{"entity": "researcher", "timestamp": "2026-08-14T13:03:58.755Z", "family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "affiliations": ["e Department of Animal Breeding and Genetics , Swedish University of Agricultural Sciences , Uppsala , Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6"}}, "publications": [{"entity": "publication", "iuid": "88ca53dd11f14b3191a5c1a38499a985", "links": {"self": {"href": "https://publications.scilifelab.se/publication/88ca53dd11f14b3191a5c1a38499a985.json"}, "display": {"href": "https://publications.scilifelab.se/publication/88ca53dd11f14b3191a5c1a38499a985"}}, "title": "Genome of the extinct Gotland cattle breed.", "authors": [{"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}], "type": "journal article", "published": "2025-12-03", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "26", "issue": "1", "pages": "1093", "issn-l": "1471-2164"}, "abstract": "The extinct cattle breed Gotland cattle lived on the island of Gotland in the Baltic Sea until the beginning of the 1950s. We sequenced the genomes of two Gotland cattle isolated from skulls from a local museum on Gotland.\n\nThe depth of coverage was 2.7X and 3.3X, respectively, with a breadth of coverage of 85% and 89%. Based on coverage of the sex chromosomes, both animals appeared to be female. We detected 19 million single nucleotide variants and 2.8 million indels in the joint dataset of Gotland cattle jointly called with modern Swedish cattle. In a principal component analysis, the two Gotland cattle placed the closest to Swedish Red cattle, rather than among the southern or northern traditional breeds. In terms of mitochondrial haplotypes, they were similar to clusters of related haplotypes involving multiple other breeds, including Swedish Mountain cattle, Swedish Red Polled and several Finnish cattle breeds.\n\nIn summary, our results suggest that Gotland cattle were genetically closer to the ancestors of Swedish Red cattle than to the extant traditional Swedish breeds.", "doi": "10.1186/s12864-025-12382-3", "pmid": "41340033", "labels": {"Ancient DNA": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12864-025-12382-3"}], "notes": [], "created": "2025-12-10T09:59:37.512Z", "modified": "2025-12-10T09:59:37.679Z"}, {"entity": "publication", "iuid": "85509550f8a04133b34f785895ed87e7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/85509550f8a04133b34f785895ed87e7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/85509550f8a04133b34f785895ed87e7"}}, "title": "Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.", "authors": [{"family": "Larsson", "given": "Martin N A", "initials": "MNA"}, {"family": "Morell Miranda", "given": "Pedro", "initials": "P"}, {"family": "Pan", "given": "Li", "initials": "L"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Kaptan", "given": "Damla", "initials": "D"}, {"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE"}, {"family": "Kivikero", "given": "Hanna", "initials": "H"}, {"family": "Kantanen", "given": "Juha", "initials": "J", "orcid": "0000-0001-6350-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd2d0b84728048f39df9c1153300252a.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M"}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F"}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}], "type": "journal article", "published": "2024-06-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "6", "issn-l": "1759-6653"}, "abstract": "Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and \u00c5land, dating from the Late Neolithic (\u223c4,100 cal BP) to historical times (\u223c1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.", "doi": "10.1093/gbe/evae114", "pmid": "38795367", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Ancient DNA": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11162877"}, {"db": "pii", "key": "7682331"}], "notes": [], "created": "2024-07-01T06:11:08.407Z", "modified": "2025-02-28T14:18:19.091Z"}, {"entity": "publication", "iuid": "1531f4fac9cd43d6aba4ef764037faa6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1531f4fac9cd43d6aba4ef764037faa6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1531f4fac9cd43d6aba4ef764037faa6"}}, "title": "Ancient Sheep Genomes reveal four Millennia of North European Short-Tailed Sheep in the Baltic Sea region", "authors": [{"family": "Larsson", "given": "Martin NA", "initials": "MN", "orcid": "0000-0002-2949-0045", "researcher": {"href": "https://publications.scilifelab.se/researcher/369e8dfabc584862b0094bd06721bc4a.json"}}, {"family": "Miranda", "given": "Pedro Morell", "initials": "PM", "orcid": "0000-0001-7678-9691", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a48ddd9e9b491ea55ec2ac0bd4328f.json"}}, {"family": "Pan", "given": "Li", "initials": "L"}, {"family": "Ba\u015fak Vural", "given": "K\u0131v\u0131lc\u0131m", "initials": "K"}, {"family": "Kaptan", "given": "Damla", "initials": "D", "orcid": "0000-0001-7953-1354", "researcher": {"href": "https://publications.scilifelab.se/researcher/d969faa7d65045298f3ef289d849dfe8.json"}}, {"family": "Rodrigues Soares", "given": "Andr\u00e9 Elias", "initials": "AE", "orcid": "0000-0002-7768-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/2270d42b20f6456a8db81f41503b0063.json"}}, {"family": "Kivikero", "given": "Hanna", "initials": "H", "orcid": "0000-0002-6396-2288", "researcher": {"href": "https://publications.scilifelab.se/researcher/754fdef753c14437a78790d13426d6ae.json"}}, {"family": "Kantanen", "given": "Juha", "initials": "J", "orcid": "0000-0001-6350-6373", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd2d0b84728048f39df9c1153300252a.json"}}, {"family": "Somel", "given": "Mehmet", "initials": "M", "orcid": "0000-0002-3138-1307", "researcher": {"href": "https://publications.scilifelab.se/researcher/13a40746adb7487e875fb0ae7c5fea9a.json"}}, {"family": "\u00d6zer", "given": "F\u00fcsun", "initials": "F", "orcid": "0000-0003-0443-5805", "researcher": {"href": "https://publications.scilifelab.se/researcher/676b684e50e04c7686e5ddfd1b9c41a1.json"}}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Stor\u00e5", "given": "Jan", "initials": "J", "orcid": "0000-0001-6319-7857", "researcher": {"href": "https://publications.scilifelab.se/researcher/57e9174cbd2a4c39be948b88b9ab2d3a.json"}}, {"family": "G\u00fcnther", "given": "Torsten", "initials": "T", "orcid": "0000-0001-9460-390X", "researcher": {"href": "https://publications.scilifelab.se/researcher/84159bff82a64a938bcff107f550c901.json"}}], "type": "posted-content", "published": "2023-06-26", "journal": {"title": "bioRxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this breed diversity goes, with formal documentation only dating back a few centuries. North European short-tailed breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia less than 6000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and \u00c5land, dating from Late Neolithic (\u223c4100 calBP) to historical times (\u223c1600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern North European short-tailed breeds, suggesting a substantial degree of long-term continuity of this breed type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit higher genetic diversity when compared to modern breeds, implying a loss of diversity in recent centuries associated with breed formation. Finally, we see a potential signature of an even earlier, genetically different form of sheep in Scandinavia as these samples do not represent the first sheep in Northern Europe. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.", "doi": "10.1101/2023.06.26.544912", "pmid": null, "labels": {"Ancient DNA": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2023-11-24T13:49:22.061Z", "modified": "2024-01-16T13:48:33.113Z"}, {"entity": "publication", "iuid": "93379f5a15c7458fac70fdb76edbaee8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93379f5a15c7458fac70fdb76edbaee8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93379f5a15c7458fac70fdb76edbaee8"}}, "title": "Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification.", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Da Silva", "given": "Vinicius H", "initials": "VH"}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Lindstr\u00f6m", "given": "Tom", "initials": "T", "orcid": "0000-0001-7856-2925", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a619b495eed4a41a65f2bc7a3c7c5dc.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Coutinho", "given": "Luiz L", "initials": "LL"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "14", "issn": "1559-2308", "issue": "7", "pages": "685-707", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic 'flexibility' in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic 'specificity' in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.", "doi": "10.1080/15592294.2019.1609868", "pmid": "31070073", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6557589"}], "notes": [], "created": "2020-01-08T12:39:10.372Z", "modified": "2021-06-18T14:18:18.038Z"}]}