcf5464c8840a71f59c535e6"}}, "title": "Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.", "authors": [{"family": "Srigyan", "given": "Megha", "initials": "M"}, {"family": "Bol\u00edvar", "given": "H\u00e9ctor", "initials": "H", "orcid": "0000-0001-5898-643X", "researcher": {"href": "https://publications.scilifelab.se/researcher/acff178f29e34a368b3f1c0105d473b7.json"}}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I", "orcid": "0000-0001-9724-9977", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b02b033776f4758acc477c75e4ec1ed.json"}}, {"family": "Santana", "given": "Jonathan", "initials": "J", "orcid": "0000-0002-9615-8560", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a4f0fc23b847b98e0d57d22a8a756d.json"}}, {"family": "Petersen", "given": "Andrew", "initials": "A", "orcid": "0000-0003-3882-0867", "researcher": {"href": "https://publications.scilifelab.se/researcher/69701b12d455487a9dd1ab55f9904327.json"}}, {"family": "Iriarte", "given": "Eneko", "initials": "E", "orcid": "0000-0001-8365-5616", "researcher": {"href": "https://publications.scilifelab.se/researcher/112f0c5761e84deea89b2b7cb68521ce.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "Mora", "given": "Alice", "initials": "A", "orcid": "0000-0002-0313-8545", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ca97200bd0442c3a9d41b84e57c448e.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Abdo", "given": "Khaled", "initials": "K"}, {"family": "Braemer", "given": "Frank", "initials": "F"}, {"family": "Smith", "given": "Colin", "initials": "C"}, {"family": "Iba\u00f1ez", "given": "Juan Jos\u00e9", "initials": "JJ"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}], "type": "journal article", "published": "2022-06-07", "journal": {"title": "Commun Biol", "issn": "2399-3642", "issn-l": "2399-3642", "volume": "5", "issue": "1", "pages": "554"}, "abstract": "The Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here we present a multidisciplinary bioarchaeological analysis of two individuals dated to the late 7th and early 8th centuries, the Umayyad Era, from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates and burial type are consistent with one of the earliest Islamic Arab burials in the Levant. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This study represents the genomic analysis of a secondary use site with characteristics consistent with an early Islamic burial in the Levant. We discuss our findings and possible historic scenarios in the light of forces such as genetic drift and their possible interaction with religious and cultural processes (including diet and subsistence practices).", "doi": "10.1038/s42003-022-03508-4", "pmid": "35672445", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9174286"}, {"db": "pii", "key": "10.1038/s42003-022-03508-4"}], "notes": [], "created": "2022-08-19T08:37:53.525Z", "modified": "2024-01-16T13:48:36.218Z"}, {"entity": "publication", "iuid": "265d3081559d435081d2d22b8a2e97da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/265d3081559d435081d2d22b8a2e97da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/265d3081559d435081d2d22b8a2e97da"}}, "title": "An empirical evaluation of genotype imputation of ancient DNA.", "authors": [{"family": "Ausmees", "given": "Kristiina", "initials": "K", "orcid": "0000-0002-6212-539X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d6a0fd5017647a7acb70bf4c667c73e.json"}}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Nettelblad", "given": "Carl", "initials": "C", "orcid": "0000-0003-0458-6902", "researcher": {"href": "https://publications.scilifelab.se/researcher/c300f2900aff429d8a3bbc72ee006df7.json"}}], "type": "journal article", "published": "2022-05-30", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "12", "issue": "6", "issn-l": "2160-1836"}, "abstract": "With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1\u00d7 coverage, and similar levels of accuracy and reference bias at levels as low as 0.75\u00d7. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1\u00d7. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.", "doi": "10.1093/g3journal/jkac089", "pmid": "35482488", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9157144"}, {"db": "pii", "key": "6575448"}], "notes": [], "created": "2022-11-29T09:07:08.055Z", "modified": "2024-01-16T13:48:36.386Z"}, {"entity": "publication", "iuid": "f6799d3e01e6445788993dca4c841552", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6799d3e01e6445788993dca4c841552.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6799d3e01e6445788993dca4c841552"}}, "title": "Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "Spinek", "given": "Anna El\u017cbieta", "initials": "AE", "orcid": "0000-0003-0304-081X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cb733a1bd8454c729d03ebd221cdf9ef.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Szostek", "given": "Krzysztof", "initials": "K"}, {"family": "Pasterkiewicz", "given": "Wojciech", "initials": "W"}, {"family": "Florek", "given": "Marek", "initials": "M"}, {"family": "Wilk", "given": "Stanis\u0142aw", "initials": "S"}, {"family": "Mnich", "given": "Barbara", "initials": "B"}, {"family": "Kruk", "given": "Janusz", "initials": "J"}, {"family": "Szmyt", "given": "Marzena", "initials": "M"}, {"family": "Kozie\u0142", "given": "S\u0142awomir", "initials": "S"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}], "type": "historical article", "published": "2021-10-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "issn-l": "0002-9483", "volume": "176", "issue": "2", "pages": "223-236"}, "abstract": "We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe.\n\nWe conducted ancient DNA studies from populations associated with Z\u0142ota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture.\n\nThe maternal genetic composition found in Z\u0142ota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Z\u0142ota group, Globular Amphora, and Funnel Beaker cultures.\n\nThe prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Z\u0142ota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Z\u0142ota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.", "doi": "10.1002/ajpa.24372", "pmid": "34308549", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2021-10-01T09:03:18.631Z", "modified": "2024-01-16T13:48:38.387Z"}, {"entity": "publication", "iuid": "7da26c536ad8449498fb9c9cf3193a48", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7da26c536ad8449498fb9c9cf3193a48.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7da26c536ad8449498fb9c9cf3193a48"}}, "title": "Genome of Pe\u015ftera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.", "authors": [{"family": "Svensson", "given": "Emma", "initials": "E"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Hoischen", "given": "Alexander", "initials": "A"}, {"family": "Hervella", "given": "Montserrat", "initials": "M"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Ioana", "given": "Mihai", "initials": "M"}, {"family": "Ridiche", "given": "Florin", "initials": "F"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "van Deuren", "given": "Rosanne C", "initials": "RC"}, {"family": "Soficaru", "given": "Andrei", "initials": "A"}, {"family": "de-la-Rua", "given": "Concepci\u00f3n", "initials": "C"}, {"family": "Netea", "given": "Mihai G", "initials": "MG"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2021-07-26", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "14", "pages": "2973-2983.e9", "issn-l": "0960-9822"}, "abstract": "Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from \"Pe\u015ftera Muierii,\" Romania who lived \u223c34,000 years ago to 13.5\u00d7 coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (\u223c3.1%) to most EUP humans but only half compared to the \u223c40,000-year-old Pe\u015ftera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.", "doi": "10.1016/j.cub.2021.04.045", "pmid": "34010592", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)00592-3"}], "notes": [], "created": "2021-05-25T06:50:37.310Z", "modified": "2024-01-16T13:48:39.094Z"}, {"entity": "publication", "iuid": "edd45af5bed64d469fc62f7ac60e5176", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edd45af5bed64d469fc62f7ac60e5176.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edd45af5bed64d469fc62f7ac60e5176"}}, "title": "Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.", "authors": [{"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "Mapelli", "given": "Igor", "initials": "I"}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "Do\u011fu", "given": "Ay\u00e7a", "initials": "A"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Erdal", "given": "\u00d6m\u00fcr Dilek", "initials": "\u00d6D"}, {"family": "Koptekin", "given": "Dilek", "initials": "D"}, {"family": "Vural", "given": "K\u0131v\u0131lc\u0131m Ba\u015fak", "initials": "KB"}, {"family": "Bayliss", "given": "Alex", "initials": "A"}, {"family": "Mazzucato", "given": "Camilla", "initials": "C"}, {"family": "Fer", "given": "Evrim", "initials": "E"}, {"family": "\u00c7oko\u011flu", "given": "Sevim Seda", "initials": "SS"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Karamurat", "given": "Cansu", "initials": "C"}, {"family": "Gemici", "given": "Hasan Can", "initials": "HC"}, {"family": "Sevkar", "given": "Arda", "initials": "A"}, {"family": "Da\u011fta\u015f", "given": "Nihan Dil\u015fad", "initials": "ND"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM"}, {"family": "Adams", "given": "Donovan", "initials": "D"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E"}, {"family": "Milella", "given": "Marco", "initials": "M"}, {"family": "Schotsmans", "given": "Eline M J", "initials": "EMJ"}, {"family": "Yurtman", "given": "Erin\u00e7", "initials": "E"}, {"family": "\u00c7etin", "given": "Mehmet", "initials": "M"}, {"family": "Yorulmaz", "given": "Sevgi", "initials": "S"}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE"}, {"family": "Ghalichi", "given": "Ayshin", "initials": "A"}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Bilgin", "given": "C Can", "initials": "CC"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "de Kleijn", "given": "Maurice", "initials": "M"}, {"family": "Mustafao\u011flu", "given": "G\u00f6khan", "initials": "G"}, {"family": "Fairbairn", "given": "Andrew", "initials": "A"}, {"family": "Pearson", "given": "Jessica", "initials": "J"}, {"family": "Togan", "given": "\u0130nci", "initials": "\u0130"}, {"family": "Kayacan", "given": "Nurcan", "initials": "N"}, {"family": "Marciniak", "given": "Arkadiusz", "initials": "A"}, {"family": "Larsen", "given": "Clark Spencer", "initials": "CS"}, {"family": "Hodder", "given": "Ian", "initials": "I"}, {"family": "Atakuman", "given": "\u00c7i\u011fdem", "initials": "\u00c7"}, {"family": "Pilloud", "given": "Marin", "initials": "M"}, {"family": "S\u00fcrer", "given": "Elif", "initials": "E"}, {"family": "Gerritsen", "given": "Fokke", "initials": "F"}, {"family": "\u00d6zbal", "given": "Rana", "initials": "R"}, {"family": "Baird", "given": "Douglas", "initials": "D"}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS"}, {"family": "Duru", "given": "G\u00fcne\u015f", "initials": "G"}, {"family": "\u00d6zba\u015faran", "given": "Mihriban", "initials": "M"}, {"family": "Haddow", "given": "Scott D", "initials": "SD"}, {"family": "Kn\u00fcsel", "given": "Christopher J", "initials": "CJ"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}], "type": "journal article", "published": "2021-06-07", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "31", "issue": "11", "pages": "2455-2468.e18", "issn-l": "0960-9822"}, "abstract": "The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from A\u015f\u0131kl\u0131 H\u00f6y\u00fck and \u00c7atalh\u00f6y\u00fck. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, A\u015f\u0131kl\u0131 H\u00f6y\u00fck and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of \u00c7atalh\u00f6y\u00fck and Barc\u0131n, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in \u00c7atalh\u00f6y\u00fck,3-5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development.", "doi": "10.1016/j.cub.2021.03.050", "pmid": "33857427", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(21)00423-1"}, {"db": "pmc", "key": "PMC8210650"}], "notes": [], "created": "2021-06-09T12:15:46.749Z", "modified": "2024-01-16T13:48:39.527Z"}, {"entity": "publication", "iuid": "a96b36a0cd1c4ae5a6c7bd698a64e2bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a96b36a0cd1c4ae5a6c7bd698a64e2bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a96b36a0cd1c4ae5a6c7bd698a64e2bf"}}, "title": "Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.", "authors": [{"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Henshilwood", "given": "Christopher S", "initials": "CS"}, {"family": "van Niekerk", "given": "Karen L", "initials": "KL"}, {"family": "Lombard", "given": "Marlize", "initials": "M"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2021-04-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "volume": "174", "issue": "4", "pages": "701-713", "issn-l": "0002-9483"}, "abstract": "Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry \"Coloured\" groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.", "doi": "10.1002/ajpa.24236", "pmid": "33539553", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2021-12-10T11:37:51.156Z", "modified": "2021-12-10T11:37:51.172Z"}, {"entity": "publication", "iuid": "886b1418f40b4c32b01fd338e3302530", "links": {"self": {"href": "https://publications.scilifelab.se/publication/886b1418f40b4c32b01fd338e3302530.json"}, "display": {"href": "https://publications.scilifelab.se/publication/886b1418f40b4c32b01fd338e3302530"}}, "title": "Multiple migrations to the Philippines during the last 50,000 years.", "authors": [{"family": "Larena", "given": "Maximilian", "initials": "M", "orcid": "0000-0002-8799-7645", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d580f1f3e584c809f5f22d7355f154f.json"}}, {"family": "Sanchez-Quinto", "given": "Federico", "initials": "F", "orcid": "0000-0002-0201-6204", "researcher": {"href": "https://publications.scilifelab.se/researcher/c554aeb35ee04ee1ac43c5291a8d7f3c.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "McKenna", "given": "James", "initials": "J"}, {"family": "Ebeo", "given": "Carlo", "initials": "C"}, {"family": "Reyes", "given": "Rebecca", "initials": "R"}, {"family": "Casel", "given": "Ophelia", "initials": "O"}, {"family": "Huang", "given": "Jin-Yuan", "initials": "JY"}, {"family": "Hagada", "given": "Kim Pullupul", "initials": "KP", "orcid": "0000-0002-1272-4132", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a2728ede8ca453c8e8c2fe8a98344bd.json"}}, {"family": "Guilay", "given": "Dennis", "initials": "D"}, {"family": "Reyes", "given": "Jennelyn", "initials": "J", "orcid": "0000-0002-9879-582X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c1a796da8c44d178de38fab6109c132.json"}}, {"family": "Allian", "given": "Fatima Pir", "initials": "FP"}, {"family": "Mori", "given": "Virgilio", "initials": "V"}, {"family": "Azarcon", "given": "Lahaina Sue", "initials": "LS"}, {"family": "Manera", "given": "Alma", "initials": "A"}, {"family": "Terando", "given": "Celito", "initials": "C", "orcid": "0000-0002-4939-1802", "researcher": {"href": "https://publications.scilifelab.se/researcher/351d926e87094101bfba53fe7322680a.json"}}, {"family": "Jamero", "given": "Lucio", "initials": "L"}, {"family": "Sireg", "given": "Gauden", "initials": "G"}, {"family": "Manginsay-Tremedal", "given": "Renefe", "initials": "R"}, {"family": "Labos", "given": "Maria Shiela", "initials": "MS"}, {"family": "Vilar", "given": "Richard Dian", "initials": "RD"}, {"family": "Latiph", "given": "Acram", "initials": "A"}, {"family": "Saway", "given": "Rodelio Linsahay", "initials": "RL", "orcid": "0000-0003-2445-048X", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c910747bc3f41369eaa95eafcb2f381.json"}}, {"family": "Marte", "given": "Erwin", "initials": "E"}, {"family": "Magbanua", "given": "Pablito", "initials": "P"}, {"family": "Morales", "given": "Amor", "initials": "A"}, {"family": "Java", "given": "Ismael", "initials": "I"}, {"family": "Reveche", "given": "Rudy", "initials": "R"}, {"family": "Barrios", "given": "Becky", "initials": "B"}, {"family": "Burton", "given": "Erlinda", "initials": "E"}, {"family": "Salon", "given": "Jesus Christopher", "initials": "JC"}, {"family": "Kels", "given": "Ma Junaliah Tuazon", "initials": "MJT"}, {"family": "Albano", "given": "Adrian", "initials": "A"}, {"family": "Cruz-Angeles", "given": "Rose Beatrix", "initials": "RB", "orcid": "0000-0003-3828-4929", "researcher": {"href": "https://publications.scilifelab.se/researcher/b6ac99916cbb41e2990452c0446e88f5.json"}}, {"family": "Molanida", "given": "Edison", "initials": "E"}, {"family": "Graneh\u00e4ll", "given": "Lena", "initials": "L", "orcid": "0000-0001-9970-4080", "researcher": {"href": "https://publications.scilifelab.se/researcher/1900cb5164304c70ab0f5aa19cf10564.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications.scilifelab.se/researcher/603244b141da49dfa9ff3a8d17f42b70.json"}}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Loo", "given": "Jun-Hun", "initials": "JH"}, {"family": "Trejaut", "given": "Jean", "initials": "J", "orcid": "0000-0002-4245-0814", "researcher": {"href": "https://publications.scilifelab.se/researcher/57eab8fc843743929a82453430b422dc.json"}}, {"family": "Ho", "given": "Simon Y W", "initials": "SYW", "orcid": "0000-0002-0361-2307", "researcher": {"href": "https://publications.scilifelab.se/researcher/00d59fd0713e440b8ddb35f58c53f19c.json"}}, {"family": "Reid", "given": "Lawrence", "initials": "L"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Schlebusch", "given": "Carina", "initials": "C", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Lambeck", "given": "Kurt", "initials": "K"}, {"family": "Endicott", "given": "Phillip", "initials": "P", "orcid": "0000-0003-2452-8507", "researcher": {"href": "https://publications.scilifelab.se/researcher/de01eeca292648eaaf16fe9480923187.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2021-03-30", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "118", "issue": "13", "issn-l": "0027-8424"}, "abstract": "Island Southeast Asia has recently produced several surprises regarding human history, but the region's complex demography remains poorly understood. Here, we report \u223c2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two \u223c8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least \u223c8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines \u223c2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive \"out-of-Taiwan\" model of farming-language-people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting \u223c1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.", "doi": "10.1073/pnas.2026132118", "pmid": "33753512", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "2026132118"}, {"db": "pmc", "key": "PMC8020671"}], "notes": [], "created": "2021-12-10T11:33:51.314Z", "modified": "2024-01-16T13:48:40.354Z"}, {"entity": "publication", "iuid": "627122d3b7f5410f829395df31d053e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/627122d3b7f5410f829395df31d053e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/627122d3b7f5410f829395df31d053e9"}}, "title": "Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians.", "authors": [{"family": "Sj\u00f6strand", "given": "Agn\u00e8s E", "initials": "AE"}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Hegay", "given": "Tatyana", "initials": "T"}, {"family": "Nikolaeva", "given": "Anna", "initials": "A"}, {"family": "Shayimkulov", "given": "Farhad", "initials": "F"}, {"family": "Blum", "given": "Michael G B", "initials": "MGB"}, {"family": "Heyer", "given": "Evelyne", "initials": "E", "orcid": "0000-0002-0266-3196", "researcher": {"href": "https://publications.scilifelab.se/researcher/aaa9ddd4afef4d28aa96f53bad9fc938.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Eur. J. Hum. Genet.", "issn": "1476-5438", "volume": "29", "issue": "2", "pages": "325-337", "issn-l": "1018-4813"}, "abstract": "Taste is essential for the interaction of animals with their food and has co-evolved with diet. Humans have peopled a large range of environments and present a wide range of diets, but little is known about the diversity and evolution of human taste perception. We measured taste recognition thresholds across populations differing in lifestyles (hunter gatherers and farmers from Central Africa, nomad herders, and farmers from Central Asia). We also generated genome-wide genotype data and performed association studies and selection scans in order to link the phenotypic variation in taste sensitivity with genetic variation. We found that hunter gatherers have lower overall sensitivity as well as lower sensitivity to quinine and fructose than their farming neighbors. In parallel, there is strong population divergence in genes associated with tongue morphogenesis and genes involved in the transduction pathway of taste signals in the African populations. We find signals of recent selection in bitter taste-receptor genes for all four populations. Enrichment analysis on association scans for the various tastes confirmed already documented associations and revealed novel GO terms that are good candidates for being involved in taste perception. Our framework permitted us to gain insight into the genetic basis of taste sensitivity variation across populations and lifestyles.", "doi": "10.1038/s41431-020-00736-2", "pmid": "33005019", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41431-020-00736-2"}, {"db": "pmc", "key": "PMC7868368"}], "notes": [], "created": "2020-10-20T06:59:23.977Z", "modified": "2024-01-16T13:48:40.806Z"}, {"entity": "publication", "iuid": "e78358779455418ba9c1128f301841ef", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e78358779455418ba9c1128f301841ef.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e78358779455418ba9c1128f301841ef"}}, "title": "Human population dynamics and Yersinia pestis in ancient northeast Asia.", "authors": [{"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N", "orcid": "0000-0002-3744-4073", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a321904793d47399adc5f73b0f58dcc.json"}}, {"family": "Koptekin", "given": "Dilek", "initials": "D", "orcid": "0000-0003-2664-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e95decb115f488ca913d25d1174711a.json"}}, {"family": "Bergfeldt", "given": "Nora", "initials": "N", "orcid": "0000-0003-2767-8156", "researcher": {"href": "https://publications.scilifelab.se/researcher/cef101ca28384bfabb088e7c87d0749e.json"}}, {"family": "D\u00f6nerta\u015f", "given": "Handan Melike", "initials": "HM", "orcid": "0000-0002-9788-6535", "researcher": {"href": "https://publications.scilifelab.se/researcher/99f355027fbd4691af8a17e78f1554f8.json"}}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Shergin", "given": "Dmitrij", "initials": "D"}, {"family": "Ivanov", "given": "Grigorij", "initials": "G", "orcid": "0000-0003-4316-7372", "researcher": {"href": "https://publications.scilifelab.se/researcher/f098ecc1f60d44e185f590c7f3b98a3d.json"}}, {"family": "Kichigin", "given": "Dmitrii", "initials": "D", "orcid": "0000-0003-3382-4199", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fbe657eebfa460eb6eabd47c6f55384.json"}}, {"family": "Pestereva", "given": "Kjunnej", "initials": "K", "orcid": "0000-0001-6270-1230", "researcher": {"href": "https://publications.scilifelab.se/researcher/c267495499114556b837c66845be6247.json"}}, {"family": "Volkov", "given": "Denis", "initials": "D", "orcid": "0000-0001-6064-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ce5ce75417640b4b778687b0dbd94a8.json"}}, {"family": "Mandryka", "given": "Pavel", "initials": "P", "orcid": "0000-0002-8647-3823", "researcher": {"href": "https://publications.scilifelab.se/researcher/5832247ccd844904b4421f7c89836815.json"}}, {"family": "Kharinskii", "given": "Artur", "initials": "A", "orcid": "0000-0002-4815-6069", "researcher": {"href": "https://publications.scilifelab.se/researcher/a4d0f94fca6d4c2388c64486891d28a4.json"}}, {"family": "Tishkin", "given": "Alexey", "initials": "A", "orcid": "0000-0002-7769-136X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff988500a4ec4fddb2b3f79b95127f77.json"}}, {"family": "Ineshin", "given": "Evgenij", "initials": "E"}, {"family": "Kovychev", "given": "Evgeniy", "initials": "E"}, {"family": "Stepanov", "given": "Aleksandr", "initials": "A"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "7", "issue": "2", "issn-l": "2375-2548"}, "abstract": "We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.", "doi": "10.1126/sciadv.abc4587", "pmid": "33523963", "labels": {"NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7/2/eabc4587"}, {"db": "pmc", "key": "PMC7787494"}], "notes": [], "created": "2021-06-09T12:15:48.048Z", "modified": "2024-01-16T13:48:41.043Z"}, {"entity": "publication", "iuid": "26891b7047fe4d50971760420593e083", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26891b7047fe4d50971760420593e083.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26891b7047fe4d50971760420593e083"}}, "title": "Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Breton", "given": "Gwenna", "initials": "G", "orcid": "0000-0002-4100-9963", "researcher": {"href": "https://publications.scilifelab.se/researcher/757353d5314b4c20ac2ef4833dd207d9.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Hollfelder", "given": "Nina", "initials": "N"}, {"family": "Sj\u00f6strand", "given": "Agnes E", "initials": "AE"}, {"family": "Xu", "given": "Jingzi", "initials": "J"}, {"family": "Gattepaille", "given": "Lucie M", "initials": "LM"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "de Jongh", "given": "Michael", "initials": "M"}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2020-10-01", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "issn-l": "0737-4038", "volume": "37", "issue": "10", "pages": "2944-2954"}, "abstract": "The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.", "doi": "10.1093/molbev/msaa140", "pmid": "32697301", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5874945"}, {"db": "pmc", "key": "PMC7530619"}], "notes": [], "created": "2020-12-08T23:26:14.491Z", "modified": "2024-01-16T13:48:41.609Z"}, {"entity": "publication", "iuid": "56bd5b3292d745ebbee0c2a369c5a13c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56bd5b3292d745ebbee0c2a369c5a13c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56bd5b3292d745ebbee0c2a369c5a13c"}}, "title": "The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.", "authors": [{"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2020-08-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "volume": "172", "issue": "4", "pages": "638-649", "issn-l": "0002-9483"}, "abstract": "In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences.\n\nWe sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools.\n\nThe genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style.\n\nWe conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.", "doi": "10.1002/ajpa.24079", "pmid": "32497286", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:25:31.764Z", "modified": "2024-01-16T13:48:41.973Z"}, {"entity": "publication", "iuid": "55dcf41e17e8459fb3c49cd79e48f71c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/55dcf41e17e8459fb3c49cd79e48f71c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/55dcf41e17e8459fb3c49cd79e48f71c"}}, "title": "Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.", "authors": [{"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Xu", "given": "Jingzi", "initials": "J"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "comparative study", "published": "2020-07-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "12", "issue": "7", "pages": "1031-1039"}, "abstract": "Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.", "doi": "10.1093/gbe/evaa098", "pmid": "32697300", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5874966"}, {"db": "pmc", "key": "PMC7375190"}], "notes": [], "created": "2020-12-08T23:25:49.670Z", "modified": "2024-01-16T13:48:42.238Z"}, {"entity": "publication", "iuid": "47c327c6229e475bad4889ad53a15767", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47c327c6229e475bad4889ad53a15767.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47c327c6229e475bad4889ad53a15767"}}, "title": "Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A", "orcid": "0000-0002-2585-127X", "researcher": {"href": "https://publications.scilifelab.se/researcher/21890fe291bb4e8e913c5eb5963bcdce.json"}}, {"family": "Makarowicz", "given": "Przemys\u0142aw", "initials": "P"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Ehler", "given": "Edvard", "initials": "E", "orcid": "0000-0003-1774-0091", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d5e30a4e46e47d8b800d5242e23d7de.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "G\u00f3rski", "given": "Jacek", "initials": "J"}, {"family": "Taras", "given": "Halina", "initials": "H"}, {"family": "Szczepanek", "given": "Anita", "initials": "A"}, {"family": "Pola\u0144ska", "given": "Marta", "initials": "M"}, {"family": "W\u0142odarczak", "given": "Piotr", "initials": "P"}, {"family": "Szyca", "given": "Agnieszka", "initials": "A"}, {"family": "Lasota-Ku\u015b", "given": "Anna", "initials": "A"}, {"family": "W\u00f3jcik", "given": "Irena", "initials": "I"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}], "type": "historical article", "published": "2020-06-00", "journal": {"title": "Am. J. Phys. Anthropol.", "issn": "1096-8644", "volume": "172", "issue": "2", "pages": "176-188", "issn-l": "0002-9483"}, "abstract": "In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes.\n\nWe performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzy\u017cow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS 14 C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples.\n\nComplete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzy\u017c\u00f3w people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study.\n\nResults revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzy\u017c\u00f3w-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.", "doi": "10.1002/ajpa.24057", "pmid": "32297323", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:25:04.935Z", "modified": "2024-01-16T13:48:42.437Z"}, {"entity": "publication", "iuid": "22a173ef02f045c28253c98404dcdc0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22a173ef02f045c28253c98404dcdc0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22a173ef02f045c28253c98404dcdc0a"}}, "title": "Patterns of African and Asian admixture in the Afrikaner population of South Africa.", "authors": [{"family": "Hollfelder", "given": "N", "initials": "N"}, {"family": "Erasmus", "given": "J C", "initials": "JC"}, {"family": "Hammaren", "given": "R", "initials": "R"}, {"family": "Vicente", "given": "M", "initials": "M"}, {"family": "Jakobsson", "given": "M", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Greeff", "given": "J M", "initials": "JM"}, {"family": "Schlebusch", "given": "C M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}], "type": "journal article", "published": "2020-02-24", "journal": {"title": "BMC Biol.", "issn": "1741-7007", "volume": "18", "issue": "1", "pages": "16", "issn-l": "1741-7007"}, "abstract": "The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%.\n\nTo investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population.\n\nWhile Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to current-day European populations.", "doi": "10.1186/s12915-020-0746-1", "pmid": "32089133", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12915-020-0746-1"}, {"db": "pmc", "key": "PMC7038537"}], "notes": [], "created": "2020-02-28T12:44:13.878Z", "modified": "2024-01-16T13:48:42.894Z"}, {"entity": "publication", "iuid": "588ea50294e0470cbaa20fdebb9123e4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/588ea50294e0470cbaa20fdebb9123e4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/588ea50294e0470cbaa20fdebb9123e4"}}, "title": "The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.", "authors": [{"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Fraser", "given": "Magdalena", "initials": "M"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "T\u00f5rv", "given": "Mari", "initials": "M"}, {"family": "Lindstr\u00f6m", "given": "Jonathan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2019-10-09", "journal": {"volume": "286", "issn": "1471-2954", "issue": "1912", "pages": "20191528", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24\u00d7 coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.", "doi": "10.1098/rspb.2019.1528", "pmid": "31594508", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6790770"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4682318"}], "notes": [], "created": "2020-01-08T12:39:39.334Z", "modified": "2021-07-07T10:46:20.330Z"}, {"entity": "publication", "iuid": "f5da15486d854d6eb5e8a778882e7721", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5da15486d854d6eb5e8a778882e7721.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5da15486d854d6eb5e8a778882e7721"}}, "title": "Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations.", "authors": [{"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Ebbesen", "given": "Peter", "initials": "P"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM"}], "type": "journal article", "published": "2019-09-01", "journal": {"volume": "36", "issn": "1537-1719", "issue": "9", "title": "Mol. Biol. Evol.", "pages": "1849-1861", "issn-l": "0737-4038"}, "abstract": "Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as \"Khoe-San\" populations and have a long history in southern Africa. Their ancestors were largely isolated up until \u223c2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has been challenging due to admixture with immigrant populations that obscure past population affinities and gene flow among these autochthonous communities. We re-evaluate a combined genome-wide data set of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx'a-language family (\u01c2Hoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.", "doi": "10.1093/molbev/msz089", "pmid": "31288264", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "5475268"}, {"db": "pmc", "key": "PMC6735883"}], "notes": [], "created": "2019-08-13T12:15:29.091Z", "modified": "2024-01-16T13:48:43.925Z"}, {"entity": "publication", "iuid": "c18fc22d368f4c109f76e74dbc4c0d6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c18fc22d368f4c109f76e74dbc4c0d6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c18fc22d368f4c109f76e74dbc4c0d6d"}}, "title": "Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications.scilifelab.se/researcher/c483febf380c4d9db683e5a73ba89816.json"}}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Koptekin", "given": "Dilek", "initials": "D"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M", "orcid": "0000-0003-1347-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/e211127b50ca4ed8ab6b2ae9bede0102.json"}}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG", "orcid": "0000-0002-3897-4607", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f103c7d36c24ac981fbd8291fea853c.json"}}, {"family": "Shcherbakov", "given": "Nikolai", "initials": "N", "orcid": "0000-0001-7731-7178", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dd678e7fb441b2a2560ec728319507.json"}}, {"family": "Shuteleva", "given": "Iia", "initials": "I", "orcid": "0000-0001-7731-7178", "researcher": {"href": "https://publications.scilifelab.se/researcher/61dd678e7fb441b2a2560ec728319507.json"}}, {"family": "Leonova", "given": "Tatiana", "initials": "T"}, {"family": "Kraeva", "given": "Liudmila", "initials": "L", "orcid": "0000-0002-6524-6998", "researcher": {"href": "https://publications.scilifelab.se/researcher/f11ac245436b40a88c66740d94f27353.json"}}, {"family": "Sungatov", "given": "Flarit A", "initials": "FA", "orcid": "0000-0001-5982-9030", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bbdcfb0afa84a899f1dead7ff3c5531.json"}}, {"family": "Sultanova", "given": "Alfija N", "initials": "AN", "orcid": "0000-0002-5409-8344", "researcher": {"href": "https://publications.scilifelab.se/researcher/bfc71e882ea64d408cb1d5201aae554a.json"}}, {"family": "Potekhina", "given": "Inna", "initials": "I"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Sinika", "given": "Vitaly", "initials": "V", "orcid": "0000-0002-1621-9205", "researcher": {"href": "https://publications.scilifelab.se/researcher/64dffb07a3a342d78eb91d9c02f87f83.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-10-00", "journal": {"volume": "4", "issn": "2375-2548", "issue": "10", "pages": "eaat4457", "title": "Sci Adv", "issn-l": "2375-2548"}, "abstract": "For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.", "doi": "10.1126/sciadv.aat4457", "pmid": "30417088", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "aat4457"}, {"db": "pmc", "key": "PMC6223350"}], "notes": [], "created": "2018-10-22T10:10:13.051Z", "modified": "2024-01-16T13:48:45.440Z"}, {"entity": "publication", "iuid": "f35cd246d7a84453b1ac19f3d163b109", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f35cd246d7a84453b1ac19f3d163b109.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f35cd246d7a84453b1ac19f3d163b109"}}, "title": "Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.", "authors": [{"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C"}, {"family": "Zachrisson", "given": "Torun", "initials": "T"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "Sobrado", "given": "Veronica", "initials": "V"}, {"family": "Evans", "given": "Jane", "initials": "J"}, {"family": "Knipper", "given": "Corina", "initials": "C"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-09-10", "journal": {"volume": "28", "issn": "1879-0445", "issue": "17", "pages": "2730-2738.e10", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.", "doi": "10.1016/j.cub.2018.06.053", "pmid": "30146150", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(18)30844-3"}], "notes": [], "created": "2018-10-31T19:48:01.236Z", "modified": "2024-01-16T13:48:45.531Z"}, {"entity": "publication", "iuid": "768c0a397b7f434a8c5c02c6d5cfaeb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/768c0a397b7f434a8c5c02c6d5cfaeb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/768c0a397b7f434a8c5c02c6d5cfaeb4"}}, "title": "Investigating Holocene human population history in North Asia using ancient mitogenomes.", "authors": [{"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM", "orcid": "0000-0002-2024-3910", "researcher": {"href": "https://publications.scilifelab.se/researcher/1bc478401dfd4be2965d23f4af757b8e.json"}}, {"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "S\u00fcmer", "given": "Arev Pelin", "initials": "AP"}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E"}, {"family": "Shergin", "given": "Dmitrij", "initials": "D"}, {"family": "Ivanov", "given": "Grigorij Leonidovich", "initials": "GL"}, {"family": "Kichigin", "given": "Dmitrii", "initials": "D"}, {"family": "Pestereva", "given": "Kjunnej", "initials": "K"}, {"family": "Volkov", "given": "Denis", "initials": "D"}, {"family": "Mandryka", "given": "Pavel", "initials": "P"}, {"family": "Kharinskii", "given": "Artur", "initials": "A"}, {"family": "Tishkin", "given": "Alexey", "initials": "A"}, {"family": "Ineshin", "given": "Evgenij", "initials": "E"}, {"family": "Kovychev", "given": "Evgeniy", "initials": "E"}, {"family": "Stepanov", "given": "Aleksandr", "initials": "A"}, {"family": "Alekseev", "given": "Aanatolij", "initials": "A"}, {"family": "Fedoseeva", "given": "Svetlana Aleksandrovna", "initials": "SA"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "historical article", "published": "2018-06-12", "journal": {"volume": "8", "issn": "2045-2322", "issue": "1", "pages": "8969", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.", "doi": "10.1038/s41598-018-27325-0", "pmid": "29895902", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-018-27325-0"}, {"db": "pmc", "key": "PMC5997703"}], "notes": [], "created": "2018-10-31T19:48:02.044Z", "modified": "2024-01-16T13:48:46.130Z"}, {"entity": "publication", "iuid": "5550cc23aeed489b8afc6a667e6dfe6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5550cc23aeed489b8afc6a667e6dfe6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5550cc23aeed489b8afc6a667e6dfe6c"}}, "title": "Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia.", "authors": [{"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Vera-Rodr\u00edguez", "given": "Juan Carlos", "initials": "JC"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Iriarte", "given": "Eneko", "initials": "E"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG"}, {"family": "Mart\u00ednez-S\u00e1nchez", "given": "Rafael M", "initials": "RM"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Rodr\u00edguez", "given": "Laura", "initials": "L"}, {"family": "Berm\u00fadez de Castro", "given": "Jos\u00e9-Mar\u00eda", "initials": "JM"}, {"family": "Carbonell", "given": "Eudald", "initials": "E"}, {"family": "Alday", "given": "Alfonso", "initials": "A"}, {"family": "Hern\u00e1ndez Vera", "given": "Jos\u00e9 Antonio", "initials": "JA"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Carretero", "given": "Jos\u00e9-Miguel", "initials": "JM"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Smith", "given": "Colin I", "initials": "CI"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2018-03-27", "journal": {"volume": "115", "issn": "1091-6490", "issue": "13", "pages": "3428-3433", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500-3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.", "doi": "10.1073/pnas.1717762115", "pmid": "29531053", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5879675"}, {"db": "pii", "key": "1717762115"}], "notes": [], "created": "2018-09-14T12:12:32.794Z", "modified": "2024-01-16T13:48:46.649Z"}, {"entity": "publication", "iuid": "79a097bcd5394e09a35047c3eb9dac7a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/79a097bcd5394e09a35047c3eb9dac7a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/79a097bcd5394e09a35047c3eb9dac7a"}}, "title": "Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "S\u00e1nchez-Quinto", "given": "Federico", "initials": "F"}, {"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah M", "initials": "GM"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Eriksson", "given": "Gunilla", "initials": "G"}, {"family": "Fraser", "given": "Magdalena", "initials": "M"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A"}, {"family": "Sim\u00f5es", "given": "Luciana G", "initials": "LG"}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M"}, {"family": "Sj\u00f6lander", "given": "Anders", "initials": "A"}, {"family": "Jansen Sellevold", "given": "Berit", "initials": "B"}, {"family": "J\u00f8rgensen", "given": "Roger", "initials": "R"}, {"family": "Claes", "given": "Peter", "initials": "P"}, {"family": "Shriver", "given": "Mark D", "initials": "MD"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Netea", "given": "Mihai G", "initials": "MG"}, {"family": "Apel", "given": "Jan", "initials": "J"}, {"family": "Lid\u00e9n", "given": "Kerstin", "initials": "K"}, {"family": "Skar", "given": "Birgitte", "initials": "B"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2018-01-00", "journal": {"volume": "16", "issn": "1545-7885", "issue": "1", "pages": "e2003703", "title": "PLoS Biol.", "issn-l": "1544-9173"}, "abstract": "Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57\u00d7 coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.", "doi": "10.1371/journal.pbio.2003703", "pmid": "29315301", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5760011"}, {"db": "pii", "key": "pbio.2003703"}], "notes": [], "created": "2018-01-11T10:03:24.352Z", "modified": "2024-01-16T13:48:47.193Z"}, {"entity": "publication", "iuid": "1b64378122df401ea8d44baa1f502671", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b64378122df401ea8d44baa1f502671.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b64378122df401ea8d44baa1f502671"}}, "title": "A female Viking warrior confirmed by genomics.", "authors": [{"family": "Hedenstierna-Jonson", "given": "Charlotte", "initials": "C"}, {"family": "Kjellstr\u00f6m", "given": "Anna", "initials": "A", "orcid": "0000-0001-8964-3771", "researcher": {"href": "https://publications.scilifelab.se/researcher/a3a47cc07e9d4b8592dba430785681b5.json"}}, {"family": "Zachrisson", "given": "Torun", "initials": "T"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Sobrado", "given": "Veronica", "initials": "V"}, {"family": "Price", "given": "Neil", "initials": "N"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}], "type": "historical article", "published": "2017-12-00", "journal": {"volume": "164", "issn": "1096-8644", "issue": "4", "title": "Am. J. Phys. Anthropol.", "pages": "853-860", "issn-l": "0002-9483"}, "abstract": "The objective of this study has been to confirm the sex and the affinity of an individual buried in a well-furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue.\n\nGenome-wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern-day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual.\n\nThe genomic results revealed the lack of a Y-chromosome and thus a female biological sex, and the mtDNA analyses support a single-individual origin of sampled elements. The genetic affinity is close to present-day North Europeans, and within Sweden to the southern and south-central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin.\n\nThe identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time-period. The results call for caution against generalizations regarding social orders in past societies.", "doi": "10.1002/ajpa.23308", "pmid": "28884802", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5724682"}], "notes": [], "created": "2017-11-03T16:18:39.012Z", "modified": "2024-01-16T13:48:47.310Z"}, {"entity": "publication", "iuid": "63a7fc722c47447b9dc981a289d38084", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63a7fc722c47447b9dc981a289d38084.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63a7fc722c47447b9dc981a289d38084"}}, "title": "Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.", "authors": [{"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Gillingwater", "given": "Thomas H", "initials": "TH"}, {"family": "MacCallum", "given": "Malcolm", "initials": "M"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Dobney", "given": "Keith", "initials": "K"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L"}], "type": "journal article", "published": "2017-11-06", "journal": {"volume": "27", "issn": "1879-0445", "issue": "21", "pages": "3396-3402.e5", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th-11th centuries CE) yielded sufficient autosomal genome coverage (0.21\u00d7 to 3.93\u00d7) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.", "doi": "10.1016/j.cub.2017.09.059", "pmid": "29107554", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(17)31257-5"}], "notes": [], "created": "2018-01-10T09:44:16.403Z", "modified": "2023-06-20T15:54:27.159Z"}, {"entity": "publication", "iuid": "61c4edd44f7c449aac10aa3423c4a688", "links": {"self": {"href": "https://publications.scilifelab.se/publication/61c4edd44f7c449aac10aa3423c4a688.json"}, "display": {"href": "https://publications.scilifelab.se/publication/61c4edd44f7c449aac10aa3423c4a688"}}, "title": "Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H", "orcid": "0000-0002-6456-8055", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b3397b2842142bea34c222f6683c0eb.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Coutinho", "given": "Alexandra", "initials": "A", "orcid": "0000-0002-1756-9469", "researcher": {"href": "https://publications.scilifelab.se/researcher/1863fb821bdf444ba26e351f764e4a70.json"}}, {"family": "Edlund", "given": "Hanna", "initials": "H", "orcid": "0000-0003-3784-4285", "researcher": {"href": "https://publications.scilifelab.se/researcher/d56063f091264c0587c973a82335c578.json"}}, {"family": "Munters", "given": "Arielle R", "initials": "AR", "orcid": "0000-0003-1512-6565", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e089ee0008a4ea3a9603fa011f973de.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications.scilifelab.se/researcher/603244b141da49dfa9ff3a8d17f42b70.json"}}, {"family": "Steyn", "given": "Maryna", "initials": "M", "orcid": "0000-0002-0215-9723", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d9921b3dba248eab7b85488dda530ad.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Lombard", "given": "Marlize", "initials": "M", "orcid": "0000-0002-0675-0414", "researcher": {"href": "https://publications.scilifelab.se/researcher/e04e97bbc9914f358864988174b9b58d.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-11-03", "journal": {"volume": "358", "issn": "1095-9203", "issue": "6363", "pages": "652-655", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.", "doi": "10.1126/science.aao6266", "pmid": "28971970", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "science.aao6266"}], "notes": [], "created": "2017-10-30T09:27:46.012Z", "modified": "2024-01-16T13:48:47.317Z"}, {"entity": "publication", "iuid": "7119a4bbab9f46d2a03b17b778804251", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7119a4bbab9f46d2a03b17b778804251.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7119a4bbab9f46d2a03b17b778804251"}}, "title": "Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations.", "authors": [{"family": "Hollfelder", "given": "Nina", "initials": "N"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}, {"family": "Babiker", "given": "Hiba", "initials": "H"}, {"family": "Hassan", "given": "Hisham Y", "initials": "HY", "orcid": "0000-0003-0026-5781", "researcher": {"href": "https://publications.scilifelab.se/researcher/df40ecb572c5470e9bd4368095fdb308.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-08-00", "journal": {"volume": "13", "issn": "1553-7404", "issue": "8", "pages": "e1006976", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400-200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.", "doi": "10.1371/journal.pgen.1006976", "pmid": "28837655", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-17-00483"}, {"db": "pmc", "key": "PMC5587336"}], "notes": [], "created": "2017-10-25T15:27:45.744Z", "modified": "2024-01-16T13:48:47.667Z"}, {"entity": "publication", "iuid": "b065ba93cc264109a62c401b02ac7cd9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b065ba93cc264109a62c401b02ac7cd9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b065ba93cc264109a62c401b02ac7cd9"}}, "title": "Adaptation to infectious disease exposure in indigenous Southern African populations.", "authors": [{"family": "Owers", "given": "Katharine A", "initials": "KA", "orcid": "0000-0002-5323-5079", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4357c52141940a1a68b6a241f4aa100.json"}}, {"family": "Sj\u00f6din", "given": "Per", "initials": "P"}, {"family": "Schlebusch", "given": "Carina M", "initials": "CM", "orcid": "0000-0002-8160-9621", "researcher": {"href": "https://publications.scilifelab.se/researcher/682f10853c1145649b8c76680605dd9b.json"}}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "journal article", "published": "2017-04-12", "journal": {"volume": "284", "issn": "1471-2954", "issue": "1852", "pages": "20170226", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "Genetic analyses can provide information about human evolutionary history that cannot always be gleaned from other sources. We evaluated evidence of selective pressure due to introduced infectious diseases in the genomes of two indigenous southern African San groups-the \u2021Khomani who had abundant contact with other people migrating into the region and the more isolated Ju|'hoansi. We used a dual approach to test for increased selection on immune genes compared with the rest of the genome in these groups. First, we calculated summary values of statistics that measure genomic signatures of adaptation to contrast selection signatures in immune genes and all genes. Second, we located regions of the genome with extreme values of three selection statistics and examined these regions for enrichment of immune genes. We found stronger and more abundant signals of selection in immune genes in the \u2021Khomani than in the Ju|'hoansi. We confirm this finding within each population to avoid effects of different demographic histories of the two populations. We identified eight immune genes that have potentially been targets of strong selection in the \u2021Khomani, whereas in the Ju|'hoansi, no immune genes were found in the genomic regions with the strongest signals of selection. We suggest that the more abundant signatures of selection at immune genes in the \u2021Khomani could be explained by their more frequent contact with immigrant groups, which likely led to increased exposure and adaptation to introduced infectious diseases.", "doi": "10.1098/rspb.2017.0226", "pmid": "28381615", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "rspb.2017.0226"}, {"db": "pmc", "key": "PMC5394675"}], "notes": [], "created": "2018-01-09T14:01:35.720Z", "modified": "2021-07-07T10:32:33.473Z"}, {"entity": "publication", "iuid": "86fb99b8bde44d8782114a6a0c9fbafe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/86fb99b8bde44d8782114a6a0c9fbafe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/86fb99b8bde44d8782114a6a0c9fbafe"}}, "title": "Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Pospieszny", "given": "\u0141ukasz", "initials": "\u0141"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Bednarczyk", "given": "J\u00f3zef", "initials": "J"}, {"family": "Piontek", "given": "Janusz", "initials": "J"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}], "type": "journal article", "published": "2017-01-00", "journal": {"volume": "26", "issn": "1878-0326", "issue": null, "pages": "30-39", "title": "Forensic Sci Int Genet", "issn-l": "1872-4973"}, "abstract": "We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq\u2122 Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS 14C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq\u2122 Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct maternal relationship in ancient individuals.", "doi": "10.1016/j.fsigen.2016.10.008", "pmid": "27771467", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S1872-4973(16)30193-4"}], "notes": [], "created": "2017-05-08T07:57:17.839Z", "modified": "2024-01-16T13:48:48.760Z"}, {"entity": "publication", "iuid": "943139d0335a490794e3bf5bb419e4ce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/943139d0335a490794e3bf5bb419e4ce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/943139d0335a490794e3bf5bb419e4ce"}}, "title": "The disappearing San of southeastern Africa and their genetic affinities.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "Prins", "given": "Frans", "initials": "F"}, {"family": "Lombard", "given": "Marlize", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Soodyall", "given": "Himla", "initials": "H"}], "type": "journal article", "published": "2016-12-00", "journal": {"volume": "135", "issn": "1432-1203", "issue": "12", "pages": "1365-1373", "title": "Hum. Genet.", "issn-l": "0340-6717"}, "abstract": "Southern Africa was likely exclusively inhabited by San hunter-gatherers before ~2000 years ago. Around that time, East African groups assimilated with local San groups and gave rise to the Khoekhoe herders. Subsequently, Bantu-speaking farmers, arriving from the north (~1800 years ago), assimilated and displaced San and Khoekhoe groups, a process that intensified with the arrival of European colonists ~350 years ago. In contrast to the western parts of southern Africa, where several Khoe-San groups still live today, the eastern parts are largely populated by Bantu speakers and individuals of non-African descent. Only a few scattered groups with oral traditions of Khoe-San ancestry remain. Advances in genetic research open up new ways to understand the population history of southeastern Africa. We investigate the genomic variation of the remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published data sets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu speakers. Specifically, we found that the Lake Chrissie San are closely related to the current southern San groups (i.e., the Karretjie people). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. This study illustrates how genetic tools can be used to assess hypotheses about the ancestry of people who seemingly lost their historic roots, only recalling a vague oral tradition of their origin.", "doi": "10.1007/s00439-016-1729-8", "pmid": "27651137", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00439-016-1729-8"}, {"db": "pmc", "key": "PMC5065584"}], "notes": [], "created": "2017-05-03T12:59:46.425Z", "modified": "2024-01-16T13:48:48.870Z"}, {"entity": "publication", "iuid": "9957a9bac4394067bd089ee19380190c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9957a9bac4394067bd089ee19380190c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9957a9bac4394067bd089ee19380190c"}}, "title": "The Demographic Development of the First Farmers in Anatolia.", "authors": [{"family": "K\u0131l\u0131n\u00e7", "given": "G\u00fcl\u015fah Merve", "initials": "GM"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "B\u00fcy\u00fckkarakaya", "given": "Ali Metin", "initials": "AM"}, {"family": "B\u0131\u00e7ak\u00e7\u0131", "given": "Erhan", "initials": "E"}, {"family": "Baird", "given": "Douglas", "initials": "D"}, {"family": "D\u00f6nerta\u015f", "given": "Handan Melike", "initials": "HM"}, {"family": "Ghalichi", "given": "Ayshin", "initials": "A"}, {"family": "Yaka", "given": "Reyhan", "initials": "R"}, {"family": "Koptekin", "given": "Dilek", "initials": "D"}, {"family": "A\u00e7an", "given": "Sinan Can", "initials": "SC"}, {"family": "Parvizi", "given": "Poorya", "initials": "P"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Daskalaki", "given": "Evangelia A", "initials": "EA"}, {"family": "Y\u00fcnc\u00fc", "given": "Eren", "initials": "E"}, {"family": "Da\u011fta\u015f", "given": "Nihan Dil\u015fad", "initials": "ND"}, {"family": "Fairbairn", "given": "Andrew", "initials": "A"}, {"family": "Pearson", "given": "Jessica", "initials": "J"}, {"family": "Mustafao\u011flu", "given": "G\u00f6khan", "initials": "G"}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS"}, {"family": "\u00c7akan", "given": "Yasin G\u00f6khan", "initials": "YG"}, {"family": "Togan", "given": "\u0130nci", "initials": "\u0130"}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "journal article", "published": "2016-10-10", "journal": {"volume": "26", "issn": "1879-0445", "issue": "19", "pages": "2659-2666", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [1-3]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [4]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.", "doi": "10.1016/j.cub.2016.07.057", "pmid": "27498567", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(16)30850-8"}, {"db": "pmc", "key": "PMC5069350"}], "notes": [], "created": "2017-05-03T12:59:50.531Z", "modified": "2024-01-16T13:48:49.199Z"}, {"entity": "publication", "iuid": "3fcdafe8bb564f759eae9e905698707a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3fcdafe8bb564f759eae9e905698707a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3fcdafe8bb564f759eae9e905698707a"}}, "title": "Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc.", "authors": [{"family": "Jeong", "given": "Choongwon", "initials": "C"}, {"family": "Ozga", "given": "Andrew T", "initials": "AT"}, {"family": "Witonsky", "given": "David B", "initials": "DB"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Edlund", "given": "Hanna", "initials": "H"}, {"family": "Hofman", "given": "Courtney A", "initials": "CA"}, {"family": "Hagan", "given": "Richard W", "initials": "RW"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Lewis", "given": "Cecil M", "initials": "CM"}, {"family": "Aldenderfer", "given": "Mark S", "initials": "MS"}, {"family": "Di Rienzo", "given": "Anna", "initials": "A"}, {"family": "Warinner", "given": "Christina", "initials": "C", "orcid": "0000-0002-4528-5877", "researcher": {"href": "https://publications.scilifelab.se/researcher/dad0e66dbd4142928a530d4596cdeee7.json"}}], "type": "journal article", "published": "2016-07-05", "journal": {"volume": "113", "issn": "1091-6490", "issue": "27", "pages": "7485-7490", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04\u00d7-7.25\u00d7, mean 2.16\u00d7) and mitochondrial genomes (20.8\u00d7-1,311.0\u00d7, mean 482.1\u00d7) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.", "doi": "10.1073/pnas.1520844113", "pmid": "27325755", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "1520844113"}, {"db": "pmc", "key": "PMC4941446"}], "notes": [], "created": "2017-05-03T13:00:04.186Z", "modified": "2024-01-16T13:48:49.855Z"}, {"entity": "publication", "iuid": "93fa171b42a84f1f9613fb95e713ab42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93fa171b42a84f1f9613fb95e713ab42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93fa171b42a84f1f9613fb95e713ab42"}}, "title": "Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool.", "authors": [{"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Kiesewetter", "given": "Henrike", "initials": "H"}, {"family": "Aylward", "given": "William", "initials": "W"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}], "type": "journal article", "published": "2016-01-25", "journal": {"volume": "26", "issn": "1879-0445", "issue": "2", "pages": "270-275", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [1-5]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [6-9]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [10]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia's central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.", "doi": "10.1016/j.cub.2015.12.019", "pmid": "26748850", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0960-9822(15)01516-X"}], "notes": [], "created": "2017-05-02T12:58:14.678Z", "modified": "2024-01-16T13:48:50.567Z"}, {"entity": "publication", "iuid": "886cc8c622b44c2397c005d7264e5eca", "links": {"self": {"href": "https://publications.scilifelab.se/publication/886cc8c622b44c2397c005d7264e5eca.json"}, "display": {"href": "https://publications.scilifelab.se/publication/886cc8c622b44c2397c005d7264e5eca"}}, "title": "Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques.", "authors": [{"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Rodriguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "Sverrisd\u00f3ttir", "given": "\u00d3ddny Osk", "initials": "\u00d3O"}, {"family": "Daskalaki", "given": "Evangelia A", "initials": "EA"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "Svensson", "given": "Emma M", "initials": "EM"}, {"family": "Berm\u00fadez de Castro", "given": "Jos\u00e9 Mar\u00eda", "initials": "JM"}, {"family": "Carbonell", "given": "Eudald", "initials": "E"}, {"family": "Dunn", "given": "Michael", "initials": "M"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "Iriarte", "given": "Eneko", "initials": "E"}, {"family": "Arsuaga", "given": "Juan Luis", "initials": "JL"}, {"family": "Carretero", "given": "Jos\u00e9-Miguel", "initials": "JM"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2015-09-22", "journal": {"volume": "112", "issn": "1091-6490", "issue": "38", "pages": "11917-11922", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The consequences of the Neolithic transition in Europe--one of the most important cultural changes in human prehistory--is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portal\u00f3n cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portal\u00f3n individuals additionally mixed with local southwestern hunter-gatherers. The proportion of hunter-gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portal\u00f3n individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portal\u00f3n genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.", "doi": "10.1073/pnas.1509851112", "pmid": "26351665", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1509851112"}, {"db": "pmc", "key": "PMC4586848"}, {"db": "BioProject", "key": "PRJEB9783"}], "notes": [], "created": "2017-05-02T12:57:09.868Z", "modified": "2023-06-20T15:54:27.281Z"}, {"entity": "publication", "iuid": "0016a8d9ada14c9a92cdaa13448ee375", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0016a8d9ada14c9a92cdaa13448ee375.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0016a8d9ada14c9a92cdaa13448ee375"}}, "title": "Human adaptation to arsenic-rich environments.", "authors": [{"family": "Schlebusch", "given": "Carina M", "initials": "CM"}, {"family": "Gattepaille", "given": "Lucie M", "initials": "LM"}, {"family": "Engstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Vahter", "given": "Marie", "initials": "M"}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}, {"family": "Broberg", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2015-06-00", "journal": {"volume": "32", "issn": "1537-1719", "issue": "6", "pages": "1544-1555", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Adaptation drives genomic changes; however, evidence of specific adaptations in humans remains limited. We found that inhabitants of the northern Argentinean Andes, an arid region where elevated arsenic concentrations in available drinking water is common, have unique arsenic metabolism, with efficient methylation and excretion of the major metabolite dimethylated arsenic and a less excretion of the highly toxic monomethylated metabolite. We genotyped women from this population for 4,301,332 single nucleotide polymorphisms (SNPs) and found a strong association between the AS3MT (arsenic [+3 oxidation state] methyltransferase) gene and mono- and dimethylated arsenic in urine, suggesting that AS3MT functions as the major gene for arsenic metabolism in humans. We found strong genetic differentiation around AS3MT in the Argentinean Andes population, compared with a highly related Peruvian population (FST = 0.014) from a region with much less environmental arsenic. Also, 13 of the 100 SNPs with the highest genome-wide Locus-Specific Branch Length occurred near AS3MT. In addition, our examination of extended haplotype homozygosity indicated a selective sweep of the Argentinean Andes population, in contrast to Peruvian and Colombian populations. Our data show that adaptation to tolerate the environmental stressor arsenic has likely driven an increase in the frequencies of protective variants of AS3MT, providing the first evidence of human adaptation to a toxic chemical.", "doi": "10.1093/molbev/msv046", "pmid": "25739736", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "msv046"}], "notes": [], "created": "2017-05-02T12:58:31.154Z", "modified": "2021-07-07T10:35:32.995Z"}, {"entity": "publication", "iuid": "fb403bdc0e494e06a76607ccbb6c84fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb403bdc0e494e06a76607ccbb6c84fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb403bdc0e494e06a76607ccbb6c84fd"}}, "title": "Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers.", "authors": [{"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Malmstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "Raghavan", "given": "Maanasa", "initials": "M"}, {"family": "Valdiosera", "given": "Cristina", "initials": "C", "orcid": "0000-0003-4948-2226", "researcher": {"href": "https://publications.scilifelab.se/researcher/113ef0dde1dd48e388f75c43bd672005.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Tambets", "given": "Kristiina", "initials": "K"}, {"family": "Parik", "given": "J\u00fcri", "initials": "J"}, {"family": "Sj\u00f6gren", "given": "Karl-G\u00f6ran", "initials": "KG"}, {"family": "Apel", "given": "Jan", "initials": "J"}, {"family": "Willerslev", "given": "Eske", "initials": "E"}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Jakobsson", "given": "Mattias", "initials": "M", "orcid": "0000-0001-7840-7853", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a4abe0fcb20492d9ec849c9fbf58a71.json"}}], "type": "historical article", "published": "2014-05-16", "journal": {"volume": "344", "issn": "1095-9203", "issue": "6185", "pages": "747-750", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains a contentious idea. Population-genomic data from 11 Scandinavian Stone Age human remains suggest that hunter-gatherers had lower genetic diversity than that of farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone Age foraging groups were historically in low numbers, likely owing to oscillating living conditions or restricted carrying capacity, and that they were partially incorporated into expanding farming groups.", "doi": "10.1126/science.1253448", "pmid": "24762536", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "science.1253448"}], "notes": [], "created": "2017-05-04T15:01:47.550Z", "modified": "2023-06-20T15:54:27.327Z"}]}