1
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Babonis LS. On the evolutionary developmental biology of the cell. Trends Genet 2024; 40:822-833. [PMID: 38971670 DOI: 10.1016/j.tig.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
Organisms are complex assemblages of cells, cells that produce light, shoot harpoons, and secrete glue. Therefore, identifying the mechanisms that generate novelty at the level of the individual cell is essential for understanding how multicellular life evolves. For decades, the field of evolutionary developmental biology (Evo-Devo) has been developing a framework for connecting genetic variation that arises during embryonic development to the emergence of diverse adult forms. With increasing access to new single cell 'omics technologies and an array of techniques for manipulating gene expression, we can now extend these inquiries inward to the level of the individual cell. In this opinion, I argue that applying an Evo-Devo framework to single cells makes it possible to explore the natural history of cells, where this was once only possible at the organismal level.
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Affiliation(s)
- Leslie S Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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2
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Zetzsche J, Fallet M. To live or let die? Epigenetic adaptations to climate change-a review. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae009. [PMID: 39139701 PMCID: PMC11321362 DOI: 10.1093/eep/dvae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/05/2024] [Accepted: 07/03/2024] [Indexed: 08/15/2024]
Abstract
Anthropogenic activities are responsible for a wide array of environmental disturbances that threaten biodiversity. Climate change, encompassing temperature increases, ocean acidification, increased salinity, droughts, and floods caused by frequent extreme weather events, represents one of the most significant environmental alterations. These drastic challenges pose ecological constraints, with over a million species expected to disappear in the coming years. Therefore, organisms must adapt or face potential extinctions. Adaptations can occur not only through genetic changes but also through non-genetic mechanisms, which often confer faster acclimatization and wider variability ranges than their genetic counterparts. Among these non-genetic mechanisms are epigenetics defined as the study of molecules and mechanisms that can perpetuate alternative gene activity states in the context of the same DNA sequence. Epigenetics has received increased attention in the past decades, as epigenetic mechanisms are sensitive to a wide array of environmental cues, and epimutations spread faster through populations than genetic mutations. Epimutations can be neutral, deleterious, or adaptative and can be transmitted to subsequent generations, making them crucial factors in both long- and short-term responses to environmental fluctuations, such as climate change. In this review, we compile existing evidence of epigenetic involvement in acclimatization and adaptation to climate change and discuss derived perspectives and remaining challenges in the field of environmental epigenetics. Graphical Abstract.
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Affiliation(s)
- Jonas Zetzsche
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro 70182, Sweden
| | - Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro 70182, Sweden
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3
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Desta TT, Wakeyo O. Breeding practice of indigenous village chickens, and traits and breed preferences of smallholder farmers. Vet Med Sci 2024; 10:e1517. [PMID: 38952253 PMCID: PMC11217597 DOI: 10.1002/vms3.1517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/18/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND Indigenous village chickens, or (IVCs), significantly contribute to rural livelihoods. Although natural selection has a disproportionate impact on the genetic structure of IVCs, farmers have developed locally tailored breeding practices to get the most out of their flocks. OBJECTIVES Small-scale farmers' insights on trait breed preferences and family flock breeding practices are presented in this cross-sectional study. METHODS A cross-sectional study was conducted in two agroecological zones using face-to-face individual interviews with 119 general informants. RESULTS Farmers prefer IVCs because they are multipurpose birds. Unlike policymakers, who usually underestimate the importance of IVCs, small-scale farmers acknowledge the coexistence of local and commercial chickens. Only 15.7% of farmers recruited homegrown cocks, whereas 47.9% outsourced breeding cocks from local markets and 36.4% from neighbours (χ-squared = 15.976, df = 2, p = 0.0003395). About 49.2% of small-scale farmers believed that consanguineous mating-induced inbreeding has only trivial effects. High flock turnover significantly reduces inbreeding. Regardless of the low production capacity, small-scale farmers prefer local (rank = 1.47) chickens to commercial (rank = 1.61). For cocks, fertility and growth traits were highly sought after, whereas for hens, maternal instincts and laying performance were prioritized. Compared to the highlands, the lowlands had a longer egg storage period (t = 2.677, df = 117, p = 0.009, 95% CI: -3.7607, -0.5622). CONCLUSIONS This study documented the wisdom of small-scale farmers and encouraged the incorporation of their insights into a sustainable genetic improvement program.
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Affiliation(s)
- Takele Taye Desta
- Wolaita Sodo AgriculturalTechnical, VocationalEducation and Training CollegeSodoEthiopia
- Present address:
Department of Biology, College of Science and Mathematics EducationKotebe University of EducationAddis AbabaEthiopia
| | - Oli Wakeyo
- Wolaita Sodo AgriculturalTechnical, VocationalEducation and Training CollegeSodoEthiopia
- Present address:
College of Agriculture and Environmental ScienceArsi UniversityAselaEthiopia
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4
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Plesnar-Bielak A, Parrett JM, Chmielewski S, Dudek K, Łukasiewicz A, Marszałek M, Babik W, Konczal M. Transcriptomics of differences in thermal plasticity associated with selection for an exaggerated male sexual trait. Heredity (Edinb) 2024; 133:43-53. [PMID: 38802597 PMCID: PMC11222471 DOI: 10.1038/s41437-024-00691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperature. Temperature decrease to 18 °C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a significant selection-by-temperature interaction effect on the expression of 40 genes, 38 of which were upregulated in fighter-selected populations in response to temperature decrease. In response to 28 °C, no selection-by-temperature interaction in gene expression was detected. Hence, differences in phenotypic response to temperature increase likely depended on genes associated with their distinct morph-specific thermal tolerance. Selection of males also drove gene expression patterns in females. These patterns could be associated with temperature-dependent fitness differences between females from fighter- vs. scrambler-selected populations reported in previous studies. Our study shows that selection for divergent male sexually selected morphologies and behaviors has a potential to drive divergence in metabolic pathways underlying plastic response to temperature in both sexes.
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Affiliation(s)
- Agata Plesnar-Bielak
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland.
| | - Jonathan M Parrett
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Sebastian Chmielewski
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Aleksandra Łukasiewicz
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Marzena Marszałek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Mateusz Konczal
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
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5
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Isdaner AJ, Levis NA, Ehrenreich IM, Pfennig DW. Genetic Variants Underlying Plasticity in Natural Populations of Spadefoot Toads: Environmental Assessment versus Phenotypic Response. Genes (Basel) 2024; 15:611. [PMID: 38790242 PMCID: PMC11121243 DOI: 10.3390/genes15050611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Many organisms facultatively produce different phenotypes depending on their environment, yet relatively little is known about the genetic bases of such plasticity in natural populations. In this study, we describe the genetic variation underlying an extreme form of plasticity--resource polyphenism--in Mexican spadefoot toad tadpoles, Spea multiplicata. Depending on their environment, these tadpoles develop into one of two drastically different forms: a carnivore morph or an omnivore morph. We collected both morphs from two ponds that differed in which morph had an adaptive advantage and performed genome-wide association studies of phenotype (carnivore vs. omnivore) and adaptive plasticity (adaptive vs. maladaptive environmental assessment). We identified four quantitative trait loci associated with phenotype and nine with adaptive plasticity, two of which exhibited signatures of minor allele dominance and two of which (one phenotype locus and one adaptive plasticity locus) did not occur as minor allele homozygotes. Investigations into the genetics of plastic traits in natural populations promise to provide novel insights into how such complex, adaptive traits arise and evolve.
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Affiliation(s)
- Andrew J. Isdaner
- Department of Biology, CB#3280, University of North Carolina, Chapel Hill, NC 27599, USA; (A.J.I.); (N.A.L.)
| | - Nicholas A. Levis
- Department of Biology, CB#3280, University of North Carolina, Chapel Hill, NC 27599, USA; (A.J.I.); (N.A.L.)
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ian M. Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - David W. Pfennig
- Department of Biology, CB#3280, University of North Carolina, Chapel Hill, NC 27599, USA; (A.J.I.); (N.A.L.)
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6
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Hu Y, Crabtree JR, Macagno ALM, Moczek AP. Histone deacetylases regulate organ-specific growth in a horned beetle. EvoDevo 2024; 15:4. [PMID: 38575982 PMCID: PMC10996171 DOI: 10.1186/s13227-024-00223-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Nutrient availability is among the most widespread means by which environmental variability affects developmental outcomes. Because almost all cells within an individual organism share the same genome, structure-specific growth responses must result from changes in gene regulation. Earlier work suggested that histone deacetylases (HDACs) may serve as epigenetic regulators linking nutritional conditions to trait-specific development. Here we expand on this work by assessing the function of diverse HDACs in the structure-specific growth of both sex-shared and sex-specific traits including evolutionarily novel structures in the horned dung beetle Onthophagus taurus. RESULTS We identified five HDAC members whose downregulation yielded highly variable mortality depending on which HDAC member was targeted. We then show that HDAC1, 3, and 4 operate in both a gene- and trait-specific manner in the regulation of nutrition-responsiveness of appendage size and shape. Specifically, HDAC 1, 3, or 4 knockdown diminished wing size similarly while leg development was differentially affected by RNAi targeting HDAC3 and HDAC4. In addition, depletion of HDAC3 transcript resulted in a more rounded shape of genitalia at the pupal stage and decreased the length of adult aedeagus across all body sizes. Most importantly, we find that HDAC3 and HDAC4 pattern the morphology and regulate the scaling of evolutionarily novel head and thoracic horns as a function of nutritional variation. CONCLUSION Collectively, our results suggest that both functional overlap and division of labor among HDAC members contribute to morphological diversification of both conventional and recently evolved appendages. More generally, our work raises the possibility that HDAC-mediated scaling relationships and their evolution may underpin morphological diversification within and across insect species broadly.
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Affiliation(s)
- Yonggang Hu
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN, 47405, USA.
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, No.2 Tiansheng Road, Beibei District, Chongqing, 400715, China.
| | - Jordan R Crabtree
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN, 47405, USA
| | - Anna L M Macagno
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN, 47405, USA
- Biostatistics Consulting Center, Department of Epidemiology and Biostatistics, School of Public Health Bloomington, Indiana University, 2719 E. 10th Street, Bloomington, IN, 47405, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN, 47405, USA
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7
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You S, Lei G, Zhou H, Li J, Chen S, Huang J, Vasseur L, Gurr GM, You M, Chen Y. Thermal acclimation uncovers a simple genetic basis of adaptation to high temperature in a cosmopolitan pest. iScience 2024; 27:109242. [PMID: 38425842 PMCID: PMC10904271 DOI: 10.1016/j.isci.2024.109242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/16/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Understanding a population's fitness heterogeneity and genetic basis of thermal adaptation is essential for predicting the responses to global warming. We examined the thermotolerance and genetic adaptation of Plutella xylostella to exposure to hot temperatures. The population fitness parameters of the hot-acclimated DBM strains varied in the thermal environments. Using genome scanning and transcription profiling, we find a number of genes potentially involved in thermal adaptation of DBM. Editing two ABCG transporter genes, PxWhite and PxABCG, confirmed their role in altering cuticle permeability and influencing thermal responses. Our results demonstrate that SNP mutations in genes and changes in gene expression can allow DBM to rapidly adapt to thermal environment. ABCG transporter genes play an important role in thermal adaptation of DBM. This work improves our understanding of genetic adaptation mechanisms of insects to thermal stress and our capacity to predict the effects of rising global temperatures on ectotherms.
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Affiliation(s)
- Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Gaoke Lei
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiling Zhou
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianyu Li
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shaoping Chen
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jieling Huang
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Department of Biological Sciences, UNESCO Chair on Community Sustainability, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Geoff M. Gurr
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Gulbali Institute, Charles Sturt University, Orange, NSW 2800, Australia
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanting Chen
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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8
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Yagound B, Sarma RR, Edwards RJ, Richardson MF, Rodriguez Lopez CM, Crossland MR, Brown GP, DeVore JL, Shine R, Rollins LA. Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad ( Rhinella marina)? Ecol Evol 2024; 14:e11127. [PMID: 38450317 PMCID: PMC10917582 DOI: 10.1002/ece3.11127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
Many organisms can adjust their development according to environmental conditions, including the presence of conspecifics. Although this developmental plasticity is common in amphibians, its underlying molecular mechanisms remain largely unknown. Exposure during development to either 'cannibal cues' from older conspecifics, or 'alarm cues' from injured conspecifics, causes reduced growth and survival in cane toad (Rhinella marina) tadpoles. Epigenetic modifications, such as changes in DNA methylation patterns, are a plausible mechanism underlying these developmental plastic responses. Here we tested this hypothesis, and asked whether cannibal cues and alarm cues trigger the same DNA methylation changes in developing cane toads. We found that exposure to both cannibal cues and alarm cues was associated with local changes in DNA methylation patterns. These DNA methylation changes affected genes putatively involved in developmental processes, but in different genomic regions for different conspecific-derived cues. Genetic background explains most of the epigenetic variation among individuals. Overall, the molecular mechanisms triggered by exposure to cannibal cues seem to differ from those triggered by alarm cues. Studies linking epigenetic modifications to transcriptional activity are needed to clarify the proximate mechanisms that regulate developmental plasticity in cane toads.
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Affiliation(s)
- Boris Yagound
- Evolution & Ecology Research Centre, Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Roshmi R. Sarma
- Evolution & Ecology Research Centre, Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
| | - Richard J. Edwards
- Evolution & Ecology Research Centre, School of Biotechnology and Biomedical SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteDeakin UniversityGeelongVictoriaAustralia
| | - Mark F. Richardson
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
- Minderoo OceanOmics Centre at UWA, Oceans InstituteDeakin UniversityGeelongVictoriaAustralia
- Deakin Genomics Research and Discovery FacilityDeakin University, Locked BagGeelongVICAustralia
| | - Carlos M. Rodriguez Lopez
- Deakin Genomics Research and Discovery FacilityDeakin University, Locked BagGeelongVICAustralia
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- Environmental Epigenetics and Genetics Group, Department of HorticultureCollege of Agriculture, Food and Environment, University of KentuckyLexingtonKentuckyUSA
| | - Michael R. Crossland
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
| | - Gregory P. Brown
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Jayna L. DeVore
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
- UMR 241 EIOUniversity of French Polynesia, IFREMER, ILM, IRDFaa’aTahitiFrench Polynesia
| | - Richard Shine
- School of Agriculture, Food and Wine, Waite Research InstituteThe University of AdelaideGlen OsmondSouth AustraliaAustralia
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Lee A. Rollins
- Evolution & Ecology Research Centre, Biological, Earth and Environmental SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityGeelongVictoriaAustralia
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9
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Steward RA, Pruisscher P, Roberts KT, Wheat CW. Genetic constraints in genes exhibiting splicing plasticity in facultative diapause. Heredity (Edinb) 2024; 132:142-155. [PMID: 38291272 PMCID: PMC10923799 DOI: 10.1038/s41437-024-00669-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Phenotypic plasticity is produced and maintained by processes regulating the transcriptome. While differential gene expression is among the most important of these processes, relatively little is known about other sources of transcriptional variation. Previous work suggests that alternative splicing plays an extensive and functionally unique role in transcriptional plasticity, though plastically spliced genes may be more constrained than the remainder of expressed genes. In this study, we explore the relationship between expression and splicing plasticity, along with the genetic diversity in those genes, in an ecologically consequential polyphenism: facultative diapause. Using 96 samples spread over two tissues and 10 timepoints, we compare the extent of differential splicing and expression between diapausing and direct developing pupae of the butterfly Pieris napi. Splicing differs strongly between diapausing and direct developing trajectories but alters a smaller and functionally unique set of genes compared to differential expression. We further test the hypothesis that among these expressed loci, plastically spliced genes are likely to experience the strongest purifying selection to maintain seasonally plastic phenotypes. Genes with unique transcriptional changes through diapause consistently had the lowest nucleotide diversity, and this effect was consistently stronger among genes that were differentially spliced compared to those with just differential expression through diapause. Further, the strength of negative selection was higher in the population expressing diapause every generation. Our results suggest that maintenance of the molecular mechanisms involved in diapause progression, including post-transcriptional modifications, are highly conserved and likely to experience genetic constraints, especially in northern populations of P. napi.
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Affiliation(s)
- Rachel A Steward
- Zoology Department, Stockholm University, Stockholm, Sweden.
- Biology Department, Lund University, Lund, Sweden.
| | - Peter Pruisscher
- Zoology Department, Stockholm University, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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10
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Lafuente E, Duneau D, Beldade P. Genetic basis of variation in thermal developmental plasticity for Drosophila melanogaster body pigmentation. Mol Ecol 2024; 33:e17294. [PMID: 38366327 DOI: 10.1111/mec.17294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Seasonal differences in insect pigmentation are attributed to the influence of ambient temperature on pigmentation development. This thermal plasticity is adaptive and heritable, and thereby capable of evolving. However, the specific genes contributing to the variation in plasticity that can drive its evolution remain largely unknown. To address this, we analysed pigmentation and pigmentation plasticity in Drosophila melanogaster. We measured two components of pigmentation in the thorax and abdomen: overall darkness and the proportion of length covered by darker pattern elements (a trident in the thorax and bands in the abdomen) in females from two developmental temperatures (17 or 28°C) and 191 genotypes. Using a GWAS approach to identify the genetic basis of variation in pigmentation and its response to temperature, we identified numerous dispersed QTLs, including some mapping to melanogenesis genes (yellow, ebony, and tan). Remarkably, we observed limited overlap between QTLs for variation within specific temperatures and those influencing thermal plasticity, as well as minimal overlap between plasticity QTLs across pigmentation components and across body parts. For most traits, consistent with selection favouring the retention of plasticity, we found that lower plasticity alleles were often at lower frequencies. The functional analysis of selected candidate QTLs and pigmentation genes largely confirmed their contributions to variation in pigmentation and/or pigmentation plasticity. Overall, our study reveals the existence and underlying basis of extensive and trait-specific genetic variation for pigmentation and pigmentation plasticity, offering a rich reservoir of raw material for natural selection to shape the evolution of these traits independently.
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Affiliation(s)
- E Lafuente
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - D Duneau
- UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - P Beldade
- cE3c (Center for Ecology, Evolution and Environmental Changes) & CHANGE (Global Change and Sustainability Institute), FCUL, Lisboa, Portugal
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11
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Pan J, Wang Y, Li C, Zhang S, Ye Z, Ni J, Li H, Li Y, Yue H, Ruan C, Zhao D, Jiang Y, Wu X, Shen X, Zufall RA, Zhang Y, Li W, Lynch M, Long H. Molecular basis of phenotypic plasticity in a marine ciliate. THE ISME JOURNAL 2024; 18:wrae136. [PMID: 39018220 PMCID: PMC11308186 DOI: 10.1093/ismejo/wrae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 07/19/2024]
Abstract
Phenotypic plasticity, which involves phenotypic transformation in the absence of genetic change, may serve as a strategy for organisms to survive in complex and highly fluctuating environments. However, its reaction norm, molecular basis, and evolution remain unclear in most organisms, especially microbial eukaryotes. In this study, we explored these questions by investigating the reaction norm, regulation, and evolution of phenotypic plasticity in the cosmopolitan marine free-living ciliates Glauconema spp., which undergo significant phenotypic changes in response to food shortages. This study led to the de novo assembly of macronuclear genomes using long-read sequencing, identified hundreds of differentially expressed genes associated with phenotypic plasticity in different life stages, validated the function of two of these genes, and revealed that the reaction norm of body shape in response to food density follows a power-law distribution. Purifying selection may be the dominant evolutionary force acting on the genes associated with phenotypic plasticity, and the overall data support the hypothesis that phenotypic plasticity is a trait maintained by natural selection. This study provides novel insight into the developmental genetics of phenotypic plasticity in non-model unicellular eukaryotes and sheds light on the complexity and long evolutionary history of this important survival strategy.
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Affiliation(s)
- Jiao Pan
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, China
| | - Yaohai Wang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Chao Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Simo Zhang
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Zhiqiang Ye
- School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
| | - Jiahao Ni
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Haichao Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yichen Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Hongwei Yue
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Chenchen Ruan
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Dange Zhao
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yujian Jiang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Xiaolin Wu
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Xiaopeng Shen
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, United States
| | - Yu Zhang
- School of Mathematics Science, Ocean University of China, Qingdao, Shandong Province 266000, China
| | - Weiyi Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, United States
| | - Hongan Long
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, China
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12
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Narayan VP, Wasana N, Wilson AJ, Chenoweth SF. Misalignment of plastic and evolutionary responses of lifespan to novel carbohydrate diets. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231732. [PMID: 38234441 PMCID: PMC10791524 DOI: 10.1098/rsos.231732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Diet elicits varied effects on longevity across a wide range of animal species where dietary discordance between an organisms' evolutionary and developmental dietary history is increasingly recognized to play a critical role in shaping lifespan. However, whether such changes, predominantly assessed in a single generation, lead to evolutionary shifts in lifespan remains unclear. In this study, we used an experimental evolution approach to test whether changes in an organisms' evolutionary and developmental dietary history, specifically carbohydrate content, causes lifespan evolution in Drosophila serrata. After 30 generations, we investigated the evolutionary potential of lifespan in response to four novel diets that varied systematically in their ratio of carbohydrate-protein content. We also examined developmental plasticity effects using a set of control populations that were raised on the four novel environments allowing us to assess the extent to which plastic responses of lifespan mirrored adaptive responses observed following experimental evolution. Both high- and low-carbohydrate diets elicited plastic effects on lifespan; however, the plastic responses for lifespan to developmental diets bore little resemblance to the evolved responses on evolutionary diets. Understanding the dietary conditions regulating the match/mismatch of plastic and evolved responses will be important in determining whether a particular match/mismatch combination is adaptive for lifespan. While the differences in evolutionary diet by developmental diet interactions are only beginning to be elucidated, this study lays the foundation for future investigations of carbohydrate contributions to evolved and plastic effects on health and lifespan.
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Affiliation(s)
- Vikram P. Narayan
- School of the Environment, The University of Queensland, St. Lucia, Queensland 4072, Australia
- College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Nidarshani Wasana
- School of the Environment, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Alastair J. Wilson
- College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Stephen F. Chenoweth
- School of the Environment, The University of Queensland, St. Lucia, Queensland 4072, Australia
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13
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Jourdan J, El Toum Abdel Fadil S, Oehlmann J, Hupało K. Rapid development of increased neonicotinoid tolerance in non-target freshwater amphipods. ENVIRONMENT INTERNATIONAL 2024; 183:108368. [PMID: 38070438 DOI: 10.1016/j.envint.2023.108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/23/2023] [Accepted: 12/02/2023] [Indexed: 01/25/2024]
Abstract
The comprehensive assessment of the long-term impacts of constant exposure to pollutants on wildlife populations remains a relatively unexplored area of ecological risk assessment. Empirical evidence to suggest that multigenerational exposure affects the susceptibility of organisms is scarce, and the underlying mechanisms in the natural environment have yet to be fully understood. In this study, we first examined the arthropod candidate species, Gammarus roeselii that - unlike closely related species - commonly occurs in many contaminated river systems of Central Europe. This makes it a suitable study organism to investigate the development of tolerances and phenotypic adaptations along pollution gradients. In a 96-h acute toxicity assay with the neonicotinoid thiacloprid, we indeed observed a successive increase in tolerance in populations coming from contaminated regions. This was accompanied by a certain phenotypic change, with increased investment into reproduction. To address the question of whether these changes are plastic or emerged from longer lasting evolutionary processes, we conducted a multigeneration experiment in the second part of our study. Here, we used closely-related Hyalella azteca and pre-exposed them for multiple generations to sublethal concentrations of thiacloprid in a semi-static design (one week renewal of media containing 0.1 or 1.0 µg/L thiacloprid). The pre-exposed individuals were then used in acute toxicity assays to see how quickly such adaptive responses can develop. Over only two generations, the tolerance to the neonicotinoid almost doubled, suggesting developmental plasticity as a plausible mechanism for the rapid adaptive response to strong selection factors such as neonicotinoid insecticides. It remains to be discovered whether the plasticity of rapidly developed tolerance is species-specific and explains why closely related species - which may not have comparable adaptive response capabilities - disappear in polluted habitats. Overall, our findings highlight the neglected role of developmental plasticity during short- and long-term exposure of natural populations to pollution. Moreover, our results show that even pollutant levels seven times lower than concentrations found in the study region have a clear impact on the developmental trajectories of non-target species.
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Affiliation(s)
- Jonas Jourdan
- Department Aquatic Ecotoxicology, Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany; Kompetenzzentrum Wasser Hessen, Max-von-Laue-Straße 13 D-60438, Frankfurt am Main, Germany.
| | - Safia El Toum Abdel Fadil
- Department Aquatic Ecotoxicology, Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany; Faculty of Life Sciences, Hamburg University of Applied Sciences, Ulmenliet 20 D-21033, Hamburg, Germany
| | - Jörg Oehlmann
- Department Aquatic Ecotoxicology, Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany; Kompetenzzentrum Wasser Hessen, Max-von-Laue-Straße 13 D-60438, Frankfurt am Main, Germany
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
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14
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Gupta A, Nair S. Epigenetic Diversity Underlying Seasonal and Annual Variations in Brown Planthopper (BPH) Populations as Revealed by Methylation- sensitive Restriction Assay. Curr Genomics 2023; 24:354-367. [PMID: 38327650 PMCID: PMC10845068 DOI: 10.2174/0113892029276542231205065843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/10/2023] [Indexed: 02/09/2024] Open
Abstract
Background The brown planthopper (BPH) is a monophagous sap-sucking insect pest of rice that is responsible for massive yield loss. BPH populations, even when genetically homogenous, can display a vast range of phenotypes, and the development of effective pest-management strategies requires a good understanding of what generates this phenotypic variation. One potential source could be epigenetic differences. Methods With this premise, we explored epigenetic diversity, structure and differentiation in field populations of BPH collected across the rice-growing seasons over a period of two consecutive years. Using a modified methylation-sensitive restriction assay (MSRA) and CpG island amplification-representational difference analysis, site-specific cytosine methylation of five stress-responsive genes (CYP6AY1, CYP6ER1, Carboxylesterase, Endoglucanase, Tf2-transposon) was estimated, for identifying methylation-based epiallelic markers and epigenetic variation across BPH populations. Results Using a cost-effective and rapid protocol, our study, for the first time, revealed the epigenetic component of phenotypic variations in the wild populations of BPH. Besides, results showed that morphologically indistinguishable populations of BPH can be epigenetically distinct. Conclusion Screening field-collected BPH populations revealed the presence of previously unreported epigenetic polymorphisms and provided a platform for future studies aimed at investigating their significance for BPH. Furthermore, these findings can form the basis for understanding the contribution(s) of DNA methylation in providing phenotypic plasticity to BPH.
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Affiliation(s)
- Ayushi Gupta
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Current Address: Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH 93BF, UK
| | - Suresh Nair
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
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15
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Dellinger M, Steele SE, Sprockel E, Philip J, Pálsson A, Benhaïm D. Variation in personality shaped by evolutionary history, genotype and developmental plasticity in response to feeding modalities in the Arctic charr. Proc Biol Sci 2023; 290:20232302. [PMID: 38087921 PMCID: PMC10716646 DOI: 10.1098/rspb.2023.2302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Animal personality has been shown to be influenced by both genetic and environmental factors and shaped by natural selection. Currently, little is known about mechanisms influencing the development of personality traits. This study examines the extent to which personality development is genetically influenced and/or environmentally responsive (plastic). We also investigated the role of evolutionary history, assessing whether personality traits could be canalized along a genetic and ecological divergence gradient. We tested the plastic potential of boldness in juveniles of five Icelandic Arctic charr morphs (Salvelinus alpinus), including two pairs of sympatric morphs, displaying various degrees of genetic and ecological divergence from the ancestral anadromous charr, split between treatments mimicking benthic versus pelagic feeding modalities. We show that differences in mean boldness are mostly affected by genetics. While the benthic treatment led to bolder individuals overall, the environmental effect was rather weak, suggesting that boldness lies under strong genetic influence with reduced plastic potential. Finally, we found hints of differences by morphs in boldness canalization through reduced variance and plasticity, and higher consistency in boldness within morphs. These findings provide new insights on how behavioural development may impact adaptive diversification.
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Affiliation(s)
- Marion Dellinger
- Department of Aquaculture and Fish Biology, Hólar University, Hólar, Iceland
- Institute of Life and Environmental Sciences, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Sarah E. Steele
- Institute of Life and Environmental Sciences, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
- Canadian Museum of Nature, Ottawa, Canada
| | - Evert Sprockel
- Department of Aquaculture and Fish Biology, Hólar University, Hólar, Iceland
- HAS University of Applied Sciences, 's-Hertogenbosch, The Netherlands
| | - Joris Philip
- Department of Aquaculture and Fish Biology, Hólar University, Hólar, Iceland
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK
| | - Arnar Pálsson
- Institute of Life and Environmental Sciences, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - David Benhaïm
- Department of Aquaculture and Fish Biology, Hólar University, Hólar, Iceland
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16
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Venney CJ, Anastasiadi D, Wellenreuther M, Bernatchez L. The Evolutionary Complexities of DNA Methylation in Animals: From Plasticity to Genetic Evolution. Genome Biol Evol 2023; 15:evad216. [PMID: 38015807 PMCID: PMC10701099 DOI: 10.1093/gbe/evad216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/22/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023] Open
Abstract
The importance of DNA methylation in plastic responses to environmental change and evolutionary dynamics is increasingly recognized. Here, we provide a Perspective piece on the diverse roles of DNA methylation on broad evolutionary timescales, including (i) short-term transient acclimation, (ii) stable phenotypic evolution, and (iii) genomic evolution. We show that epigenetic responses vary along a continuum, ranging from short-term acclimatory responses in variable environments within a generation to long-term modifications in populations and species. DNA methylation thus unlocks additional potential for organisms to rapidly acclimate to their environment over short timeframes. If these changes affect fitness, they can circumvent the need for adaptive changes at the genome level. However, methylation has a complex reciprocal relationship with genetic variation as it can be genetically controlled, yet it can also induce point mutations and contribute to genomic evolution. When habitats remain constant over many generations, or populations are separated across habitats, initially plastic phenotypes can become hardwired through epigenetically facilitated mutagenesis. It remains unclear under what circumstances plasticity contributes to evolutionary outcomes, and when plastic changes will become permanently encoded into genotype. We highlight how studies investigating the evolution of epigenetic plasticity need to carefully consider how plasticity in methylation state could evolve among different evolutionary scenarios, the possible phenotypic outcomes, its effects on genomic evolution, and the proximate energetic and ultimate fitness costs of methylation. We argue that accumulating evidence suggests that DNA methylation can contribute toward evolution on various timescales, spanning a continuum from acclimatory plasticity to genomic evolution.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, Canada
| | - Dafni Anastasiadi
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, Nelson, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, Canada
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17
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Isdaner AJ, Levis NA, Pfennig DW. Comparative transcriptomics reveals that a novel form of phenotypic plasticity evolved via lineage-specific changes in gene expression. Ecol Evol 2023; 13:e10646. [PMID: 37869437 PMCID: PMC10589077 DOI: 10.1002/ece3.10646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
Novel forms of phenotypic plasticity may evolve by lineage-specific changes or by co-opting mechanisms from more general forms of plasticity. Here, we evaluated whether a novel resource polyphenism in New World spadefoot toads (genus Spea) evolved by co-opting mechanisms from an ancestral form of plasticity common in anurans-accelerating larval development rate in response to pond drying. We compared overlap in differentially expressed genes between alternative trophic morphs constituting the polyphenism in Spea versus those found between tadpoles of Old World spadefoot toads (genus Pelobates) when experiencing different pond-drying regimes. Specifically, we (1) generated a de novo transcriptome and conducted differential gene expression analysis in Spea multiplicata, (2) utilized existing gene expression data and a recently published transcriptome for Pelobates cultripes when exposed to different drying regimes, and (3) identified unique and overlapping differentially expressed transcripts. We found thousands of differentially expressed genes between S. multiplicata morphs that were involved in major developmental reorganization, but the vast majority of these were not differentially expressed in P. cultripes. Thus, S. multiplicata's novel polyphenism appears to have arisen primarily through lineage-specific changes in gene expression and not by co-opting existing patterns of gene expression involved in pond-drying plasticity. Therefore, although ancestral stress responses might jump-start evolutionary innovation, substantial lineage-specific modification might be needed to refine these responses into more complex forms of plasticity.
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Affiliation(s)
- Andrew J. Isdaner
- Department of BiologyUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Nicholas A. Levis
- Department of BiologyUniversity of North CarolinaChapel HillNorth CarolinaUSA
- Department of BiologyIndiana UniversityBloomingtonIndianaUSA
| | - David W. Pfennig
- Department of BiologyUniversity of North CarolinaChapel HillNorth CarolinaUSA
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18
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DiVito Evans A, Fairbanks RA, Schmidt P, Levine MT. Histone methylation regulates reproductive diapause in Drosophila melanogaster. PLoS Genet 2023; 19:e1010906. [PMID: 37703303 PMCID: PMC10499233 DOI: 10.1371/journal.pgen.1010906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Fluctuating environments threaten fertility and viability. To better match the immediate, local environment, many organisms adopt alternative phenotypic states, a phenomenon called "phenotypic plasticity." Natural populations that predictably encounter fluctuating environments tend to be more plastic than conspecific populations that encounter a constant environment, suggesting that phenotypic plasticity can be adaptive. Despite pervasive evidence of such "adaptive phenotypic plasticity," gene regulatory mechanisms underlying plasticity remains poorly understood. Here we test the hypothesis that environment-dependent phenotypic plasticity is mediated by epigenetic factors. To test this hypothesis, we exploit the adaptive reproductive arrest of Drosophila melanogaster females, called diapause. Using an inbred line from a natural population with high diapause plasticity, we demonstrate that diapause is determined epigenetically: only a subset of genetically identical individuals enter diapause and this diapause plasticity is epigenetically transmitted for at least three generations. Upon screening a suite of epigenetic marks, we discovered that the active histone marks H3K4me3 and H3K36me1 are depleted in diapausing ovaries. Using ovary-specific knockdown of histone mark writers and erasers, we demonstrate that H3K4me3 and H3K36me1 depletion promotes diapause. Given that diapause is highly polygenic, that is, distinct suites of alleles mediate diapause plasticity across distinct genotypes, we also investigated the potential for genetic variation in diapause-determining epigenetic marks. Specifically, we asked if these histone marks were similarly depleted in diapause of a genotypically distinct line. We found evidence of divergence in both the gene expression program and histone mark abundance. This study reveals chromatin determinants of phenotypic plasticity and suggests that these determinants may be genotype-dependent, offering new insight into how organisms may exploit and evolve epigenetic mechanisms to persist in fluctuating environments.
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Affiliation(s)
- Abigail DiVito Evans
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Regina A. Fairbanks
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Paul Schmidt
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mia T. Levine
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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19
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Hanly JJ, Francescutti CM, Loh LS, Corning OBWH, Long DJ, Nakatani MA, Porter AH, Martin A. Genetics of yellow-orange color variation in a pair of sympatric sulphur butterflies. Cell Rep 2023; 42:112820. [PMID: 37481719 DOI: 10.1016/j.celrep.2023.112820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/02/2023] [Accepted: 06/29/2023] [Indexed: 07/25/2023] Open
Abstract
Continuous color polymorphisms can serve as a tractable model for the genetic and developmental architecture of traits. Here we investigated continuous color variation in Colias eurytheme and Colias philodice, two species of sulphur butterflies that hybridize in sympatry. Using quantitative trait locus (QTL) analysis and high-throughput color quantification, we found two interacting large-effect loci affecting orange-to-yellow chromaticity. Knockouts of red Malpighian tubules (red), likely involved in endosomal maturation, result in depigmented wing scales. Additionally, the transcription factor bric-a-brac can act as a modulator of orange pigmentation. We also describe the QTL architecture of other continuously varying traits, together supporting a large-X effect model where the genetic control of species-defining traits is enriched on sex chromosomes. This study sheds light on the range of possible genetic architectures that can underpin a continuously varying trait and illustrates the power of using automated measurement to score phenotypes that are not always conspicuous to the human eye.
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Affiliation(s)
- Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC, USA; Smithsonian Tropical Research Institute, Gamboa, Panama.
| | | | - Ling S Loh
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Olaf B W H Corning
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Derek J Long
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Marshall A Nakatani
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Adam H Porter
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA.
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC, USA.
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20
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Casasa S, Katsougia E, Ragsdale EJ. A Mediator subunit imparts robustness to a polyphenism decision. Proc Natl Acad Sci U S A 2023; 120:e2308816120. [PMID: 37527340 PMCID: PMC10410750 DOI: 10.1073/pnas.2308816120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/21/2023] [Indexed: 08/03/2023] Open
Abstract
Polyphenism is a type of developmental plasticity that translates continuous environmental variability into discontinuous phenotypes. Such discontinuity likely requires a switch between alternative gene-regulatory networks, a principle that has been borne out by mechanisms found to promote morph-specific gene expression. However, whether robustness is required to execute a polyphenism decision has awaited testing at the molecular level. Here, we used a nematode model for polyphenism, Pristionchus pacificus, to identify the molecular regulatory factors that ensure the development of alternative forms. This species has a dimorphism in its adult feeding structures, specifically teeth, which are a morphological novelty that allows predation on other nematodes. Through a forward genetic screen, we determined that a duplicate homolog of the Mediator subunit MDT-15/MED15, P. pacificus MDT-15.1, is necessary for the polyphenism and the robustness of the resulting phenotypes. This transcriptional coregulator, which has a conserved role in metabolic responses to nutritional stress, coordinates these processes with its effects on this diet-induced polyphenism. Moreover, this MED15 homolog genetically interacts with two nuclear receptors, NHR-1 and NHR-40, to achieve dimorphism: Single and double mutants for these three factors result in morphologies that together produce a continuum of forms between the extremes of the polyphenism. In summary, we have identified a molecular regulator that confers discontinuity to a morphological polyphenism, while also identifying a role for MED15 as a plasticity effector.
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Affiliation(s)
- Sofia Casasa
- Department of Biology, Indiana University, Bloomington, IN47405
| | - Eleni Katsougia
- Department of Biology, Indiana University, Bloomington, IN47405
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21
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Iguchi Y. Allometric approach to the two male morphs in the Japanese firefly Luciola parvula. FRONTIERS IN INSECT SCIENCE 2023; 3:1230363. [PMID: 38469470 PMCID: PMC10926417 DOI: 10.3389/finsc.2023.1230363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/06/2023] [Indexed: 03/13/2024]
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22
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Anas M, Diniz WJS, Menezes ACB, Reynolds LP, Caton JS, Dahlen CR, Ward AK. Maternal Mineral Nutrition Regulates Fetal Genomic Programming in Cattle: A Review. Metabolites 2023; 13:metabo13050593. [PMID: 37233634 DOI: 10.3390/metabo13050593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Maternal mineral nutrition during the critical phases of fetal development may leave lifetime impacts on the productivity of an individual. Most research within the developmental origins of the health and disease (DOHaD) field is focused on the role of macronutrients in the genome function and programming of the developing fetus. On the other hand, there is a paucity of knowledge about the role of micronutrients and, specifically, minerals in regulating the epigenome of livestock species, especially cattle. Therefore, this review will address the effects of the maternal dietary mineral supply on the fetal developmental programming from the embryonic to the postnatal phases in cattle. To this end, we will draw a parallel between findings from our cattle model research with data from model animals, cell lines, and other livestock species. The coordinated role and function of different mineral elements in feto-maternal genomic regulation underlies the establishment of pregnancy and organogenesis and, ultimately, affects the development and functioning of metabolically important tissues, such as the fetal liver, skeletal muscle, and, importantly, the placenta. Through this review, we will delineate the key regulatory pathways involved in fetal programming based on the dietary maternal mineral supply and its crosstalk with epigenomic regulation in cattle.
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Affiliation(s)
- Muhammad Anas
- Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 36849, USA
| | | | - Ana Clara B Menezes
- Department of Animal Science, South Dakota State University, Brookings, SD 57007, USA
| | - Lawrence P Reynolds
- Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 36849, USA
| | - Joel S Caton
- Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 36849, USA
| | - Carl R Dahlen
- Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 36849, USA
| | - Alison K Ward
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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23
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Yoon KJ, Cunningham CB, Bretman A, Duncan EJ. One genome, multiple phenotypes: decoding the evolution and mechanisms of environmentally induced developmental plasticity in insects. Biochem Soc Trans 2023; 51:675-689. [PMID: 36929376 PMCID: PMC10246940 DOI: 10.1042/bst20210995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/18/2023]
Abstract
Plasticity in developmental processes gives rise to remarkable environmentally induced phenotypes. Some of the most striking and well-studied examples of developmental plasticity are seen in insects. For example, beetle horn size responds to nutritional state, butterfly eyespots are enlarged in response to temperature and humidity, and environmental cues also give rise to the queen and worker castes of eusocial insects. These phenotypes arise from essentially identical genomes in response to an environmental cue during development. Developmental plasticity is taxonomically widespread, affects individual fitness, and may act as a rapid-response mechanism allowing individuals to adapt to changing environments. Despite the importance and prevalence of developmental plasticity, there remains scant mechanistic understanding of how it works or evolves. In this review, we use key examples to discuss what is known about developmental plasticity in insects and identify fundamental gaps in the current knowledge. We highlight the importance of working towards a fully integrated understanding of developmental plasticity in a diverse range of species. Furthermore, we advocate for the use of comparative studies in an evo-devo framework to address how developmental plasticity works and how it evolves.
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Affiliation(s)
- Kane J. Yoon
- School of Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, U.K
| | | | - Amanda Bretman
- School of Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, U.K
| | - Elizabeth J. Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, U.K
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24
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Prabh N, Linnenbrink M, Jovicic M, Guenther A. Fast adjustment of pace-of-life and risk-taking to changes in food quality by altered gene expression in house mice. Ecol Lett 2023; 26:99-110. [PMID: 36366786 DOI: 10.1111/ele.14137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/13/2022]
Abstract
The pace-of-life syndrome hypothesis provides a framework for the adaptive integration of behaviour, physiology and life history between and within species. It suggests that behaviours involving a risk of death or injury should co-vary with a higher allocation to fast reproduction. Empirical support for this hypothesis is mixed, presumably because important influencing factors such as environmental variation, are usually neglected. By experimentally manipulating food quality of wild mice living under semi-natural conditions for three generations, we show that individuals adjust their life history strategies and risk-taking behaviours as well as trait covariation (Nindividuals = 1442). These phenotypic differences are correlated to differences in transcriptomic gene expression of primary metabolic processes in the liver while no changes in gene frequencies occurred. Our discussion emphasises the need to integrate the role of environmental conditions and phenotypic plasticity in shaping relationships among behaviour, physiology and life history in response to changing environmental conditions.
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Affiliation(s)
- Neel Prabh
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | | | - Milan Jovicic
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Anja Guenther
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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25
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Mateus ARA, Beldade P. Developmental Plasticity in Butterfly Eyespot Mutants: Variation in Thermal Reaction Norms Across Genotypes and Pigmentation Traits. INSECTS 2022; 13:1000. [PMID: 36354827 PMCID: PMC9699518 DOI: 10.3390/insects13111000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Developmental plasticity refers to the property by which a genotype corresponds to distinct phenotypes depending on the environmental conditions experienced during development. This dependence of phenotype expression on environment is graphically represented by reaction norms, which can differ between traits and between genotypes. Even though genetic variation for reaction norms provides the basis for the evolution of plasticity, we know little about the genes that contribute to that variation. This includes understanding to what extent those are the same genes that contribute to inter-individual variation in a fixed environment. Here, we quantified thermal plasticity in butterfly lines that differ in pigmentation phenotype to test the hypothesis that alleles affecting pigmentation also affect plasticity therein. We characterized thermal reaction norms for eyespot color rings of distinct Bicyclus anynana genetic backgrounds, corresponding to allelic variants affecting eyespot size and color composition. Our results reveal genetic variation for the slope and curvature of reaction norms, with differences between eyespots and between eyespot color rings, as well as between sexes. Our report of prevalent temperature-dependent and compartment-specific allelic effects underscores the complexity of genotype-by-environment interactions and their consequence for the evolution of developmental plasticity.
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Affiliation(s)
| | - Patrícia Beldade
- Instituto Gulbenkian de Ciência (IGC), 2780-156 Oeiras, Portugal
- CNRS—UMR 5174, Evolution et Diversité Biologique (EDB), Université Paul Sabatier (UPS), 31077 Toulouse, France
- Center for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculty of Sciences, University of Lisbon (FCUL), 1749-016 Lisbon, Portugal
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26
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Rodrigues LR, Montserrat M, Magalhães S. Evolution in agricultural systems: Moving toward the understanding of complexity. Evol Appl 2022; 15:1483-1489. [PMID: 36330296 PMCID: PMC9624076 DOI: 10.1111/eva.13490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 12/01/2022] Open
Abstract
Agricultural fields are typically simplified ecosystems compared to natural sites, a characteristic that has long-attracted researchers in Ecology and Evolution. In recent years, there has been a rising interest in understanding how agricultural systems are shaped by evolution in the context of changing agricultural practices by integrating biological information of crop systems. This editorial introduces the special issue "Evolution in agricultural systems," incorporating the articles published within this issue into three general areas of research: phenotypic and genetic responses to the environment, biotic interactions and the role of microbes. Together, this body of work unveils unforeseen complexity at all levels, from microbes to trophic chains. Understanding such complexity is critical not only to better understand natural systems, but also if we wish to improve the sustainability of the food system.
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Affiliation(s)
- Leonor R. Rodrigues
- cE3c: Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisbonPortugal
| | - Marta Montserrat
- IHSM La Mayora‐UMA‐CSIC: Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”MálagaSpain
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisbonPortugal
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27
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La Fortezza M, Rendueles O, Keller H, Velicer GJ. Hidden paths to endless forms most wonderful: ecology latently shapes evolution of multicellular development in predatory bacteria. Commun Biol 2022; 5:977. [PMID: 36114258 PMCID: PMC9481553 DOI: 10.1038/s42003-022-03912-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/30/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractEcological causes of developmental evolution, for example from predation, remain much investigated, but the potential importance of latent phenotypes in eco-evo-devo has received little attention. Using the predatory bacterium Myxococcus xanthus, which undergoes aggregative fruiting body development upon starvation, we tested whether adaptation to distinct growth environments that do not induce development latently alters developmental phenotypes under starvation conditions that do induce development. In an evolution experiment named MyxoEE-3, growing M. xanthus populations swarmed across agar surfaces while adapting to conditions varying at factors such as surface stiffness or prey identity. Such ecological variation during growth was found to greatly impact the latent evolution of development, including fruiting body morphology, the degree of morphological trait correlation, reaction norms, degrees of developmental plasticity and stochastic diversification. For example, some prey environments promoted retention of developmental proficiency whereas others led to its systematic loss. Our results have implications for understanding evolutionary interactions among predation, development and motility in myxobacterial life cycles, and, more broadly, how ecology can profoundly shape the evolution of developmental systems latently rather than by direct selection on developmental features.
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28
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Lin WC, Liu C, Kosillo P, Tai LH, Galarce E, Bateup HS, Lammel S, Wilbrecht L. Transient food insecurity during the juvenile-adolescent period affects adult weight, cognitive flexibility, and dopamine neurobiology. Curr Biol 2022; 32:3690-3703.e5. [PMID: 35863352 PMCID: PMC10519557 DOI: 10.1016/j.cub.2022.06.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 04/01/2022] [Accepted: 06/29/2022] [Indexed: 10/17/2022]
Abstract
A major challenge for neuroscience, public health, and evolutionary biology is to understand the effects of scarcity and uncertainty on the developing brain. Currently, a significant fraction of children and adolescents worldwide experience insecure access to food. The goal of our work was to test in mice whether the transient experience of insecure versus secure access to food during the juvenile-adolescent period produced lasting differences in learning, decision-making, and the dopamine system in adulthood. We manipulated feeding schedules in mice from postnatal day (P)21 to P40 as food insecure or ad libitum and found that when tested in adulthood (after P60), males with different developmental feeding history showed significant differences in multiple metrics of cognitive flexibility in learning and decision-making. Adult females with different developmental feeding history showed no differences in cognitive flexibility but did show significant differences in adult weight. We next applied reinforcement learning models to these behavioral data. The best fit models suggested that in males, developmental feeding history altered how mice updated their behavior after negative outcomes. This effect was sensitive to task context and reward contingencies. Consistent with these results, in males, we found that the two feeding history groups showed significant differences in the AMPAR/NMDAR ratio of excitatory synapses on nucleus-accumbens-projecting midbrain dopamine neurons and evoked dopamine release in dorsal striatal targets. Together, these data show in a rodent model that transient differences in feeding history in the juvenile-adolescent period can have significant impacts on adult weight, learning, decision-making, and dopamine neurobiology.
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Affiliation(s)
- Wan Chen Lin
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Christine Liu
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Polina Kosillo
- Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Lung-Hao Tai
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ezequiel Galarce
- Robert Wood Johnson Foundation Health and Society Scholar, University of California Berkeley, Berkeley, CA 94720, USA
| | - Helen S Bateup
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Stephan Lammel
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Linda Wilbrecht
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA 94720, USA; Department of Psychology, University of California Berkeley, Berkeley, CA 94720, USA.
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29
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Bolkhovitinov L, Weselman BT, Shaw GA, Dong C, Giribhattanavar J, Saha MS. Tissue Rotation of the Xenopus Anterior-Posterior Neural Axis Reveals Profound but Transient Plasticity at the Mid-Gastrula Stage. J Dev Biol 2022; 10:38. [PMID: 36135371 PMCID: PMC9503425 DOI: 10.3390/jdb10030038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
The establishment of anterior-posterior (AP) regional identity is an essential step in the appropriate development of the vertebrate central nervous system. An important aspect of AP neural axis formation is the inherent plasticity that allows developing cells to respond to and recover from the various perturbations that embryos continually face during the course of development. While the mechanisms governing the regionalization of the nervous system have been extensively studied, relatively less is known about the nature and limits of early neural plasticity of the anterior-posterior neural axis. This study aims to characterize the degree of neural axis plasticity in Xenopus laevis by investigating the response of embryos to a 180-degree rotation of their AP neural axis during gastrula stages by assessing the expression of regional marker genes using in situ hybridization. Our results reveal the presence of a narrow window of time between the mid- and late gastrula stage, during which embryos are able undergo significant recovery following a 180-degree rotation of their neural axis and eventually express appropriate regional marker genes including Otx, Engrailed, and Krox. By the late gastrula stage, embryos show misregulation of regional marker genes following neural axis rotation, suggesting that this profound axial plasticity is a transient phenomenon that is lost by late gastrula stages.
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Affiliation(s)
- Lyuba Bolkhovitinov
- Department of Molecular Biology, Massachusetts General Hospital, Harvard University, Boston, MA 02114, USA
| | - Bryan T. Weselman
- School of Medicine, Georgetown University, Washington, DC 20007, USA
| | - Gladys A. Shaw
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Chen Dong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Margaret S. Saha
- Department of Biology, College of William and Mary, Williamsburg, VA 23185, USA
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30
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Zhang L, Dayananda B, Xia JG, Sun BJ. Editorial: Ecophysiological analysis of vulnerability to climate warming in ectotherms. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.946836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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31
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Wrozyna C, Mischke S, Hoehle M, Gross M, Piller WE. Large-Scale Geographic Size Variability of Cyprideis torosa (Ostracoda) and Its Taxonomic and Ecologic Implications. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.857499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Body-size variability results from a variety of extrinsic and intrinsic factors (environmental and biological influences) underpinned by phylogeny. In ostracodes it is assumed that body size is predominantly controlled by ecological conditions, but investigations have mostly focused on local or regional study areas. In this study, we investigate the geographical size variability (length, height, and width) of Holocene and Recent valves of the salinity-tolerant ostracode species Cyprideis torosa within a large geographical area (31°–51° latitude, and 12°–96° longitude). It is shown that distant local size clusters of Cyprideis torosa are framed within two large-scale geographical patterns. One pattern describes the separation of two different size classes (i.e., morphotypes) at around ∼42° N. The co-occurrence of both size morphotypes in the same habitats excludes an environmental control on the distribution of the morphotypes but rather could point to the existence of two differentiated lineages. Generally, correlations between valve size and environmental parameters (salinity, geographical positions) strongly depend on the taxonomic resolution. While latitude explains the overall size variability of C. torosa sensu lato (i.e., undifferentiated for morphotypes), salinity-size correlations are restricted to the morphotype scale. Another large-scale pattern represents a continuous increase in valve size of C. torosa with latitude according to the macroecological pattern referred as Bergmann trend. Existing explanations for Bergmann trends insufficiently clarify the size cline of C. torosa which might be because these models are restricted to intraspecific levels. The observed size-latitude relationship of C. torosa may, therefore, result from interspecific divergence (i.e., size ordered spatially may result from interspecific divergence sorting) while environmental influence is of minor importance. Our results imply that geographical body-size patterns of ostracodes are not straightforward and are probably not caused by universal mechanisms. Consideration of phylogenetic relationships of ostracodes is therefore necessary before attempting to identify the role of environmental controls on body size variability.
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32
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Differences in phenology, daily timing of activity, and associations of temperature utilization with survival in three threatened butterflies. Sci Rep 2022; 12:7534. [PMID: 35534513 PMCID: PMC9085768 DOI: 10.1038/s41598-022-10676-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
We used observational data collected during a mark-recapture study that generated a total of 7503 captures of 6108 unique individuals representing three endangered butterfly species to quantify inter-and intraindividual variation in temperature utilization and examine how activity patterns vary according to season, time of day, and ambient temperature. The Marsh Fritillary, the Apollo, and the Large Blue differed in utilized temperatures and phenology. Their daily activity patterns responded differently to temperature, in part depending on whether they were active in the beginning, middle or end of the season, in part reflecting interindividual variation and intraindividual flexibility, and in part owing to differences in ecology, morphology, and colouration. Activity temperatures varied over the season, and the Apollo and the Large Blue were primarily active at the highest available ambient temperatures (on the warmest days and during the warmest part of the day). The Marsh Fritillary was active early in the season and decreased activity during the highest temperatures. The relationship between individual lifespan and the average temperature was qualitatively different in the three species pointing to species-specific selection. Lifespan increased with an increasing range of utilized temperatures in all species, possibly reflecting that intra-individual flexibility comes with a general survival benefit.
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33
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Maulana MI, Riksen JAG, Snoek BL, Kammenga JE, Sterken MG. The genetic architecture underlying body-size traits plasticity over different temperatures and developmental stages in Caenorhabditis elegans. Heredity (Edinb) 2022; 128:313-324. [PMID: 35383317 PMCID: PMC9076863 DOI: 10.1038/s41437-022-00528-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 01/25/2023] Open
Abstract
Most ectotherms obey the temperature-size rule, meaning they grow larger in a colder environment. This raises the question of how the interplay between genes and temperature affects the body size of ectotherms. Despite the growing body of literature on the physiological life-history and molecular genetic mechanism underlying the temperature-size rule, the overall genetic architecture orchestrating this complex phenotype is not yet fully understood. One approach to identify genetic regulators of complex phenotypes is quantitative trait locus (QTL) mapping. Here, we explore the genetic architecture of body-size phenotypes, and plasticity of body-size phenotypes at different temperatures using Caenorhabditis elegans as a model ectotherm. We used 40 recombinant inbred lines (RILs) derived from N2 and CB4856, which were reared at four different temperatures (16, 20, 24, and 26 °C) and measured at two developmental stages (L4 and adult). The animals were measured for body length, width at vulva, body volume, length/width ratio, and seven other body-size traits. The genetically diverse RILs varied in their body-size phenotypes with heritabilities ranging from 0.0 to 0.99. We detected 18 QTL underlying the body-size traits across all treatment combinations, with the majority clustering on Chromosome X. We hypothesize that the Chromosome X QTL could result from a known pleiotropic regulator-npr-1-known to affect the body size of C. elegans through behavioral changes. We also found five plasticity QTL of body-size traits where three colocalized with body-size QTL. In conclusion, our findings shed more light on multiple loci affecting body-size plasticity and the possibility of co-regulation of traits and traits plasticity by the same loci under different environments.
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Affiliation(s)
- Muhammad I Maulana
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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34
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Oomen RA, Hutchings JA. Genomic reaction norms inform predictions of plastic and adaptive responses to climate change. J Anim Ecol 2022; 91:1073-1087. [PMID: 35445402 PMCID: PMC9325537 DOI: 10.1111/1365-2656.13707] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common‐garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity. Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change. Here, we describe the utility of integrating genomics with common‐garden‐gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential. An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco‐evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high‐dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts. We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco‐evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common‐garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.
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Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway
| | - Jeffrey A Hutchings
- Centre for Coastal Research (CCR), University of Agder, Kristiansand, Norway.,Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
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35
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Steward RA, de Jong MA, Oostra V, Wheat CW. Alternative splicing in seasonal plasticity and the potential for adaptation to environmental change. Nat Commun 2022; 13:755. [PMID: 35136048 PMCID: PMC8825856 DOI: 10.1038/s41467-022-28306-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022] Open
Abstract
Seasonal plasticity is accomplished via tightly regulated developmental cascades that translate environmental cues into trait changes. Little is known about how alternative splicing and other posttranscriptional molecular mechanisms contribute to plasticity or how these mechanisms impact how plasticity evolves. Here, we use transcriptomic and genomic data from the butterfly Bicyclus anynana, a model system for seasonal plasticity, to compare the extent of differential expression and splicing and test how these axes of transcriptional plasticity differ in their potential for evolutionary change. Between seasonal morphs, we find that differential splicing affects a smaller but functionally unique set of genes compared to differential expression. Further, we find strong support for the novel hypothesis that spliced genes are more susceptible than differentially expressed genes to erosion of genetic variation due to selection on seasonal plasticity. Our results suggest that splicing plasticity is especially likely to experience genetic constraints that could affect the potential of wild populations to respond to rapidly changing environments.
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Affiliation(s)
| | | | - Vicencio Oostra
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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36
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Levis NA, Ragsdale EJ. Linking Molecular Mechanisms and Evolutionary Consequences of Resource Polyphenism. Front Integr Neurosci 2022; 16:805061. [PMID: 35210995 PMCID: PMC8861301 DOI: 10.3389/fnint.2022.805061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
Resource polyphenism-the occurrence of environmentally induced, discrete, and intraspecific morphs showing differential niche use-is taxonomically widespread and fundamental to the evolution of ecological function where it has arisen. Despite longstanding appreciation for the ecological and evolutionary significance of resource polyphenism, only recently have its proximate mechanisms begun to be uncovered. Polyphenism switches, especially those influencing and influenced by trophic interactions, offer a route to integrating proximate and ultimate causation in studies of plasticity, and its potential influence on evolution more generally. Here, we use the major events in generalized polyphenic development as a scaffold for linking the molecular mechanisms of polyphenic switching with potential evolutionary outcomes of polyphenism and for discussing challenges and opportunities at each step in this process. Not only does the study of resource polyphenism uncover interesting details of discrete plasticity, it also illuminates and informs general principles at the intersection of development, ecology, and evolution.
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Affiliation(s)
- Nicholas A. Levis
- Department of Biology, Indiana University, Bloomington, IN, United States
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37
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Colombo M, Montazeaud G, Viader V, Ecarnot M, Prosperi J, David J, Fort F, Violle C, Freville H. A genome‐wide analysis suggests pleiotropic effects of Green Revolution genes on shade avoidance in wheat. Evol Appl 2022; 15:1594-1604. [PMID: 36330302 PMCID: PMC9624089 DOI: 10.1111/eva.13349] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/26/2022] Open
Abstract
A classic example of phenotypic plasticity in plants is the suit of phenotypic responses induced by a change in the ratio of red to far-red light (R∶FR) as a result of shading, also known as the shade avoidance syndrome (SAS). While the adaptive consequences of this syndrome have been extensively discussed in natural ecosystems, how SAS varies within crop populations and how SAS evolved during crop domestication and breeding remain poorly known. In this study, we grew a panel of 180 durum wheat (Triticum turgidum ssp. durum) genotypes spanning diversity from wild, early domesticated, and elite genetic compartments under two light treatments: low R:FR light (shaded treatment) and high R:FR light (unshaded treatment). We first quantified the genetic variability of SAS, here measured as a change in plant height at the seedling stage. We then dissected the genetic basis of this variation through genome-wide association mapping. Genotypes grown in shaded conditions were taller than those grown under unshaded conditions. Interaction between light quality and genotype did not affect plant height. We found six QTLs affecting plant height. Three significantly interacted with light quality among which the well-known Rht1 gene introgressed in elite germplasm during the Green Revolution. Interestingly at three loci, short genotypes systematically expressed reduced SAS, suggesting a positive genetic correlation between plant height and plant height plasticity. Overall, our study sheds light on the evolutionary history of crops and illustrates the relevance of genetic approaches to tackle agricultural challenges.
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Affiliation(s)
- Michel Colombo
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
- CEFE Univ. Montpellier Institut Agro CNRS EPHE, IRD Univ Valéry Montpellier France
| | - Germain Montazeaud
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
- CEFE Univ. Montpellier Institut Agro CNRS EPHE, IRD Univ Valéry Montpellier France
- Department of Ecology and Evolution University of Lausanne 1015 Lausanne Switzerland
| | - Veronique Viader
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
| | - Martin Ecarnot
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
| | | | - Jacques David
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
| | - Florian Fort
- CEFE Univ. Montpellier Institut Agro CNRS EPHE, IRD Univ Valéry Montpellier France
| | - Cyrille Violle
- CEFE Univ. Montpellier CNRS EPHE, IRD Univ Valéry Montpellier France
| | - Helene Freville
- AGAP Univ Montpellier CIRAD, INRAE Institut Agro Montpellier France
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38
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Rodrigues LR, Zwoinska MK, Axel W Wiberg R, Snook RR. The genetic basis and adult reproductive consequences of developmental thermal plasticity. J Anim Ecol 2022; 91:1119-1134. [PMID: 35060127 PMCID: PMC9373847 DOI: 10.1111/1365-2656.13664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022]
Abstract
Increasing temperature and thermal variability generate profound selection on populations. Given the fast rate of environmental change, understanding the role of plasticity and genetic adaptation in response to increasing temperatures is critical. This may be especially true for thermal effects on reproductive traits in which thermal fertility limits at high temperatures may be lower than for survival traits. Consequences of changing environments during development on adult phenotypes may be particularly problematic for core traits such as reproduction that begin early in development. Here we examine the consequences of developmental thermal plasticity on subsequent adult reproductive traits and its genetic basis. We used a panel of Drosophila melanogaster (the Drosophila Genetic Reference Panel; DGRP) in which male fertility performance was previously defined as either showing relatively little (status = ‘high’‐performing lines) or substantial (‘low’‐performing lines) decline when exposed to increasing developmental temperatures. We used a thermal reaction norm approach to quantify variation in the consequences of developmental thermal plasticity on multiple adult reproductive traits, including sex‐specific responses, and to identify candidate genes underlying such variation. Developmental thermal stress impacted the means and thermal reaction norms of all reproductive traits except offspring sex ratio. Mating success declined as temperature increased with no difference between high and low lines, whereas increasing temperature resulted in declines for both male and female fertility and productivity but depended on line status. Fertility and offspring number were positively correlated within and between the sexes across lines, but males were more affected than females. We identified 933 SNPs with significant evolved genetic differentiation between high and low lines. In all, 54 of these lie within genomic windows of overall high differentiation, have significant effects of genotype on the male thermal reaction norm for productivity and are associated with 16 genes enriched for phenotypes affecting reproduction, stress responses and autophagy in Drosophila and other organisms. Our results illustrate considerable plasticity in male thermal limits on several reproductive traits following development at high temperature, and we identify differentiated loci with relevant phenotypic effects that may contribute to this population variation. While our work is on a single population, phenotypic results align with an increasing number of studies demonstrating the potential for stronger selection of thermal stress on reproductive traits, particularly in males. Such large fitness costs may have both short‐ and long‐term consequences for the evolution of populations in response to a warming world.
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Affiliation(s)
| | | | | | - Rhonda R Snook
- Department of Zoology Stockholm University Stockholm Sweden
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39
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Lafuente E, Lürig MD, Rövekamp M, Matthews B, Buser C, Vorburger C, Räsänen K. Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.748212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Interactions between organisms and their environments are central to how biological diversity arises and how natural populations and ecosystems respond to environmental change. These interactions involve processes by which phenotypes are affected by or respond to external conditions (e.g., via phenotypic plasticity or natural selection) as well as processes by which organisms reciprocally interact with the environment (e.g., via eco-evolutionary feedbacks). Organism-environment interactions can be highly dynamic and operate on different hierarchical levels, from genes and phenotypes to populations, communities, and ecosystems. Therefore, the study of organism-environment interactions requires integrative approaches and model systems that are suitable for studies across different hierarchical levels. Here, we introduce the freshwater isopod Asellus aquaticus, a keystone species and an emerging invertebrate model system, as a prime candidate to address fundamental questions in ecology and evolution, and the interfaces therein. We review relevant fields of research that have used A. aquaticus and draft a set of specific scientific questions that can be answered using this species. Specifically, we propose that studies on A. aquaticus can help understanding (i) the influence of host-microbiome interactions on organismal and ecosystem function, (ii) the relevance of biotic interactions in ecosystem processes, and (iii) how ecological conditions and evolutionary forces facilitate phenotypic diversification.
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40
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Bailey NW, Desjonquères C, Drago A, Rayner JG, Sturiale SL, Zhang X. A neglected conceptual problem regarding phenotypic plasticity's role in adaptive evolution: The importance of genetic covariance and social drive. Evol Lett 2021; 5:444-457. [PMID: 34621532 PMCID: PMC8484725 DOI: 10.1002/evl3.251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/12/2021] [Accepted: 07/19/2021] [Indexed: 01/16/2023] Open
Abstract
There is tantalizing evidence that phenotypic plasticity can buffer novel, adaptive genetic variants long enough to permit their evolutionary spread, and this process is often invoked in explanations for rapid adaptive evolution. However, the strength and generality of evidence for it is controversial. We identify a conceptual problem affecting this debate: recombination, segregation, and independent assortment are expected to quickly sever associations between genes controlling novel adaptations and genes contributing to trait plasticity that facilitates the novel adaptations by reducing their indirect fitness costs. To make clearer predictions about this role of plasticity in facilitating genetic adaptation, we describe a testable genetic mechanism that resolves the problem: genetic covariance between new adaptive variants and trait plasticity that facilitates their persistence within populations. We identify genetic architectures that might lead to such a covariance, including genetic coupling via physical linkage and pleiotropy, and illustrate the consequences for adaptation rates using numerical simulations. Such genetic covariances may also arise from the social environment, and we suggest the indirect genetic effects that result could further accentuate the process of adaptation. We call the latter mechanism of adaptation social drive, and identify methods to test it. We suggest that genetic coupling of plasticity and adaptations could promote unusually rapid ‘runaway’ evolution of novel adaptations. The resultant dynamics could facilitate evolutionary rescue, adaptive radiations, the origin of novelties, and other commonly studied processes.
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Affiliation(s)
- Nathan W Bailey
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom
| | - Camille Desjonquères
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom.,Department of Biological Sciences University of Wisconsin-Milwaukee Milwaukee Wisconsin 53201
| | - Ana Drago
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom
| | - Jack G Rayner
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom
| | - Samantha L Sturiale
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom.,Current Address: Department of Biology Georgetown University Washington DC 20057
| | - Xiao Zhang
- School of Biology University of St Andrews St Andrews KY16 9TH United Kingdom
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41
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Suzuki Y, Toh L. Constraints and Opportunities for the Evolution of Metamorphic Organisms in a Changing Climate. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.734031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We argue that developmental hormones facilitate the evolution of novel phenotypic innovations and timing of life history events by genetic accommodation. Within an individual’s life cycle, metamorphic hormones respond readily to environmental conditions and alter adult phenotypes. Across generations, the many effects of hormones can bias and at times constrain the evolution of traits during metamorphosis; yet, hormonal systems can overcome constraints through shifts in timing of, and acquisition of tissue specific responses to, endocrine regulation. Because of these actions of hormones, metamorphic hormones can shape the evolution of metamorphic organisms. We present a model called a developmental goblet, which provides a visual representation of how metamorphic organisms might evolve. In addition, because developmental hormones often respond to environmental changes, we discuss how endocrine regulation of postembryonic development may impact how organisms evolve in response to climate change. Thus, we propose that developmental hormones may provide a mechanistic link between climate change and organismal adaptation.
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42
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Estrada-Cortés E, Ortiz W, Rabaglino MB, Block J, Rae O, Jannaman EA, Xiao Y, Hansen PJ. Choline acts during preimplantation development of the bovine embryo to program postnatal growth and alter muscle DNA methylation. FASEB J 2021; 35:e21926. [PMID: 34533870 DOI: 10.1096/fj.202100991r] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 01/09/2023]
Abstract
The preimplantation period of embryonic development can be a key window for programming of postnatal development because extensive epigenetic remodeling occurs during this time. It was hypothesized that modification of one-carbon metabolism of the bovine embryo by addition of the methyl-donor choline to culture medium would change postnatal phenotype through epigenetic modification. Embryos produced in vitro were cultured with 1.8 mM choline chloride or control medium. Blastocysts were transferred into females and pregnancy outcomes and postnatal phenotype of the resultant calves determined. Exposure of embryos to choline increased gestation length and calf birth weight. Calves derived from choline-treated embryos were also heavier at weaning and had increased ratio of body weight to hip height than control calves. Choline altered muscle DNA methylation of calves 4 months after birth. A total of 670 of the 8149 CpG examined were differentially methylated, with the predominant effect of choline being hypomethylation. Among the genes associated with differentially methylated CpG were ribosomal RNAs and genes in AMPK, mTOR, integrin, and BEX2 canonical pathways and cellular functions involved in growth and proliferation. Results demonstrate that provision of the methyl-donor choline to the preimplantation embryo can alter its developmental program to increase gestation length, birth weight, and weaning weight and cause postnatal changes in muscle DNA methylation including those associated with genes related to anabolic processes and cellular growth. The importance of the nutritional status of the embryo with respect to one-carbon metabolism for ensuring health and well-being after birth is emphasized by these observations.
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Affiliation(s)
- Eliab Estrada-Cortés
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida, USA.,Campo Experimental Centro Altos de Jalisco, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos, Mexico
| | - William Ortiz
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Maria B Rabaglino
- Quantitative Genetics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Jeremy Block
- Department of Animal Science, University of Wyoming, Laramie, Wyoming, USA
| | - Owen Rae
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Elizabeth A Jannaman
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Yao Xiao
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Peter J Hansen
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida, USA
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43
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Inferring multilayer interactome networks shaping phenotypic plasticity and evolution. Nat Commun 2021; 12:5304. [PMID: 34489412 PMCID: PMC8421358 DOI: 10.1038/s41467-021-25086-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Phenotypic plasticity represents a capacity by which the organism changes its phenotypes in response to environmental stimuli. Despite its pivotal role in adaptive evolution, how phenotypic plasticity is genetically controlled remains elusive. Here, we develop a unified framework for coalescing all single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) into a quantitative graph. This framework integrates functional genetic mapping, evolutionary game theory, and predator-prey theory to decompose the net genetic effect of each SNP into its independent and dependent components. The independent effect arises from the intrinsic capacity of a SNP, only expressed when it is in isolation, whereas the dependent effect results from the extrinsic influence of other SNPs. The dependent effect is conceptually beyond the traditional definition of epistasis by not only characterizing the strength of epistasis but also capturing the bi-causality of epistasis and the sign of the causality. We implement functional clustering and variable selection to infer multilayer, sparse, and multiplex interactome networks from any dimension of genetic data. We design and conduct two GWAS experiments using Staphylococcus aureus, aimed to test the genetic mechanisms underlying the phenotypic plasticity of this species to vancomycin exposure and Escherichia coli coexistence. We reconstruct the two most comprehensive genetic networks for abiotic and biotic phenotypic plasticity. Pathway analysis shows that SNP-SNP epistasis for phenotypic plasticity can be annotated to protein-protein interactions through coding genes. Our model can unveil the regulatory mechanisms of significant loci and excavate missing heritability from some insignificant loci. Our multilayer genetic networks provide a systems tool for dissecting environment-induced evolution.
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44
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Espinosa-Soto C, Hernández U, Posadas-García YS. Recombination facilitates genetic assimilation of new traits in gene regulatory networks. Evol Dev 2021; 23:459-473. [PMID: 34455697 DOI: 10.1111/ede.12391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/11/2021] [Accepted: 08/04/2021] [Indexed: 11/30/2022]
Abstract
A new phenotypic variant may appear first in organisms through plasticity, that is, as a response to an environmental signal or other nongenetic perturbation. If such trait is beneficial, selection may increase the frequency of alleles that enable and facilitate its development. Thus, genes may take control of such traits, decreasing dependence on nongenetic disturbances, in a process called genetic assimilation. Despite an increasing amount of empirical studies supporting genetic assimilation, its significance is still controversial. Whether genetic assimilation is widespread depends, to a great extent, on how easily mutation and recombination reduce the trait's dependence on nongenetic perturbations. Previous research suggests that this is the case for mutations. Here we use simulations of gene regulatory network dynamics to address this issue with respect to recombination. We find that recombinant offspring of parents that produce a new phenotype through plasticity are more likely to produce the same phenotype without requiring any perturbation. They are also prone to preserve the ability to produce that phenotype after genetic and nongenetic perturbations. Our work also suggests that ancestral plasticity can play an important role for setting the course that evolution takes. In sum, our results indicate that the manner in which phenotypic variation maps unto genetic variation facilitates evolution through genetic assimilation in gene regulatory networks. Thus, we contend that the importance of this evolutionary mechanism should not be easily neglected.
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Affiliation(s)
- Carlos Espinosa-Soto
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Ulises Hernández
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
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45
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Crespi E, Burnap R, Chen J, Das M, Gassman N, Rosa E, Simmons R, Wada H, Wang ZQ, Xiao J, Yang B, Yin J, Goldstone JV. Resolving the Rules of Robustness and Resilience in Biology Across Scales. Integr Comp Biol 2021; 61:2163-2179. [PMID: 34427654 DOI: 10.1093/icb/icab183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022] Open
Abstract
Why do some biological systems and communities persist while others fail? Robustness, a system's stability, and resilience, the ability to return to a stable state, are key concepts that span multiple disciplines within and outside the biological sciences. Discovering and applying common rules that govern the robustness and resilience of biological systems is a critical step toward creating solutions for species survival in the face of climate change, as well as the for the ever-increasing need for food, health, and energy for human populations. We propose that network theory provides a framework for universal scalable mathematical models to describe robustness and resilience and the relationship between them, and hypothesize that resilience at lower organization levels contribute to robust systems. Insightful models of biological systems can be generated by quantifying the mechanisms of redundancy, diversity, and connectivity of networks, from biochemical processes to ecosystems. These models provide pathways towards understanding how evolvability can both contribute to and result from robustness and resilience under dynamic conditions. We now have an abundance of data from model and non-model systems and the technological and computational advances for studying complex systems. Several conceptual and policy advances will allow the research community to elucidate the rules of robustness and resilience. Conceptually, a common language and data structure that can be applied across levels of biological organization needs to be developed. Policy advances such as cross-disciplinary funding mechanisms, access to affordable computational capacity, and the integration of network theory and computer science within the standard biological science curriculum will provide the needed research environments. This new understanding of biological systems will allow us to derive ever more useful forecasts of biological behaviors and revolutionize the engineering of biological systems that can survive changing environments or disease, navigate the deepest oceans, or sustain life throughout the solar system.
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Affiliation(s)
- Erica Crespi
- School of Biological Sciences, Washington State University
| | - Robert Burnap
- Microbiology and Molecular Genetics, Oklahoma State University
| | - Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology
| | | | - Epaminondas Rosa
- Department of Physics and School of Biological Sciences, Illinois State University
| | | | - Haruka Wada
- Department of Biological Sciences, Auburn University
| | - Zhen Q Wang
- Department of Biological Sciences, University at Buffalo
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine
| | - Bing Yang
- Division of Plant Sciences, University of Missouri
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison
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46
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Estrada-Cortés E, Jannaman EA, Block J, Amaral TF, Hansen PJ. Programming of postnatal phenotype caused by exposure of cultured embryos from Brahman cattle to colony-stimulating factor 2 and serum. J Anim Sci 2021; 99:6291391. [PMID: 34079989 DOI: 10.1093/jas/skab180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022] Open
Abstract
Alterations in the environment of the preimplantation embryo can affect competence to establish pregnancy and phenotype of resultant calves. In this study, the bovine embryo produced in vitro was used to evaluate postnatal programming actions of the embryokine colony-stimulating factor 2 (CSF2) and serum, which is a common additive of culture media. Oocytes were collected by ovum pick up from Brahman donors and fertilized with semen from Brahman bulls. Embryos were randomly assigned to one of the three treatments: vehicle, CSF2 10 ng/mL, or 1% (v/v) serum. Treatments were added to the culture medium from day 5 to 7 after fertilization. Blastocysts were harvested on day 7 and transferred into crossbred recipients. Postnatal body growth and Longissimus dorsi muscle characteristics of the resultant calves were measured. The percent of cleaved embryos becoming blastocysts was increased by serum and, to a lesser extent, CSF2. Treatment did not affect survival after embryo transfer but gestation length was shortest for pregnancies established with serum-treated embryos. Treatment did not significantly affect postnatal body weight or growth. At 3 mo of age, CSF2 calves had lower fat content in the Longissimus dorsi muscle and less subcutaneous fat over the muscle than vehicle calves. There was a tendency for cross-sectional area of the muscle to be smaller for serum calves than vehicle calves. Results confirm the importance of the preimplantation period as a window to modulate postnatal phenotype of resultant calves. In particular, CSF2 exerted actions during the preimplantation period to program characteristics of accumulation of intramuscular and subcutaneous fat of resultant calves. The use of a low serum concentration in culture medium from day 5 to 7 of development can increase the yield of transferrable embryos without causing serious negative consequences for the offspring.
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Affiliation(s)
- Eliab Estrada-Cortés
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA.,Campo Experimental Centro Altos de Jalisco, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tepatitlán de Morelos, Jalisco, 47600, México
| | - Elizabeth A Jannaman
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
| | - Jeremy Block
- Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA
| | - Thiago F Amaral
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
| | - Peter J Hansen
- Department of Animal Sciences and D.H. Barron Reproductive and Perinatal Biology Research Program, Genetics Institute, University of Florida, Gainesville, FL 32611-0910, USA
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47
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Tong Y, Zhang S, Riddle S, Zhang L, Song R, Yue D. Intrauterine Hypoxia and Epigenetic Programming in Lung Development and Disease. Biomedicines 2021; 9:944. [PMID: 34440150 PMCID: PMC8394854 DOI: 10.3390/biomedicines9080944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Clinically, intrauterine hypoxia is the foremost cause of perinatal morbidity and developmental plasticity in the fetus and newborn infant. Under hypoxia, deviations occur in the lung cell epigenome. Epigenetic mechanisms (e.g., DNA methylation, histone modification, and miRNA expression) control phenotypic programming and are associated with physiological responses and the risk of developmental disorders, such as bronchopulmonary dysplasia. This developmental disorder is the most frequent chronic pulmonary complication in preterm labor. The pathogenesis of this disease involves many factors, including aberrant oxygen conditions and mechanical ventilation-mediated lung injury, infection/inflammation, and epigenetic/genetic risk factors. This review is focused on various aspects related to intrauterine hypoxia and epigenetic programming in lung development and disease, summarizes our current knowledge of hypoxia-induced epigenetic programming and discusses potential therapeutic interventions for lung disease.
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Affiliation(s)
- Yajie Tong
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China;
| | - Shuqing Zhang
- School of Pharmacy, China Medical University, Shenyang 110122, China;
| | - Suzette Riddle
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Lubo Zhang
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA;
| | - Rui Song
- Lawrence D. Longo, MD Center for Perinatal Biology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA;
| | - Dongmei Yue
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China;
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48
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Rodrigues YK, van Bergen E, Alves F, Duneau D, Beldade P. Additive and non-additive effects of day and night temperatures on thermally plastic traits in a model for adaptive seasonal plasticity. Evolution 2021; 75:1805-1819. [PMID: 34097756 DOI: 10.1111/evo.14271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/26/2021] [Accepted: 05/12/2021] [Indexed: 12/17/2022]
Abstract
Developmental plasticity can match organismal phenotypes to ecological conditions, helping populations to deal with the environmental heterogeneity of alternating seasons. In contrast to natural situations, experimental studies of plasticity often use environmental conditions that are held constant during development. To explore potential interactions between day and night temperatures, we tested effects of circadian temperature fluctuations on thermally plastic traits in a seasonally plastic butterfly, Bicyclus anynana. Comparing phenotypes for four treatments corresponding to a full-factorial analysis of cooler and warmer temperatures, we found evidence of significant interaction effects between day and night temperatures. We then focused on comparing phenotypes between individuals reared under two types of temperature fluctuations (warmer days with cooler nights, and cooler days with warmer nights) and individuals reared under a constant temperature of the same daily mean. We found evidence of additive-like effects (for body size), and different types of dominance-like effects, with one particular period of the light cycle (for development time) or one particular extreme temperature (for eyespot size) having a larger impact on phenotype. Differences between thermally plastic traits, which together underlie alternative seasonal strategies for survival and reproduction, revealed their independent responses to temperature. This study underscores the value of studying how organisms integrate complex environmental information toward a complete understanding of natural phenotypic variation and of the impact of environmental change thereon.
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Affiliation(s)
- Yara Katia Rodrigues
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Current address: Atlantic Technical University (UTA), Mindelo, São Vicente island, Cabo Verde
| | - Erik van Bergen
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Current address: Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
| | - Filipa Alves
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - David Duneau
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,UMR 5174 - CNRS, Evolution et Diversité Biologique, University Paul Sabatier, Toulouse, France
| | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.,UMR 5174 - CNRS, Evolution et Diversité Biologique, University Paul Sabatier, Toulouse, France.,CE3C: Centre for Ecology, Evolution, and Environmental Changes, Faculty of Sciences, University of Lisbon, Portugal
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Levis NA, Kelly PW, Harmon EA, Ehrenreich IM, McKay DJ, Pfennig DW. Transcriptomic bases of a polyphenism. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:482-495. [PMID: 34142757 DOI: 10.1002/jez.b.23066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/22/2021] [Accepted: 05/22/2021] [Indexed: 11/06/2022]
Abstract
Polyphenism-in which multiple distinct phenotypes are produced from a single genotype owing to differing environmental conditions-is commonplace, but its molecular bases are poorly understood. Here, we examine the transcriptomic bases of a polyphenism in Mexican spadefoot toads (Spea multiplicata). Depending on their environment, their tadpoles develop into either a default "omnivore" morph or a novel "carnivore" morph. We compared patterns of gene expression among sibships that exhibited high versus low production of carnivores when reared in conditions that induce the carnivore morph versus those that do not. We found that production of the novel carnivore morph actually involved changes in fewer genes than did the maintenance of the default omnivore morph in the inducing environment. However, only body samples showed this pattern; head samples showed the opposite pattern. We also found that changes to lipid metabolism (especially cholesterol biosynthesis) and peroxisome contents and function might be crucial for establishing and maintaining differences between the morphs. Thus, our findings suggest that carnivore phenotype might have originally evolved following the breakdown of robustness mechanisms that maintain the default omnivore phenotype, and that the carnivore morph is developmentally regulated by lipid metabolism and peroxisomal form, function, and/or signaling. This study also serves as a springboard for further exploration into the nature and causes of plasticity in an emerging model system.
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Affiliation(s)
- Nicholas A Levis
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA.,Current affiliation: Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Patrick W Kelly
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Emily A Harmon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, University of Southern, Los Angeles, California, USA
| | - Daniel J McKay
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - David W Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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Casasa S, Biddle JF, Koutsovoulos GD, Ragsdale EJ. Polyphenism of a Novel Trait Integrated Rapidly Evolving Genes into Ancestrally Plastic Networks. Mol Biol Evol 2021; 38:331-343. [PMID: 32931588 PMCID: PMC7826178 DOI: 10.1093/molbev/msaa235] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Developmental polyphenism, the ability to switch between phenotypes in response to environmental variation, involves the alternating activation of environmentally sensitive genes. Consequently, to understand how a polyphenic response evolves requires a comparative analysis of the components that make up environmentally sensitive networks. Here, we inferred coexpression networks for a morphological polyphenism, the feeding-structure dimorphism of the nematode Pristionchus pacificus. In this species, individuals produce alternative forms of a novel trait—moveable teeth, which in one morph enable predatory feeding—in response to environmental cues. To identify the origins of polyphenism network components, we independently inferred coexpression modules for more conserved transcriptional responses, including in an ancestrally nonpolyphenic nematode species. Further, through genome-wide analyses of these components across the nematode family (Diplogastridae) in which the polyphenism arose, we reconstructed how network components have changed. To achieve this, we assembled and resolved the phylogenetic context for five genomes of species representing the breadth of Diplogastridae and a hypothesized outgroup. We found that gene networks instructing alternative forms arose from ancestral plastic responses to environment, specifically starvation-induced metabolism and the formation of a conserved diapause (dauer) stage. Moreover, loci from rapidly evolving gene families were integrated into these networks with higher connectivity than throughout the rest of the P. pacificus transcriptome. In summary, we show that the modular regulatory outputs of a polyphenic response evolved through the integration of conserved plastic responses into networks with genes of high evolutionary turnover.
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Affiliation(s)
- Sofia Casasa
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
| | - Joseph F Biddle
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
| | | | - Erik J Ragsdale
- Department of Biology, Indiana University, Bloomington, Bloomington, IN
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