{"entity": "researcher", "timestamp": "2026-08-08T16:12:12.797Z", "family": "Hasselquist", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0056-6616", "affiliations": ["Department of Biology, Lund University, Lund, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb"}}, "publications": [{"entity": "publication", "iuid": "411c02d828c14370a99a8a2b57b28e22", "links": {"self": {"href": "https://publications.scilifelab.se/publication/411c02d828c14370a99a8a2b57b28e22.json"}, "display": {"href": "https://publications.scilifelab.se/publication/411c02d828c14370a99a8a2b57b28e22"}}, "title": "Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Ponnikas", "given": "Suvi", "initials": "S", "orcid": "0000-0003-3526-2118", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ddd324bbfbb4833b25ba6dfe4c7dcb4.json"}}, {"family": "Hasselquist", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0056-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2024-09-04", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "volume": "14", "issue": "9", "issn-l": "2160-1836"}, "abstract": "Recombination plays a crucial role in evolution by generating novel haplotypes and disrupting linkage between genes, thereby enhancing the efficiency of selection. Here, we analyze the genomes of 12 great reed warblers (Acrocephalus arundinaceus) in a 3-generation pedigree to identify precise crossover positions along the chromosomes. We located more than 200 crossovers and found that these were highly concentrated toward the telomeric ends of the chromosomes. Apart from this major pattern in the recombination landscape, we found significantly higher frequencies of crossovers in genic compared with intergenic regions, and in exons compared with introns. Moreover, while the number of recombination events was similar between the sexes, the crossovers were located significantly closer to the ends of paternal compared with maternal chromosomes. In conclusion, our study of the great reed warbler revealed substantial variation in crossover frequencies within chromosomes, with a distinct bias toward the sub-telomeric regions, particularly on the paternal side. These findings emphasize the importance of thoroughly screening the entire length of chromosomes to characterize the recombination landscape and uncover potential sex-biases in recombination.", "doi": "10.1093/g3journal/jkae150", "pmid": "38985659", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11373659"}, {"db": "pii", "key": "7710635"}], "notes": [], "created": "2024-10-21T11:19:13.917Z", "modified": "2024-11-25T10:23:45.131Z"}, {"entity": "publication", "iuid": "f361c17689bc48929bd23e7d629f9f1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f361c17689bc48929bd23e7d629f9f1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f361c17689bc48929bd23e7d629f9f1b"}}, "title": "Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird.", "authors": [{"family": "Zhang", "given": "Hongkai", "initials": "H", "orcid": "0000-0001-7371-9612", "researcher": {"href": "https://publications.scilifelab.se/researcher/33b4db2c681b400c9106f8d27b6fb714.json"}}, {"family": "Lundberg", "given": "Max", "initials": "M", "orcid": "0000-0002-1895-3622", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b6a6dafa8fe4371ab26ed02ca5a550c.json"}}, {"family": "Tarka", "given": "Maja", "initials": "M", "orcid": "0000-0001-9651-1101", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a0abfbfc5bb4d5fb77f356c6ad80a34.json"}}, {"family": "Hasselquist", "given": "Dennis", "initials": "D", "orcid": "0000-0002-0056-6616", "researcher": {"href": "https://publications.scilifelab.se/researcher/73a24d358af64f22b81735f577c33bbb.json"}}, {"family": "Hansson", "given": "Bengt", "initials": "B", "orcid": "0000-0001-6694-8169", "researcher": {"href": "https://publications.scilifelab.se/researcher/01f0144e207c41dcbc4d5aec68690e4b.json"}}], "type": "journal article", "published": "2023-11-01", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "15", "issue": "11", "issn-l": "1759-6653"}, "abstract": "Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 \u00d7 10-9 mutations per site per generation (m/s/g) for the autosomes and 5.10 \u00d7 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.", "doi": "10.1093/gbe/evad180", "pmid": "37793164", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10627410"}, {"db": "pii", "key": "7289221"}], "notes": [], "created": "2023-11-29T10:54:38.925Z", "modified": "2024-01-16T13:48:31.754Z"}]}