| 1. |
- Arnqvist, Göran, Professor, 1961-, et al.
(author)
-
A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements
- 2024
-
In: G3. - : Oxford University Press. - 2160-1836. ; 14:2
-
Journal article (peer-reviewed)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.
|
|
| 2. |
- Arnqvist, Göran, Professor, 1961-, et al.
(author)
-
A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?
- 2022
-
In: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 12:10
-
Journal article (peer-reviewed)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.
|
|
| 3. |
- Arnqvist, Göran, Professor, 1961-, et al.
(author)
-
Concerted evolution of metabolic rate, economics of mating, ecology, and pace of life across seed beetles
- 2022
-
In: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Science. - 0027-8424 .- 1091-6490. ; 119:33
-
Journal article (peer-reviewed)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.
|
|
| 4. |
- Arnqvist, Göran, Professor, 1961-, et al.
(author)
-
Direct and indirect effects of male genital elaboration in female seed beetles
- 2021
-
In: Proceedings of the Royal Society of London. Biological Sciences. - London : Royal Society. - 0962-8452 .- 1471-2954. ; 288:1954
-
Journal article (peer-reviewed)abstract
- Our understanding of coevolution between male genitalia and female traits remains incomplete. This is perhaps especially true for genital traits that cause internal injuries in females, such as the spiny genitalia of seed beetles where males with relatively long spines enjoy a high relative fertilization success. We report on a new set of experiments, based on extant selection lines, aimed at assessing the effects of long male spines on females in Callosobruchus maculatus . We first draw on an earlier study using microscale laser surgery, and demonstrate that genital spines have a direct negative (sexually antagonistic) effect on female fecundity. We then ask whether artificial selection for long versus short spines resulted in direct or indirect effects on female lifetime offspring production. Reference females mating with males from long-spine lines had higher offspring production, presumably due to an elevated allocation in males to those ejaculate components that are beneficial to females. Remarkably, selection for long male genital spines also resulted in an evolutionary increase in female offspring production as a correlated response. Our findings thus suggest that female traits that affect their response to male spines are both under direct selection to minimize harm but are also under indirect selection (a good genes effect), consistent with the evolution of mating and fertilization biases being affected by several simultaneous processes.
|
|
| 5. |
- Arnqvist, Göran, Professor, 1961-, et al.
(author)
-
Ecology, the pace‐of‐life, epistatic selection and the maintenance of genetic variation in life‐history genes
- 2023
-
In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 32:17, s. 4713-4724
-
Journal article (peer-reviewed)abstract
- Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.
|
|
| 6. |
- Arnqvist, Göran, Professor, 1961-
(author)
-
Mixed Models Offer No Freedom from Degress Of Freedom
- 2020
-
In: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 35:4, s. 329-335
-
Research review (peer-reviewed)abstract
- Statistics matter greatly in biology, whether we like it or not. As a discipline with an empirical inclination, we are faced with data every day and we rely on inferential statistical models to make sense of it and to provide us with novel insights. Much of the time, the growing level of complexity and sophistication of the models we put to use in ecology and evolution have led to more appropriate analyses of our data. However, this is not always the case. Here, I draw attention to a classic flaw in inferential statistics that has resurfaced in a new flavor as a result of increased reliance on complex linear mixed models -the multifaceted and disturbingly persistent problem of pseudoreplication.
|
|
| 7. |
- Arnqvist, Göran, Professor, 1961-, et al.
(author)
-
The pace-of-life : A sex-specific link between metabolic rate and life history in bean beetles
- 2017
-
In: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435. ; 31:12, s. 2299-2309
-
Journal article (peer-reviewed)abstract
- Metabolic rate (MR) is a key functional trait simply because metabolism converts resources into population growth rate. Yet, our empirical understanding of the sources of within species variation in MR, as well as of its life history and ecological correlates, is rather limited. Here, we assess whether MR lies at the root of a syndrome of correlated rate-dependent life-history traits in an insect.Selection for early (E) or late (L) age-at-reproduction for >160 generations in the bean beetle Acanthoscelides obtectus has produced beetles that differ markedly in juvenile development, body size, fecundity schedules, ageing and life span. Here, we use micro-respirometry to test whether this has been associated with the evolution of age- and sex-specific metabolic phenotypes.We find that mass-specific MR is 18% higher in E lines compared to L lines and that MR decreases more rapidly with chronological, but not biological, age in E lines. Males, under sexual selection to “live-fast-die-young”, show 50% higher MR than females and MR decreased more rapidly with age in males.Our results are consistent with a central role for MR for the divergence in “pace-of-life” seen in these beetles, supporting the view that MR lies at the root of ecologically relevant life-history trait variation within species.
|
|
| 8. |
- Bagchi, Basabi, et al.
(author)
-
Sexual conflict drives micro- and macroevolution of sexual dimorphism in immunity
- 2021
-
In: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 19:1
-
Journal article (peer-reviewed)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.
|
|
| 9. |
- Bayram, Helen L., et al.
(author)
-
Identification of novel ejaculate proteins in a seed beetle and division of labour across male accessory reproductive glands
- 2019
-
In: Insect biochemistry and molecular biology. - : Pergamon. - 0965-1748 .- 1879-0240. ; 104, s. 50-57
-
Journal article (peer-reviewed)abstract
- The male ejaculate contains a multitude of seminal fluid proteins (SFPs), many of which are key reproductive molecules, as well as sperm. However, the identification of SFPs is notoriously difficult and a detailed understanding of this complex phenotype has only been achieved in a few model species. We employed a recently developed proteomic method involving whole-organism stable isotope labelling coupled with proteomic and transcriptomic analyses to characterize ejaculate proteins in the seed beetle Callosobruchus maculatus. We identified 317 proteins that were transferred to females at mating, and a great majority of these showed signals of secretion and were highly male-biased in expression in the abdomen. These male-derived proteins were enriched with proteins involved in general metabolic and catabolic processes but also with proteolytic enzymes and proteins involved in protection against oxidative stress. Thirty-seven proteins showed significant homology with SFPs previously identified in other insects. However, no less than 92 C. maculatus ejaculate proteins were entirely novel, receiving no significant blast hits and lacking homologs in extant data bases, consistent with a rapid and divergent evolution of SFPs. We used 3D micro-tomography in conjunction with proteomic methods to identify 5 distinct pairs of male accessory reproductive glands and to show that certain ejaculate proteins were only recovered in certain male glands. Finally, we provide a tentative list of 231 candidate female-derived reproductive proteins, some of which are likely important in ejaculate processing and/or sperm storage.
|
|
| 10. |
- Boman, Jesper, et al.
(author)
-
Larger genomes show improved buffering of adult fitness against environmental stress in seed beetles
- 2023
-
In: Biology Letters. - : Royal Society. - 1744-9561 .- 1744-957X. ; 19:1
-
Journal article (peer-reviewed)abstract
- Our general understanding of the evolution of genome size (GS) is incomplete, and it has long been clear that GS does not reflect organismal complexity. Here, we assess the hypothesis that larger genomes may allow organisms to better cope with environmental variation. It is, for example, possible that genome expansion due to proliferation of transposable elements or gene duplications may affect the ability to regulate and fine-tune transcriptional profiles. We used 18 populations of the seed beetle Callosobruchus maculatus, which differ in GS by up to 4.5%, and exposed adults and juveniles to environmental stress in a series of experiments where stage-specific fitness was assayed. We found that populations with larger genomes were indeed better buffered against environmental stress for adult, but not for juvenile, fitness. The genetic correlation across populations between GS and canalization of adult fitness is consistent with a role for natural selection in the evolution of GS.
|
|
