| 1. |
- Arnqvist, Göran, Professor, 1961-, et al.
(författare)
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A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
- 2024
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Ingår i: G3. - : Oxford University Press. - 2160-1836. ; 14:2
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Tidskriftsartikel (refereegranskat)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.
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| 2. |
- Arnqvist, Göran, et al.
(författare)
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A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
- 2024
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Ingår i: G3. - 2160-1836. ; 14:2
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Tidskriftsartikel (refereegranskat)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.
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| 3. |
- Arnqvist, Göran, Professor, 1961-, et al.
(författare)
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Concerted evolution of metabolic rate, economics of mating, ecology, and pace of life across seed beetles
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Science. - 0027-8424 .- 1091-6490. ; 119:33
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Tidskriftsartikel (refereegranskat)abstract
- Male-female coevolution has taken different paths among closely related species, but our understanding of the factors that govern its direction is limited. While it is clear that ecological factors, life history, and the economics of reproduction are connected, the divergent links are often obscure. We propose that a complete understanding requires the conceptual integration of metabolic phenotypes. Metabolic rate, a nexus of life history evolution, is constrained by ecological factors and may exert important direct and indirect effects on the evolution of sexual dimorphism. We performed standardized experiments in 12 seed beetle species to gain a rich set of sex-specific measures of metabolic phenotypes, life history traits, and the economics of mating and analyzed our multivariate data using phylogenetic comparative methods. Resting metabolic rate (RMR) showed extensive evolution and evolved more rapidly in males than in females. The evolution of RMR was tightly coupled with a suite of life history traits, describing a pace-of-life syndrome (POLS), with indirect effects on the economics of mating. As predicted, high resource competition was associated with a low RMR and a slow POLS. The cost of mating showed sexually antagonistic coevolution, a hallmark of sexual conflict. The sex-specific costs and benefits of mating were predictably related to ecology, primarily through the evolution of male ejaculate size. Overall, our results support the tenet that resource competition affects metabolic processes that, in turn, have predictable effects on both life history evolution and reproduction, such that ecology shows both direct and indirect effects on male-female coevolution.
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| 4. |
- Bagchi, Basabi, et al.
(författare)
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Sexual conflict drives micro- and macroevolution of sexual dimorphism in immunity
- 2021
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Ingår i: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Sexual dimorphism in immunity is believed to reflect sex differences in reproductive strategies and trade-offs between competing life history demands. Sexual selection can have major effects on mating rates and sex-specific costs of mating and may thereby influence sex differences in immunity as well as associated host-pathogen dynamics. Yet, experimental evidence linking the mating system to evolved sexual dimorphism in immunity are scarce and the direct effects of mating rate on immunity are not well established. Here, we use transcriptomic analyses, experimental evolution and phylogenetic comparative methods to study the association between the mating system and sexual dimorphism in immunity in seed beetles, where mating causes internal injuries in females.RESULTS: We demonstrate that female phenoloxidase (PO) activity, involved in wound healing and defence against parasitic infections, is elevated relative to males. This difference is accompanied by concomitant sex differences in the expression of genes in the prophenoloxidase activating cascade. We document substantial phenotypic plasticity in female PO activity in response to mating and show that experimental evolution under enforced monogamy (resulting in low remating rates and reduced sexual conflict relative to natural polygamy) rapidly decreases female (but not male) PO activity. Moreover, monogamous females had evolved increased tolerance to bacterial infection unrelated to mating, implying that female responses to costly mating may trade off with other aspects of immune defence, an hypothesis which broadly accords with the documented sex differences in gene expression. Finally, female (but not male) PO activity shows correlated evolution with the perceived harmfulness of male genitalia across 12 species of seed beetles, suggesting that sexual conflict has a significant influence on sexual dimorphisms in immunity in this group of insects.CONCLUSIONS: Our study provides insights into the links between sexual conflict and sexual dimorphism in immunity and suggests that selection pressures moulded by mating interactions can lead to a sex-specific mosaic of immune responses with important implications for host-pathogen dynamics in sexually reproducing organisms.
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| 5. |
- Bomström, Henri, et al.
(författare)
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Digital Twins About Humans—Design Objectives From Three Projects
- 2022
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Ingår i: Journal of Computing and Information Science in Engineering. - : The American Society of Mechanical Engineers. - 1530-9827 .- 1944-7078. ; 22:5
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Tidskriftsartikel (refereegranskat)abstract
- Digital twin (DT) emerges as a key concept of the Industry 4.0 paradigm and beyond. However, the current literature lacks focus on humans and human activities as a part of complex system DTs. Acknowledging human aspects in DTs can enhance work performance, well-being, motivation, and personal development of professionals. This study examines emerging requirements for human digital twins (HDTs) in three use cases of industry–academia collaboration on complex systems. The results draw together the overall design problem and four design objectives for HDTs. We propose to combine the machine and human-related aspects of DTs and highlight the need for virtual-to-virtual interoperability between HDTs and machines alike. Furthermore, we outline differences between humans and machines regarding digital twinning by addressing human activities and knowledge-based behavior on systems. Design of HDTs requires understanding of individual professional characteristics, such as skills and information preferences, together with twinning between the physical and digital machine entities and interactions between the human and machine DTs. As the field moves toward including humans as a part of the DT concept, incorporating HDTs in complex systems emerges as an increasingly significant issue.
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| 6. |
- Höök, Lars, 1980-
(författare)
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The Evolution of Sex Chromosomes and Dosage Compensation in Structurally Dynamic Butterfly Genomes
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Dimorphic sex chromosomes have evolved independently throughout evolution from initially homologous autosomes. Recombination suppression between the sex chromosomes causes one sex chromosome to degenerate, which will influence evolution of sex-linked genes. This thesis investigated the evolution of genes and regulatory mechanisms on the sex chromosomes in Leptidea butterflies. Butterflies are female heterogametic, and females carry a dimorphic Z/W pair, while males have two homologous Z chromosomes. Dosage compensation is expected to evolve to equalize gene expression differences which are caused by this imbalance. Our analyses showed that Z-linked gene expression was reduced in males to parity with females, and reduced compared to autosomal levels. This is likely an adaptation to homogenize expression patterns between the sexes. However, the Z chromosome was enriched with male-biased genes, and sex-biased genes were not downregulated, suggesting that specific tuning occur for subsets of genes. An exploration of the Leptidea genomes revealed an unprecedented amount of chromosomal rearrangements, and detection of chromosomal heterozygotes suggests that the process is ongoing. Transposable elements were enriched in fused chromosome regions and are likely promoting rearrangements. The observed restructuring has formed several neo-sex chromosomes, which makes Leptidea useful for studies of evolutionary dynamics of sex chromosomes. Z-linked genes showed a faster-Z effect, which was strongest for female-biased genes. In addition, the neo-Z chromosomes revealed a temporal dynamic, with younger Z chromosomes diverging faster. This could potentially be caused by an increased adaptive potential compared to the ancestral Z chromosome. Dualistic dosage compensation was found on the neo-Z chromosomes, with some chromosome regions being downregulated in males, and some regions being upregulated in females, in both cases resulting in inter-sexual expression balance. One Leptidea neo-W chromosome is largely intact, and analyses of allele specific expression provided strong evidence for W gametolog expression. Furthermore, male Z-linked expression was reduced for genes that lacked W gametologs, indicating that gene regulation has evolved rapidly to achieve dosage balance. This work has led to several interesting discoveries about gene regulation, chromosome rearrangements and sequence divergence of sex chromosomes, and in general revealed a more complex picture of how these specific chromosomes evolve.
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| 7. |
- Immonen, Elina, et al.
(författare)
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An experimental test of temperature-dependent selection on mitochondrial haplotypes in Callosobruchus maculatus seed beetles
- 2020
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Ingår i: Ecology and Evolution. - : WILEY. - 2045-7758. ; 10:20, s. 11387-11398
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondrial DNA (mtDNA) consists of few but vital maternally inherited genes that interact closely with nuclear genes to produce cellular energy. How important mtDNA polymorphism is for adaptation is still unclear. The assumption in population genetic studies is often that segregating mtDNA variation is selectively neutral. This contrasts with empirical observations of mtDNA haplotypes affecting fitness-related traits and thermal sensitivity, and latitudinal clines in mtDNA haplotype frequencies. Here, we experimentally test whether ambient temperature affects selection on mtDNA variation, and whether such thermal effects are influenced by intergenomic epistasis due to interactions between mitochondrial and nuclear genes, using replicated experimental evolution inCallosobruchus maculatusseed beetle populations seeded with a mixture of different mtDNA haplotypes. We also test for sex-specific consequences of mtDNA evolution on reproductive success, given that mtDNA mutations can have sexually antagonistic fitness effects. Our results demonstrate natural selection on mtDNA haplotypes, with some support for thermal environment influencing mtDNA evolution through mitonuclear epistasis. The changes in male and female reproductive fitness were both aligned with changes in mtDNA haplotype frequencies, suggesting that natural selection on mtDNA is sexually concordant in stressful thermal environments. We discuss the implications of our findings for the evolution of mtDNA.
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| 8. |
- Immonen, Elina, et al.
(författare)
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Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles
- 2023
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653 .- 1759-6653. ; 15:1
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Tidskriftsartikel (refereegranskat)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.
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| 9. |
- Kaufmann, Philipp, et al.
(författare)
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Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance
- 2021
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Ingår i: Nature Ecology & Evolution. - : Springer Nature. - 2397-334X. ; 5:10, s. 1394-1402
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Tidskriftsartikel (refereegranskat)abstract
- Sexual dimorphism is ubiquitous in nature but its evolution is puzzling given that the mostly shared genome constrains independent evolution in the sexes. Sex differences should result from asymmetries between the sexes in selection or genetic variation but studies investigating both simultaneously are lacking. Here, we combine a quantitative genetic analysis of body size variation, partitioned into autosomal and sex chromosome contributions and ten generations of experimental evolution to dissect the evolution of sexual body size dimorphism in seed beetles (Callosobruchus maculatus) subjected to sexually antagonistic or sex-limited selection. Female additive genetic variance (VA) was primarily linked to autosomes, exhibiting a strong intersexual genetic correlation with males (?am,f = 0.926), while X- and Y-linked genes further contributed to the male VA and X-linked genes contributed to female dominance variance. Consistent with these estimates, sexual body size dimorphism did not evolve in response to female-limited selection but evolved by 30–50% under male-limited and sexually antagonistic selection. Remarkably, Y-linked variance alone could change dimorphism by 30%, despite the C. maculatus Y chromosome being small and heterochromatic. Our results demonstrate how the potential for sexual dimorphism to evolve depends on both its underlying genetic basis and the nature of sex-specific selection.
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| 10. |
- Kaufmann, Philipp, 1991-, et al.
(författare)
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Sexually antagonistic selection maintains genetic variance when sexual dimorphism evolves
- 2023
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : Royal Society. - 0962-8452 .- 1471-2954. ; 290:1995
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Tidskriftsartikel (refereegranskat)abstract
- Genetic variance (VG) in fitness related traits is often unexpectedly high, evoking the question how VG can be maintained in the face of selection. Sexually antagonistic (SA) selection favouring alternative alleles in the sexes is common and predicted to maintain VG, while directional selection should erode it. Both SA and sex-limited directional selection can lead to sex-specific adaptations but how each affect VG when sexual dimorphism evolves remain experimentally untested. Using replicated artificial selection on the seed beetle Callosobruchus maculatus body size we recently demonstrated an increase in size dimorphism under SA and male-limited (ML) selection by 50% and 32%, respectively. Here we test their consequences on genetic variation. We show that SA selection maintained significantly more ancestral, autosomal additive genetic variance than ML selection, while both eroded sex-linked additive variation equally. Ancestral female-specific dominance variance was completely lost under ML, while SA selection consistently sustained it. Further, both forms of selection preserved a high genetic correlation between the sexes (rm,f). These results demonstrate the potential for sexual antagonism to maintain more genetic variance while fueling sex-specific adaptation in a short evolutionary timescale, and are in line with predicted importance of sex-specific dominance reducing sexual conflict over alternative alleles.
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