{"entity": "researcher", "timestamp": "2026-07-20T01:31:24.168Z", "family": "Isaksson", "given": "Caroline", "initials": "C", "orcid": "0000-0002-6889-1386", "affiliations": ["Evolutionary Ecology, Biology Department Lund University Lund Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/30ddbca044f64cb1b1feef58baf539ba.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/30ddbca044f64cb1b1feef58baf539ba"}}, "publications": [{"entity": "publication", "iuid": "0e37ae638f8a41589a54a60d69ead29f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e37ae638f8a41589a54a60d69ead29f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e37ae638f8a41589a54a60d69ead29f"}}, "title": "Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe.", "authors": [{"family": "Salm\u00f3n", "given": "Pablo", "initials": "P", "orcid": "0000-0001-9718-6611", "researcher": {"href": "https://publications.scilifelab.se/researcher/b60bfa8b60174680a1546f283c2ccbc1.json"}}, {"family": "Jacobs", "given": "Arne", "initials": "A", "orcid": "0000-0001-7635-5447", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c375694c76e48279bdc6e7dcc2808a6.json"}}, {"family": "Ahr\u00e9n", "given": "Dag", "initials": "D"}, {"family": "Biard", "given": "Clotilde", "initials": "C", "orcid": "0000-0001-7474-5345", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f2845cc669e41f38f4abc7be2d749c2.json"}}, {"family": "Dingemanse", "given": "Niels J", "initials": "NJ", "orcid": "0000-0003-3320-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/364e2f2173244470bc7f9c1feff13bc9.json"}}, {"family": "Dominoni", "given": "Davide M", "initials": "DM", "orcid": "0000-0003-2063-9955", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5c5e5b23a174cecb550e7a68cd0b0d7.json"}}, {"family": "Helm", "given": "Barbara", "initials": "B", "orcid": "0000-0002-6648-1463", "researcher": {"href": "https://publications.scilifelab.se/researcher/54eeba33656a4e44a2a8281b9a1d9c6d.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M"}, {"family": "Senar", "given": "Juan Carlos", "initials": "JC", "orcid": "0000-0001-9955-3892", "researcher": {"href": "https://publications.scilifelab.se/researcher/9acb6c1702bf4ce88d24eb8a35b39ae3.json"}}, {"family": "Sprau", "given": "Philipp", "initials": "P"}, {"family": "Visser", "given": "Marcel E", "initials": "ME", "orcid": "0000-0002-1456-1939", "researcher": {"href": "https://publications.scilifelab.se/researcher/87e0c4d6e845447ab627a26c7d12d989.json"}}, {"family": "Isaksson", "given": "Caroline", "initials": "C", "orcid": "0000-0002-6889-1386", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ddbca044f64cb1b1feef58baf539ba.json"}}], "type": "journal article", "published": "2021-05-20", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "2983", "issn-l": "2041-1723"}, "abstract": "Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.", "doi": "10.1038/s41467-021-23027-w", "pmid": "34016968", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-23027-w"}, {"db": "pmc", "key": "PMC8137928"}], "notes": [], "created": "2021-12-10T09:50:47.664Z", "modified": "2021-12-10T09:50:47.897Z"}, {"entity": "publication", "iuid": "f5bd5ff4af6e4311aaa2b84a04fff62b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5bd5ff4af6e4311aaa2b84a04fff62b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5bd5ff4af6e4311aaa2b84a04fff62b"}}, "title": "Urbanization is associated with modifications in DNA methylation in a small passerine bird.", "authors": [{"family": "Watson", "given": "Hannah", "initials": "H", "orcid": "0000-0003-4656-0647", "researcher": {"href": "https://publications.scilifelab.se/researcher/897ef477ef2e4fa290cb67b245bdf3f5.json"}}, {"family": "Powell", "given": "Daniel", "initials": "D", "orcid": "0000-0001-6323-7791", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8bd7fa790f9432d9d61cc1ab8d9b2d8.json"}}, {"family": "Salm\u00f3n", "given": "Pablo", "initials": "P", "orcid": "0000-0001-9718-6611", "researcher": {"href": "https://publications.scilifelab.se/researcher/b60bfa8b60174680a1546f283c2ccbc1.json"}}, {"family": "Jacobs", "given": "Arne", "initials": "A", "orcid": "0000-0001-7635-5447", "researcher": {"href": "https://publications.scilifelab.se/researcher/7c375694c76e48279bdc6e7dcc2808a6.json"}}, {"family": "Isaksson", "given": "Caroline", "initials": "C", "orcid": "0000-0002-6889-1386", "researcher": {"href": "https://publications.scilifelab.se/researcher/30ddbca044f64cb1b1feef58baf539ba.json"}}], "type": "journal article", "published": "2021-01-00", "journal": {"title": "Evol Appl", "issn": "1752-4571", "volume": "14", "issue": "1", "pages": "85-98", "issn-l": "1752-4571"}, "abstract": "Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome-wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban- and forest-dwelling birds were over-represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over-represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban- and forest-dwelling birds were under-represented in regulatory regions, more likely to occur in nonexpressed genes and not over-represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.", "doi": "10.1111/eva.13160", "pmid": "33519958", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "EVA13160"}, {"db": "pmc", "key": "PMC7819559"}], "notes": [], "created": "2021-02-02T12:30:56.264Z", "modified": "2024-01-16T13:48:40.994Z"}]}