{"entity": "researcher", "timestamp": "2026-07-17T08:46:18.005Z", "family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "affiliations": ["Animal Ecology, Department of Ecology and Genetics, EBC Uppsala University Uppsala Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f"}}, "publications": [{"entity": "publication", "iuid": "234306780e8e4d429ab2d566fe419047", "links": {"self": {"href": "https://publications.scilifelab.se/publication/234306780e8e4d429ab2d566fe419047.json"}, "display": {"href": "https://publications.scilifelab.se/publication/234306780e8e4d429ab2d566fe419047"}}, "title": "Sex-Specific Dominance of Gene Expression in Seed Beetles.", "authors": [{"family": "Kaufmann", "given": "Philipp", "initials": "P", "orcid": "0000-0002-7164-6867", "researcher": {"href": "https://publications.scilifelab.se/researcher/4214ade17fff4c30a690c13c43623ee7.json"}}, {"family": "R\u00f6nn", "given": "Johanna Liljestrand", "initials": "JL", "orcid": "0000-0002-8112-152X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9446e0b8115a427c945830849d0b0205.json"}}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2024-12-06", "journal": {"title": "Mol. Biol. Evol.", "issn": "1537-1719", "volume": "41", "issue": "12", "issn-l": "0737-4038"}, "abstract": "When different alleles are favored in different environments, dominance reversal where alternate alleles are dominant in the environment in which they are favored can generate net balancing selection. The sexes represent two distinct genetic environments and sexually antagonistic (SA) selection can maintain genetic variation, especially when the alleles involved show sex-specific dominance. Sexual dimorphism in gene expression is pervasive and has been suggested to result from SA selection. Yet, whether gene-regulatory variation shows sex-specific dominance is poorly understood. We tested for sex-specific dominance in gene expression using three crosses between homozygous lines derived from a population of a seed beetle, where a previous study documented a signal of dominance reversal for fitness between the sexes. Overall, we found that the dominance effects of variants affecting gene expression were positively correlated between the sexes (r = 0.33 to 0.44). Yet, 586 transcripts showed significant differences in dominance between the sexes. Sex-specific dominance was significantly more common in transcripts with more sex-biased expression, in two of three of our crosses. Among transcripts showing sex-specific dominance, lesser sexual dimorphism in gene expression among heterozygotes was somewhat more common than greater. Gene ontology enrichment analyses showed that functional categories associated with known SA phenotypes in Callosobruchus maculatus were overrepresented among transcripts with sex-specific dominance, including genes involved in metabolic processes and the target-of-rapamycin pathway. Our results support the suggestion that sex-specific dominance of regulatory variants contributes to the maintenance of genetic variation in fitness mediated by SA selection in this species.", "doi": "10.1093/molbev/msae244", "pmid": "39692633", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11653567"}, {"db": "pii", "key": "7927672"}], "notes": [], "created": "2025-02-28T14:19:00.427Z", "modified": "2025-02-28T14:19:00.540Z"}, {"entity": "publication", "iuid": "c8247c4a542e4c94ae4a3ee22db83900", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8247c4a542e4c94ae4a3ee22db83900"}}, "title": "Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.", "authors": [{"family": "Papachristos", "given": "Konstantinos", "initials": "K", "orcid": "0000-0002-4777-9088", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bf7a545a218455fa134b3dd8bb1b895.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A", "orcid": "0000-0002-5662-9145", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f74f301499b4f888e0ac7c5161ae161.json"}}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2024-07-03", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "16", "issue": "7", "pages": null}, "abstract": "Male seminal fluid proteins often show signs of positive selection and divergent evolution, believed to reflect male-female coevolution. Yet, our understanding of the predicted concerted evolution of seminal fluid proteins and female reproductive proteins is limited. We sequenced, assembled, and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding seminal fluid proteins and female reproductive proteins with those in digestive protein genes and well-conserved reference genes. We found that female reproductive proteins showed an overall ratio of nonsynonymous to synonymous substitutions (\u03c9) similar to that of conserved genes, while seminal fluid proteins and digestive proteins exhibited higher overall \u03c9 values. Further, seminal fluid proteins and digestive proteins showed a higher proportion of sites putatively under positive selection, and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among seminal fluid proteins were on average more closely correlated with those in female reproductive proteins than with either digestive or conserved genes. Gene expression showed the expected negative covariation with \u03c9 values, except for male-biased genes where this negative relationship was reversed. In conclusion, seminal fluid proteins showed relatively rapid evolution and signs of positive selection. In contrast, female reproductive proteins evolved at a lower rate under selective constraints, on par with genes known to be well conserved. Although our findings provide support for concerted evolution of seminal fluid proteins and female reproductive proteins, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.", "doi": "10.1093/gbe/evae143", "pmid": "38941482", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Long-term Support WABI": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11251426"}, {"db": "pii", "key": "7701342"}], "notes": [], "created": "2024-11-12T10:52:28.961Z", "modified": "2024-11-25T10:24:28.390Z"}, {"entity": "publication", "iuid": "10b805170fe94fe1acccfcec55db793d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10b805170fe94fe1acccfcec55db793d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10b805170fe94fe1acccfcec55db793d"}}, "title": "A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements.", "authors": [{"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}, {"family": "Westerberg", "given": "Ivar", "initials": "I"}, {"family": "Galbraith", "given": "James", "initials": "J"}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Scofield", "given": "Douglas G", "initials": "DG", "orcid": "0000-0001-5235-6461", "researcher": {"href": "https://publications.scilifelab.se/researcher/62a8063a48a446a7947d55f9900894a6.json"}}, {"family": "Olsen", "given": "Remi-Andr\u00e9", "initials": "RA"}, {"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}, {"family": "Bonath", "given": "Franziska", "initials": "F"}, {"family": "Ewels", "given": "Philip", "initials": "P"}, {"family": "Suh", "given": "Alexander", "initials": "A"}], "type": "journal article", "published": "2023-12-13", "journal": {"title": "G3 (Bethesda)", "issn": "2160-1836", "issn-l": "2160-1836"}, "abstract": "Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.", "doi": "10.1093/g3journal/jkad266", "pmid": "38092066", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Other": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "7471854"}], "notes": [], "created": "2024-01-02T13:29:05.665Z", "modified": "2024-01-16T13:48:31.509Z"}, {"entity": "publication", "iuid": "18d1940c083c4e4780bea26c0c4df967", "links": {"self": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967.json"}, "display": {"href": "https://publications.scilifelab.se/publication/18d1940c083c4e4780bea26c0c4df967"}}, "title": "Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles.", "authors": [{"family": "Immonen", "given": "Elina", "initials": "E", "orcid": "0000-0003-1121-6950", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6c9af5588c64dfdacba192b65524d43.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}, {"family": "Stojkovi\u0107", "given": "Biljana", "initials": "B"}, {"family": "Savkovi\u0107", "given": "Uro\u0161", "initials": "U"}, {"family": "\u0110or\u0111evi\u0107", "given": "Mirko", "initials": "M"}, {"family": "Liljestrand-R\u00f6nn", "given": "Johanna", "initials": "J"}, {"family": "Wiberg", "given": "R Axel W", "initials": "RAW"}, {"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}], "type": "journal article", "published": "2023-01-04", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "issn-l": "1759-6653", "volume": "15", "issue": "1", "pages": null}, "abstract": "The patterns of reproductive timing and senescence vary within and across species owing to differences in reproductive strategies, but our understanding of the molecular underpinnings of such variation is incomplete. This is perhaps particularly true for sex differences. We investigated the evolution of sex-specific gene expression associated with life history divergence in replicated populations of the seed beetle Acanthoscelides obtectus, experimentally evolving under (E)arly or (L)ate life reproduction for >200 generations which has resulted in strongly divergent life histories. We detected 1,646 genes that were differentially expressed in E and L lines, consistent with a highly polygenic basis of life history evolution. Only 30% of differentially expressed genes were similarly affected in males and females. The evolution of long life was associated with significantly reduced sex differences in expression, especially in non-reproductive tissues. The expression differences were overall more pronounced in females, in accordance with their greater phenotypic divergence in lifespan. Functional enrichment analysis revealed differences between E and L beetles in gene categories previously implicated in aging, such as mitochondrial function and defense response. The results show that divergent life history evolution can be associated with profound changes in gene expression that alter the transcriptome in a sex-specific way, highlighting the importance of understanding the mechanisms of aging in each sex.", "doi": "10.1093/gbe/evac177", "pmid": "36542472", "labels": {"Bioinformatics Support and Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9830990"}, {"db": "pii", "key": "6948356"}], "notes": [], "created": "2023-12-01T12:26:26.019Z", "modified": "2024-07-01T06:04:47.982Z"}, {"entity": "publication", "iuid": "b5b41e59d80945f0b7a009d2dd268562", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b41e59d80945f0b7a009d2dd268562.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b41e59d80945f0b7a009d2dd268562"}}, "title": "A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?", "authors": [{"family": "Arnqvist", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0002-3501-3376", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2e926bfdd22419eb57d2c375041150f.json"}}, {"family": "Sayadi", "given": "Ahmed", "initials": "A"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Ecol Evol", "issn": "2045-7758", "volume": "12", "issue": "10", "pages": "e9440", "issn-l": "2045-7758"}, "abstract": "Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome-wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate-dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean F ST = 0.23-0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's D NS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (d XY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome-wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.", "doi": "10.1002/ece3.9440", "pmid": "36311399", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9608792"}, {"db": "pii", "key": "ECE39440"}], "notes": [], "created": "2022-11-29T09:34:26.276Z", "modified": "2022-11-29T09:34:26.313Z"}]}