{"entity": "researcher", "timestamp": "2026-08-10T19:50:13.047Z", "family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "affiliations": ["Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden. anders.gotherstrom@arklab.su.se jan.stora@ofl.su.se gulsahkilinc@hacettepe.edu.tr.", "Centre for Palaeogenetics, 10691 Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a"}}, "publications": [{"entity": "publication", "iuid": "dcbd5db61afd44e1a12825cbf9aa3ab7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcbd5db61afd44e1a12825cbf9aa3ab7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcbd5db61afd44e1a12825cbf9aa3ab7"}}, "title": "Population genomics of the muskox' resilience in the near absence of genetic variation.", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Garcia-Erill", "given": "Gen\u00eds", "initials": "G", "orcid": "0000-0003-3150-1708", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f24c82ea67a4df19363eb616a422eb4.json"}}, {"family": "Hangh\u00f8j", "given": "Kristian", "initials": "K", "orcid": "0000-0003-1941-5495", "researcher": {"href": "https://publications.scilifelab.se/researcher/b992ca7293ea408185d741d2af179ab4.json"}}, {"family": "Rasmussen", "given": "Malthe Sebro", "initials": "MS", "orcid": "0000-0002-2982-6258", "researcher": {"href": "https://publications.scilifelab.se/researcher/56f925cfd53d46e3a20889d86bb75361.json"}}, {"family": "Meisner", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9540-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/b04643f766854c2ebd98d74592fe2f03.json"}}, {"family": "Liu", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-8839-2659", "researcher": {"href": "https://publications.scilifelab.se/researcher/fabce70bd90a4bfe8923d6167e236cff.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Santander", "given": "Cindy G", "initials": "CG", "orcid": "0000-0003-3021-6809", "researcher": {"href": "https://publications.scilifelab.se/researcher/da5878fe3c394895ad89147310debb7e.json"}}, {"family": "Quinn", "given": "Liam", "initials": "L", "orcid": "0000-0002-3597-2948", "researcher": {"href": "https://publications.scilifelab.se/researcher/b8670190c2054747876bf67f9509284b.json"}}, {"family": "Lin", "given": "Long", "initials": "L", "orcid": "0000-0002-1075-6800", "researcher": {"href": "https://publications.scilifelab.se/researcher/b26a9f7b72764d298b2f1fbd618ce7a5.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S", "orcid": "0000-0001-8118-8313", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8eebb29461c4496a1b4e1b033f1afec.json"}}, {"family": "Car\u00f8e", "given": "Christian", "initials": "C", "orcid": "0000-0001-9601-6768", "researcher": {"href": "https://publications.scilifelab.se/researcher/fb28fc94b3ad42139d7e739566f8dd90.json"}}, {"family": "Dalerum", "given": "Fredrik", "initials": "F", "orcid": "0000-0001-9737-8242", "researcher": {"href": "https://publications.scilifelab.se/researcher/7bec76c703ab493cb883105e2ec6b2e9.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1088a8b6a9af4cc396c610383576690f.json"}}, {"family": "M\u00e5sviken", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2660-7081", "researcher": {"href": "https://publications.scilifelab.se/researcher/b060865f580a44f29d46bf1bb6030f1f.json"}}, {"family": "Vartanyan", "given": "Sergey", "initials": "S", "orcid": "0000-0001-7806-4053", "researcher": {"href": "https://publications.scilifelab.se/researcher/0c472e06d8fa43a0b8a5575d5aec48e8.json"}}, {"family": "Raundrup", "given": "Katrine", "initials": "K", "orcid": "0000-0002-2110-3709", "researcher": {"href": "https://publications.scilifelab.se/researcher/0076f2642729447c887937c94b6b6df8.json"}}, {"family": "Al-Chaer", "given": "Amal", "initials": "A"}, {"family": "Rasmussen", "given": "Linett", "initials": "L", "orcid": "0000-0002-8050-5732", "researcher": {"href": "https://publications.scilifelab.se/researcher/d011adfb3d1d4074b3a404967b36a415.json"}}, {"family": "Hvilsom", "given": "Christina", "initials": "C", "orcid": "0000-0001-7870-6888", "researcher": {"href": "https://publications.scilifelab.se/researcher/19e68386a9414dad9162026abafad7ce.json"}}, {"family": "Heide-J\u00f8rgensen", "given": "Mads Peter", "initials": "MP", "orcid": "0000-0003-4846-7622", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9e5faf23cc44a0cb5d1c122a4e30ce1.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Aastrup", "given": "Peter", "initials": "P", "orcid": "0000-0003-4258-3358", "researcher": {"href": "https://publications.scilifelab.se/researcher/27511a58dd334aebbe0947cac97cb1bb.json"}}, {"family": "Van Coeverden de Groot", "given": "Peter J", "initials": "PJ"}, {"family": "Schmidt", "given": "Niels Martin", "initials": "NM", "orcid": "0000-0002-4166-6218", "researcher": {"href": "https://publications.scilifelab.se/researcher/0248915d131f49869c9c34312664b57a.json"}}, {"family": "Albrechtsen", "given": "Anders", "initials": "A", "orcid": "0000-0001-7306-031X", "researcher": {"href": "https://publications.scilifelab.se/researcher/876472bb22b141bf8d20ac3f8d04077b.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Heller", "given": "Rasmus", "initials": "R", "orcid": "0000-0001-6583-6923", "researcher": {"href": "https://publications.scilifelab.se/researcher/0289add03723441ab92592b4e3702a2c.json"}}, {"family": "Moltke", "given": "Ida", "initials": "I", "orcid": "0000-0001-7052-8554", "researcher": {"href": "https://publications.scilifelab.se/researcher/9529133a359142b89858b1fad77ac265.json"}}, {"family": "Siegismund", "given": "Hans Redlef", "initials": "HR", "orcid": "0000-0001-5757-3131", "researcher": {"href": "https://publications.scilifelab.se/researcher/e6451365bb8d4e86933d6c1c44e77de2.json"}}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "33", "issue": "2", "pages": "e17205", "issn-l": "0962-1083"}, "abstract": "Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.", "doi": "10.1111/mec.17205", "pmid": "37971141", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2024-01-02T13:39:50.306Z", "modified": "2024-11-25T10:27:04.091Z"}, {"entity": "publication", "iuid": "15b298c3dbdc466f99868b9b5e5aed52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15b298c3dbdc466f99868b9b5e5aed52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15b298c3dbdc466f99868b9b5e5aed52"}}, "title": "A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition.", "authors": [{"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE", "orcid": "0000-0003-0653-4292", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0ad7b1c36784c0092fd82f6d792c4bb.json"}}, {"family": "Kazanc\u0131", "given": "Duygu Deniz", "initials": "DD", "orcid": "0000-0002-8333-4027", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f28aea0bd7e4bb7b6ac3d8843cae17f.json"}}, {"family": "Aydo\u011fan", "given": "Ay\u00e7a", "initials": "A", "orcid": "0000-0003-0171-6978", "researcher": {"href": "https://publications.scilifelab.se/researcher/191b5ce05f6343e4825ef86d5703f8df.json"}}, {"family": "Gemici", "given": "Hasan Can", "initials": "HC", "orcid": "0000-0003-4424-2864", "researcher": {"href": "https://publications.scilifelab.se/researcher/e57ecd0264874105bb04cf9eb0cfce25.json"}}, {"family": "Erdal", "given": "\u00d6m\u00fcr Dilek", "initials": "\u00d6D", "orcid": "0000-0002-1559-4062", "researcher": {"href": "https://publications.scilifelab.se/researcher/43a1b606e9644c3794a02cf3e5c77984.json"}}, {"family": "Sar\u0131altun", "given": "Sava\u015f", "initials": "S", "orcid": "0000-0003-4190-3727", "researcher": {"href": "https://publications.scilifelab.se/researcher/70e2757acc7047bf8e33983e6585be80.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": "Koptekin", "given": "Dilek", "initials": "D", "orcid": "0000-0003-2664-5774", "researcher": {"href": "https://publications.scilifelab.se/researcher/0e95decb115f488ca913d25d1174711a.json"}}, {"family": "G\u00fcr\u00fcn", "given": "Kanat", "initials": "K", "orcid": "0000-0002-0433-2593", "researcher": {"href": "https://publications.scilifelab.se/researcher/ecc7d8b8f978438e8812dee4049122df.json"}}, {"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E", "orcid": "0000-0001-8646-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/b98a6e55a69644cda1e305da05c6838d.json"}}, {"family": "Fernandes", "given": "Daniel", "initials": "D", "orcid": "0000-0002-7434-6552", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9a0a0289d9a46518acfa124747e38bf.json"}}, {"family": "\u00c7akan", "given": "G\u00f6khan", "initials": "G", "orcid": "0000-0002-1840-4252", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef6138f4d74e4270b91f894300b40d3f.json"}}, {"family": "Koruyucu", "given": "Meliha Melis", "initials": "MM", "orcid": "0000-0002-1579-4478", "researcher": {"href": "https://publications.scilifelab.se/researcher/f034fb30cc694e00b12d060be03a7081.json"}}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Karamurat", "given": "Cansu", "initials": "C", "orcid": "0000-0002-3596-9036", "researcher": {"href": "https://publications.scilifelab.se/researcher/04c6c312d10a4d5a8c806b8550709016.json"}}, {"family": "\u00d6zkan", "given": "Mustafa", "initials": "M", "orcid": "0000-0002-7520-4572", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d994334753f4081811a1897ab1a3317.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": "Sevkar", "given": "Arda", "initials": "A", "orcid": "0000-0003-4573-6778", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c781bd3197040a3a9e4dee03b57dc65.json"}}, {"family": "S\u00fcrer", "given": "Elif", "initials": "E", "orcid": "0000-0002-0738-6669", "researcher": {"href": "https://publications.scilifelab.se/researcher/8061a22cfed349b18cdee6c00e8661c9.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Atakuman", "given": "\u00c7i\u011fdem", "initials": "\u00c7", "orcid": "0000-0001-8675-6236", "researcher": {"href": "https://publications.scilifelab.se/researcher/acefd01d35f04a0b99350ec4828adfcb.json"}}, {"family": "Erdal", "given": "Y\u0131lmaz Selim", "initials": "YS", "orcid": "0000-0001-8143-8159", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7f77cf0f580409f98004f71cf99c001.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Erim \u00d6zdo\u011fan", "given": "Asl\u0131", "initials": "A"}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}], "type": "journal article", "published": "2022-11-04", "journal": {"title": "Sci Adv", "issn": "2375-2548", "issn-l": "2375-2548", "volume": "8", "issue": "44", "pages": "eabo3609"}, "abstract": "Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic \u00c7ay\u00f6n\u00fc in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that \u00c7ay\u00f6n\u00fc was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting \u00c7ay\u00f6n\u00fc's cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.", "doi": "10.1126/sciadv.abo3609", "pmid": "36332018", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9635823"}], "notes": [], "created": "2022-12-19T10:42:53.985Z", "modified": "2023-10-16T15:30:26.817Z"}, {"entity": "publication", "iuid": "a2d409c477d843b68f024873b1ebc0eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a2d409c477d843b68f024873b1ebc0eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a2d409c477d843b68f024873b1ebc0eb"}}, "title": "Mammuthus sp. (Early and Middle Pleistocene Mammoths).", "authors": [{"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Trends Genet.", "issn": "0168-9525", "volume": "37", "issue": "7", "pages": "682-683", "issn-l": null}, "abstract": null, "doi": "10.1016/j.tig.2021.04.006", "pmid": "33985817", "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": "S0168-9525(21)00102-5"}], "notes": [], "created": "2021-06-09T12:16:52.282Z", "modified": "2024-01-16T13:48:39.270Z"}, {"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": "735c9b9d0c6245a788a78a937efb44eb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/735c9b9d0c6245a788a78a937efb44eb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/735c9b9d0c6245a788a78a937efb44eb"}}, "title": "Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1324-7489", "researcher": {"href": "https://publications.scilifelab.se/researcher/caeaa61758c4474ebd104ec232041341.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f80fb4d234c4f2fa2179ad1e7c6a6db.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Steiner", "given": "Cynthia C", "initials": "CC", "orcid": "0000-0002-2131-8072", "researcher": {"href": "https://publications.scilifelab.se/researcher/74c6c6b31d4e49628a2a74a1f7377ce5.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications.scilifelab.se/researcher/873e2383b99a43d7848bf387264cf0e8.json"}}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS", "orcid": "0000-0003-1371-219X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c37b07e1cb9643279b8801c45dde9dbe.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications.scilifelab.se/researcher/84b8b0757f02429b9bd419acb42ab6a3.json"}}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Brace", "given": "Selina", "initials": "S", "orcid": "0000-0003-2126-6732", "researcher": {"href": "https://publications.scilifelab.se/researcher/476fbd04aaaf453f943f5eea976c3cff.json"}}, {"family": "Chan", "given": "Yvonne L", "initials": "YL"}, {"family": "Wheat", "given": "Christopher W", "initials": "CW"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Goossens", "given": "Benoit", "initials": "B"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "historical article", "published": "2021-04-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2393", "issn-l": "2041-1723"}, "abstract": "Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.", "doi": "10.1038/s41467-021-22386-8", "pmid": "33896938", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Stockholm (Genomics Production)": null, "NGI Stockholm (Genomics Applications)": null, "National Genomics Infrastructure": null, "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-22386-8"}, {"db": "pmc", "key": "PMC8071806"}], "notes": [], "created": "2021-04-30T07:55:37.656Z", "modified": "2024-01-16T13:48:39.991Z"}, {"entity": "publication", "iuid": "a28f46bafc084df78efa91e2f3f049c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a28f46bafc084df78efa91e2f3f049c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a28f46bafc084df78efa91e2f3f049c7"}}, "title": "Million-year-old DNA sheds light on the genomic history of mammoths.", "authors": [{"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications.scilifelab.se/researcher/f56ca19cfa4f4909be996b2c99ec24f1.json"}}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P", "orcid": "0000-0001-9350-1987", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d148327b05a4c7ea53d5567eb87c74e.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}, {"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Oppenheimer", "given": "Jonas", "initials": "J"}, {"family": "Hartmann", "given": "Stefanie", "initials": "S", "orcid": "0000-0002-3476-0169", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d5ae4f0b70c4c33a7070830804670f8.json"}}, {"family": "Xenikoudakis", "given": "Georgios", "initials": "G"}, {"family": "Thomas", "given": "Jessica A", "initials": "JA"}, {"family": "Dehasque", "given": "Marianne", "initials": "M", "orcid": "0000-0002-4640-8306", "researcher": {"href": "https://publications.scilifelab.se/researcher/cdb54cf4aebb4cde9e3030a801fc9746.json"}}, {"family": "Sa\u011fl\u0131can", "given": "Ekin", "initials": "E", "orcid": "0000-0001-8646-1163", "researcher": {"href": "https://publications.scilifelab.se/researcher/b98a6e55a69644cda1e305da05c6838d.json"}}, {"family": "Fidan", "given": "Fatma Rabia", "initials": "FR", "orcid": "0000-0001-5877-7945", "researcher": {"href": "https://publications.scilifelab.se/researcher/75d1cb5fb5754f25b1adbad44e9f4adf.json"}}, {"family": "Barnes", "given": "Ian", "initials": "I", "orcid": "0000-0001-8322-6918", "researcher": {"href": "https://publications.scilifelab.se/researcher/daed8b59096b411dac9ad2bbe6ac84b4.json"}}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Nikolskiy", "given": "Pavel", "initials": "P"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Hofreiter", "given": "Michael", "initials": "M"}, {"family": "Lister", "given": "Adrian M", "initials": "AM", "orcid": "0000-0002-7985-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/156889b432944198909e4842f841a296.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "591", "issue": "7849", "pages": "265-269"}, "abstract": "Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.", "doi": "10.1038/s41586-021-03224-9", "pmid": "33597750", "labels": {"NGI Stockholm (Genomics Production)": null, "National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03224-9"}, {"db": "pmc", "key": "PMC7116897"}, {"db": "mid", "key": "EMS114570"}], "notes": [], "created": "2021-02-22T13:16:35.556Z", "modified": "2024-01-16T13:48:40.588Z"}, {"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": "3e21cc6163c14d55a5a03727b870e2d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e21cc6163c14d55a5a03727b870e2d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e21cc6163c14d55a5a03727b870e2d1"}}, "title": "Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.", "authors": [{"family": "Feuerborn", "given": "Tatiana R", "initials": "TR"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Munters", "given": "Arielle R", "initials": "AR"}, {"family": "Pe\u010dnerov\u00e1", "given": "Patr\u00edcia", "initials": "P"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Ure\u00f1a", "given": "Irene", "initials": "I"}, {"family": "Ersmark", "given": "Erik", "initials": "E"}, {"family": "Lagerholm", "given": "Vendela Kempe", "initials": "VK"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Rodr\u00edguez-Varela", "given": "Ricardo", "initials": "R"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D", "orcid": "0000-0002-9701-5940", "researcher": {"href": "https://publications.scilifelab.se/researcher/abb3bf815a954e039100104597097b68.json"}}], "type": "journal article", "published": "2020-11-30", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "21", "issue": "1", "pages": "844", "issn-l": "1471-2164"}, "abstract": "After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.\n\nHere we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.\n\nWe propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.", "doi": "10.1186/s12864-020-07229-y", "pmid": "33256612", "labels": {"NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-020-07229-y"}, {"db": "pmc", "key": "PMC7708127"}], "notes": [], "created": "2020-12-07T16:36:42.754Z", "modified": "2024-01-16T13:48:41.282Z"}, {"entity": "publication", "iuid": "ffa17d5833774c64ae24d57daf592ed5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffa17d5833774c64ae24d57daf592ed5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffa17d5833774c64ae24d57daf592ed5"}}, "title": "Origins and genetic legacy of prehistoric dogs.", "authors": [{"family": "Bergstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0002-4096-9268", "researcher": {"href": "https://publications.scilifelab.se/researcher/77429e0da9574e9ab3d1a14ae5dbb803.json"}}, {"family": "Frantz", "given": "Laurent", "initials": "L", "orcid": "0000-0001-8030-3885", "researcher": {"href": "https://publications.scilifelab.se/researcher/76b1179f8ee34ebbbdd466fb977f3ce7.json"}}, {"family": "Schmidt", "given": "Ryan", "initials": "R"}, {"family": "Ersmark", "given": "Erik", "initials": "E", "orcid": "0000-0003-4186-7498", "researcher": {"href": "https://publications.scilifelab.se/researcher/7061c3d9591b40488954083d06ed2e17.json"}}, {"family": "Lebrasseur", "given": "Ophelie", "initials": "O", "orcid": "0000-0003-0687-8538", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f100bd635446739f54bcabbf1840bc.json"}}, {"family": "Girdland-Flink", "given": "Linus", "initials": "L"}, {"family": "Lin", "given": "Audrey T", "initials": "AT", "orcid": "0000-0003-2505-1480", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f1f6e691ce04fd396757c4918535cc2.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "Sj\u00f6gren", "given": "Karl-G\u00f6ran", "initials": "KG", "orcid": "0000-0003-1791-3175", "researcher": {"href": "https://publications.scilifelab.se/researcher/1fe55ca79f7a438dbbda3e97e3780223.json"}}, {"family": "Anthony", "given": "David", "initials": "D", "orcid": "0000-0001-9122-0313", "researcher": {"href": "https://publications.scilifelab.se/researcher/dfe0401df8e44a82a3c69a7a0478007d.json"}}, {"family": "Antipina", "given": "Ekaterina", "initials": "E", "orcid": "0000-0002-3003-942X", "researcher": {"href": "https://publications.scilifelab.se/researcher/52c0ad9634824dabbef732e81a68ec60.json"}}, {"family": "Amiri", "given": "Sarieh", "initials": "S", "orcid": "0000-0002-6835-373X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae40113ed34f4ed1a173637c864e1c38.json"}}, {"family": "Bar-Oz", "given": "Guy", "initials": "G"}, {"family": "Bazaliiskii", "given": "Vladimir I", "initials": "VI"}, {"family": "Bulatovi\u0107", "given": "Jelena", "initials": "J", "orcid": "0000-0002-0672-067X", "researcher": {"href": "https://publications.scilifelab.se/researcher/977f7acdf2e94256bc664d52f8b99922.json"}}, {"family": "Brown", "given": "Dorcas", "initials": "D"}, {"family": "Carmagnini", "given": "Alberto", "initials": "A"}, {"family": "Davy", "given": "Tom", "initials": "T", "orcid": "0000-0002-9466-5497", "researcher": {"href": "https://publications.scilifelab.se/researcher/2c9e9bebf8ad41d2a53d4c475f719b88.json"}}, {"family": "Fedorov", "given": "Sergey", "initials": "S", "orcid": "0000-0001-8179-740X", "researcher": {"href": "https://publications.scilifelab.se/researcher/856215bb926b471c9d74e7408715f8e6.json"}}, {"family": "Fiore", "given": "Ivana", "initials": "I", "orcid": "0000-0001-5721-0760", "researcher": {"href": "https://publications.scilifelab.se/researcher/48a313be55974f488d3804f980eb0dd0.json"}}, {"family": "Fulton", "given": "Deirdre", "initials": "D"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M", "orcid": "0000-0001-8865-0937", "researcher": {"href": "https://publications.scilifelab.se/researcher/79253311b1c64b599c8987b947459391.json"}}, {"family": "Haile", "given": "James", "initials": "J", "orcid": "0000-0002-8521-8337", "researcher": {"href": "https://publications.scilifelab.se/researcher/253913f4bc03438fb7e5c075014d2f6e.json"}}, {"family": "Irving-Pease", "given": "Evan K", "initials": "EK", "orcid": "0000-0003-1940-2192", "researcher": {"href": "https://publications.scilifelab.se/researcher/02e144af5864412baa97c9fa5defbfd5.json"}}, {"family": "Jamieson", "given": "Alexandra", "initials": "A", "orcid": "0000-0003-0979-5762", "researcher": {"href": "https://publications.scilifelab.se/researcher/b70ced169df04e52af5047b555159daf.json"}}, {"family": "Janssens", "given": "Luc", "initials": "L"}, {"family": "Kirillova", "given": "Irina", "initials": "I"}, {"family": "Horwitz", "given": "Liora Kolska", "initials": "LK"}, {"family": "Kuzmanovic-Cvetkovi\u0107", "given": "Julka", "initials": "J"}, {"family": "Kuzmin", "given": "Yaroslav", "initials": "Y", "orcid": "0000-0002-4512-2269", "researcher": {"href": "https://publications.scilifelab.se/researcher/1326bb181c944b00a73d940f87ddf298.json"}}, {"family": "Losey", "given": "Robert J", "initials": "RJ", "orcid": "0000-0003-3615-8160", "researcher": {"href": "https://publications.scilifelab.se/researcher/4fae0ee7f4f24212ba68d26087deaf88.json"}}, {"family": "Dizdar", "given": "Daria Lo\u017enjak", "initials": "DL", "orcid": "0000-0002-5769-2269", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb0100bc6c5d459aa8f9b05b2e236ba5.json"}}, {"family": "Mashkour", "given": "Marjan", "initials": "M", "orcid": "0000-0003-3630-9459", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d45bd37c43f4f7fba2c62c9a26e18c7.json"}}, {"family": "Novak", "given": "Mario", "initials": "M", "orcid": "0000-0002-4567-8742", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae952c508a1d444c9e3ee6cdb0c5a2ae.json"}}, {"family": "Onar", "given": "Vedat", "initials": "V", "orcid": "0000-0002-8359-243X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d129588489cb4684b204c29aba54b1fc.json"}}, {"family": "Orton", "given": "David", "initials": "D", "orcid": "0000-0003-4069-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b0e6ccfd34e49a1878181fa931114de.json"}}, {"family": "Pasari\u0107", "given": "Maja", "initials": "M"}, {"family": "Radivojevi\u0107", "given": "Miljana", "initials": "M", "orcid": "0000-0001-7329-305X", "researcher": {"href": "https://publications.scilifelab.se/researcher/19d71e76741c4d7eacc555b9328291c7.json"}}, {"family": "Rajkovi\u0107", "given": "Dragana", "initials": "D"}, {"family": "Roberts", "given": "Benjamin", "initials": "B"}, {"family": "Ryan", "given": "Hannah", "initials": "H", "orcid": "0000-0002-4320-4594", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a07befb801c478692e3508b663d1a97.json"}}, {"family": "Sablin", "given": "Mikhail", "initials": "M", "orcid": "0000-0002-2773-7454", "researcher": {"href": "https://publications.scilifelab.se/researcher/3355f7b5b291492b8ff2119fd74adbaf.json"}}, {"family": "Shidlovskiy", "given": "Fedor", "initials": "F"}, {"family": "Stojanovi\u0107", "given": "Ivana", "initials": "I", "orcid": "0000-0001-5271-680X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d603204ff3c04194a7246468a9f1754e.json"}}, {"family": "Tagliacozzo", "given": "Antonio", "initials": "A"}, {"family": "Trantalidou", "given": "Katerina", "initials": "K"}, {"family": "Ull\u00e9n", "given": "Inga", "initials": "I"}, {"family": "Villaluenga", "given": "Aritza", "initials": "A"}, {"family": "Wapnish", "given": "Paula", "initials": "P"}, {"family": "Dobney", "given": "Keith", "initials": "K", "orcid": "0000-0001-9036-4681", "researcher": {"href": "https://publications.scilifelab.se/researcher/29ea25869ffa4984a013051452969efb.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Linderholm", "given": "Anna", "initials": "A", "orcid": "0000-0002-1613-9926", "researcher": {"href": "https://publications.scilifelab.se/researcher/27c319330d1e4827858b5612dc203c69.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Pinhasi", "given": "Ron", "initials": "R", "orcid": "0000-0003-1629-8131", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd8eedf480ae494d9e6249ec58dd1867.json"}}, {"family": "Larson", "given": "Greger", "initials": "G", "orcid": "0000-0002-4092-0392", "researcher": {"href": "https://publications.scilifelab.se/researcher/8313c5d2d5a148349ad14e51deca8ab5.json"}}, {"family": "Skoglund", "given": "Pontus", "initials": "P", "orcid": "0000-0002-3021-5913", "researcher": {"href": "https://publications.scilifelab.se/researcher/338a5f8f37fb48b3887230dfd81786d3.json"}}], "type": "journal article", "published": "2020-10-30", "journal": {"title": "Science", "issn": "1095-9203", "volume": "370", "issue": "6516", "pages": "557-564", "issn-l": "0036-8075"}, "abstract": "Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.", "doi": "10.1126/science.aba9572", "pmid": "33122379", "labels": {"NGI Stockholm (Genomics Applications)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "370/6516/557"}, {"db": "pmc", "key": "PMC7116352"}, {"db": "mid", "key": "EMS103415"}], "notes": [], "created": "2021-01-08T16:29:50.956Z", "modified": "2021-11-10T12:45:57.753Z"}, {"entity": "publication", "iuid": "d65d460e50e0405eaa0e81048974930c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d65d460e50e0405eaa0e81048974930c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d65d460e50e0405eaa0e81048974930c"}}, "title": "Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.", "authors": [{"family": "Lord", "given": "Edana", "initials": "E", "orcid": "0000-0002-4717-1988", "researcher": {"href": "https://publications.scilifelab.se/researcher/05d936191b3c4ff3acbe71db566da595.json"}}, {"family": "Dussex", "given": "Nicolas", "initials": "N", "orcid": "0000-0002-9179-8593", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8ce91163131424a99f8815c2cb96953.json"}}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Ryder", "given": "Oliver A", "initials": "OA"}, {"family": "Stanton", "given": "David W G", "initials": "DWG", "orcid": "0000-0002-9753-3166", "researcher": {"href": "https://publications.scilifelab.se/researcher/2732b89a34b54967bcb87811cdc3fb1c.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "S\u00e1nchez-Barreiro", "given": "F\u00e1tima", "initials": "F"}, {"family": "Zhang", "given": "Guojie", "initials": "G"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Lorenzen", "given": "Eline D", "initials": "ED"}, {"family": "Willerslev", "given": "Eske", "initials": "E", "orcid": "0000-0002-7081-6748", "researcher": {"href": "https://publications.scilifelab.se/researcher/da0055841300427e85d9af38b1863ef1.json"}}, {"family": "Protopopov", "given": "Albert", "initials": "A"}, {"family": "Shidlovskiy", "given": "Fedor", "initials": "F"}, {"family": "Fedorov", "given": "Sergey", "initials": "S"}, {"family": "Bocherens", "given": "Herv\u00e9", "initials": "H"}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Goossens", "given": "Benoit", "initials": "B"}, {"family": "van der Plicht", "given": "Johannes", "initials": "J", "orcid": "0000-0003-4298-7037", "researcher": {"href": "https://publications.scilifelab.se/researcher/c115c95efd014b748c698a802f25f2d5.json"}}, {"family": "Chan", "given": "Yvonne L", "initials": "YL", "orcid": "0000-0002-8073-4025", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fdb2d9af4bc439eb1572abe7000190d.json"}}, {"family": "Prost", "given": "Stefan", "initials": "S", "orcid": "0000-0002-6229-3596", "researcher": {"href": "https://publications.scilifelab.se/researcher/809ba200bb864ec9abf0d0cad09c5a42.json"}}, {"family": "Potapova", "given": "Olga", "initials": "O", "orcid": "0000-0002-3589-2489", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a8a3f7d32434226be4d637673845820.json"}}, {"family": "Kirillova", "given": "Irina", "initials": "I"}, {"family": "Lister", "given": "Adrian M", "initials": "AM"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd81ccff05904164be2bcceaa65422f7.json"}}, {"family": "Kapp", "given": "Joshua D", "initials": "JD"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2020-10-05", "journal": {"title": "Curr. Biol.", "issn": "1879-0445", "volume": "30", "issue": "19", "pages": "3871-3879.e7", "issn-l": "0960-9822"}, "abstract": "Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a \u223c18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the B\u00f8lling-Aller\u00f8d interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.", "doi": "10.1016/j.cub.2020.07.046", "pmid": "32795436", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0960-9822(20)31071-X"}], "notes": [], "created": "2020-08-24T09:00:42.045Z", "modified": "2024-01-16T13:48:41.594Z"}, {"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": "b58a481da1744ca8b371ca73d93972c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b58a481da1744ca8b371ca73d93972c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b58a481da1744ca8b371ca73d93972c6"}}, "title": "Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox.", "authors": [{"family": "Larsson", "given": "Petter", "initials": "P"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Hagen", "given": "Ingerid J", "initials": "IJ"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Androsov", "given": "Semyon", "initials": "S"}, {"family": "Germonpr\u00e9", "given": "Mietje", "initials": "M"}, {"family": "Bergfeldt", "given": "Nora", "initials": "N"}, {"family": "Fedorov", "given": "Sergey", "initials": "S"}, {"family": "Eide", "given": "Nina E", "initials": "NE"}, {"family": "Sokolova", "given": "Natalia", "initials": "N"}, {"family": "Berteaux", "given": "Dominique", "initials": "D"}, {"family": "Angerbj\u00f6rn", "given": "Anders", "initials": "A"}, {"family": "Flagstad", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Plotnikov", "given": "Valeri", "initials": "V"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "D\u00edez-Del-Molino", "given": "David", "initials": "D"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2019-12-23", "journal": {"volume": "374", "issn": "1471-2970", "issue": "1788", "pages": "20190212", "title": "Philos. Trans. R. Soc. Lond., B, Biol. Sci.", "issn-l": "0962-8436"}, "abstract": "Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'", "doi": "10.1098/rstb.2019.0212", "pmid": "31679495", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6863501"}, {"db": "figshare", "key": "10.6084/m9.figshare.c.4669517"}], "notes": [], "created": "2019-11-20T09:28:56.670Z", "modified": "2024-01-16T13:48:43.259Z"}, {"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": "88ca69fe4ed541d0ad898f7f989c34b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88ca69fe4ed541d0ad898f7f989c34b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88ca69fe4ed541d0ad898f7f989c34b0"}}, "title": "Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.", "authors": [{"family": "Cappellini", "given": "Enrico", "initials": "E"}, {"family": "Welker", "given": "Frido", "initials": "F"}, {"family": "Pandolfi", "given": "Luca", "initials": "L"}, {"family": "Ramos-Madrigal", "given": "Jazm\u00edn", "initials": "J"}, {"family": "Samodova", "given": "Diana", "initials": "D"}, {"family": "R\u00fcther", "given": "Patrick L", "initials": "PL"}, {"family": "Fotakis", "given": "Anna K", "initials": "AK"}, {"family": "Lyon", "given": "David", "initials": "D"}, {"family": "Moreno-Mayar", "given": "J V\u00edctor", "initials": "JV"}, {"family": "Bukhsianidze", "given": "Maia", "initials": "M"}, {"family": "Rakownikow Jersie-Christensen", "given": "Rosa", "initials": "R"}, {"family": "Mackie", "given": "Meaghan", "initials": "M"}, {"family": "Ginolhac", "given": "Aur\u00e9lien", "initials": "A"}, {"family": "Ferring", "given": "Reid", "initials": "R"}, {"family": "Tappen", "given": "Martha", "initials": "M"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Dickinson", "given": "Marc R", "initials": "MR"}, {"family": "Stafford", "given": "Thomas W", "initials": "TW"}, {"family": "Chan", "given": "Yvonne L", "initials": "YL"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Nathan", "given": "Senthilvel K S S", "initials": "SKSS"}, {"family": "Heintzman", "given": "Peter D", "initials": "PD"}, {"family": "Kapp", "given": "Joshua D", "initials": "JD"}, {"family": "Kirillova", "given": "Irina", "initials": "I"}, {"family": "Moodley", "given": "Yoshan", "initials": "Y"}, {"family": "Agusti", "given": "Jordi", "initials": "J"}, {"family": "Kahlke", "given": "Ralf-Dietrich", "initials": "RD"}, {"family": "Kiladze", "given": "Gocha", "initials": "G"}, {"family": "Mart\u00ednez-Navarro", "given": "Bienvenido", "initials": "B"}, {"family": "Liu", "given": "Shanlin", "initials": "S"}, {"family": "Sandoval Velasco", "given": "Marcela", "initials": "M"}, {"family": "Sinding", "given": "Mikkel-Holger S", "initials": "MS"}, {"family": "Kelstrup", "given": "Christian D", "initials": "CD"}, {"family": "Allentoft", "given": "Morten E", "initials": "ME"}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "Penkman", "given": "Kirsty", "initials": "K"}, {"family": "Shapiro", "given": "Beth", "initials": "B"}, {"family": "Rook", "given": "Lorenzo", "initials": "L"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Olsen", "given": "Jesper V", "initials": "JV"}, {"family": "Lordkipanidze", "given": "David", "initials": "D"}, {"family": "Willerslev", "given": "Eske", "initials": "E"}], "type": "historical article", "published": "2019-10-00", "journal": {"volume": "574", "issn": "1476-4687", "issue": "7776", "pages": "103-107", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.", "doi": "10.1038/s41586-019-1555-y", "pmid": "31511700", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-019-1555-y"}, {"db": "pmc", "key": "PMC6894936"}, {"db": "mid", "key": "EMS84015"}], "notes": [], "created": "2019-12-02T16:53:09.503Z", "modified": "2021-07-07T20:31:10.850Z"}, {"entity": "publication", "iuid": "74d4aa31e7774b5d81c9f6b39c75f31c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74d4aa31e7774b5d81c9f6b39c75f31c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74d4aa31e7774b5d81c9f6b39c75f31c"}}, "title": "Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.", "authors": [{"family": "Kashuba", "given": "Natalija", "initials": "N"}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E"}, {"family": "Damlien", "given": "Hege", "initials": "H"}, {"family": "Manninen", "given": "Mikael A", "initials": "MA", "orcid": "0000-0002-8906-6502", "researcher": {"href": "https://publications.scilifelab.se/researcher/ce8d3c355c374e8794526fdfeb1c87e8.json"}}, {"family": "Nordqvist", "given": "Bengt", "initials": "B"}, {"family": "Persson", "given": "Per", "initials": "P"}, {"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": "2019-05-15", "journal": {"volume": "2", "issn": "2399-3642", "issue": null, "pages": "185", "title": "Commun Biol", "issn-l": "2399-3642"}, "abstract": "Human demography research in grounded on the information derived from ancient DNA and archaeology. For example, the study on the early postglacial dual-route colonisation of the Scandinavian Peninsula is largely based on associating genomic data with the early dispersal of lithic technology from the East European Plain. However, a clear connection between material culture and genetics has been lacking. Here, we demonstrate that direct connection by analysing human DNA from chewed birch bark pitch mastics. These samples were discovered at Huseby Klev in western Sweden, a Mesolithic site with eastern lithic technology. We generated genome-wide data for three individuals, and show their affinity to the Scandinavian hunter-gatherers. Our samples date to 9880-9540 calBP, expanding the temporal range and distribution of the early Scandinavian genetic group. We propose that DNA from ancient mastics can be used to study environment and ecology of prehistoric populations.", "doi": "10.1038/s42003-019-0399-1", "pmid": "31123709", "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": "399"}, {"db": "pmc", "key": "PMC6520363"}, {"db": "Dryad", "key": "10.5061/dryad.j3k19p9"}], "notes": [], "created": "2019-12-02T17:20:27.160Z", "modified": "2024-01-16T13:48:44.340Z"}, {"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": "233b062d1f5d47e5ac0971cd9ea0a47f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/233b062d1f5d47e5ac0971cd9ea0a47f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/233b062d1f5d47e5ac0971cd9ea0a47f"}}, "title": "Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians.", "authors": [{"family": "Juras", "given": "Anna", "initials": "A"}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M"}, {"family": "Nikitin", "given": "Alexey G", "initials": "AG"}, {"family": "Ehler", "given": "Edvard", "initials": "E"}, {"family": "Chyle\u0144ski", "given": "Maciej", "initials": "M"}, {"family": "\u0141ukasik", "given": "Sylwia", "initials": "S"}, {"family": "Krenz-Niedba\u0142a", "given": "Marta", "initials": "M"}, {"family": "Sinika", "given": "Vitaly", "initials": "V"}, {"family": "Piontek", "given": "Janusz", "initials": "J"}, {"family": "Ivanova", "given": "Svetlana", "initials": "S"}, {"family": "Dabert", "given": "Miroslawa", "initials": "M"}, {"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": "2017-03-07", "journal": {"volume": "7", "issn": "2045-2322", "issue": null, "pages": "43950", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.", "doi": "10.1038/srep43950", "pmid": "28266657", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "srep43950"}, {"db": "pmc", "key": "PMC5339713"}], "notes": [], "created": "2017-11-03T16:18:39.704Z", "modified": "2021-07-07T10:48:05.331Z"}, {"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": "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": "242a899e5ba144c19d809a35fd9d24cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/242a899e5ba144c19d809a35fd9d24cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/242a899e5ba144c19d809a35fd9d24cc"}}, "title": "Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth.", "authors": [{"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Mallick", "given": "Swapan", "initials": "S"}, {"family": "Skoglund", "given": "Pontus", "initials": "P"}, {"family": "Enk", "given": "Jacob", "initials": "J"}, {"family": "Rohland", "given": "Nadin", "initials": "N"}, {"family": "Li", "given": "Heng", "initials": "H"}, {"family": "Omrak", "given": "Ay\u00e7a", "initials": "A"}, {"family": "Vartanyan", "given": "Sergey", "initials": "S"}, {"family": "Poinar", "given": "Hendrik", "initials": "H"}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications.scilifelab.se/researcher/2a1a0a680ab8456cbf5a941e9718fd5a.json"}}, {"family": "Reich", "given": "David", "initials": "D"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-8270-7613", "researcher": {"href": "https://publications.scilifelab.se/researcher/48ecf726779249ac9d12f4f7a1cc62bf.json"}}], "type": "journal article", "published": "2015-05-18", "journal": {"volume": "25", "issn": "1879-0445", "issue": "10", "pages": "1395-1400", "title": "Curr. Biol.", "issn-l": "0960-9822"}, "abstract": "The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding. However, whether such genetic factors have had an impact on species prior to their extinction is unclear; examining this would require a detailed reconstruction of a species' demographic history as well as changes in genome-wide diversity leading up to its extinction. Here, we present high-quality complete genome sequences from two woolly mammoths (Mammuthus primigenius). The first mammoth was sequenced at 17.1-fold coverage and dates to \u223c4,300 years before present, representing one of the last surviving individuals on Wrangel Island. The second mammoth, sequenced at 11.2-fold coverage, was obtained from an \u223c44,800-year-old specimen from the Late Pleistocene population in northeastern Siberia. The demographic trajectories inferred from the two genomes are qualitatively similar and reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel mammoth at the end of the last glaciation. A comparison of the two genomes shows that the Wrangel mammoth has a 20% reduction in heterozygosity as well as a 28-fold increase in the fraction of the genome that comprises runs of homozygosity. We conclude that the population on Wrangel Island, which was the last surviving woolly mammoth population, was subject to reduced genetic diversity shortly before it became extinct.", "doi": "10.1016/j.cub.2015.04.007", "pmid": "25913407", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0960-9822(15)00420-0"}, {"db": "pmc", "key": "PMC4439331"}, {"db": "mid", "key": "NIHMS678983"}], "notes": [], "created": "2017-05-02T12:58:15.555Z", "modified": "2021-07-07T20:31:10.723Z"}, {"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"}]}