{"entity": "researcher", "timestamp": "2026-07-15T17:18:06.751Z", "family": "Kierczak", "given": "M", "initials": "M", "orcid": "0000-0003-2629-5655", "affiliations": ["Department of Cell and Molecular Biology, Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e"}}, "publications": [{"entity": "publication", "iuid": "6a3ba31b04c54d138e7e1e4e193684e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6a3ba31b04c54d138e7e1e4e193684e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6a3ba31b04c54d138e7e1e4e193684e0"}}, "title": "GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.", "authors": [{"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": "van der Valk", "given": "Tom", "initials": "T"}, {"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Dehasque", "given": "Marianne", "initials": "M"}, {"family": "Stanton", "given": "David W G", "initials": "DWG"}, {"family": "Khoonsari", "given": "Payam Emami", "initials": "PE"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"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": "2022-06-13", "journal": {"title": "BMC Bioinformatics", "issn": "1471-2105", "volume": "23", "issue": "1", "pages": "228", "issn-l": "1471-2105"}, "abstract": "Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.\n\nHere, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub ( https://github.com/NBISweden/GenErode ).\n\nGenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.", "doi": "10.1186/s12859-022-04757-0", "pmid": "35698034", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Long-term Support WABI": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC9195343"}, {"db": "pii", "key": "10.1186/s12859-022-04757-0"}], "notes": [], "created": "2022-08-01T12:22:30.120Z", "modified": "2024-01-16T13:48:36.134Z"}, {"entity": "publication", "iuid": "9c25f649010d4c10b0c89f067f250b61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9c25f649010d4c10b0c89f067f250b61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9c25f649010d4c10b0c89f067f250b61"}}, "title": "Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.", "authors": [{"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Rafati", "given": "Nima", "initials": "N"}, {"family": "H\u00f6glund", "given": "Julia", "initials": "J", "orcid": "0000-0001-8061-3947", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b02049b625d47a69324be23e35f5b58.json"}}, {"family": "Gourl\u00e9", "given": "Hadrien", "initials": "H", "orcid": "0000-0001-9807-1082", "researcher": {"href": "https://publications.scilifelab.se/researcher/4143a879fa2043e7873be9e2aa72d051.json"}}, {"family": "Lo Faro", "given": "Valeria", "initials": "V", "orcid": "0000-0003-4931-7327", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e77657632e1469d9f0382673f54d071.json"}}, {"family": "Schmitz", "given": "Daniel", "initials": "D", "orcid": "0000-0003-4480-891X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b1d0c4505854c7d9ab7a2ed3116b7ae.json"}}, {"family": "Ek", "given": "Weronica E", "initials": "WE", "orcid": "0000-0003-2194-496X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7398a2bfa9154e15a4295828bc0f5bb8.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U", "orcid": "0000-0002-6316-3355", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8739f0f42c44019ab88a49db350a4f2.json"}}, {"family": "Enroth", "given": "Stefan", "initials": "S", "orcid": "0000-0002-5056-9137", "researcher": {"href": "https://publications.scilifelab.se/researcher/16bb97ef16ee49f3ae0c7ea0495fd971.json"}}, {"family": "Ekman", "given": "Diana", "initials": "D"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}, {"family": "Karlsson", "given": "Torgny", "initials": "T", "orcid": "0000-0001-8095-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/691d6823b8e04c5abf1613513da32b08.json"}}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5", "orcid": "0000-0002-2915-4498", "researcher": {"href": "https://publications.scilifelab.se/researcher/76265c54961046e99bdb0439f9ae1d34.json"}}], "type": "journal article", "published": "2022-05-09", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "13", "issue": "1", "pages": "2532"}, "abstract": "Despite the success of genome-wide association studies, much of the genetic contribution to complex traits remains unexplained. Here, we analyse high coverage whole-genome sequencing data, to evaluate the contribution of rare genetic variants to 414 plasma proteins. The frequency distribution of genetic variants is skewed towards the rare spectrum, and damaging variants are more often rare. We estimate that less than 4.3% of the narrow-sense heritability is expected to be explained by rare variants in our cohort. Using a gene-based approach, we identify Cis-associations for 237 of the proteins, which is slightly more compared to a GWAS (N = 213), and we identify 34 associated loci in Trans. Several associations are driven by rare variants, which have larger effects, on average. We therefore conclude that rare variants could be of importance for precision medicine applications, but have a more limited contribution to the missing heritability of complex diseases.", "doi": "10.1038/s41467-022-30208-8", "pmid": "35534486", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9085767"}, {"db": "pii", "key": "10.1038/s41467-022-30208-8"}], "notes": [], "created": "2022-06-10T08:49:57.584Z", "modified": "2024-01-16T13:48:36.679Z"}, {"entity": "publication", "iuid": "bac07fae3c0e4214bca1d4ff1a326f39", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bac07fae3c0e4214bca1d4ff1a326f39.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bac07fae3c0e4214bca1d4ff1a326f39"}}, "title": "A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.", "authors": [{"family": "Christmas", "given": "Matthew J", "initials": "MJ"}, {"family": "Jones", "given": "Julia C", "initials": "JC"}, {"family": "Olsson", "given": "Anna", "initials": "A"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Bunikis", "given": "Ignas", "initials": "I"}, {"family": "Kierczak", "given": "Marcin", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Whitley", "given": "Kaitlyn M", "initials": "KM"}, {"family": "Sullivan", "given": "Isabel", "initials": "I"}, {"family": "Geib", "given": "Jennifer C", "initials": "JC"}, {"family": "Miller-Struttmann", "given": "Nicole E", "initials": "NE"}, {"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": "2022-02-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "31", "issue": "4", "pages": "1111-1127"}, "abstract": "Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species (\"incognitus\"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.", "doi": "10.1111/mec.16291", "pmid": "34837435", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "NGI Long read": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-11-30T12:41:55.744Z", "modified": "2024-01-16T13:48:37.663Z"}, {"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": "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": "ce6d56617d5243ee9bf1a8d1257c006e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ce6d56617d5243ee9bf1a8d1257c006e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ce6d56617d5243ee9bf1a8d1257c006e"}}, "title": "Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin.", "authors": [{"family": "Tengvall", "given": "K", "initials": "K", "orcid": "0000-0003-0424-3571", "researcher": {"href": "https://publications.scilifelab.se/researcher/59b02aaaf03b4cd39150c3034888c81d.json"}}, {"family": "Bergvall", "given": "K", "initials": "K"}, {"family": "Olsson", "given": "M", "initials": "M", "orcid": "0000-0002-7228-2575", "researcher": {"href": "https://publications.scilifelab.se/researcher/a544f6e122da4b1ebf7a2ad70fd5bceb.json"}}, {"family": "Ardesj\u00f6-Lundgren", "given": "B", "initials": "B"}, {"family": "Farias", "given": "F H G", "initials": "FHG", "orcid": "0000-0002-5215-7304", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b8a07dda61d4fc3a3f837cdb5dbcd5a.json"}}, {"family": "Kierczak", "given": "M", "initials": "M", "orcid": "0000-0003-2629-5655", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c13f96fb81f4ae2bfff5e91ac45388e.json"}}, {"family": "Hedhammar", "given": "\u00c5", "initials": "\u00c5", "orcid": "0000-0001-7048-3851", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa01be589a4b4939a01c06ad57bfc356.json"}}, {"family": "Lindblad-Toh", "given": "K", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Andersson", "given": "G", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Immunogenetics", "issn": "1432-1211", "volume": "72", "issue": "5", "pages": "315-323", "issn-l": "0093-7711"}, "abstract": "Canine atopic dermatitis (CAD) is an inflammatory and pruritic allergic skin disease with both genetic and environmental risk factors described. We performed mRNA sequencing of non-lesional axillary skin biopsies from nine German shepherd dogs. Obtained RNA sequences were mapped to the dog genome (CanFam3.1) and a high-quality skin transcriptome was generated with 23,510 expressed gene transcripts. Differentially expressed genes (DEGs) were defined by comparing three controls to five treated CAD cases. Using a leave-one-out analysis, we identified seven DEGs: five known to encode proteins with functions related to an activated immune system (CD209, CLEC4G, LOC102156842 (lipopolysaccharide-binding protein-like), LOC480601 (regakine-1-like), LOC479668 (haptoglobin-like)), one (OBP) encoding an odorant-binding protein potentially connected to rhinitis, and the last (LOC607095) encoding a novel long non-coding RNA. Furthermore, high mRNA expression of inflammatory genes was found in axillary skin from an untreated mild CAD case compared with healthy skin. In conclusion, we define genes with different expression patterns in CAD case skin helping us understand post-treatment atopic skin. Further studies in larger sample sets are warranted to confirm and to transfer these results into clinical practice.", "doi": "10.1007/s00251-020-01169-3", "pmid": "32556497", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1007/s00251-020-01169-3"}, {"db": "pmc", "key": "PMC7320941"}], "notes": [], "created": "2020-07-03T05:20:56.396Z", "modified": "2024-01-16T13:48:42.253Z"}]}