{"entity": "researcher", "timestamp": "2026-04-20T22:33:47.929Z", "family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "affiliations": ["Department of Population Ecology Institute of Ecology and Evolution Friedrich Schiller University Jena Jena Germany"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e"}}, "publications": [{"entity": "publication", "iuid": "eaf9b454889b42e98966f350d0a69e84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eaf9b454889b42e98966f350d0a69e84"}}, "title": "A mosaic of modular variation at a single gene underpins convergent plumage coloration.", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Chase", "given": "Madeline A", "initials": "MA", "orcid": "0000-0002-7916-3560", "researcher": {"href": "https://publications.scilifelab.se/researcher/3053121df4b64418bc1dcc2d7e50d87c.json"}}, {"family": "Kakhki", "given": "Niloofar Alaei", "initials": "NA"}, {"family": "Lammers", "given": "Fritjof", "initials": "F", "orcid": "0000-0002-3110-8220", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a13a19d3594543a30c5146011aaa3a.json"}}, {"family": "de Souza", "given": "Stacey G", "initials": "SG", "orcid": "0000-0001-6596-5522", "researcher": {"href": 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"given": "Fabian", "initials": "F"}, {"family": "Shurulinkov", "given": "Petar", "initials": "P"}, {"family": "Sklyarenko", "given": "Sergey", "initials": "S", "orcid": "0000-0002-7443-347X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0de4c8591f1b4929ae73d3ea81ca2c17.json"}}, {"family": "Stumberger", "given": "Borut", "initials": "B"}, {"family": "Tagiyev", "given": "Abulfaz", "initials": "A"}, {"family": "Uboldi", "given": "Alessia", "initials": "A", "orcid": "0009-0001-3940-3697", "researcher": {"href": "https://publications.scilifelab.se/researcher/53c73538105e441eb6a5402ad0883799.json"}}, {"family": "Vogiatzis", "given": "Nikitas", "initials": "N", "orcid": "0009-0008-9592-923X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9be0f74759fd4d429c3cb891c51d6e83.json"}}, {"family": "Taborsak-Lines", "given": "Fanny", "initials": "F"}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Yao", "given": "Liqun", "initials": "L"}, {"family": "Peichel", "given": "Catherine L", "initials": "CL", "orcid": "0000-0002-7731-8944", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b4d7c680f69458dbde56257ff4820c5.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Gagnaire", "given": "Pierre-Alexandre", "initials": "PA", "orcid": "0000-0002-1908-3235", "researcher": {"href": "https://publications.scilifelab.se/researcher/10f9487cea1d40938b3f9f00f72e6433.json"}}, {"family": "Kirschel", "given": "Alexander N G", "initials": "ANG", "orcid": "0000-0003-4379-7956", "researcher": {"href": "https://publications.scilifelab.se/researcher/d533e6378c094ef7bf44e570bcbb1145.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2025-10-16", "journal": {"title": "Science", "issn": "1095-9203", "volume": "390", "issue": "6770", "pages": "eado8005", "issn-l": "0036-8075"}, "abstract": "The reshuffling of genomic variation from multiple origins is an important contributor to phenotypic diversification, yet insights into the evolutionary trajectories of this combinatorial process and their interplay with genetic architecture remain scarce. We show that convergent plumage color evolution in wheatears involves a monogenic architecture with modular variation introgressed at the agouti signaling protein (ASIP) locus. Introgression of a new transposable element insertion and linked protein-coding variation underpin a transspecific throat color polymorphism, which stable isotopes suggest is associated with alternative foraging niches. Cointrogression of linked regulatory ASIP variation resulted in mantle color convergence in one species, whereas convergent color evolution at the genus level required new variation. Our results demonstrate evolutionary trajectories from introgressed variation realized within the constraints of a monogenic architecture.", "doi": "10.1126/science.ado8005", "pmid": "41100596", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Short read": "Service", "NGI Other": "Service"}, "xrefs": [], "notes": [], "created": "2026-01-26T14:53:27.788Z", "modified": "2026-01-26T14:53:31.469Z"}, {"entity": "publication", "iuid": "2c9906a7c1a0408f8006e723a38f488c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c9906a7c1a0408f8006e723a38f488c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c9906a7c1a0408f8006e723a38f488c"}}, "title": "An annotated chromosome-scale reference genome for Eastern black-eared wheatear (Oenanthe melanoleuca).", "authors": [{"family": "Peona", "given": "Valentina", "initials": "V", "orcid": "0000-0001-5119-1837", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4903a935025452f88e4f1c02483829b.json"}}, {"family": "Palacios-Gimenez", "given": "Octavio Manuel", "initials": "OM", "orcid": "0000-0002-1472-9949", "researcher": {"href": "https://publications.scilifelab.se/researcher/f90e29ecd5724ff19509983e65891915.json"}}, {"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Olsen", "given": "Remi Andr\u00e9", "initials": "RA"}, {"family": "Alaei Kakhki", "given": "Niloofar", "initials": "N"}, {"family": "Andriopoulos", "given": "Pavlos", "initials": "P", "orcid": "0000-0002-5377-2974", "researcher": {"href": "https://publications.scilifelab.se/researcher/ef8407f9cb79440d80f580cef8536175.json"}}, {"family": "Bontzorlos", "given": "Vasileios", "initials": "V", "orcid": "0000-0002-1276-3385", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebafa22103ec46ab87ce2b5fa878519d.json"}}, {"family": "Schweizer", "given": "Manuel", "initials": "M", "orcid": "0000-0002-7555-8450", "researcher": {"href": "https://publications.scilifelab.se/researcher/5a043d6f016b46709ace7f181d8cd3b8.json"}}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2023-06-01", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "13", "issue": "6", "pages": null}, "abstract": "Pervasive convergent evolution and in part high incidences of hybridization distinguish wheatears (songbirds of the genus Oenanthe) as a versatile system to address questions at the forefront of research on the molecular bases of phenotypic and species diversification. To prepare the genomic resources for this venture, we here generated and annotated a chromosome-scale assembly of the Eastern black-eared wheatear (Oenanthe melanoleuca). This species is part of the Oenanthe hispanica complex that is characterized by convergent evolution of plumage coloration and high rates of hybridization. The long-read-based male nuclear genome assembly comprises 1.04 Gb in 32 autosomes, the Z chromosome, and the mitogenome. The assembly is highly contiguous (contig N50, 12.6 Mb; scaffold N50, 70 Mb), with 96% of the genome assembled at the chromosome level and 95.5% benchmarking universal single-copy orthologs (BUSCO) completeness. The nuclear genome was annotated with 18,143 protein-coding genes and 31,333 mRNAs (annotation BUSCO completeness, 98.0%), and about 10% of the genome consists of repetitive DNA. The annotated chromosome-scale reference genome of Eastern black-eared wheatear provides a crucial resource for research into the genomics of adaptation and speciation in an intriguing group of passerines.", "doi": "10.1093/g3journal/jkad088", "pmid": "37097035", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10234393"}, {"db": "pii", "key": "7141353"}], "notes": [], "created": "2023-08-15T06:59:21.634Z", "modified": "2024-01-16T13:48:33.264Z"}, {"entity": "publication", "iuid": "217d4684484246f2aec3ad0c479d36a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/217d4684484246f2aec3ad0c479d36a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/217d4684484246f2aec3ad0c479d36a0"}}, "title": "Linked-read sequencing enables haplotype-resolved resequencing at population scale.", "authors": [{"family": "Lutgen", "given": "Dave", "initials": "D", "orcid": "0000-0003-0793-3930", "researcher": {"href": "https://publications.scilifelab.se/researcher/68173a10b32e4dca953933b92e0cec4e.json"}}, {"family": "Ritter", "given": "Raphael", "initials": "R"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Schielzeth", "given": "Holger", "initials": "H", "orcid": "0000-0002-9124-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/56d7e24b36a24560bafa92f08848ac46.json"}}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Garc\u00eda", "given": "Jes\u00fas T", "initials": "JT", "orcid": "0000-0003-4126-9658", "researcher": {"href": "https://publications.scilifelab.se/researcher/699bf85902454a43aeef0a075ed38a39.json"}}, {"family": "Shirihai", "given": "Hadoram", "initials": "H"}, {"family": "Schweizer", "given": "Manuel", "initials": "M"}, {"family": "Suh", "given": "Alexander", "initials": "A", "orcid": "0000-0002-8979-9992", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e39e1313d894596a6c4ed949e43e019.json"}}, {"family": "Burri", "given": "Reto", "initials": "R", "orcid": "0000-0002-1813-0079", "researcher": {"href": "https://publications.scilifelab.se/researcher/68f21e70e2864b42ab9fc532c14c069c.json"}}], "type": "journal article", "published": "2020-09-00", "journal": {"volume": "20", "issn": "1755-0998", "issue": "5", "pages": "1311-1322", "title": "Mol Ecol Resour", "issn-l": "1755-098X"}, "abstract": "The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences - including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps - are still limited by the lack of high-quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25\u00d7, 20\u00d7, 15\u00d7, 10\u00d7, 7\u00d7, and 5\u00d7) with high-coverage data (46-68\u00d7) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15\u00d7 coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15\u00d7 coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25\u00d7 coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing at population scale.", "doi": "10.1111/1755-0998.13192", "pmid": "32419391", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-06-01T16:55:32.608Z", "modified": "2024-01-16T13:48:41.811Z"}]}