{"entity": "researcher", "timestamp": "2026-08-20T20:36:39.874Z", "family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "affiliations": ["Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3"}}, "publications": [{"entity": "publication", "iuid": "139b06c68a8941ef87d34e80188f8132", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/139b06c68a8941ef87d34e80188f8132.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/139b06c68a8941ef87d34e80188f8132"}}, "title": "Chromosome-level genome assembly of Norwegian wild alpine reindeer (Rangifer tarandus tarandus).", "authors": [{"family": "T\u00f8rresen", "given": "Ole K", "initials": "OK", "orcid": "0000-0002-1932-8212", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d2f90dfcdde43d597ac37a347c44ff5.json"}}, {"family": "Tooming-Klunderud", "given": "Ave", "initials": "A", "orcid": "0009-0008-0057-2873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a83f56872d6a4b0fb91504e15cafa9eb.json"}}, {"family": "Skage", "given": "Morten", "initials": "M", "orcid": "0000-0002-5312-8038", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3f666519e7d400fa772046cad3844f4.json"}}, {"family": "Streitlien", "given": "Anne Eline", "initials": "AE"}, {"family": "Strand", "given": "Olav", "initials": "O", "orcid": "0009-0002-6189-6309", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccbd166b26bc483593f68d185d65a2c1.json"}}, {"family": "Rolandsen", "given": "Christer M", "initials": "CM", "orcid": "0000-0002-5628-0385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72a91e483949447789bd7230f8bc5b7e.json"}}, {"family": "Ferrari", "given": "Giada", "initials": "G", "orcid": "0000-0002-0850-1518", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6679779a21914fb496849057cccbf984.json"}}, {"family": "Cerca", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-7788-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9119ffe17f1400ea74e0eaf43c105fc.json"}}, {"family": "Mysterud", "given": "Atle", "initials": "A", "orcid": "0000-0001-8993-7382", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f36192bbe8634b818745104303041e90.json"}}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}], "type": "journal article", "published": "2026-05-06", "journal": {"title": "J. Hered.", "issn": "1465-7333", "volume": "117", "issue": "3", "pages": "557-565", "issn-l": "0022-1503"}, "abstract": "We describe a chromosome-level genome assembly from a wild alpine reindeer individual (Rangifer tarandus tarandus) from the Rondane area in Southern Norway. The assembly is resolved into two pseudo-haplotypes: hap 1 spanning 3,081 Mb and hap 2 spanning 2,633 Mb. Contig N50 and scaffold N50 lengths are in the range of 31 to 41 and 66 to 69 Mb, respectively. A large part of these two haplotypes (83.8% and 90.4%, respectively) are scaffolded into 34 autosomal chromosomal pseudomolecules, and in sex chromosomes X and Y for hap 1. The BUSCO completeness scores are 98.0% and 95.2%, respectively, and gene annotations of the assemblies identified 37,998 and 36,977 protein-coding genes. We also present an updated and improved genome assembly for Svalbard reindeer (Rangifer tarandus platyrhynchus; contig N50 46 to 48 Mb, scaffold N50 67 to 71 Mb, BUSCO 95.4% to 98.0%) and a comparison with previously published genome assemblies of reindeer.", "doi": "10.1093/jhered/esaf094", "pmid": "41182255", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC13147171"}, {"db": "pii", "key": "8313328"}], "notes": [], "created": "2026-08-20T09:42:07.920Z", "modified": "2026-08-20T09:42:08.225Z"}, {"entity": "publication", "iuid": "138b39dd98a64e34b572a06dc7a23268", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/138b39dd98a64e34b572a06dc7a23268.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/138b39dd98a64e34b572a06dc7a23268"}}, "title": "Pangenomes as a framework for adaptive radiation, speciation, and adaptation.", "authors": [{"family": "Tellini", "given": "Nicol\u00f2", "initials": "N", "orcid": "0000-0002-2406-2906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a07df210a708474ca042a58742697844.json"}}, {"family": "T\u00f8rresen", "given": "Ole K", "initials": "OK", "orcid": "0000-0002-1932-8212", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d2f90dfcdde43d597ac37a347c44ff5.json"}}, {"family": "Edwards", "given": "David", "initials": "D", "orcid": "0000-0001-7599-6760", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce49135f9a0b4268adb4fc7e0bd3f6de.json"}}, {"family": "Rieseberg", "given": "Loren H", "initials": "LH", "orcid": "0000-0002-2712-2417", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ccc872959fc4264b9f530e85a09437a.json"}}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}, {"family": "Cerca", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-7788-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9119ffe17f1400ea74e0eaf43c105fc.json"}}], "type": "journal article", "published": "2025-12-00", "journal": {"title": "American journal of botany", "issn": "1537-2197", "volume": "112", "issue": "12", "pages": "e70130", "issn-l": "0002-9122"}, "abstract": "Understanding the genomic basis of diversification is a central goal in evolutionary biology. In recent years, the development and use of pangenomes, a genomic representation of multiple individuals within a lineage (a set of related populations, subspecies, ecotypes, or species), has enabled researchers to differentiate between DNA sequences shared by all individuals of a given lineage (core regions) from those present only in some individuals (accessory or variable regions). Differentiating between core and accessory regions has highlighted a key limitation of relying on a single reference genome: It captures the genetic code of only one individual and this biases genomic analyses and our understanding of diversification. Here, we propose that by identifying genes associated with both core and accessory regions, we can deepen our understanding of the processes underlying diversification. We suggest that analyzing pangenomes and accessory regions will provide deeper insights into diversification, hybridization, and the genetic basis of adaptation and speciation.", "doi": "10.1002/ajb2.70130", "pmid": "41345855", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12712766"}], "notes": [], "created": "2026-08-20T06:28:24.994Z", "modified": "2026-08-20T06:28:25.286Z"}, {"entity": "publication", "iuid": "fb29b512feb245c88b3146865fab9555", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fb29b512feb245c88b3146865fab9555.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fb29b512feb245c88b3146865fab9555"}}, "title": "Reference genome bias in light of species-specific chromosomal reorganization and translocations.", "authors": [{"family": "Maurstad", "given": "Marius F", "initials": "MF", "orcid": "0000-0001-7894-1693", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/958ec319e3674f9683957590400c48e2.json"}}, {"family": "Hoff", "given": "Siv Nam Khang", "initials": "SNK", "orcid": "0000-0001-8113-338X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db76a491cfab4d5c9227443701eaed37.json"}}, {"family": "Cerca", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-7788-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9119ffe17f1400ea74e0eaf43c105fc.json"}}, {"family": "Ravinet", "given": "Mark", "initials": "M", "orcid": "0000-0002-2841-1798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01b9b7c21953456e8c12a46803d6ab78.json"}}, {"family": "Bradbury", "given": "Ian", "initials": "I"}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}, {"family": "Pr\u00e6bel", "given": "Kim", "initials": "K", "orcid": "0000-0002-0681-1854", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95c9602002d042cf874a93c895f37776.json"}}, {"family": "Jentoft", "given": "Sissel", "initials": "S", "orcid": "0000-0001-8707-531X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/52961bc2c6574c6085059f52a16b5fb6.json"}}], "type": "journal article", "published": "2025-10-15", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "volume": "26", "issue": "1", "pages": "355", "issn-l": "1474-7596"}, "abstract": "Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements-such as chromosomal inversions-in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses.\n\nHere, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod (Arctogadus glacialis), polar cod (Boreogadus saida), and Atlantic cod (Gadus morhua) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20 \u00d7 coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (\u03c0), and cross-species genetic divergence (DXY). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference.\n\nInaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.", "doi": "10.1186/s13059-025-03761-w", "pmid": "41094588", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12523119"}, {"db": "pii", "key": "10.1186/s13059-025-03761-w"}], "notes": [], "created": "2026-08-20T12:21:55.840Z", "modified": "2026-08-20T12:21:56.087Z"}, {"entity": "publication", "iuid": "d26c5004293a4ea7b4613b8f3053e8ac", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d26c5004293a4ea7b4613b8f3053e8ac.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d26c5004293a4ea7b4613b8f3053e8ac"}}, "title": "Chromosome-level genome assembly of Norwegian wild alpine reindeer ( Rangifer tarandus tarandus )", "authors": [{"family": "T\u00f8rresen", "given": "Ole K", "initials": "OK", "orcid": "0000-0002-1932-8212", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d2f90dfcdde43d597ac37a347c44ff5.json"}}, {"family": "Tooming-Klunderud", "given": "Ave", "initials": "A", "orcid": "0009-0008-0057-2873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a83f56872d6a4b0fb91504e15cafa9eb.json"}}, {"family": "Skage", "given": "Morten", "initials": "M", "orcid": "0000-0002-5312-8038", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3f666519e7d400fa772046cad3844f4.json"}}, {"family": "Streitlien", "given": "Anne Eline", "initials": "AE"}, {"family": "Strand", "given": "Olav", "initials": "O"}, {"family": "Rolandsen", "given": "Christer M", "initials": "CM", "orcid": "0000-0002-5628-0385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72a91e483949447789bd7230f8bc5b7e.json"}}, {"family": "Ferrari", "given": "Giada", "initials": "G", "orcid": "0000-0002-0850-1518", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6679779a21914fb496849057cccbf984.json"}}, {"family": "Cerca", "given": "Jos\u00e9", "initials": "J", "orcid": "0000-0001-7788-4367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9119ffe17f1400ea74e0eaf43c105fc.json"}}, {"family": "Mysterud", "given": "Atle", "initials": "A", "orcid": "0000-0001-8993-7382", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f36192bbe8634b818745104303041e90.json"}}, {"family": "Jakobsen", "given": "Kjetill S", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2fe02e097b342508301397260ef7cc3.json"}}], "type": "posted-content", "published": "2025-05-16", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.05.15.652595", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:03:51.677Z", "modified": "2026-08-20T11:05:35.656Z"}, {"entity": "publication", "iuid": "626310cbddb14ff48c80c0f9372c585b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/626310cbddb14ff48c80c0f9372c585b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/626310cbddb14ff48c80c0f9372c585b"}}, "title": "The Earth BioGenome Project 2020: Starting the clock.", "authors": [{"family": "Lewin", "given": "Harris A", "initials": "HA", "orcid": "0000-0002-1043-7287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5059da24204049c696aec45b62526759.json"}}, {"family": "Richards", "given": "Stephen", "initials": "S", "orcid": "0000-0001-8959-5466", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8005cf3b343461388e2b82a2c61c293.json"}}, {"family": "Lieberman Aiden", "given": "Erez", "initials": "E"}, {"family": "Allende", "given": "Miguel L", "initials": "ML", "orcid": "0000-0002-2783-2152", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27d6fdda2e7b4487b651c852c3f3cd11.json"}}, {"family": "Archibald", "given": "John M", "initials": "JM"}, {"family": "B\u00e1lint", "given": "Mikl\u00f3s", "initials": "M"}, {"family": "Barker", "given": "Katharine B", "initials": "KB"}, {"family": "Baumgartner", "given": "Bridget", "initials": "B"}, {"family": "Belov", "given": "Katherine", "initials": "K"}, {"family": "Bertorelle", "given": "Giorgio", "initials": "G"}, {"family": "Blaxter", "given": "Mark L", "initials": "ML", "orcid": "0000-0003-2861-949X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b785bc131a241c4815ab5ef1576709b.json"}}, {"family": "Cai", "given": "Jing", "initials": "J"}, {"family": "Caperello", "given": "Nicolette D", "initials": "ND"}, {"family": "Carlson", "given": "Keith", "initials": "K"}, {"family": "Castilla-Rubio", "given": "Juan Carlos", "initials": "JC"}, {"family": "Chaw", "given": "Shu-Miaw", "initials": "SM"}, {"family": "Chen", "given": "Lei", "initials": "L"}, {"family": "Childers", "given": "Anna K", "initials": "AK"}, {"family": "Coddington", "given": "Jonathan A", "initials": "JA", "orcid": "0000-0001-6004-7730", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/efae0bfdf0c64e86a175c8921b1af0b4.json"}}, {"family": "Conde", "given": "Dalia A", "initials": "DA", "orcid": "0000-0002-7923-8163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5b73243e2df04c5a8d771456b262a4bf.json"}}, {"family": "Corominas", "given": "Montserrat", "initials": "M", "orcid": "0000-0002-0724-8346", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0805b84e0e824c93a51262f4fdc8f8e2.json"}}, {"family": "Crandall", "given": "Keith A", "initials": "KA", "orcid": "0000-0002-0836-3389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/853c5da68a5a4c96bd2248b21bd15ba7.json"}}, {"family": "Crawford", "given": "Andrew J", "initials": "AJ"}, {"family": "DiPalma", "given": "Federica", "initials": "F"}, {"family": "Durbin", "given": "Richard", "initials": "R", "orcid": "0000-0002-9130-1006", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a8972546b724b0d9c6ed69a766cc41b.json"}}, {"family": "Ebenezer", "given": "ThankGod E", "initials": "TE"}, {"family": "Edwards", "given": "Scott V", "initials": "SV", "orcid": "0000-0003-2535-6217", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/249a83cc8fb240609cd7bd76c6c79e2c.json"}}, {"family": "Fedrigo", "given": "Olivier", "initials": "O"}, {"family": "Flicek", "given": "Paul", "initials": "P"}, {"family": "Formenti", "given": "Giulio", "initials": "G"}, {"family": "Gibbs", "given": "Richard A", "initials": "RA"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP", "orcid": "0000-0002-5805-7195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/93cbe282154844588f63bc7cc6983b30.json"}}, {"family": "Goldstein", "given": "Melissa M", "initials": "MM"}, {"family": "Graves", "given": "Jennifer Marshall", "initials": "JM", "orcid": "0000-0001-6480-7856", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/48044e7f378c41e28b58ae92e1102efb.json"}}, {"family": "Greely", "given": "Henry T", "initials": "HT", "orcid": "0000-0002-1105-6734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea9e4bfb13764d13b4418be1ecc2d27d.json"}}, {"family": "Grigoriev", "given": "Igor V", "initials": "IV", "orcid": "0000-0002-3136-8903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5cb43708257842149fbbeed91293d400.json"}}, {"family": "Hackett", "given": "Kevin J", "initials": "KJ"}, {"family": "Hall", "given": "Neil", "initials": "N"}, {"family": "Haussler", "given": "David", "initials": "D"}, {"family": "Helgen", "given": "Kristofer M", "initials": "KM"}, {"family": "Hogg", "given": "Carolyn J", "initials": "CJ", "orcid": "0000-0002-6328-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faf4b7a234c84bdbac97cf9b0e8f5531.json"}}, {"family": "Isobe", "given": "Sachiko", "initials": "S"}, {"family": "Jakobsen", "given": "Kjetill Sigurd", "initials": "KS", "orcid": "0000-0002-8861-5397", "researcher": {"href": 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