{"entity": "researcher", "timestamp": "2026-08-12T23:56:21.317Z", "family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e"}}, "publications": [{"entity": "publication", "iuid": "a1a66eb9378f48bcbb9c32923b5503e3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a1a66eb9378f48bcbb9c32923b5503e3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a1a66eb9378f48bcbb9c32923b5503e3"}}, "title": "Genome Variation in Three Anthophora Bee Species Reflects Divergent Demographic Histories", "authors": [{"family": "Taliadoros", "given": "Demetris", "initials": "D"}, {"family": "Soares", "given": "Andr\u00e9 E R", "initials": "AER", "orcid": "0000-0002-7768-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/2270d42b20f6456a8db81f41503b0063.json"}}, {"family": "Dias", "given": "Guilherme", "initials": "G", "orcid": "0000-0002-1459-3148", "researcher": {"href": "https://publications.scilifelab.se/researcher/73778a1096e04b5d94f8d5c6f3584d99.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Pippel", "given": "Martin", "initials": "M", "orcid": "0000-0002-8134-5929", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f59d0c98de64ac1a62234792258ee62.json"}}, {"family": "Olsson", "given": "Anna", "initials": "A", "orcid": "0000-0002-5438-7293", "researcher": {"href": "https://publications.scilifelab.se/researcher/57ec91022afd4c1390433d6383a06fc0.json"}}, {"family": "Mosbech", "given": "Mai\u2010Britt", "initials": "M", "orcid": "0000-0002-6068-0971", "researcher": {"href": "https://publications.scilifelab.se/researcher/efde81e53e6e48cba694e82e6fa8d38c.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Lager", "given": "Nina", "initials": "N"}, {"family": "Strand", "given": "Anna\u2010Sofi", "initials": "A"}, {"family": "Pettersson", "given": "Mats", "initials": "M", "orcid": "0000-0002-7372-9076", "researcher": {"href": "https://publications.scilifelab.se/researcher/27011c7fbb8a44dda536a4fc876675b0.json"}}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Cederberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Lindblad\u2010Toh", "given": "Kerstin", "initials": "K"}, {"family": "Webster", "given": "Matthew T", "initials": "MT", "orcid": "0000-0003-1141-2863", "researcher": {"href": "https://publications.scilifelab.se/researcher/579df0da95b94e5087512b76d7f1c058.json"}}], "type": "journal-article", "published": "2025-12-00", "journal": {"title": "Mol Ecol", "issn": "0962-1083", "pages": "e70204", "volume": "34", "issue": "24", "issn-l": "0962-1083"}, "abstract": "Population genomics can reveal trends and drivers of biodiversity loss, but it is still unclear how best to use measures of genome variation to understand population vulnerability in insects. Here we study genome variation in three species of Anthophora bees that show contrasting population trends in northern Europe. Two species, Anthophora plagiata and Anthophora retusa , have experienced declines and recoveries of different magnitudes in the last 50 years, whereas a third species, Anthophora quadrimaculata , has relative population stability. We generate highly contiguous genome assemblies and use them to study genome variation in 136 samples of these species collected throughout Sweden. We find exceedingly low genetic variation in A. plagiata , which has experienced a severe recent bottleneck, but high genetic variation in A. retusa , despite a similar recent population trajectory. Fragmented populations of the threatened species A. plagiata appear isolated from each other, but in A. retusa, there is a lack of deep population structure among geographically separated subpopulations. We infer population size in the distant past using MSMC2 and recent past using GONE. These methods are remarkably concordant and indicate ancient fluctuations in population size dating back to the Pleistocene, with moderate expansions in the past century in all three species. These results are comparable to some other studies of endangered insects, which have experienced population declines that predate the modern era. We detect long blocks of identity-by-state in A. plagiata , indicative of severe recent inbreeding. Translocations between isolated populations of this species could have a positive effect on their resilience.", "doi": "10.1111/mec.70204", "pmid": "41387163", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Short read": "Service", "NGI Long read": "Service"}, "xrefs": [], "notes": [], "created": "2025-12-17T11:40:16.625Z", "modified": "2025-12-21T19:08:10.173Z"}, {"entity": "publication", "iuid": "3f77b47c2c9d4cb4b7c69ccd9596688c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f77b47c2c9d4cb4b7c69ccd9596688c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f77b47c2c9d4cb4b7c69ccd9596688c"}}, "title": "A chromosome-level genome assembly of the European green toad (Bufotes viridis).", "authors": [{"family": "R\u00f6din-M\u00f6rch", "given": "Patrik", "initials": "P", "orcid": "0000-0001-6737-1488", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e6abe040b284d67b11f45db1e58540e.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Choi", "given": "Eunkyoung", "initials": "E", "orcid": "0009-0007-7147-9468", "researcher": {"href": "https://publications.scilifelab.se/researcher/e4255b0cdeec4f43885e730affd1246b.json"}}, {"family": "Ciofi", "given": "Claudio", "initials": "C", "orcid": "0000-0001-8537-8659", "researcher": {"href": "https://publications.scilifelab.se/researcher/f15012e62daf4c28b3c101550f460d35.json"}}, {"family": "Diedericks", "given": "Genevieve", "initials": "G", "orcid": "0000-0001-7700-8906", "researcher": {"href": "https://publications.scilifelab.se/researcher/7506eb0e88da4e4da970947289df5c4c.json"}}, {"family": "Diroma", "given": "Maria Angela", "initials": "MA", "orcid": "0000-0003-1427-8946", "researcher": {"href": "https://publications.scilifelab.se/researcher/93fd5ac3fe64467d9e617b2bf14fea71.json"}}, {"family": "Einarsd\u00f3ttir", "given": "El\u00edsabet", "initials": "E", "orcid": "0000-0003-3101-2285", "researcher": {"href": "https://publications.scilifelab.se/researcher/0db39539bdd94519a418e6dd7a287cc8.json"}}, {"family": "F\u00f6rs\u00e4ter", "given": "Kristofer", "initials": "K", "orcid": "0009-0009-7670-215X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2e8576dc5354bef84f13f2e6a3fc1b6.json"}}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Jons\u00e4ll", "given": "Linnea", "initials": "L", "orcid": "0009-0004-6729-0185", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c8f571a5be4dfeb7ebf5b35f4b4ae7.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Laurila", "given": "Anssi", "initials": "A", "orcid": "0000-0001-8090-3776", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b55d6c459ef448c992a37db2a02c3ea.json"}}, {"family": "Leit\u00e3o", "given": "Henrique G", "initials": "HG", "orcid": "0000-0002-9212-4590", "researcher": {"href": "https://publications.scilifelab.se/researcher/991f0492e152466f8f02cb6b7365ca6b.json"}}, {"family": "Mosbech", "given": "Mai-Britt", "initials": "M"}, {"family": "Natali", "given": "Chiara", "initials": "C", "orcid": "0000-0002-0293-171X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df472019f49541f3bd455f1d8b1aea91.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "R"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O", "orcid": "0000-0002-5597-1870", "researcher": {"href": "https://publications.scilifelab.se/researcher/31689f508a984d0680d285c294669615.json"}}, {"family": "Soler", "given": "Lucile", "initials": "L", "orcid": "0000-0002-0121-2393", "researcher": {"href": "https://publications.scilifelab.se/researcher/f701059f90fe4c7c9b969079e74aac57.json"}}, {"family": "Svardal", "given": "Hannes", "initials": "H", "orcid": "0000-0001-7866-7313", "researcher": {"href": "https://publications.scilifelab.se/researcher/4aee397f0ff64641a9c2033d56c6effb.json"}}, {"family": "Proux-W\u00e9ra", "given": "Estelle", "initials": "E", "orcid": "0000-0003-3752-1806", "researcher": {"href": "https://publications.scilifelab.se/researcher/9257ccdfc6484cd9a95f9b2f17f9a8d1.json"}}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J", "orcid": "0000-0002-5840-779X", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e1eb3c1903f4a97a4c585a2dee3b05f.json"}}], "type": "journal article", "published": "2025-03-18", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "15", "issue": "3", "pages": null}, "abstract": "The European green toad (Bufotes viridis) is geographically widely distributed. While the species global conservation status is labeled as of least concern by the IUCN, it is declining in many parts of its range where populations are fragmented and isolated. A high-quality reference genome is an important resource for conservation genomic researchers who are trying to understand and interpret the genomic signals of population decline, inbreeding, and the accumulation of deleterious mutations. Here, we assembled and annotated a chromosome-level reference genome for B. viridis as part of the European Reference Genome Atlas pilot project. The genome assembly, with a size of \u223c3.89 Gb consists of 11 chromosomes and an additional 2,096 unplaced scaffolds. The final assembly had a scaffold N50 value of 478.39 Mb and covered 90.4% single copy tetrapod orthologs, and 46.7% repetitive elements. Finally, a total of 23,830 protein-coding genes matching a known gene, together with 56,974 mRNAs were predicted. This high-quality reference genome will benefit amphibian evolutionary genomics research and enable conservation genetic studies to inform practical conservation work on this species.", "doi": "10.1093/g3journal/jkaf002", "pmid": "39969399", "labels": {"NGI Stockholm (Genomics Production)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11917475"}, {"db": "pii", "key": "8024180"}], "notes": [], "created": "2025-02-28T07:50:03.734Z", "modified": "2025-11-21T12:40:15.314Z"}, {"entity": "publication", "iuid": "6dfa6120b7ef4380a12e3374d03f0f95", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dfa6120b7ef4380a12e3374d03f0f95.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dfa6120b7ef4380a12e3374d03f0f95"}}, "title": "The genome sequence of the white-tailed eagle, Haliaeetus albicilla (Linnaeus, 1758).", "authors": [{"family": "P\u00e1lsson", "given": "Sn\u00e6bj\u00f6rn", "initials": "S"}, {"family": "Skarph\u00e9\u00f0insson", "given": "Kristinn Haukur", "initials": "KH"}, {"family": "Heintz", "given": "Julia", "initials": "J", "orcid": "0009-0001-9345-1358", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7ebbb1f975844f7910676091d05a61e.json"}}, {"family": "Quarfordt", "given": "Pernilla", "initials": "P"}, {"family": "Strand", "given": "Ann-Sofi", "initials": "AS"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Pettersson", "given": "Olga Vinnere", "initials": "OV"}, {"family": "Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team", "given": "", "initials": ""}, {"family": "Wellcome Sanger Institute Scientific Operations: Sequencing Operations", "given": "", "initials": ""}, {"family": "Wellcome Sanger Institute Tree of Life Core Informatics team", "given": "", "initials": ""}, {"family": "Tree of Life Core Informatics collective", "given": "", "initials": ""}, {"family": "Darwin Tree of Life Consortium", "given": "", "initials": ""}], "type": "journal article", "published": "2024-10-09", "journal": {"title": "Wellcome Open Res", "issn": "2398-502X", "volume": "9", "pages": "575", "issn-l": "2398-502X"}, "abstract": "We present a genome assembly from an individual female Haliaeetus albicilla (the white-tailed eagle; Chordata; Aves; Accipitriformes; Accipitridae). The genome sequence has a total length of 1,320.30 megabases. Most of the assembly is scaffolded into 34 chromosomal pseudomolecules, including the Z and W sex chromosomes. Gene annotation of this assembly on Ensembl identified 17,501 protein-coding genes.", "doi": "10.12688/wellcomeopenres.23089.1", "pmid": "39534533", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11555360"}], "notes": [], "created": "2024-11-04T20:48:53.042Z", "modified": "2024-11-25T10:31:35.253Z"}]}