{"entity": "researcher", "timestamp": "2026-07-13T09:31:49.944Z", "family": "Guerrero-Bosagna", "given": "Carlos M", "initials": "CM", "orcid": "0000-0003-1935-5875", "affiliations": ["AVIAN Behavioural Genomics and Physiology Group, Link\u00f6ping University, Link\u00f6ping, Sweden.", "Evolutionary Biology Centrum, Dept of Organismal Biology, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669"}}, "publications": [{"entity": "publication", "iuid": "9e4daf0046b8477fbc62333829667614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e4daf0046b8477fbc62333829667614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e4daf0046b8477fbc62333829667614"}}, "title": "Epigenetic changes as regulatory mechanism for the expression of life history stages in Zonotrichia capensis inhabiting an aseasonal environment", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Gonzalez\u2010 Gomez", "given": "Paulina L", "initials": "PL", "orcid": "0000-0002-1219-8881", "researcher": {"href": "https://publications.scilifelab.se/researcher/636c42cfcc1f46c4bc83ffaa6f99c597.json"}}, {"family": "Wingfield", "given": "John C", "initials": "JC"}, {"family": "Guerrero\u2010Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal-article", "published": "2026-05-00", "journal": {"title": "Journal of Avian Biology", "issn": "0908-8857", "volume": "2026", "issue": "3", "issn-l": null}, "abstract": null, "doi": "10.1002/jav.03516", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-06-01T11:10:53.812Z", "modified": "2026-06-01T11:10:54.000Z"}, {"entity": "publication", "iuid": "6af44bc75c7b4fe19763db841169ec45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6af44bc75c7b4fe19763db841169ec45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6af44bc75c7b4fe19763db841169ec45"}}, "title": "Genetic and neuro-epigenetic effects of divergent artificial selection for feather pecking behaviour in chickens.", "authors": [{"family": "de Haas", "given": "Elske N", "initials": "EN"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Kjaer", "given": "Joergen B", "initials": "JB"}, {"family": "Jensen", "given": "Per", "initials": "P", "orcid": "0000-0001-5491-0649", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83892cd7d6a46898629107a11205254.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal article", "published": "2024-12-19", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "1219", "issn-l": "1471-2164"}, "abstract": "Feather pecking (FP) is a repetitive behaviour in chickens, influenced by genetic, epigenetic, and environmental factors, similar to behaviours seen in human developmental disorders (e.g., hyperactivity, autism). This study examines genetic and neuro-epigenetic factors in the thalamus of chickens from lines selected for seven generations for high or low FP behaviour (HFP or LFP). We integrate data on Differentially Methylated Regions (DMRs), Single Nucleotide Polymorphisms (SNPs), and Copy Number Variations (CNVs) in this controlled artificial selection process. Significant differences in behaviour, immunology, and neurology have been reported in these lines. We identified 710 SNPs in these lines that indicate new potentially important genes for FP such as TMPRSS6 (implicated in autism), and SST and ARNT2 (somatostatin function). CNV were the omic level most affected during selection. The largest CNVs found were in RIC3 (gain in HFP) and SH3RF2 (gain in LFP) genes, linked to nicotinic acetylcholine receptor regulation and human oncogenesis, respectively. Our study also suggests that promoters and introns are hotspots for CpG depletion. The overlapping of the omic levels investigated here with data from a public FP Quantitative Trait Loci (QTL) database revealed novel candidate genes for understanding repetitive behaviours, such as RTKN2, associated with Alzheimer's disease in humans. This study suggests CNVs as a crucial initial step for genomic diversification, potentially more impactful than SNPs.", "doi": "10.1186/s12864-024-11137-w", "pmid": "39702044", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11657628"}, {"db": "pii", "key": "10.1186/s12864-024-11137-w"}], "notes": [], "created": "2025-02-28T14:22:16.646Z", "modified": "2025-04-07T07:29:14.100Z"}, {"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": "93379f5a15c7458fac70fdb76edbaee8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93379f5a15c7458fac70fdb76edbaee8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93379f5a15c7458fac70fdb76edbaee8"}}, "title": "Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification.", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Da Silva", "given": "Vinicius H", "initials": "VH"}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Lindstr\u00f6m", "given": "Tom", "initials": "T", "orcid": "0000-0001-7856-2925", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a619b495eed4a41a65f2bc7a3c7c5dc.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Coutinho", "given": "Luiz L", "initials": "LL"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "14", "issn": "1559-2308", "issue": "7", "pages": "685-707", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic 'flexibility' in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic 'specificity' in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.", "doi": "10.1080/15592294.2019.1609868", "pmid": "31070073", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6557589"}], "notes": [], "created": "2020-01-08T12:39:10.372Z", "modified": "2021-06-18T14:18:18.038Z"}]}