{"entity": "researcher", "timestamp": "2026-08-09T07:03:08.723Z", "family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "affiliations": ["AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Link\u00f6ping University, 58183 Link\u00f6ping, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241"}}, "publications": [{"entity": "publication", "iuid": "355af91bf856401ab8f7a654af8b92ad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/355af91bf856401ab8f7a654af8b92ad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/355af91bf856401ab8f7a654af8b92ad"}}, "title": "Multi-layered dosage compensation of the avian Z chromosome by increased transcriptional burst frequency and elevated translational rates.", "authors": [{"family": "Papanicolaou", "given": "Natali", "initials": "N", "orcid": "0000-0002-2931-3241", "researcher": {"href": "https://publications.scilifelab.se/researcher/439a0a25106742c893178f4151d71291.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications.scilifelab.se/researcher/e282901d24c64b16a540eff0d57776f4.json"}}, {"family": "Wettersten", "given": "Sebastian", "initials": "S"}, {"family": "Hagemann-Jensen", "given": "Michael", "initials": "M", "orcid": "0000-0002-6423-8216", "researcher": {"href": "https://publications.scilifelab.se/researcher/26cb45960bd042c498f4914a342312a0.json"}}, {"family": "Kr\u00fcger", "given": "Annika", "initials": "A", "orcid": "0000-0002-2482-0316", "researcher": {"href": "https://publications.scilifelab.se/researcher/74e46d93b561473189588abecdb96f93.json"}}, {"family": "Zhang", "given": "Jilin", "initials": "J", "orcid": "0000-0002-9976-1605", "researcher": {"href": "https://publications.scilifelab.se/researcher/b595931cc9c045dbbeb2dba7f3913d05.json"}}, {"family": "Coucoravas", "given": "Christos", "initials": "C"}, {"family": "Petrosian", "given": "Ioannis", "initials": "I"}, {"family": "Xin", "given": "Xian", "initials": "X", "orcid": "0000-0003-1460-5978", "researcher": {"href": "https://publications.scilifelab.se/researcher/612e837e68e44339b8a9a110beb38125.json"}}, {"family": "Ceyhan", "given": "Ilhan", "initials": "I", "orcid": "0009-0001-9504-6647", "researcher": {"href": "https://publications.scilifelab.se/researcher/c79c334d1b6747159586eca778e2f2df.json"}}, {"family": "Rorbach", "given": "Joanna", "initials": "J", "orcid": "0000-0002-2891-2840", "researcher": {"href": "https://publications.scilifelab.se/researcher/a069374613a7403b818ce7ca400f3627.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb82c502293d424cb266e1c4e405485f.json"}}], "type": "journal article", "published": "2025-10-13", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "9088", "issn-l": "2041-1723"}, "abstract": "Sex-chromosome dosage poses a challenge for heterogametic species in maintaining the proper balance of gene products across chromosomes in each sex. While therian mammals (XX/XY system) achieve near-perfect balance of X-chromosome mRNAs through X-upregulation and X-inactivation, birds (ZW/ZZ system) have been found to lack efficient compensation at RNA level, challenging the necessity of resolving major gene-dosage asymmetries in avian cells. Through comprehensive allele-resolved multiome analyses, we examine dosage compensation in female (ZW), male (ZZ), and rare intersex (ZZW) chicken. Our data reveal that females upregulate their single Z chromosome through increased transcriptional burst frequency, mirroring mammalian X upregulation. Z-protein levels are further balanced in females through enhanced translation efficiency. Additionally, we present a global analysis of promoter elements regulating transcriptional burst kinetics in birds, revealing evolutionary conservation of the genomic encoding of burst kinetics between birds and mammals. Our study provides insights into the regulation of avian dosage compensation, and when considering all regulatory layers collectively, an unexpected similarity between avian and mammalian dosage compensation becomes apparent.", "doi": "10.1038/s41467-025-64817-w", "pmid": "41083481", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12518621"}, {"db": "pii", "key": "10.1038/s41467-025-64817-w"}], "notes": [], "created": "2025-12-08T12:39:47.612Z", "modified": "2025-12-08T12:39:48.467Z"}, {"entity": "publication", "iuid": "5b6d8c72800145a294f1fab88be77e43", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b6d8c72800145a294f1fab88be77e43.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b6d8c72800145a294f1fab88be77e43"}}, "title": "Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication-Related Brain Composition.", "authors": [{"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F"}, {"family": "Moradinour", "given": "Zahra", "initials": "Z"}, {"family": "Katajama", "given": "Rebecca", "initials": "R"}, {"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML", "orcid": "0000-0003-3952-2853", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e025902fc04455ad70a33ba146c003.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2025-05-19", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "pages": "e17788", "issn-l": "0962-1083"}, "abstract": "Domestication involves huge phenotypic shifts via strong directional selection. The resulting changes, often termed the Domestication Syndrome, typically encompass numerous traits; however, the most universal of these are changes in reduced fear of humans (tameness) and brain composition. To assess how early domestication selection may have focused on tameness and its interaction with brain composition, a Red Junglefowl (Gallus gallus) population (the wild progenitor of the domestic chicken) was used to create two lines bidirectionally selected for fear of humans over eight generations of selection. These selection lines were then used to make an intercross population. Using a combination of genome-wide mapping in the intercross and between-line analysis of the selection lines, we show that the genetic loci for tameness co-localise with genetic loci for brain composition and anxiety behaviour. Furthermore, the detected loci for brain composition also co-localise with brain composition loci identified in a separate wild \u00d7 domestic intercross. These results indicate that tameness and brain composition are either pleiotropic or genetically linked, and that tameness selection appears to recapitulate the same loci that have been selected by domestication itself. Therefore, selection for increased tameness could be the initial selection pressure driving the core of the domestication syndrome.", "doi": "10.1111/mec.17788", "pmid": "40386851", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T11:37:29.894Z", "modified": "2025-11-28T10:51:37.135Z"}, {"entity": "publication", "iuid": "0d08036c5f154cf0b2c0036250a0fa7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0d08036c5f154cf0b2c0036250a0fa7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0d08036c5f154cf0b2c0036250a0fa7e"}}, "title": "The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken.", "authors": [{"family": "H\u00f6glund", "given": "Andrey", "initials": "A", "orcid": "0000-0002-1130-374X", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a484451caf40f2a1a196b36bb9c423.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Churcher", "given": "Allison M", "initials": "AM", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos M", "initials": "CM"}, {"family": "Martinez-Barrio", "given": "Alvaro", "initials": "A", "orcid": "0000-0001-5064-2093", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ff319fe64340f2bb2350121848ecff.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M", "orcid": "0000-0003-1262-4585", "researcher": {"href": "https://publications.scilifelab.se/researcher/02b768197c08422aaad526f35c526eaf.json"}}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "20", "issue": "3", "pages": "e1010719", "issn-l": "1553-7390"}, "abstract": "DNA methylation is a key regulator of eukaryote genomes, and is of particular relevance in the regulation of gene expression on the sex chromosomes, with a key role in dosage compensation in mammalian XY systems. In the case of birds, dosage compensation is largely absent, with it being restricted to two small Male Hyper-Methylated (MHM) regions on the Z chromosome. To investigate how variation in DNA methylation is regulated on the Z chromosome we utilised a wild x domestic advanced intercross in the chicken, with both hypothalamic methylomes and transcriptomes assayed in 124 individuals. The relatively large numbers of individuals allowed us to identify additional genomic MHM regions on the Z chromosome that were significantly differentially methylated between the sexes. These regions appear to down-regulate local gene expression in males, but not remove it entirely (unlike the lncRNAs identified in the initial MHM regions). These MHM regions were further tested and the most balanced genes appear to show decreased expression in males, whilst methylation appeared to be far more correlated with gene expression in the less balanced, as compared to the most balanced genes. In addition, quantitative trait loci (QTL) that regulate variation in methylation on the Z chromosome, and those loci that regulate methylation on the autosomes that derive from the Z chromosome were mapped. Trans-effect hotspots were also identified that were based on the autosomes but affected the Z, and also one that was based on the Z chromosome but that affected both autosomal and sex chromosome DNA methylation regulation. We show that both cis and trans loci that originate from the Z chromosome never exhibit an interaction with sex, whereas trans loci originating from the autosomes but affecting the Z chromosome always display such an interaction. Our results highlight how additional MHM regions are actually present on the Z chromosome, and they appear to have smaller-scale effects on gene expression in males. Quantitative variation in methylation is also regulated both from the autosomes to the Z chromosome, and from the Z chromosome to the autosomes.", "doi": "10.1371/journal.pgen.1010719", "pmid": "38457441", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10954189"}, {"db": "pii", "key": "PGENETICS-D-23-00328"}], "notes": [], "created": "2024-11-12T10:39:26.077Z", "modified": "2024-11-25T10:31:41.001Z"}, {"entity": "publication", "iuid": "0766864994cb473684058b77c01738ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0766864994cb473684058b77c01738ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0766864994cb473684058b77c01738ac"}}, "title": "Population structure and hybridisation in a population of Hawaiian feral chickens.", "authors": [{"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML", "orcid": "0000-0003-3952-2853", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e025902fc04455ad70a33ba146c003.json"}}, {"family": "L\u00f3pez", "given": "Saioa", "initials": "S", "orcid": "0000-0003-2936-4070", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc2378f261d1489cba776ae5426cbd0d.json"}}, {"family": "van Dorp", "given": "Lucy", "initials": "L", "orcid": "0000-0002-6211-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/40a0b4ff087f4c03af169b07eae84ece.json"}}, {"family": "Hellenthal", "given": "Garrett", "initials": "G"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Gering", "given": "Eben", "initials": "E", "orcid": "0000-0002-1270-6727", "researcher": {"href": "https://publications.scilifelab.se/researcher/24122f6cfea1415cb03db379203fbf14.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2023-03-00", "journal": {"title": "Heredity (Edinb)", "issn": "1365-2540", "volume": "130", "issue": "3", "pages": "154-162", "issn-l": "0018-067X"}, "abstract": "Chickens are believed to have inhabited the Hawaiian island of Kauai since the first human migrations around 1200AD, but numbers have peaked since the tropical storms Iniki and Iwa in the 1980s and 1990s that destroyed almost all the chicken coops on the island and released large numbers of domestic chickens into the wild. Previous studies have shown these now feral chickens are an admixed population between Red Junglefowl (RJF) and domestic chickens. Here, using genetic haplotypic data, we estimate the time of the admixture event between the feral population on the island and the RJF to 1981 (1976-1995), coinciding with the timings of storm Iwa and Iniki. Analysis of genetic structure reveals a greater similarity between individuals inhabiting the northern and western part of the island to RJF than individuals from the eastern part of the island. These results point to the possibility of introgression events between feral chickens and the wild chickens in areas surrounding the Koke'e State Park and the Alaka'i plateau, posited as two of the major RJF reservoirs in the island. Furthermore, we have inferred haplotype blocks from pooled data to determine the most plausible source of the feral population. We identify a clear contribution from RJF and layer chickens of the White Leghorn (WL) breed. This work provides independent confirmation of the traditional hypothesis surrounding the origin of the feral populations and draws attention to the possibility of introgression of domestic alleles into the wild reservoir.", "doi": "10.1038/s41437-022-00589-z", "pmid": "36725960", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9981564"}, {"db": "pii", "key": "10.1038/s41437-022-00589-z"}], "notes": [], "created": "2023-10-30T09:49:37.992Z", "modified": "2024-01-16T13:48:33.905Z"}, {"entity": "publication", "iuid": "75a1fcfdbb4d43ac9dab3cba90b8ece5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/75a1fcfdbb4d43ac9dab3cba90b8ece5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/75a1fcfdbb4d43ac9dab3cba90b8ece5"}}, "title": "Genomic and gene expression associations to morphology of a sexual ornament in the chicken.", "authors": [{"family": "Bakovic", "given": "Vid", "initials": "V", "orcid": "0000-0001-9506-5816", "researcher": {"href": "https://publications.scilifelab.se/researcher/613026a563c543c794e0094c0239920b.json"}}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML", "orcid": "0000-0003-3952-2853", "researcher": {"href": "https://publications.scilifelab.se/researcher/53e025902fc04455ad70a33ba146c003.json"}}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2022-08-25", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836", "volume": "12", "issue": "9", "pages": "jkac174"}, "abstract": "How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (>30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication.", "doi": "10.1093/g3journal/jkac174", "pmid": "35801935", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "6633936"}, {"db": "pmc", "key": "PMC9434260"}], "notes": [], "created": "2022-08-16T13:29:35.931Z", "modified": "2024-01-16T13:48:35.097Z"}, {"entity": "publication", "iuid": "9249d1bd183c4a2dbece43a7d7e1db47", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9249d1bd183c4a2dbece43a7d7e1db47.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9249d1bd183c4a2dbece43a7d7e1db47"}}, "title": "The genomics of phenotypically differentiated Asellus aquaticus cave, surface stream and lake ecotypes.", "authors": [{"family": "Bakovic", "given": "Vid", "initials": "V", "orcid": "0000-0001-9506-5816", "researcher": {"href": "https://publications.scilifelab.se/researcher/613026a563c543c794e0094c0239920b.json"}}, {"family": "Martin Cerezo", "given": "Maria Luisa", "initials": "ML"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Hargeby", "given": "Anders", "initials": "A"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "volume": "30", "issue": "14", "pages": "3530-3547", "issn-l": "0962-1083"}, "abstract": "Organisms well suited for the study of ecotype formation have wide distribution ranges, where they adapt to multiple drastically different habitats repeatedly over space and time. Here we study such ecotypes in a Crustacean model, Asellus aquaticus, a commonly occurring isopod found in freshwater habitats as diverse as streams, caves and lakes. Previous studies focusing on cave vs. surface ecotypes have attributed depigmentation, eye loss and prolonged antennae to several south European cave systems. Likewise, surveys across multiple Swedish lakes have identified the presence of dark-pigmented \"reed\" and light-pigmented \"stonewort\" ecotypes, which can be found within the same lake. In this study, we sequenced the first draft genome of A. aquaticus, and subsequently use this to map reads and call variants in surface stream, cave and two lake ecotypes. In addition, the draft genome was combined with a RADseq approach to perform a quantitative trait locus (QTL) mapping study using a laboratory bred F2 and F4 cave \u00d7 surface intercross. We identified genomic regions associated with body pigmentation, antennae length and body size. Furthermore, we compared genome-wide differentiation between natural populations and found several genes potentially associated with these habitats. The assessment of the cave QTL regions in the light-dark comparison of lake populations suggests that the regions associated with cave adaptation are also involved with genomic differentiation in the lake ecotypes. These demonstrate how troglomorphic adaptations can be used as a model for related ecotype formation.", "doi": "10.1111/mec.15987", "pmid": "34002902", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "Dryad", "key": "10.5061/dryad.2547d7wqj"}], "notes": [], "created": "2021-10-01T09:01:08.974Z", "modified": "2024-01-16T13:48:39.201Z"}, {"entity": "publication", "iuid": "d787ebed6379499b968ca423e460aa66", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d787ebed6379499b968ca423e460aa66.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d787ebed6379499b968ca423e460aa66"}}, "title": "The methylation landscape and its role in domestication and gene regulation in the chicken.", "authors": [{"family": "H\u00f6glund", "given": "Andrey", "initials": "A"}, {"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "Fogelholm", "given": "Jesper", "initials": "J"}, {"family": "Churcher", "given": "Allison M", "initials": "AM", "orcid": "0000-0003-1902-3002", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97e6fb500a043f08d4f882e802cd91b.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos M", "initials": "CM", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}, {"family": "Martinez-Barrio", "given": "Alvaro", "initials": "A", "orcid": "0000-0001-5064-2093", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6ff319fe64340f2bb2350121848ecff.json"}}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2020-12-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "4", "issue": "12", "pages": "1713-1724", "issn-l": "2397-334X"}, "abstract": "Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.", "doi": "10.1038/s41559-020-01310-1", "pmid": "32958860", "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-020-01310-1"}, {"db": "figshare", "key": "10.6084/m9.figshare.12803873"}, {"db": "figshare", "key": "10.6084/m9.figshare.12803876"}, {"db": "figshare", "key": "10.6084/m9.figshare.12803870"}], "notes": [], "created": "2020-09-25T11:36:26.073Z", "modified": "2024-01-16T13:48:41.219Z"}, {"entity": "publication", "iuid": "fdff2262424e46cc949c4ce71f7b8f59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fdff2262424e46cc949c4ce71f7b8f59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fdff2262424e46cc949c4ce71f7b8f59"}}, "title": "Intra-Individual Behavioural Variability: A Trait under Genetic Control.", "authors": [{"family": "Henriksen", "given": "Rie", "initials": "R"}, {"family": "H\u00f6glund", "given": "Andrey", "initials": "A", "orcid": "0000-0002-1130-374X", "researcher": {"href": "https://publications.scilifelab.se/researcher/70a484451caf40f2a1a196b36bb9c423.json"}}, {"family": "Fogelholm", "given": "Jesper", "initials": "J", "orcid": "0000-0002-0868-8722", "researcher": {"href": "https://publications.scilifelab.se/researcher/5dc8c561c04f437991504aca4c86593d.json"}}, {"family": "Abbey-Lee", "given": "Robin", "initials": "R"}, {"family": "Johnsson", "given": "Martin", "initials": "M"}, {"family": "Dingemanse", "given": "Niels J", "initials": "NJ", "orcid": "0000-0003-3320-0861", "researcher": {"href": "https://publications.scilifelab.se/researcher/364e2f2173244470bc7f9c1feff13bc9.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D", "orcid": "0000-0003-2329-2635", "researcher": {"href": "https://publications.scilifelab.se/researcher/6447b896ea3b453ab10136b5f44ae241.json"}}], "type": "journal article", "published": "2020-10-29", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "issn-l": null, "volume": "21", "issue": "21", "pages": "8069"}, "abstract": "When individuals are measured more than once in the same context they do not behave in exactly the same way each time. The degree of predictability differs between individuals, with some individuals showing low levels of variation around their behavioural mean while others show high levels of variation. This intra-individual variability in behaviour has received much less attention than between-individual variability in behaviour, and very little is known about the underlying mechanisms that affect this potentially large but understudied component of behavioural variation. In this study, we combine standardized behavioural tests in a chicken intercross to estimate intra-individual behavioural variability with a large-scale genomics analysis to identify genes affecting intra-individual behavioural variability in an avian population. We used a variety of different anxiety-related behavioural phenotypes for this purpose. Our study shows that intra-individual variability in behaviour has a direct genetic basis that is largely unique compared to the genetic architecture for the standard behavioural measures they are based on (at least in the detected quantitative trait locus). We identify six suggestive candidate genes that may underpin differences in intra-individual behavioural variability, with several of these candidates having previously been linked to behaviour and mental health. These findings demonstrate that intra-individual variability in behaviour appears to be a heritable trait in and of itself on which evolution can act.", "doi": "10.3390/ijms21218069", "pmid": "33138119", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "ijms21218069"}, {"db": "pmc", "key": "PMC7663371"}], "notes": [], "created": "2021-01-12T13:47:04.128Z", "modified": "2024-01-16T13:48:41.496Z"}]}