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Wierzbicki F, Kofler R, Signor S. Evolutionary dynamics of piRNA clusters in Drosophila. Mol Ecol 2023; 32:1306-1322. [PMID: 34878692 DOI: 10.1111/mec.16311] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 12/21/2022]
Abstract
Small RNAs produced from transposable element (TE)-rich sections of the genome, termed piRNA clusters, are a crucial component in the genomic defence against selfish DNA. In animals, it is thought the invasion of a TE is stopped when a copy of the TE inserts into a piRNA cluster, triggering the production of cognate small RNAs that silence the TE. Despite this importance for TE control, little is known about the evolutionary dynamics of piRNA clusters, mostly because these repeat-rich regions are difficult to assemble and compare. Here, we establish a framework for studying the evolution of piRNA clusters quantitatively. Previously introduced quality metrics and a newly developed software for multiple alignments of repeat annotations (Manna) allow us to estimate the level of polymorphism segregating in piRNA clusters and the divergence among homologous piRNA clusters. By studying 20 conserved piRNA clusters in multiple assemblies of four Drosophila species, we show that piRNA clusters are evolving rapidly. While 70%-80% of the clusters are conserved within species, the clusters share almost no similarity between species as closely related as D. melanogaster and D. simulans. Furthermore, abundant insertions and deletions are segregating within the Drosophila species. We show that the evolution of clusters is mainly driven by large insertions of recently active TEs and smaller deletions mostly in older TEs. The effect of these forces is so rapid that homologous clusters often do not contain insertions from the same TE families.
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Affiliation(s)
- Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
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Bailey NW, Desjonquères C. The Indirect Genetic Effect Interaction Coefficient ψ: Theoretically Essential and Empirically Neglected. J Hered 2022; 113:79-90. [PMID: 34791332 PMCID: PMC8851666 DOI: 10.1093/jhered/esab056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/20/2021] [Indexed: 12/23/2022] Open
Abstract
The interaction effect coefficient ψ has been a much-discussed, fundamental parameter of indirect genetic effect (IGE) models since its formal mathematical description in 1997. The coefficient simultaneously describes the form of changes in trait expression caused by genes in the social environment and predicts the evolutionary consequences of those IGEs. Here, we report a striking mismatch between theoretical emphasis on ψ and its usage in empirical studies. Surveying all IGE research, we find that the coefficient ψ has not been equivalently conceptualized across studies. Several issues related to its proper empirical measurement have recently been raised, and these may severely distort interpretations about the evolutionary consequences of IGEs. We provide practical advice on avoiding such pitfalls. The majority of empirical IGE studies use an alternative variance-partitioning approach rooted in well-established statistical quantitative genetics, but several hundred estimates of ψ (from 15 studies) have been published. A significant majority are positive. In addition, IGEs with feedback, that is, involving the same trait in both interacting partners, are far more likely to be positive and of greater magnitude. Although potentially challenging to measure without bias, ψ has critically-developed theoretical underpinnings that provide unique advantages for empirical work. We advocate for a shift in perspective for empirical work, from ψ as a description of IGEs, to ψ as a robust predictor of evolutionary change. Approaches that "run evolution forward" can take advantage of ψ to provide falsifiable predictions about specific trait interactions, providing much-needed insight into the evolutionary consequences of IGEs.
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Affiliation(s)
- Nathan W Bailey
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
| | - Camille Desjonquères
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
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Baud A, McPeek S, Chen N, Hughes KA. Indirect Genetic Effects: A Cross-disciplinary Perspective on Empirical Studies. J Hered 2022; 113:1-15. [PMID: 34643239 PMCID: PMC8851665 DOI: 10.1093/jhered/esab059] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Indirect genetic effects (IGE) occur when an individual's phenotype is influenced by genetic variation in conspecifics. Opportunities for IGE are ubiquitous, and, when present, IGE have profound implications for behavioral, evolutionary, agricultural, and biomedical genetics. Despite their importance, the empirical study of IGE lags behind the development of theory. In large part, this lag can be attributed to the fact that measuring IGE, and deconvoluting them from the direct genetic effects of an individual's own genotype, is subject to many potential pitfalls. In this Perspective, we describe current challenges that empiricists across all disciplines will encounter in measuring and understanding IGE. Using ideas and examples spanning evolutionary, agricultural, and biomedical genetics, we also describe potential solutions to these challenges, focusing on opportunities provided by recent advances in genomic, monitoring, and phenotyping technologies. We hope that this cross-disciplinary assessment will advance the goal of understanding the pervasive effects of conspecific interactions in biology.
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Affiliation(s)
- Amelie Baud
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,the Universitat Pompeu Fabra (UPF), Barcelona,Spain
| | - Sarah McPeek
- the Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Nancy Chen
- the Department of Biology, University of Rochester, Rochester, NY 14627,USA
| | - Kimberly A Hughes
- the Department of Biological Science, Florida State University, Tallahassee, FL 32303,USA
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Signor SA. Evolution of Plasticity in Response to Ethanol between Sister Species with Different Ecological Histories ( Drosophila melanogaster and D. simulans). Am Nat 2020; 196:620-633. [PMID: 33064591 DOI: 10.1086/710763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractWhen populations evolve adaptive reaction norms in response to novel environments, it can occur through a process termed genetic accommodation. Under this model, the initial response to the environment is widely variable between genotypes as a result of cryptic genetic variation, which is then refined by selection to a single adaptive response. Here, I empirically test these predictions from genetic accommodation by measuring reaction norms in individual genotypes and across several time points. I compare two species of Drosophila that differ in their adaptation to ethanol (D. melanogaster and D. simulans). Both species are human commensals with a recent cosmopolitan expansion, but only D. melanogaster is adapted to ethanol exposure. Using gene expression as a phenotype and an approach that combines information about expression and alternative splicing, I find that D. simulans exhibits cryptic genetic variation in the response to ethanol, while D. melanogaster has almost no genotype-specific variation in reaction norm. This is evidence for adaptation to ethanol through genetic accommodation, suggesting that the evolution of phenotypic plasticity could be an important contributor to the ability to exploit novel resources.
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Halmenschelager PT, da Rocha JBT. Biochemical CuSO 4 Toxicity in Drosophila melanogaster Depends on Sex and Developmental Stage of Exposure. Biol Trace Elem Res 2019; 189:574-585. [PMID: 30178145 DOI: 10.1007/s12011-018-1475-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/07/2018] [Indexed: 01/01/2023]
Abstract
Copper is a transition metal that exists in different chemical forms (e.g., Cu2+,Cu+, and Cu0) and at high concentrations it is toxic. Here, we investigated the Cu2+-induced toxicity in Drosophila melanogaster, evaluating the survival, locomotion, and the activity of acetylcholinesterase (AChE) and glutathione S-transferase (GST) enzymes. Flies were exposed to Cu2+(0.1-1 mmol CuSO4/kg of diet or approximately 0.1-1 mM Cu2+) and allowed to mate during 24 h. GST and AChE enzymes were evaluated in the larvae and in the head and the body (thorax + abdomen) of the adult male and females flies. The total number of adult females (0.4-1 mM) and males (0.75 and 1 mM) was decreased by CuSO4. The climbing ability was hampered in flies exposed to 1 mM Cu2+. In larvae, Cu2+(0.4-1 mM) increased AChE activity (P < 0.002). In males' heads, 0.4 mM Cu2+ increased the AChE activity (P < 0.01). In adults' bodies, Cu2+inhibited the activity in both sexes, but with greater effectiveness in males (0.1 to 1 mM) than in females (1 mM). Regarding GST activity, 0.1 mM Cu2+increased, but 1 mM decrease GST in larvae. In the head of flies, Cu2+decreased the GST activity at intermediate (0.4 mM) and increased GST at the highest concentration (1 mM) in males. In the bodies, the effect of Cu2+was similar. In conclusion, Cu2+exposure in D. melanogaster disrupted locomotion and enzymatic parameters that can be related to changes in AChE and in the detoxifying GST enzyme.
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Affiliation(s)
- Paula Tais Halmenschelager
- Department of Biochemistry and Molecular Biology, Center for Natural and Exact Sciences, Federal University of Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - João Batista Teixeira da Rocha
- Department of Biochemistry and Molecular Biology, Center for Natural and Exact Sciences, Federal University of Santa Maria, Santa Maria, Rio Grande do Sul, Brazil.
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Signor S, Nuzhdin S. Dynamic changes in gene expression and alternative splicing mediate the response to acute alcohol exposure in Drosophila melanogaster. Heredity (Edinb) 2018; 121:342-360. [PMID: 30143789 DOI: 10.1038/s41437-018-0136-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/21/2018] [Accepted: 07/19/2018] [Indexed: 12/18/2022] Open
Abstract
Environmental changes typically cause rapid gene expression responses in the exposed organisms, including changes in the representation of gene isoforms with different functions or properties. Identifying the genes that respond to environmental change, including in genotype-specific ways, is an important step in treating the undesirable physiological effects of stress, such as exposure to toxins or ethanol. Ethanol is a unique environmental stress in that chronic exposure results in permanent physiological changes and the development of alcohol use disorders. Drosophila is a classic model for deciphering the mechanisms of the response to alcohol exposure, as it meets the criteria for the development of alcohol use disorders, and has similar physiological underpinnings with vertebrates. Because many studies on the response to ethanol have relied on a priori candidate genes, broad surveys of gene expression and splicing are required and have been investigated here. Further, we expose Drosophila to ethanol in an environment that is genetically, socially, and ecologically relevant. Both expression and splicing differences, inasmuch as they can be decomposed, contribute to the response to ethanol in Drosophila melanogaster. However, we find that while D. melanogaster responds to ethanol, there is very little genetic variation in how it responds to ethanol. In addition, the response to alcohol over time is dynamic, suggesting that incorporating time into studies on the response to the environment is important.
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Affiliation(s)
- Sarah Signor
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
| | - Sergey Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
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Signor SA, Abbasi M, Marjoram P, Nuzhdin SV. Conservation of social effects (Ψ ) between two species of Drosophila despite reversal of sexual dimorphism. Ecol Evol 2017; 7:10031-10041. [PMID: 29238534 PMCID: PMC5723616 DOI: 10.1002/ece3.3523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 12/15/2022] Open
Abstract
Indirect genetic effects (IGEs) describe the effect of the genes of social partners on the phenotype of a focal individual. Here, we measure indirect genetic effects using the “coefficient of interaction” (Ψ) to test whether Ψ evolved between Drosophila melanogaster and D. simulans. We compare Ψ for locomotion between ethanol and nonethanol environments in both species, but only D. melanogaster utilizes ethanol ecologically. We find that while sexual dimorphism for locomotion has been reversed in D. simulans, there has been no evolution of social effects between these two species. What did evolve was the interaction between genotype‐specific Ψ and the environment, as D. melanogaster varies unpredictably between environments and D. simulans does not. In this system, this suggests evolutionary lability of sexual dimorphism but a conservation of social effects, which brings forth interesting questions about the role of the social environment in sexual selection.
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Affiliation(s)
- Sarah A Signor
- Program in Molecular and Computational Biology Dornsife College of Letters, Arts and Sciences University of Southern California Los Angeles CA USA
| | - Mohammad Abbasi
- Graduate Program in Computational Biology Dornsife College of Letters, Arts and Sciences University of Southern California Los Angeles CA USA
| | - Paul Marjoram
- Program in Molecular and Computational Biology Dornsife College of Letters, Arts and Sciences University of Southern California Los Angeles CA USA.,Department of Preventive Medicine Keck School of Medicine University of Southern California Los Angeles CA USA
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology Dornsife College of Letters, Arts and Sciences University of Southern California Los Angeles CA USA
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