| 1. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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| 2. |
- Abbott, Jessica K., et al.
(författare)
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Sex chromosome evolution : Historical insights and future perspectives
- 2017
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Ingår i: Proceedings of the Royal Society B: Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 284:1854
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Forskningsöversikt (refereegranskat)abstract
- Many separate-sexed organisms have sex chromosomes controlling sex determination. Sex chromosomes often have reduced recombination, specialized (frequently sex-specific) gene content, dosage compensation and heteromorphic size. Research on sex determination and sex chromosome evolution has increased over the past decade and is today a very active field. However, some areas within the field have not received as much attention as others.We therefore believe that a historic overviewof key findings and empirical discoveries will put current thinking into context and help us better understand where to go next. Here, we present a timeline of important conceptual and analytical models, as well as empirical studies that have advanced the field and changed our understanding of the evolution of sex chromosomes. Finally, we highlight gaps in our knowledge so far and propose some specific areas within the field that we recommend a greater focus on in the future, including the role of ecology in sex chromosome evolution and newmultilocus models of sex chromosome divergence.
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| 3. |
- Abbott, Jessica K., 1978-, et al.
(författare)
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Sexual conflict in wing size and shape in Drosophila melanogaster
- 2010
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Ingår i: Journal of Evolutionary Biology. - : Wiley. - 1010-061X .- 1420-9101. ; 23:9, s. 1989-1997
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Tidskriftsartikel (refereegranskat)abstract
- Intralocus sexual conflict occurs when opposing selection pressures operate on loci expressed in both sexes, constraining the evolution of sexual dimorphism and displacing one or both sexes from their optimum. We eliminated intralocus conflict in Drosophila melanogaster by limiting transmission of all major chromosomes to males, thereby allowing them to win the intersexual tug-of-war. Here, we show that this male-limited (ML) evolution treatment led to the evolution (in both sexes) of masculinized wing morphology, body size, growth rate, wing loading, and allometry. In addition to more male-like size and shape, ML evolution resulted in an increase in developmental stability for males. However, females expressing ML chromosomes were less developmentally stable, suggesting that being ontogenetically more male-like was disruptive to development. We suggest that sexual selection over size and shape of the imago may therefore explain the persistence of substantial genetic variation in these characters and the ontogenetic processes underlying them.
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| 4. |
- Abbott, Jessica K., et al.
(författare)
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The microevolutionary response to male-limited X-chromosome evolution in Drosophila melanogaster reflects macroevolutionary patterns
- 2020
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Ingår i: Journal of Evolutionary Biology. - : Wiley-Blackwell. - 1010-061X .- 1420-9101. ; 33:6, s. 738-750
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Tidskriftsartikel (refereegranskat)abstract
- Due to its hemizygous inheritance and role in sex determination, the X-chromosome is expected to play an important role in the evolution of sexual dimorphism and to be enriched for sexually antagonistic genetic variation. By forcing the X-chromosome to only be expressed in males over >40 generations, we changed the selection pressures on the X to become similar to those experienced by the Y. This releases the X from any constraints arising from selection in females and should lead to specialization for male fitness, which could occur either via direct effects of X-linked loci or trans-regulation of autosomal loci by the X. We found evidence of masculinization via up-regulation of male-benefit sexually antagonistic genes and down-regulation of X-linked female-benefit genes. Potential artefacts of the experimental evolution protocol are discussed and cannot be wholly discounted, leading to several caveats. Interestingly, we could detect evidence of microevolutionary changes consistent with previously documented macroevolutionary patterns, such as changes in expression consistent with previously established patterns of sexual dimorphism, an increase in the expression of metabolic genes related to mito-nuclear conflict and evidence that dosage compensation effects can be rapidly altered. These results confirm the importance of the X in the evolution of sexual dimorphism and as a source for sexually antagonistic genetic variation and demonstrate that experimental evolution can be a fruitful method for testing theories of sex chromosome evolution.
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| 5. |
- Abbott, Jessica K., et al.
(författare)
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Why is measuring and predicting fitness under genomic conflict so hard?
- 2023
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Ingår i: Current Opinion in Genetics and Development. - 0959-437X. ; 81
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Forskningsöversikt (refereegranskat)abstract
- The genomic conflict between the sexes is caused by differences in the optimal male and female reproductive strategies, and is a major contributor to genetic, phenotypic, and life history variation. While early experimental work appeared to strongly support predictions from sexual conflict, recent work has produced more ambiguous results. Recent advances in experimental evolution studies combined with theoretical arguments can shed light on why measuring fitness under a conflict is so challenging, including the incidental alteration of mating dynamics, demographic effects, and inherent complexity in what quantity selection maximizes. We stress that non-intuitive results do not necessarily mean the absence of conflict, and follow-up experiments to determine why a priori predictions failed can ultimately teach us more than if they had been confirmed.
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| 6. |
- Cīrulis, Aivars, et al.
(författare)
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Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite
- 2024
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of gonochorism from hermaphroditism is linked with the formation of sex chromosomes, as well as the evolution of sex-biased and sex-specific gene expression to allow both sexes to reach their fitness optimum. There is evidence that sexual selection drives the evolution of male-biased gene expression in particular. However, previous research in this area in animals comes from either theoretical models or comparative studies of already old sex chromosomes. We therefore investigated changes in gene expression under 3 different selection regimes for the simultaneous hermaphrodite Macrostomum lignano subjected to sex-limited experimental evolution (i.e. selection for fitness via eggs, sperm, or a control regime allowing both). After 21 and 22 generations of selection for male-specific or female-specific fitness, we characterized changes in whole-organism gene expression. We found that female-selected lines had changed the most in their gene expression. Although annotation for this species is limited, gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggest that metabolic changes (e.g. biosynthesis of amino acids and carbon metabolism) are an important adaptive component. As predicted, we found that the expression of genes previously identified as testis-biased candidates tended to be downregulated in the female-selected lines. We did not find any significant expression differences for previously identified candidates of other sex-specific organs, but this may simply reflect that few transcripts have been characterized in this way. In conclusion, our experiment suggests that changes in testis-biased gene expression are important in the early evolution of sex chromosomes and gonochorism.
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| 7. |
- Kapun, Martin, et al.
(författare)
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Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource
- 2021
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 38:12, s. 5782-5805
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Tidskriftsartikel (refereegranskat)abstract
- Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
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| 8. |
- Lund-Hansen, Katrine K., et al.
(författare)
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Female-limited X chromosome evolution reveals that lifespan is mainly modulated by interlocus rather than intralocus sexual conflict
- 2022
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Ingår i: Behavioral Ecology and Sociobiology. - : Springer Science and Business Media LLC. - 0340-5443 .- 1432-0762. ; 76:9
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Tidskriftsartikel (refereegranskat)abstract
- Abstract: Sexual dimorphism in somatic investment may be shaped by two distinct forms of sexual conflict; under intralocus sexual conflict (IASC), males and females have different optimal levels of somatic investment but are constrained from reaching their respective optima by their shared genome, while under interlocus sexual conflict (IRSC), males and females have different optimal sexual strategies, which could have direct or indirect effects on levels of somatic investment. We investigated effects of IASC and IRSC on two aspects of somatic investment, immune defence strategies and longevity, using previously established female-limited experimental evolution lines in Drosophila melanogaster. We found little evidence for any effect of either type of sexual conflict on investment in the immune defence resistance or tolerance. Nor did we find convincing evidence that longevity is subject to IASC in this species. However, we did find evidence that increased female control over mating rate had important and opposite effects on longevity between the sexes. Specifically, females that had adapted to high levels of female control over mating had a longer lifespan when kept in mixed-sex groups, while males had shorter longevity, perhaps due to increased investment in post-copulatory sexual selection. These novel results show that female control over mating rates may have important and unexpected effects on patterns of somatic investment. Significance statement: Sexual conflict occurs between the two sexes over numerous life history traits, and it is complex to disentangle how these traits interact and affect each other. Here we use a long-term evolution experiment to investigate sexual dimorphism in somatic maintenance. We found no effect of feminising the X chromosome on female immune defence. However, we did find that increased female control over mating rate resulted in longer female lifespan, but reduced male lifespan, and that these effects were dependent on social context (isolated or in mixed-sex groups). Unlike previous studies on the effect of sexual conflict on longevity, our experiment did not manipulate environmental conditions nor the adult sex ratio, which is likely to reduce both pre- and post-copulatory sexual selection.
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| 9. |
- Lund-Hansen, Katrine K., et al.
(författare)
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Feminization of complex traits in Drosophila melanogaster via female-limited X chromosome evolution
- 2020
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 74:12, s. 2703-2713
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Tidskriftsartikel (refereegranskat)abstract
- A handful of studies have investigated sexually antagonistic constraints on achieving sex-specific fitness optima, although exclusively through male-genome-limited evolution experiments. In this article, we established a female-limited X chromosome evolution experiment, where we used an X chromosome balancer to enforce the inheritance of the X through the matriline, thus removing exposure to male selective constraints. This approach eliminates the effects of sexually antagonistic selection on the X chromosome, permitting evolution toward a single sex-specific optimum. After multiple generations of selection, we found strong evidence that body size and development time had moved toward a female-specific optimum, whereas reproductive fitness and locomotion activity remained unchanged. The changes in body size and development time are consistent with previous results, and suggest that the X chromosome is enriched for sexually antagonistic genetic variation controlling these particular traits. The lack of change in reproductive fitness and locomotion activity could be due to a number of mutually nonexclusive explanations, including a lack of sexually antagonistic variance on the X chromosome for those traits or confounding effects of the use of the balancer chromosome. This study is the first to employ female-genome-limited selection and adds to the understanding of the complexity of sexually antagonistic genetic variation.
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| 10. |
- Lund-Hansen, Katrine K., et al.
(författare)
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Sexually antagonistic coevolution between the sex chromosomes of Drosophila melanogaster
- 2021
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National academy of Science. - 0027-8424 .- 1091-6490. ; 118:8
-
Tidskriftsartikel (refereegranskat)abstract
- Antagonistic interactions between the sexes are important drivers of evolutionary divergence. Interlocus sexual conflict is generally described as a conflict between alleles at two interacting loci whose identity and genomic location are arbitrary, but with opposite fitness effects in each sex. We build on previous theory by suggesting that when loci under interlocus sexual conflict are located on the sex chromosomes it can lead to cycles of antagonistic coevolution between them and therefore between the sexes. We tested this hypothesis by performing experimental crosses using Drosophila melanogaster where we reciprocally exchanged the sex chromosomes between five allopatric wild-type populations in a round-robin design. Disrupting putatively coevolved sex chromosome pairs resulted in increased male reproductive success in 16 of 20 experimental populations (10 of which were individually significant), but also resulted in lower offspring egg-to-adult viability that affected both male and female fitness. After 25 generations of experimental evolution these sexually antagonistic fitness effects appeared to be resolved. To formalize our hypothesis, we developed population genetic models of antagonistic coevolution using fitness expressions based on our empirical results. Our model predictions support the conclusion that antagonistic coevolution between the sex chromosomes is plausible under the fitness effects observed in our experiments. Together, our results lend both empirical and theoretical support to the idea that cycles of antagonistic coevolution can occur between sex chromosomes and illustrate how this process, in combination with autosomal coadaptation, may drive genetic and phenotypic divergence between populations.
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| 11. |
- Manat, Yesbol, et al.
(författare)
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Female-limited X-chromosome evolution effects on male pre- and post-copulatory success
- 2021
-
Ingår i: Biology letters. - : The Royal Society. - 1744-9561 .- 1744-957X. ; 17:3
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Tidskriftsartikel (refereegranskat)abstract
- Intralocus sexual conflict arises when the expression of shared alleles at a single locus generates opposite fitness effects in each sex (i.e. sexually antagonistic alleles), preventing each sex from reaching its sex-specific optimum. Despite its importance to reproductive success, the relative contribution of intralocus sexual conflict to male pre- and post-copulatory success is not well-understood. Here, we used a female-limited X-chromosome (FLX) evolution experiment in Drosophila melanogaster to limit the inheritance of the X-chromosome to the matriline, eliminating possible counter-selection in males and allowing the X-chromosome to accumulate female-benefit alleles. After more than 100 generations of FLX evolution, we studied the effect of the evolved X-chromosome on male attractiveness and sperm competitiveness. We found a non-significant increase in attractiveness and decrease in sperm offence ability in males expressing the evolved X-chromosomes, but a significant increase in their ability to avoid displacement by other males' sperm. This is consistent with a trade-off between these traits, perhaps mediated by differences in body size, causing a small net reduction in overall male fitness in the FLX lines. These results indicate that the X-chromosome in D. melanogaster is subject to selection via intralocus sexual conflict in males.
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| 12. |
- Nordén, Anna K., et al.
(författare)
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Rapid evolution of sex role specialization in a hermaphrodite under sex-limited selection
- 2023
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Ingår i: Evolution; international journal of organic evolution. - : Oxford University Press (OUP). - 1558-5646. ; 77:4, s. 1066-1076
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of separate sexes from hermaphroditism is thought to have occurred independently many times, and may be linked to the evolution of sex chromosomes. Even though we have a good understanding of the theoretical steps in the evolution of sex chromosomes from a hermaphrodite ancestor, the initial stages are still hard to study in animals because many well-studied animal sex chromosome systems are old. We addressed this problem by experimentally selecting a hermaphrodite via sex-limited experimental evolution for several generations, simulating the early stages in the evolution of a sex chromosome. After 14 generations, a fitness assay revealed evidence of incipient sex role specialization in the female-selected lines, presumably reflecting the release from constraints usually imposed by selection on the other sex role. Importantly, however, this was not simply explained by morphology because testis and ovary sizes did not diverge among treatments. There was no evidence of a change in the male-selected lines. Our study shows that sex role specialization can occur rapidly as a result of sex-limited selection, which is consistent with genetic constraints between sex roles, and in line with the first predicted steps toward the evolution of a new sex chromosome system.
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| 13. |
- Abbott, Jessica, et al.
(författare)
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Epigenetics and Sex-Specific Fitness : An Experimental Test Using Male-Limited Evolution in Drosophila melanogaster
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:7, s. e70493-
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Tidskriftsartikel (refereegranskat)abstract
- When males and females have different fitness optima for the same trait but share loci, intralocus sexual conflict is likely to occur. Epigenetic mechanisms such as genomic imprinting (in which expression is altered according to parent-of-origin) and sex-specific maternal effects have been suggested as ways by which this conflict can be resolved. However these ideas have not yet been empirically tested. We designed an experimental evolution protocol in Drosophila melanogaster that enabled us to look for epigenetic effects on the X-chromosome-a hotspot for sexually antagonistic loci. We used special compound-X females to enforce father-to-son transmission of the X-chromosome for many generations, and compared fitness and gene expression levels between Control males, males with a Control X-chromosome that had undergone one generation of father-son transmission, and males with an X-chromosome that had undergone many generations of father-son transmission. Fitness differences were dramatic, with experimentally-evolved males approximately 20% greater than controls, and with males inheriting a non-evolved X from their father about 20% lower than controls. These data are consistent with both strong intralocus sexual conflict and misimprinting of the X-chromosome under paternal inheritance. However, expression differences suggested that reduced fitness under paternal X inheritance was largely due to deleterious maternal effects. Our data confirm the sexually-antagonistic nature of Drosophila's X-chromosome and suggest that the response to male-limited X-chromosome evolution entails compensatory evolution for maternal effects, and perhaps modification of other epigenetic effects via coevolution of the sex chromosomes.
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| 14. |
- Abbott, Jessica K.
(författare)
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Intra-locus sexual conflict and sexually antagonistic genetic variation in hermaphroditic animals
- 2011
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 278:1703, s. 161-169
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Forskningsöversikt (refereegranskat)abstract
- Intra-locus sexual conflict results when sex-specific selection pressures for a given trait act against the intra-sexual genetic correlation for that trait. It has been found in a wide variety of taxa in both laboratory and natural populations, but the importance of intra-locus sexual conflict and sexually antagonistic genetic variation in hermaphroditic organisms has rarely been considered. This is not so surprising given the conceptual and theoretical association of intra-locus sexual conflict with sexual dimorphism, but there is no a priori reason why intra-locus sexual conflict cannot occur in hermaphroditic organisms as well. Here, I discuss the potential for intra-locus sexual conflict in hermaphroditic animals and review the available evidence for such conflict, and for the existence of sexually antagonistic genetic variation in hermaphrodites. I argue that mutations with asymmetric effects are particularly likely to be important in mediating sexual antagonism in hermaphroditic organisms. Moreover, sexually antagonistic genetic variation is likely to play an important role in inter-individual variation in sex allocation and in transitions to and from gonochorism (separate sexes) in simultaneous hermaphrodites. I also describe how sequential hermaphrodites may experience a unique form of intra-locus sexual conflict via antagonistic pleiotropy. Finally, I conclude with some suggestions for further research.
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| 15. |
- Abbott, Jessica K., et al.
(författare)
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Obtaining snapshots of genetic variation using hemiclonal analysis
- 2011
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Ingår i: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 26:7, s. 359-368
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Forskningsöversikt (refereegranskat)abstract
- Hemiclones are naturally occurring or artificially produced individuals that share a single specific genetic haplotype. Natural hemiclones are produced via hybridization between two closely related species, whereas hemiclonal analysis in Drosophila is carried out in the laboratory via crosses with artificially created 'clone-generator' females with a specific genetic make-up. Hemiclonal analysis in Drosophila has been applied successfully to date to obtain measures of standing genetic variation for numerous traits. Here, we review the current hemiclonal literature and suggest future directions for hemiclonal research, including its application in molecular and genomic studies, and the adaptation of natural hemiclonal systems to carry out Drosophila-type studies of standing genetic variation.
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| 16. |
- Cīrulis, Aivars, et al.
(författare)
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Sex-limited chromosomes and non-reproductive traits
- 2022
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Ingår i: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 20
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Forskningsöversikt (refereegranskat)abstract
- Sex chromosomes are typically viewed as having originated from a pair of autosomes, and differentiated as the sex-limited chromosome (e.g. Y) has degenerated by losing most genes through cessation of recombination. While often thought that degenerated sex-limited chromosomes primarily affect traits involved in sex determination and sex cell production, accumulating evidence suggests they also influence traits not sex-limited or directly involved in reproduction. Here, we provide an overview of the effects of sex-limited chromosomes on non-reproductive traits in XY, ZW or UV sex determination systems, and discuss evolutionary processes maintaining variation at sex-limited chromosomes and molecular mechanisms affecting non-reproductive traits.
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| 17. |
- Epstein, Yaffa, et al.
(författare)
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Science and the legal rights of nature
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 380:6646
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Forskningsöversikt (refereegranskat)abstract
- We review the use of science by lawmakers and courts in implementing or rejecting legal rights for nature in Ecuador, India, the United States, and other jurisdictions where some type of rights of nature have been recognized in the legal system. We then use the "right to evolve" to exemplify how interdisciplinary work can (i) help courts effectively define what this right might entail; (ii) inform how might be applied in different circumstances; and (iii) provide a template for how scientists and legal scholars can generate the interdisciplinary scholarship necessary to understand and implement the growing body of rights-of-nature laws, and environmental law more generally. We conclude by pointing to what further research is needed to understand and effectively implement the growing body of rights-of-nature laws.
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| 18. |
- Epstein, Yaffa, et al.
(författare)
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Science and the legal rights of nature
- 2023
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Ingår i: Science. - 0036-8075. ; 380:6646
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Forskningsöversikt (refereegranskat)abstract
- We review the use of science by lawmakers and courts in implementing or rejecting legal rights for nature in Ecuador, India, the United States, and other jurisdictions where some type of rights of nature have been recognized in the legal system. We then use the “right to evolve” to exemplify how interdisciplinary work can (i) help courts effectively define what this right might entail; (ii) inform how it might be applied in different circumstances; and (iii) provide a template for how scientists and legal scholars can generate the interdisciplinary scholarship necessary to understand and implement the growing body of rights-of-nature laws, and environmental law more generally. We conclude by pointing to what further research is needed to understand and effectively implement the growing body of rights-of-nature laws.
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| 19. |
- Ferraro, Gino B., et al.
(författare)
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Fatty acid synthesis is required for breast cancer brain metastasis
- 2021
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Ingår i: Nature Cancer. - : Springer Science and Business Media LLC. - 2662-1347. ; 2:4, s. 414-428
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Tidskriftsartikel (refereegranskat)abstract
- Brain metastases are refractory to therapies that control systemic disease in patients with human epidermal growth factor receptor 2-positive breast cancer and the brain microenvironment contributes to this therapy resistance. Nutrient availability can vary across tissues, therefore metabolic adaptations required for brain metastatic breast cancer growth may introduce liabilities that can be exploited for therapy. Here we assessed how metabolism differs between breast tumors in brain versus extracranial sites and found that fatty acid synthesis is elevated in breast tumors growing in the brain. We determine that this phenotype is an adaptation to decreased lipid availability in the brain relative to other tissues, resulting in site-specific dependency on fatty acid synthesis for breast tumors growing at this site. Genetic or pharmacological inhibition of fatty acid synthase reduces human epidermal growth factor receptor 2-positive breast tumor growth in the brain, demonstrating that differences in nutrient availability across metastatic sites can result in targetable metabolic dependencies.
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| 20. |
- Hoedjes, Katja M., et al.
(författare)
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From whole bodies to single cells : A guide to transcriptomic approaches for ecology and evolutionary biology
- 2024
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X.
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Tidskriftsartikel (refereegranskat)abstract
- RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.
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| 21. |
- Jansson, Samuel, et al.
(författare)
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Correlation of mosquito wing-beat harmonics to aid in species classification and flight heading assessment
- 2019
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Ingår i: Novel Biophotonics Techniques and Applications V. - : SPIE. - 1605-7422 .- 2410-9045. - 9781510628434 ; 20:60
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Konferensbidrag (refereegranskat)abstract
- Surveying disease vectors is currently excessively laborious for continuous and widespread monitoring. Wing beat modulation spectroscopy gives opportunity for species and sex recognition in electronic traps or mosquito target classification in lidar. We used a polarimetric dual-wavelength-band laboratory system to record kHz modulated backscattered light from insects. The system operates in the near and short-wave infrared at 808 nm and 1550 nm and retrieves both co- and depolarized light. Here we give clues on the harmonic content and covariance of four mosquito species and fruit flies. Further, we interpret the interdependence of harmonic strengths when insects transit the probe volume with random heading direction and provide correlation matrices for coherent and incoherent light. Using the obtained parameters, we demonstrate that species that are difficult to distinguish with microscope can be classified with high accuracy. The results are valuable for understanding wingbeat harmonics in relation to heading and valuable for optimal sensor design for disease vector surveillance.
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| 22. |
- Liotta, Melissa N., et al.
(författare)
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Antagonistic selection on body size and sword length in a wild population of the swordtail fish, Xiphophorus multilineatus : Potential for intralocus tactical conflict
- 2021
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 11:9, s. 3941-3955
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Tidskriftsartikel (refereegranskat)abstract
- Alternative reproductive tactics (ARTs) have provided valuable insights into how sexual selection and life history trade-offs can lead to variation within a sex. However, the possibility that tactics may constrain evolution through intralocus tactical conflict (IATC) is rarely considered. In addition, when IATC has been considered, the focus has often been on the genetic correlations between the ARTs, while evidence that the ARTs have different optima for associated traits and that at least one of the tactics is not at its optimum is often missing. Here, we investigate selection on three traits associated with the ARTs in the swordtail fish Xiphophorus multilineatus; body size, body shape, and the sexually selected trait for which these fishes were named, sword length (elongation of the caudal fin). All three traits are tactically dimorphic, with courter males being larger, deeper bodied and having longer swords, and the sneaker males being smaller, more fusiform and having shorter swords. Using measures of reproductive success in a wild population we calculated selection differentials, as well as linear and quadratic gradients. We demonstrated that the tactics have different optima and at least one of the tactics is not at its optimum for body size and sword length. Our results provide the first evidence of selection in the wild on the sword, an iconic trait for sexual selection. In addition, given the high probability that these traits are genetically correlated to some extent between the two tactics, our study suggests that IATC is constraining both body size and the sword from reaching their phenotypic optima. We discuss the importance of considering the role of IATC in the evolution of tactical dimorphism, how this conflict can be present despite tactical dimorphism, and how it is important to consider this conflict when explaining not only variation within a species but differences across species as well.
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| 23. |
- Liotta, Melissa N., et al.
(författare)
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Evidence for genetic integration of mating behavior and morphology in a behaviorally plastic alternative reproductive tactic
- 2021
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Ingår i: Evolutionary Ecology. - : Springer Science and Business Media LLC. - 0269-7653 .- 1573-8477. ; 35:44687, s. 723-737
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Tidskriftsartikel (refereegranskat)abstract
- Alternative reproductive tactics (ARTs) often exhibit more than one mating behavior depending on social context (i.e., behavioral plasticity). It has been hypothesized that by constraining an ART from reaching optimal morphological states, intralocus tactical conflict could promote the maintenance of behavioral plasticity in ARTs, rather than the use of a fixed mating behavior to match an optimal morphological state. For selection on either behavior or morphology to influence one another, there would need to be genetic integration between these traits within the behaviorally plastic males. To examine this possibility, we compared the relationship between body shape, body size and propensity to use sneak-chase behavior across experienced wild-caught males and inexperienced lab reared males from the behaviorally plastic ART (sneaker males) of the swordtail fish Xiphophorus multilineatus. The smaller, more narrow-bodied sneaker males use both force copulatory sneak-chases and courtship behavior to access females, while the larger, deeper-bodied courter males are fixed in their use of courtship behavior. We detected similar relationships between body size and the propensity to use sneak-chase behavior within the sneaker males when they were alone with a female (no competitor present) for both experienced and inexperienced males, suggesting genetic integration between behavior and body size. Body shape, on the other hand, was more complex and suggested both genetic integration (more fusiform males from both groups were more likely to use sneak-chase), as well as learning depending on subtle differences in body shape. We discuss how intralocus tactical conflict on morphological traits that are genetically integrated with behaviors has the potential to maintain behavioral plasticity in the X. multilineatus sneaker males and influence the evolution of ARTs in general.
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| 24. |
- Liotta, Melissa N, et al.
(författare)
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Tactical dimorphism : the interplay between body shape and mating behaviour in the swordtail Xiphophorus multilineatus (Cyprinodontiformes: Poeciliidae)
- 2019
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Ingår i: Biological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4066 .- 1095-8312. ; 127:2, s. 337-350
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Tidskriftsartikel (refereegranskat)abstract
- Alternative reproductive tactics (ARTs) are characterized by dimorphism for reproductive phenotypes (i.e. tactical dimorphism). Tactical dimorphism often evolves as a response to differing phenotypic optima for a shared reproductive trait between members of the same sex in a species. We characterized dimorphism for body shape between ARTs in the swordtail fish Xiphophorus multilineatus and investigated the relationship between body shape and mating behaviours. Xiphophorus multilineatus possesses two ARTs, a courter male that uses only courtship to attract females, and a sneaker male that is contextually plastic and uses both courtship and force copulatory sneak chases. We found that courter and sneaker males are dimorphic for body shape; however, we did not detect a significant difference in the allometric relationship between body shape and size. Additionally, we found that more fusiform sneaker males were more likely to use sneak-chase behaviour in the absence of a competitor. These results suggest that the ARTs in X. multilineatus have different phenotypic optima for body shape and that a fusiform body shape might be more optimal for sneak-chase behaviour. Understanding tactical dimorphism in this species will allow us to explore further how the ARTs evolved and the potential for intralocus tactical conflict to constrain the evolution of each ART from reaching their respective optima.
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| 25. |
- Olito, Colin, et al.
(författare)
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Consequences of partially recessive deleterious genetic variation for the evolution of inversions suppressing recombination between sex chromosomes
- 2022
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 76:6, s. 1320-1330
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of suppressed recombination between sex chromosomes is widely hypothesized to be driven by sexually antagonistic selection (SA), where tighter linkage between the sex-determining gene(s) and nearby SA loci is favored when it couples male-beneficial alleles to the proto-Y chromosome, and female-beneficial alleles to the proto-X. Despite limited empirical evidence, the SA selection hypothesis overshadows several alternatives, including an incomplete but often-repeated “sheltering hypothesis” that suggests that expansion of the sex-linked region (SLR) reduces homozygous expression of partially recessive deleterious mutations at selected loci. Here, we use population genetic models to evaluate the consequences of deleterious mutational variation for the evolution of neutral chromosomal inversions expanding the SLR on proto-Y chromosomes. We find that SLR-expanding inversions face a race against time: lightly loaded inversions are initially beneficial, but eventually become deleterious as they accumulate new mutations, and must fix before this window of opportunity closes. The outcome of this race is strongly influenced by inversion size, the mutation rate, and the dominance coefficient of deleterious mutations. Yet, small inversions have elevated fixation probabilities relative to neutral expectations for biologically plausible parameter values. Our results demonstrate that deleterious genetic variation can plausibly drive recombination suppression in small steps and would be most consistent with empirical patterns of small evolutionary strata or gradual recombination arrest.
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| 26. |
- Olito, Colin, et al.
(författare)
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The evolution of suppressed recombination between sex chromosomes and the lengths of evolutionary strata
- 2023
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Ingår i: Evolution; international journal of organic evolution. - : Oxford University Press (OUP). - 1558-5646. ; 77:4, s. 1077-1090
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Tidskriftsartikel (refereegranskat)abstract
- The idea that sex differences in selection drive the evolution of suppressed recombination between sex chromosomes is well developed in population genetics. Yet, despite a now classic body of theory, empirical evidence that sexually antagonistic selection drives the evolution of recombination arrest remains equivocal and alternative hypotheses underdeveloped. Here, we investigate whether the length of "evolutionary strata" formed by chromosomal inversions (or other large-effect recombination modifiers) expanding the non-recombining sex-linked region (SLR) on sex chromosomes can be informative of how selection influenced their fixation. We develop population genetic models to show how the length of an SLR-expanding inversion, and the presence of partially recessive deleterious mutational variation, affect the fixation probability of three different classes of inversions: (1) intrinsically neutral, (2) directly beneficial (i.e., due to breakpoint or positional effects), and (3) those capturing sexually antagonistic (SA) loci. Our models indicate that neutral inversions, and those capturing an SA locus in linkage disequilibrium with the ancestral SLR, will exhibit a strong fixation bias toward small inversions; while unconditionally beneficial inversions, and those capturing a genetically unlinked SA locus, will favor fixation of larger inversions. The footprint of evolutionary stratum size left behind by different selection regimes is strongly influenced by parameters affecting the deleterious mutation load, the physical position of the ancestral SLR, and the distribution of new inversion lengths.
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| 27. |
- Olito, Colin, et al.
(författare)
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The interaction between sex-specific selection and local adaptation in species without separate sexes
- 2018
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Ingår i: Philosophical Transactions of the Royal Society B: Biological Sciences. - : The Royal Society. - 1471-2970 .- 0962-8436. ; 373:1757
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Tidskriftsartikel (refereegranskat)abstract
- Local adaptation in hermaphrodite species can be based on a variety of fitness components, including survival, as well as both female and male sex-functions within individuals. When selection via female and male fitness components varies spatially (e.g. due to environmental heterogeneity), local adaptation will depend, in part, on variation in selection through each fitness component, and the extent to which genetic trade-offs between sex-functions maintain genetic variation necessary for adaptation. Local adaptation will also depend on the hermaphrodite mating system because self-fertilization alters several key factors influencing selection and the maintenance of genetic variance underlying trade-offs between the sex-functions (sexually antagonistic polymorphism). As a first step to guide intuition regarding sex-specific adaptation in hermaphrodites, we develop a simple theoretical model incorporating the essential features of hermaphrodite mating and adaptation in a spatially heterogeneous environment, and explore the interaction between sex-specific selection, self-fertilization and local adaptation. Our results suggest that opportunities for sex-specific local adaptation in hermaphrodites depend strongly on the extent of self-fertilization and inbreeding depression. Using our model as a conceptual framework, we provide a broad overview of the literature on sex-specific selection and local adaptation in hermaphroditic plants and animals, emphasizing promising future directions in light of our theoretical predictions.
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| 28. |
- Ponnikas, Suvi, et al.
(författare)
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Why Do Sex Chromosomes Stop Recombining?
- 2018
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Ingår i: Trends in Genetics. - : Elsevier BV. - 0168-9525. ; 34:7, s. 492-503
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Tidskriftsartikel (refereegranskat)abstract
- It is commonly assumed that sex chromosomes evolve recombination suppression because selection favours linkage between sex-determining and sexually antagonistic genes. However, although the role of sexual antagonism during sex chromosome evolution has attained strong support from theory, experimental and observational evidence is rare or equivocal. Here, we highlight alternative, often neglected, hypotheses for recombination suppression on sex chromosomes, which invoke meiotic drive, heterozygote advantage, and genetic drift, respectively. We contrast the hypotheses, the situations when they are likely to be of importance, and outline why it is surprisingly difficult to test them. Lastly, we discuss future research directions (including modelling, population genomics, comparative approaches, and experiments) to disentangle the different hypotheses of sex chromosome evolution.
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| 29. |
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