{"entity": "researcher", "timestamp": "2026-09-09T10:14:17.313Z", "family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c"}}, "publications": [{"entity": "publication", "iuid": "4cbaa979b3cc49c3bb40ccc04b73b5a0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4cbaa979b3cc49c3bb40ccc04b73b5a0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4cbaa979b3cc49c3bb40ccc04b73b5a0"}}, "title": "The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts", "authors": [{"family": "Guinet", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-9922-2118", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c17993b1fc0450eb9808706576983eb.json"}}, {"family": "Sharif", "given": "Bilal Muhammad", "initials": "BM", "orcid": "0000-0002-0581-0542", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2deb1c150e3942dfbb9b33c7b875dd21.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}], "type": "posted-content", "published": "2025-07-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.07.16.665190", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:06:33.990Z", "modified": "2026-08-20T11:06:34.096Z"}, {"entity": "publication", "iuid": "dbd9f08cebd64013a251af7cb65f8352", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dbd9f08cebd64013a251af7cb65f8352.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dbd9f08cebd64013a251af7cb65f8352"}}, "title": "Disinfecting eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data", "authors": [{"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}, {"family": "Jin", "given": "Chenyu", "initials": "C", "orcid": "0000-0002-2392-7090", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afcc4905564e41868967d9cfef968b07.json"}}, {"family": "Clinton", "given": "Samantha L\u00f3pez", "initials": "SL", "orcid": "0000-0003-1364-9135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb3097a7dd3342e6ae0d1532ae0d18f3.json"}}, {"family": "Guinet", "given": "Benjamin", "initials": "B", "orcid": "0000-0002-9922-2118", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4c17993b1fc0450eb9808706576983eb.json"}}, {"family": "Wijnands", "given": "Flore", "initials": "F", "orcid": "0009-0009-6254-8964", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/557893083c5a469ea1285294e2a2ac3a.json"}}, {"family": "Johnson", "given": "Ernst", "initials": "E", "orcid": "0009-0004-0745-2437", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ff7522013ba43ebb1fe72b5e3d4037d.json"}}, {"family": "Kutschera", "given": "Verena E", "initials": "VE", "orcid": "0000-0002-8930-534X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c7185df2f7d44872960d604e9c70c551.json"}}, {"family": "Kinsella", "given": "Cormac M", "initials": "CM", "orcid": "0000-0001-9865-4608", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/772bfbaa9ca14161980526ba81082d3c.json"}}, {"family": "Heintzman", "given": "Peter D", "initials": "PD", "orcid": "0000-0002-6449-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/54774bc7db094262b111c5245207579f.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}], "type": "posted-content", "published": "2025-03-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2025.03.19.644176", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:01:37.613Z", "modified": "2026-08-20T11:01:37.948Z"}, {"entity": "publication", "iuid": "f5e0c130e1784f818079a60a79ae857f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f5e0c130e1784f818079a60a79ae857f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f5e0c130e1784f818079a60a79ae857f"}}, "title": "aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow", "authors": [{"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86bda59888834d6889a108f8abbdb0fa.json"}}, {"family": "Bergfeldt", "given": "Nora", "initials": "N", "orcid": "0000-0003-2767-8156", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9141014a18c54129b99af1006ff76f9b.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E", "orcid": "0000-0003-0500-1208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a60c96525a642b4be97e15a53de250b.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70f79b138afe4df99b780eb97ebdbc13.json"}}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE", "orcid": "0000-0003-0653-4292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f06df27a24874d5e9b11db34a31730d1.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02faff0c060a4c25a13a9c7556dd30c3.json"}}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff87fd5aabe4a38954dd96d8e6c261d.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c4e61575ab14fe3aa59190a82521921.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4ca88bb3cf24e2591c447ec929502e6.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dae455224d4af4a35865907088f0b1.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}], "type": "journal-article", "published": "2023-10-23", "journal": {"title": "Genome Biol.", "issn": "1474-760X", "issn-l": "1474-7596", "volume": "24", "issue": "1", "pages": "242"}, "abstract": "Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.", "doi": "10.1186/s13059-023-03083-9", "pmid": "37872569", "labels": {"Tom van der Valk": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10591440"}, {"db": "pii", "key": "10.1186/s13059-023-03083-9"}], "notes": [], "created": "2022-12-02T13:45:21.283Z", "modified": "2025-12-04T16:53:57.886Z"}, {"entity": "publication", "iuid": "05f038f754da4f4781f21a4937cf7db3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/05f038f754da4f4781f21a4937cf7db3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/05f038f754da4f4781f21a4937cf7db3"}}, "title": "Ghost admixture in eastern gorillas", "authors": [{"family": "Pawar", "given": "Harvinder", "initials": "H", "orcid": "0000-0002-3852-4999", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1eab80604aac428f880af679461e32ac.json"}}, {"family": "Rymbekova", "given": "Aigerim", "initials": "A"}, {"family": "Cuadros", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-6240-281X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a56b2cee5df84075abf3a87573937347.json"}}, {"family": "Huang", "given": "Xin", "initials": "X", "orcid": "0000-0002-9918-9602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/27a6d482c13b437a8ba45a652135aef7.json"}}, {"family": "de Manuel", "given": "Marc", "initials": "M", "orcid": "0000-0002-1245-0127", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/32a9a768dceb47d682d91f91799b35fa.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Lobon", "given": "Irene", "initials": "I"}, {"family": "Alvarez-Estape", "given": "Marina", "initials": "M", "orcid": "0000-0001-8242-1092", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92207dc6de3d4bfaa8614bcdb3738cfb.json"}}, {"family": "Haber", "given": "Marc", "initials": "M", "orcid": "0000-0003-1000-1448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f33d7d7019084d4c9973df74a53b58da.json"}}, {"family": "Dolgova", "given": "Olga", "initials": "O", "orcid": "0000-0001-5231-9388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51a65f7fb8544946b506f69b37b414b0.json"}}, {"family": "Han", "given": "Sojung", "initials": "S", "orcid": "0000-0002-6113-1042", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec6576ca2d1a480e8e5aec022199bcb5.json"}}, {"family": "Esteller-Cucala", "given": "Paula", "initials": "P", "orcid": "0000-0003-3048-4280", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/610f0a88c36a4acd80c59acbca72cc8a.json"}}, {"family": "Juan", "given": "David", "initials": "D", "orcid": "0000-0003-1912-9667", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/027154f54530486eac69b942138bc07f.json"}}, {"family": "Ayub", "given": "Qasim", "initials": "Q"}, {"family": "Bautista", "given": "Ruben", "initials": "R"}, {"family": "Kelley", "given": "Joanna L", "initials": "JL"}, {"family": "Cornejo", "given": "Omar E", "initials": "OE"}, {"family": "Lao", "given": "Oscar", "initials": "O", "orcid": "0000-0002-8525-9649", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f3a9334fa5dd44198f1cde45246d8480.json"}}, {"family": "Andr\u00e9s", "given": "Aida M", "initials": "AM", "orcid": "0000-0002-8590-9672", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58f57f8eb741498a95bcb05b3c9c7dd6.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e062373c6bc46b98e56215d3ec89eeb.json"}}, {"family": "Ssebide", "given": "Benard", "initials": "B"}, {"family": "Cranfield", "given": "Mike", "initials": "M"}, {"family": "Tyler-Smith", "given": "Chris", "initials": "C", "orcid": "0000-0002-6492-5403", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9c0139811de45f9bf0f31b69b31e846.json"}}, {"family": "Xue", "given": "Yali", "initials": "Y", "orcid": "0000-0002-4501-6909", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/367981d027d44ff9ba2c8ad927ca15e4.json"}}, {"family": "Prado-Martinez", "given": "Javier", "initials": "J", "orcid": "0000-0001-5402-2721", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43966b07053e4841948de2d54d41b2f3.json"}}, {"family": "Marques-Bonet", "given": "Tomas", "initials": "T", "orcid": "0000-0002-5597-3075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1091cb5bfe394d459969d24bb1c22c66.json"}}, {"family": "Kuhlwilm", "given": "Martin", "initials": "M", "orcid": "0000-0002-0115-1797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c21afe591ec14eeab27425b903e4db99.json"}}], "type": "posted-content", "published": "2022-12-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.12.19.521012", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:43:03.727Z", "modified": "2026-08-20T10:43:04.442Z"}, {"entity": "publication", "iuid": "df4795e44b4949ed85aa1a9c3a966746", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df4795e44b4949ed85aa1a9c3a966746.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df4795e44b4949ed85aa1a9c3a966746"}}, "title": "Genomic trajectories of a near-extinction event in the Chatham Island black robin.", "authors": [{"family": "von Seth", "given": "Johanna", "initials": "J"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Lord", "given": "Edana", "initials": "E"}, {"family": "Sigeman", "given": "Hanna", "initials": "H"}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Knapp", "given": "Michael", "initials": "M"}, {"family": "Kardailsky", "given": "Olga", "initials": "O"}, {"family": "Robertson", "given": "Fiona", "initials": "F"}, {"family": "Hale", "given": "Marie", "initials": "M"}, {"family": "Houston", "given": "Dave", "initials": "D"}, {"family": "Kennedy", "given": "Euan", "initials": "E"}, {"family": "Dal\u00e9n", "given": "Love", "initials": "L"}, {"family": "Nor\u00e9n", "given": "Karin", "initials": "K"}, {"family": "Massaro", "given": "Melanie", "initials": "M"}, {"family": "Robertson", "given": "Bruce C", "initials": "BC"}, {"family": "Dussex", "given": "Nicolas", "initials": "N"}], "type": "journal article", "published": "2022-11-10", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "23", "issue": "1", "pages": "747", "issn-l": "1471-2164"}, "abstract": "Understanding the micro--evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.\n\nWe found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.\n\nOur results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.", "doi": "10.1186/s12864-022-08963-1", "pmid": "36357860", "labels": {"Tom van der Valk": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC9647977"}, {"db": "pii", "key": "10.1186/s12864-022-08963-1"}], "notes": [], "created": "2022-12-02T13:45:19.103Z", "modified": "2025-04-29T07:05:08.598Z"}, {"entity": "publication", "iuid": "76358c9d2a394794ad8a06a269f1bca3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/76358c9d2a394794ad8a06a269f1bca3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/76358c9d2a394794ad8a06a269f1bca3"}}, "title": "aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow", "authors": [{"family": "Pochon", "given": "Zo\u00e9", "initials": "Z", "orcid": "0000-0001-7981-5795", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/86bda59888834d6889a108f8abbdb0fa.json"}}, {"family": "Bergfeldt", "given": "Nora", "initials": "N", "orcid": "0000-0003-2767-8156", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9141014a18c54129b99af1006ff76f9b.json"}}, {"family": "K\u0131rd\u00f6k", "given": "Emrah", "initials": "E", "orcid": "0000-0003-0500-1208", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3a60c96525a642b4be97e15a53de250b.json"}}, {"family": "Vicente", "given": "M\u00e1rio", "initials": "M", "orcid": "0000-0002-9122-4530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/70f79b138afe4df99b780eb97ebdbc13.json"}}, {"family": "Naidoo", "given": "Thijessen", "initials": "T"}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Alt\u0131n\u0131\u015f\u0131k", "given": "N Ezgi", "initials": "NE", "orcid": "0000-0003-0653-4292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f06df27a24874d5e9b11db34a31730d1.json"}}, {"family": "Krzewi\u0144ska", "given": "Maja", "initials": "M", "orcid": "0000-0002-6702-8724", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02faff0c060a4c25a13a9c7556dd30c3.json"}}, {"family": "Dalen", "given": "Love", "initials": "L", "orcid": "0000-0001-6307-8188", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6ff87fd5aabe4a38954dd96d8e6c261d.json"}}, {"family": "G\u00f6therstr\u00f6m", "given": "Anders", "initials": "A", "orcid": "0000-0001-8579-1304", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0c4e61575ab14fe3aa59190a82521921.json"}}, {"family": "Mirabello", "given": "Claudio", "initials": "C", "orcid": "0000-0001-7868-034X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4ca88bb3cf24e2591c447ec929502e6.json"}}, {"family": "Unneberg", "given": "Per", "initials": "P", "orcid": "0000-0001-5735-3315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47dae455224d4af4a35865907088f0b1.json"}}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c448f1b878442c687d58549f90ba4e9.json"}}], "type": "posted-content", "published": "2022-10-05", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.10.03.510579", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:41:14.984Z", "modified": "2026-08-20T10:41:15.936Z"}, {"entity": "publication", "iuid": "8c142158f5404cbdbaa3962fe7825832", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8c142158f5404cbdbaa3962fe7825832.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8c142158f5404cbdbaa3962fe7825832"}}, "title": "Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.", "authors": [{"family": "Hooper", "given": "Rebecca", "initials": "R"}, {"family": "Brealey", "given": "Jaelle C", "initials": "JC", "orcid": "0000-0001-7068-2017", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/94980a28c68b44c8a2c709ac6a4c6dc7.json"}}, {"family": "van der Valk", "given": "Tom", "initials": "T", "orcid": "0000-0001-6582-3452", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa0dba3cc12143cba213f7f3a052216c.json"}}, {"family": "Alberdi", "given": "Antton", "initials": "A", "orcid": "0000-0002-2875-6446", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7db6c63c5480449c8791411cffa3b2a5.json"}}, {"family": "Durban", "given": "John W", "initials": "JW"}, {"family": "Fearnbach", "given": "Holly", "initials": "H"}, {"family": "Robertson", "given": "Kelly M", "initials": "KM", "orcid": "0000-0002-0090-8604", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd34e649cf2148a382009e97594c4d9a.json"}}, {"family": "Baird", "given": "Robin W", "initials": "RW"}, {"family": "Bradley Hanson", "given": "M", "initials": "M"}, {"family": "Wade", "given": "Paul", "initials": "P"}, {"family": "Gilbert", "given": "M Thomas P", "initials": "MTP"}, {"family": "Morin", "given": "Phillip A", "initials": "PA", "orcid": "0000-0002-3279-1519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6068e888748e4995b6e7f2d39702c8b0.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW"}, {"family": "Foote", "given": "Andrew D", "initials": "AD", "orcid": "0000-0001-7384-1634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d685d768b18a41b6ae4ece4569cb99b7.json"}}, {"family": "Guschanski", "given": "Katerina", "initials": "K", "orcid": "0000-0002-8493-5457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e062373c6bc46b98e56215d3ec89eeb.json"}}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "28", "issue": "2", "pages": "484-502", "issn-l": "0962-1083"}, "abstract": "Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.", "doi": "10.1111/mec.14860", "pmid": "30187987", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6487819"}, {"db": "GENBANK", "key": "ERS554424"}, {"db": "GENBANK", "key": "ERS554471"}, {"db": "GENBANK", "key": "ANOL00000000.2"}], "notes": [], "created": "2026-08-20T11:18:52.996Z", "modified": "2026-08-20T11:18:53.273Z"}]}