{"entity": "researcher", "timestamp": "2026-06-09T03:21:47.862Z", "family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "affiliations": ["Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden. j.wolf@biologie.uni-muenchen.de.", "Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany. j.wolf@biologie.uni-muenchen.de."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d"}}, "publications": [{"entity": "publication", "iuid": "d936680b828c47f8a2753c7de07ce0de", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d936680b828c47f8a2753c7de07ce0de.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d936680b828c47f8a2753c7de07ce0de"}}, "title": "DNA Methylation Reflects Cis-Genetic Differentiation Across the European Crow Hybrid Zone.", "authors": [{"family": "Merondun", "given": "Justin", "initials": "J", "orcid": "0000-0001-5077-4096", "researcher": {"href": "https://publications.scilifelab.se/researcher/38e6336366e1418685f36244f39ecde6.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}], "type": "journal article", "published": "2025-07-10", "journal": {"title": "Mol. Ecol.", "issn": "1365-294X", "issn-l": "0962-1083", "volume": "34", "issue": "21", "pages": "e70026"}, "abstract": "Chromatin modifications provide a substrate for epigenetic variation with evolutionary potential. To quantify the contribution of this layer of variation during speciation in crows, we leveraged genome and methylome sequencing data from an incipient avian species: all-black carrion crows, grey-coated hooded crows, and their hybrids. Combining controlled experimentation under common garden conditions and sampling of natural genetic variation across the hybrid zone, we show that 5mC methylation variation was largely explained by genome properties and the ontogenetic programme of the organism. Taxonomically related methylation divergence clustered in intergenic space, with the only genomic region of strongly elevated genetic differentiation encoding the diagnostic colour contrast between taxa. We conclude that methylation variation with relevance to speciation largely follows cis-genetic polymorphism in this system and does not constitute an autonomous axis of evolution.", "doi": "10.1111/mec.70026", "pmid": "40637207", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2025-09-08T06:59:29.504Z", "modified": "2025-11-03T08:42:37.319Z"}, {"entity": "publication", "iuid": "6aed2fd0f7a9458cb4150da23a7ab56d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6aed2fd0f7a9458cb4150da23a7ab56d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6aed2fd0f7a9458cb4150da23a7ab56d"}}, "title": "Experimental evolution of adaptive divergence under varying degrees of gene flow.", "authors": [{"family": "Tusso", "given": "Sergio", "initials": "S", "orcid": "0000-0002-0612-9230", "researcher": {"href": "https://publications.scilifelab.se/researcher/027fc05d9bd843afaa82aeecce0747e8.json"}}, {"family": "Nieuwenhuis", "given": "Bart P S", "initials": "BPS", "orcid": "0000-0001-8159-4784", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e3278c557ff403aa061ee99a8631d6e.json"}}, {"family": "Weissensteiner", "given": "Bernadette", "initials": "B"}, {"family": "Immler", "given": "Simone", "initials": "S"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}], "type": "journal article", "published": "2021-03-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "5", "issue": "3", "pages": "338-349", "issn-l": "2397-334X"}, "abstract": "Adaptive divergence is the key evolutionary process generating biodiversity by means of natural selection. Yet, the conditions under which it can arise in the presence of gene flow remain contentious. To address this question, we subjected 132 sexually reproducing fission yeast populations, sourced from two independent genetic backgrounds, to disruptive ecological selection and manipulated the level of migration between environments. Contrary to theoretical expectations, adaptive divergence was most pronounced when migration was either absent (allopatry) or maximal (sympatry), but was much reduced at intermediate rates (parapatry and local mating). This effect was apparent across central life-history components (survival, asexual growth and mating) but differed in magnitude between ancestral genetic backgrounds. The evolution of some fitness components was constrained by pervasive negative correlations (trade-off between asexual growth and mating), while others changed direction under the influence of migration (for example, survival and mating). In allopatry, adaptive divergence was mainly conferred by standing genetic variation and resulted in ecological specialization. In sympatry, divergence was mainly mediated by novel mutations enriched in a subset of genes and was characterized by the repeated emergence of two strategies: an ecological generalist and an asexual growth specialist. Multiple loci showed consistent evidence for antagonistic pleiotropy across migration treatments providing a conceptual link between adaptation and divergence. This evolve-and-resequence experiment shows that rapid ecological differentiation can arise even under high rates of gene flow. It further highlights that adaptive trajectories are governed by complex interactions of gene flow, ancestral variation and genetic correlations.", "doi": "10.1038/s41559-020-01363-2", "pmid": "33432131", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-020-01363-2"}], "notes": [], "created": "2022-11-09T15:53:31.559Z", "modified": "2024-01-16T13:48:40.602Z"}, {"entity": "publication", "iuid": "2ec4096268f347c79eedea7bb77234a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ec4096268f347c79eedea7bb77234a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ec4096268f347c79eedea7bb77234a9"}}, "title": "Determinants of genetic variation across eco-evolutionary scales in pinnipeds.", "authors": [{"family": "Peart", "given": "Claire R", "initials": "CR", "orcid": "0000-0002-0433-0299", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ca9ce827fb435195a0d5bee245ba6a.json"}}, {"family": "Tusso", "given": "Sergio", "initials": "S", "orcid": "0000-0002-0612-9230", "researcher": {"href": "https://publications.scilifelab.se/researcher/027fc05d9bd843afaa82aeecce0747e8.json"}}, {"family": "Pophaly", "given": "Saurabh D", "initials": "SD"}, {"family": "Botero-Castro", "given": "Fidel", "initials": "F", "orcid": "0000-0002-5062-8272", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ef9abb38c5d4c259d64e6f59ee7440c.json"}}, {"family": "Wu", "given": "Chi-Chih", "initials": "CC"}, {"family": "Aurioles-Gamboa", "given": "David", "initials": "D"}, {"family": "Baird", "given": "Amy B", "initials": "AB"}, {"family": "Bickham", "given": "John W", "initials": "JW", "orcid": "0000-0001-9624-7806", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b8ef9c3991c4da38ad3010bb30977be.json"}}, {"family": "Forcada", "given": "Jaume", "initials": "J", "orcid": "0000-0002-2115-0150", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9fddd47f5b64f779913b9fd631edb2e.json"}}, {"family": "Galimberti", "given": "Filippo", "initials": "F", "orcid": "0000-0001-5537-6409", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d82a8f8835145619fbac351091bfbec.json"}}, {"family": "Gemmell", "given": "Neil J", "initials": "NJ", "orcid": "0000-0003-0671-3637", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ca2b0a676d84b878b3f9faa8748e148.json"}}, {"family": "Hoffman", "given": "Joseph I", "initials": "JI", "orcid": "0000-0001-5895-8949", "researcher": {"href": "https://publications.scilifelab.se/researcher/5455275134754093b050bee85b8f88c5.json"}}, {"family": "Kovacs", "given": "Kit M", "initials": "KM"}, {"family": "Kunnasranta", "given": "Mervi", "initials": "M"}, {"family": "Lydersen", "given": "Christian", "initials": "C"}, {"family": "Nyman", "given": "Tommi", "initials": "T"}, {"family": "de Oliveira", "given": "Larissa Rosa", "initials": "LR"}, {"family": "Orr", "given": "Anthony J", "initials": "AJ"}, {"family": "Sanvito", "given": "Simona", "initials": "S", "orcid": "0000-0003-1427-6414", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f65216b298b4575adb46bfeea38d8d3.json"}}, {"family": "Valtonen", "given": "Mia", "initials": "M", "orcid": "0000-0003-2034-2019", "researcher": {"href": "https://publications.scilifelab.se/researcher/601fe0084ca1460486e607e509f46c3a.json"}}, {"family": "Shafer", "given": "Aaron B A", "initials": "ABA", "orcid": "0000-0001-7652-225X", "researcher": {"href": "https://publications.scilifelab.se/researcher/65325cc227b74704ab85e14385a1673e.json"}}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}], "type": "journal article", "published": "2020-08-00", "journal": {"title": "Nat Ecol Evol", "issn": "2397-334X", "volume": "4", "issue": "8", "pages": "1095-1104", "issn-l": "2397-334X"}, "abstract": "The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimated the long-term coalescent Ne for 17 pinniped species represented by 36 population samples (total n = 458 individuals). Ne estimates ranged from 8,936 to 91,178, were highly consistent within (sub)species and showed a strong positive correlation with NC ([Formula: see text] = 0.59; P = 0.0002). Ne/NC ratios were low (mean, 0.31; median, 0.13) and co-varied strongly with demographic history and, to a lesser degree, with species' ecological and life-history variables such as breeding habitat. Residual variation in Ne/NC, after controlling for past demographic fluctuations, contained information about recent population size changes during the Anthropocene. Specifically, species of conservation concern typically had positive residuals indicative of a smaller contemporary NC than would be expected from their long-term Ne. This study highlights the value of comparative population genomic analyses for gauging the evolutionary processes governing genetic variation in natural populations, and provides a framework for identifying populations deserving closer conservation attention.", "doi": "10.1038/s41559-020-1215-5", "pmid": "32514167", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41559-020-1215-5"}], "notes": [], "created": "2020-12-08T23:33:13.775Z", "modified": "2024-01-16T13:48:42.060Z"}, {"entity": "publication", "iuid": "8458cb81480843a097988562512b7c30", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8458cb81480843a097988562512b7c30.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8458cb81480843a097988562512b7c30"}}, "title": "In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation.", "authors": [{"family": "Wu", "given": "Chi-Chih", "initials": "C"}, {"family": "Klaesson", "given": "Axel", "initials": "A"}, {"family": "Buskas", "given": "Julia", "initials": "J"}, {"family": "Ranefall", "given": "Petter", "initials": "P"}, {"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JBW", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}], "type": "journal article", "published": "2019-03-08", "journal": {"title": "J Exp Biol", "issn": "1477-9145", "issn-l": "0022-0949", "volume": "222", "issue": "Pt 5", "pages": "jeb194431"}, "abstract": "Functional validation of candidate genes involved in adaptation and speciation remains challenging. Here, we exemplify the utility of a method quantifying individual mRNA transcripts in revealing the molecular basis of divergence in feather pigment synthesis during early-stage speciation in crows. Using a padlock probe assay combined with rolling circle amplification, we quantified cell-type-specific gene expression in the histological context of growing feather follicles. Expression of Tyrosinase Related Protein 1 ( TYRP1), Solute Carrier Family 45 member 2 (SLC45A2) and Hematopoietic Prostaglandin D Synthase (HPGDS) was melanocyte-limited and significantly reduced in follicles from hooded crow, explaining the substantially lower eumelanin content in grey versus black feathers. The central upstream Melanocyte Inducing Transcription Factor (MITF) only showed differential expression specific to melanocytes - a feature not captured by bulk RNA-seq. Overall, this study provides insight into the molecular basis of an evolutionary young transition in pigment synthesis, and demonstrates the power of histologically explicit, statistically substantiated single-cell gene expression quantification for functional genetic inference in natural populations.", "doi": "10.1242/jeb.194431", "pmid": "30718374", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "jeb.194431"}, {"db": "pmc", "key": "PMC6650291"}, {"db": "mid", "key": "EMS83767"}, {"db": "figshare", "key": "10.6084/m9.figshare.7635791"}], "notes": [], "created": "2019-11-18T08:46:40.714Z", "modified": "2024-01-16T13:48:44.622Z"}, {"entity": "publication", "iuid": "164404029f4a4a9a9c060ce21f1eb099", "links": {"self": {"href": "https://publications.scilifelab.se/publication/164404029f4a4a9a9c060ce21f1eb099.json"}, "display": {"href": "https://publications.scilifelab.se/publication/164404029f4a4a9a9c060ce21f1eb099"}}, "title": "Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.", "authors": [{"family": "K\u00fcnstner", "given": "Axel", "initials": "A"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JB", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Whitney", "given": "Osceola", "initials": "O"}, {"family": "Balakrishnan", "given": "Christopher N", "initials": "CN", "orcid": "0000-0002-0788-0659", "researcher": {"href": "https://publications.scilifelab.se/researcher/363e6c4a51b647bba7e02e1c8e5464fd.json"}}, {"family": "Day", "given": "Lainy", "initials": "L", "orcid": "0000-0002-9122-3044", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a99dd326b9640629732a9fdbded2662.json"}}, {"family": "Edwards", "given": "Scott V", "initials": "SV"}, {"family": "Janes", "given": "Daniel E", "initials": "DE"}, {"family": "Schlinger", "given": "Barney A", "initials": "BA"}, {"family": "Wilson", "given": "Richard K", "initials": "RK"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Warren", "given": "Wesley C", "initials": "WC"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2010-03-00", "journal": {"volume": "19 Suppl 1", "issn": "1365-294X", "issue": "Suppl 1", "pages": "266-276", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with approximately 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.", "doi": "10.1111/j.1365-294X.2009.04487.x", "pmid": "20331785", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "mid", "key": "NIHMS216459"}, {"db": "pmc", "key": "PMC2904817"}, {"db": "pii", "key": "MEC4487"}], "notes": [], "created": "2017-05-04T14:57:12.592Z", "modified": "2023-06-19T11:19:36.049Z"}]}