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Santos MA, Carromeu-Santos A, Quina AS, Antunes MA, Kristensen TN, Santos M, Matos M, Fragata I, Simões P. Experimental Evolution in a Warming World: The Omics Era. Mol Biol Evol 2024; 41:msae148. [PMID: 39034684 DOI: 10.1093/molbev/msae148] [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: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024] Open
Abstract
A comprehensive understanding of the genetic mechanisms that shape species responses to thermal variation is essential for more accurate predictions of the impacts of climate change on biodiversity. Experimental evolution with high-throughput resequencing approaches (evolve and resequence) is a highly effective tool that has been increasingly employed to elucidate the genetic basis of adaptation. The number of thermal evolve and resequence studies is rising, yet there is a dearth of efforts to integrate this new wealth of knowledge. Here, we review this literature showing how these studies have contributed to increase our understanding on the genetic basis of thermal adaptation. We identify two major trends: highly polygenic basis of thermal adaptation and general lack of consistency in candidate targets of selection between studies. These findings indicate that the adaptive responses to specific environments are rather independent. A review of the literature reveals several gaps in the existing research. Firstly, there is a paucity of studies done with organisms of diverse taxa. Secondly, there is a need to apply more dynamic and ecologically relevant thermal environments. Thirdly, there is a lack of studies that integrate genomic changes with changes in life history and behavioral traits. Addressing these issues would allow a more in-depth understanding of the relationship between genotype and phenotype. We highlight key methodological aspects that can address some of the limitations and omissions identified. These include the need for greater standardization of methodologies and the utilization of new technologies focusing on the integration of genomic and phenotypic variation in the context of thermal adaptation.
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Affiliation(s)
- Marta A Santos
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Carromeu-Santos
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Ana S Quina
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Almada, Portugal
| | - Marta A Antunes
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - Mauro Santos
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departament de Genètica i de Microbiologia, Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GBBE), Universitat Autonòma de Barcelona, Bellaterra, Spain
| | - Margarida Matos
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Inês Fragata
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Pedro Simões
- CE3C-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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2
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van Heerwaarden B, Sgrò C, Kellermann VM. Threshold shifts and developmental temperature impact trade-offs between tolerance and plasticity. Proc Biol Sci 2024; 291:20232700. [PMID: 38320612 PMCID: PMC10846935 DOI: 10.1098/rspb.2023.2700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Mounting evidence suggests that ectotherms are already living close to their upper physiological thermal limits. Phenotypic plasticity has been proposed to reduce the impact of climate change in the short-term providing time for adaptation, but the tolerance-plasticity trade-off hypothesis predicts organisms with higher tolerance have lower plasticity. Empirical evidence is mixed, which may be driven by methodological issues such as statistical artefacts, nonlinear reaction norms, threshold shifts or selection. Here, we examine whether threshold shifts (organisms with higher tolerance require stronger treatments to induce maximum plastic responses) influence tolerance-plasticity trade-offs in hardening capacity for desiccation tolerance and critical thermal maximum (CTMAX) across Drosophila species with varying distributions/sensitivity to desiccation/heat stress. We found evidence for threshold shifts in both traits; species with higher heat/desiccation tolerance required longer hardening treatments to induce maximum hardening responses. Species with higher heat tolerance also showed reductions in hardening capacity at higher developmental acclimation temperatures. Trade-off patterns differed depending on the hardening treatment used and the developmental temperature flies were exposed to. Based on these findings, studies that do not consider threshold shifts, or that estimate plasticity under a narrow set of environments, will have a limited ability to assess trade-off patterns and differences in plasticity across species/populations more broadly.
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Affiliation(s)
| | - Carla Sgrò
- School of Biological Sciences, Monash University, Clayton 3800, Victoria, Australia
| | - Vanessa M. Kellermann
- School of Biological Sciences, Monash University, Clayton 3800, Victoria, Australia
- School of Agriculture Biomedicine and Environment, La Trobe University, Bundoora 3086, Victoria, Australia
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3
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Gowri V, Monteiro A. Acquired preferences for a novel food odor do not become stronger or stable after multiple generations of odor feeding in Bicyclus anynana butterfly larvae. Ann N Y Acad Sci 2024; 1531:84-94. [PMID: 38113288 DOI: 10.1111/nyas.15090] [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] [Indexed: 12/21/2023]
Abstract
Many herbivorous insects have specific host-plant preferences, and it is unclear how these preferences evolved. Previously, we found that Bicyclus anynana larvae can learn to prefer novel food odors from eating leaves with those odors and transmit those learned preferences to the next generation. It is uncertain whether such acquired odor preferences can increase across generations of repeated odor feeding and be maintained even in the absence of odor. In this study, we fed larvae with novel banana odor-coated leaves (odor-fed larvae) for five consecutive generations, without selection on behavioral choices, and measured how larval innate preferences changed over time. Then, we removed the odor stimulus from a larval subgroup, while the other group continued to be odor-fed. Our results show that larvae learned to prefer the novel odor within a generation of odor feeding and transmitted the learned preference to the next generation, as previously found. Odor-fed larvae preferred odor significantly more compared to control larvae across five generations of repeated odor or control feeding. However, this led neither to increased odor preference, nor its stabilization. This suggests that when butterfly larvae feed on a new host, a preference for that novel food plant may develop and be transmitted to the next generation, but this preference lasts for a single generation and disappears once the odor stimulus is removed.
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Affiliation(s)
- V Gowri
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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4
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Liu J, Liu T, Liu Y, Wang Y, Liu L, Gong L, Liu B, Lü Z. Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies. Curr Issues Mol Biol 2023; 46:153-170. [PMID: 38248314 PMCID: PMC10813846 DOI: 10.3390/cimb46010012] [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: 11/16/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Adaptation to thermal conditions in tidal mudflats always involves tolerating frequent fluctuations and often extreme environmental temperatures. Regulation of gene expression plays a fundamental role in the evolution of these thermal adaptations. To identify the key gene regulatory networks associated with the thermal adaptation, we investigated the capability of cold tolerance, as well as the transcriptomic changes under cold stress in two mudflat inhabitants (Odontamblyopus lacepedii and O. rebecca) with contrasting latitude affinity. Our results revealed a remarkable divergent capacity of cold tolerance (CTmin: 0.61 °C vs. 9.57 °C) between the two gobies. Analysis of transcriptomic changes under cold stress unveiled 193 differentially expressed genes exhibiting similar expression profiles across all tissues and species, including several classic metabolic and circadian rhythm molecules such as ACOD and CIART that may represent the core cold response machinery in eel gobies. Meanwhile, some genes show a unique expression spectrum in the more cold-tolerant O. lacepedii suggesting their roles in the enhanced cold tolerance and hence the extreme thermal adaptations. In addition, a weighted gene co-expression network analysis (WGCNA) revealed a subset of metabolic hub genes including MYH11 and LIPT2 showing distinct down-regulation in O. lacepedii when exposed to cold stress which highlights the role of reduced energy consumption in the enhanced cold tolerance of eel gobies. These findings not only provide new insights into how mudflat teleosts could cope with cold stress and their potential evolutionary strategies for adapting to their thermal environment, but also have important implications for sound management and conservation of their fishery resources in a scenario of global climate warming in the marine realm.
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Affiliation(s)
- Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Yantao Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Yuzhen Wang
- National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
| | - Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (J.L.); (T.L.); (Y.L.); (L.L.); (L.G.); (B.L.)
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5
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Fatemi E, Jung C. Pathogenicity of the root lesion nematode Pratylenchus neglectus depends on pre-culture conditions. Sci Rep 2023; 13:19642. [PMID: 37949971 PMCID: PMC10638436 DOI: 10.1038/s41598-023-46551-9] [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: 09/01/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
The ability of a plant parasitic nematode to infect and reproduce within a host plant depends on its genotype and the environmental conditions before and during infection. We studied the culturing conditions of the root lesion nematode Pratylenchus neglectus to produce inoculum for plant infection tests. Nematodes were either cultivated on carrot calli for different periods or directly isolated from the roots of the host plants. After infection of wheat and barley plants in the greenhouse, nematodes were quantified by RT-qPCR and by visual counting of the nematodes. We observed drastically reduced infection rates after long-term (> 96 weeks) cultivation on carrot callus. In contrast, fresh isolates from cereal roots displayed much higher pathogenicity. We recommend using root lesion nematodes cultivated on carrot calli no longer than 48 weeks to guarantee uniform infection rates.
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Affiliation(s)
- Ehsan Fatemi
- Plant Breeding Institute, Christian-Albrechts University, Kiel, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts University, Kiel, Germany.
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6
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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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7
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Gunderson AR, Revell LJ. Testing for genetic assimilation with phylogenetic comparative analysis: Conceptual, methodological, and statistical considerations. Evolution 2022; 76:1942-1952. [PMID: 35851667 DOI: 10.1111/evo.14570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/21/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
Genetic assimilation is a process that leads to reduced phenotypic plasticity during adaptation to novel conditions, a potentially important phenomenon under global environmental change. Null expectations when testing for genetic assimilation, however, are not always clear. For instance, the statistical artifact of regression to the mean could bias us toward detecting genetic assimilation when it has not occurred. Likewise, the specific mechanism underlying plasticity expression may affect null expectations under neutral evolution. We used macroevolutionary numerical simulations to examine both of these important issues and their interaction, varying whether plasticity evolves, the evolutionary mechanism, trait measurement error, and experimental design. We also modified an existing reaction norm correction method to account for phylogenetic nonindependence. We found (1) regression to the mean is pervasive and can generate spurious support for genetic assimilation; (2) experimental design and post hoc correction can minimize this spurious effect; and (3) neutral evolution can produce patterns consistent with genetic assimilation without constraint or selection, depending on the mechanism of plasticity expression. Additionally, we reanalyzed published macroevolutionary data supporting genetic assimilation, and found that support was reduced after proper correction. Considerable caution is thus required whenever investigating genetic assimilation and reaction norm evolution at macroevolutionary scales.
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Affiliation(s)
- Alex R Gunderson
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, 70118
| | - Liam J Revell
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, 02125.,Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
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8
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Brennan RS, deMayo JA, Dam HG, Finiguerra MB, Baumann H, Pespeni MH. Loss of transcriptional plasticity but sustained adaptive capacity after adaptation to global change conditions in a marine copepod. Nat Commun 2022; 13:1147. [PMID: 35241657 PMCID: PMC8894427 DOI: 10.1038/s41467-022-28742-6] [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: 10/23/2020] [Accepted: 02/04/2022] [Indexed: 12/04/2022] Open
Abstract
Adaptive evolution and phenotypic plasticity will fuel resilience in the geologically unprecedented warming and acidification of the earth’s oceans, however, we have much to learn about the interactions and costs of these mechanisms of resilience. Here, using 20 generations of experimental evolution followed by three generations of reciprocal transplants, we investigated the relationship between adaptation and plasticity in the marine copepod, Acartia tonsa, in future global change conditions (high temperature and high CO2). We found parallel adaptation to global change conditions in genes related to stress response, gene expression regulation, actin regulation, developmental processes, and energy production. However, reciprocal transplantation showed that adaptation resulted in a loss of transcriptional plasticity, reduced fecundity, and reduced population growth when global change-adapted animals were returned to ambient conditions or reared in low food conditions. However, after three successive transplant generations, global change-adapted animals were able to match the ambient-adaptive transcriptional profile. Concurrent changes in allele frequencies and erosion of nucleotide diversity suggest that this recovery occurred via adaptation back to ancestral conditions. These results demonstrate that while plasticity facilitated initial survival in global change conditions, it eroded after 20 generations as populations adapted, limiting resilience to new stressors and previously benign environments. Rapid adaptation will facilitate species resilience under global climate change, but its effects on plasticity are less commonly investigated. This study shows that 20 generations of experimental adaptation in a marine copepod drives a rapid loss of plasticity that carries costs and might have impacts on future resilience to environmental change.
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Affiliation(s)
- Reid S Brennan
- Department of Biology, University of Vermont, Burlington, VT, USA. .,Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
| | - James A deMayo
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA.,Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Hans G Dam
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Michael B Finiguerra
- Department of Ecology and Evolutionary Biology, University of Connecticut, Groton, CT, USA
| | - Hannes Baumann
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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Gowri V, Monteiro A. Inheritance of Acquired Traits in Insects and Other Animals and the Epigenetic Mechanisms That Break the Weismann Barrier. J Dev Biol 2021; 9:41. [PMID: 34698204 PMCID: PMC8544363 DOI: 10.3390/jdb9040041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/21/2021] [Accepted: 10/01/2021] [Indexed: 01/29/2023] Open
Abstract
The credibility of the Weismann barrier has come into question. Several studies in various animal systems, from mice to worms, have shown that novel environmental stimuli can generate an altered developmental or behavioral trait that can be transmitted to offspring of the following generation. Recently, insects have become ideal models to study the inheritance of acquired traits. This is because insects can be reared in high numbers at low cost, they have short generation times and produce abundant offspring. Numerous studies have shown that an insect can modify its phenotype in response to a novel stimulus to aid its survival, and also that this modified phenotypic trait can be inherited by its offspring. Epigenetic mechanisms are likely at play but, most studies do not address the mechanisms that underlie the inheritance of acquired traits in insects. Here we first review general epigenetic mechanisms such as DNA methylation, histone acetylation and small noncoding RNAs that have been implicated in the transmission of acquired traits in animals, then we focus on the few insect studies in which these mechanisms have been investigated.
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Affiliation(s)
- V. Gowri
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
- Science Division, Yale-NUS College, Singapore 138609, Singapore
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10
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Barley JM, Cheng BS, Sasaki M, Gignoux-Wolfsohn S, Hays CG, Putnam AB, Sheth S, Villeneuve AR, Kelly M. Limited plasticity in thermally tolerant ectotherm populations: evidence for a trade-off. Proc Biol Sci 2021; 288:20210765. [PMID: 34493077 PMCID: PMC8424342 DOI: 10.1098/rspb.2021.0765] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
Many species face extinction risks owing to climate change, and there is an urgent need to identify which species' populations will be most vulnerable. Plasticity in heat tolerance, which includes acclimation or hardening, occurs when prior exposure to a warmer temperature changes an organism's upper thermal limit. The capacity for thermal acclimation could provide protection against warming, but prior work has found few generalizable patterns to explain variation in this trait. Here, we report the results of, to our knowledge, the first meta-analysis to examine within-species variation in thermal plasticity, using results from 20 studies (19 species) that quantified thermal acclimation capacities across 78 populations. We used meta-regression to evaluate two leading hypotheses. The climate variability hypothesis predicts that populations from more thermally variable habitats will have greater plasticity, while the trade-off hypothesis predicts that populations with the lowest heat tolerance will have the greatest plasticity. Our analysis indicates strong support for the trade-off hypothesis because populations with greater thermal tolerance had reduced plasticity. These results advance our understanding of variation in populations' susceptibility to climate change and imply that populations with the highest thermal tolerance may have limited phenotypic plasticity to adjust to ongoing climate warming.
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Affiliation(s)
- Jordanna M. Barley
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Brian S. Cheng
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Matthew Sasaki
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | | | - Cynthia G. Hays
- Department of Biology, Keene State College, Keene, NH 03435, USA
| | - Alysha B. Putnam
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Seema Sheth
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Andrew R. Villeneuve
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Morgan Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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11
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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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12
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deMayo JA, Girod A, Sasaki MC, Dam HG. Adaptation to simultaneous warming and acidification carries a thermal tolerance cost in a marine copepod. Biol Lett 2021; 17:20210071. [PMID: 34256577 PMCID: PMC8278047 DOI: 10.1098/rsbl.2021.0071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
The ocean is undergoing warming and acidification. Thermal tolerance is affected both by evolutionary adaptation and developmental plasticity. Yet, thermal tolerance in animals adapted to simultaneous warming and acidification is unknown. We experimentally evolved the ubiquitous copepod Acartia tonsa to future combined ocean warming and acidification conditions (OWA approx. 22°C, 2000 µatm CO2) and then compared its thermal tolerance relative to ambient conditions (AM approx. 18°C, 400 µatm CO2). The OWA and AM treatments were reciprocally transplanted after 65 generations to assess effects of developmental conditions on thermal tolerance and potential costs of adaptation. Treatments transplanted from OWA to AM conditions were assessed at the F1 and F9 generations following transplant. Adaptation to warming and acidification, paradoxically, reduces both thermal tolerance and phenotypic plasticity. These costs of adaptation to combined warming and acidification may limit future population resilience.
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Affiliation(s)
- James A. deMayo
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340-6048, USA
| | - Amanda Girod
- Department of Molecular Biology and Biochemistry, Middlebury College, Middlebury, VT 05753, USA
| | - Matthew C. Sasaki
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340-6048, USA
| | - Hans G. Dam
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340-6048, USA
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13
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He F, Steige KA, Kovacova V, Göbel U, Bouzid M, Keightley PD, Beyer A, de Meaux J. Cis-regulatory evolution spotlights species differences in the adaptive potential of gene expression plasticity. Nat Commun 2021; 12:3376. [PMID: 34099660 PMCID: PMC8184852 DOI: 10.1038/s41467-021-23558-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
Phenotypic plasticity is the variation in phenotype that a single genotype can produce in different environments and, as such, is an important component of individual fitness. However, whether the effect of new mutations, and hence evolution, depends on the direction of plasticity remains controversial. Here, we identify the cis-acting modifications that have reshaped gene expression in response to dehydration stress in three Arabidopsis species. Our study shows that the direction of effects of most cis-regulatory variants differentiating the response between A. thaliana and the sister species A. lyrata and A. halleri depends on the direction of pre-existing plasticity in gene expression. A comparison of the rate of cis-acting variant accumulation in each lineage indicates that the selective forces driving adaptive evolution in gene expression favors regulatory changes that magnify the stress response in A. lyrata. The evolutionary constraints measured on the amino-acid sequence of these genes support this interpretation. In contrast, regulatory changes that mitigate the plastic response to stress evolved more frequently in A. halleri. Our results demonstrate that pre-existing plasticity may be a stepping stone for adaptation, but its selective remodeling differs between lineages.
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Affiliation(s)
- F He
- CEPLAS, University of Cologne, Cologne, Germany
| | - K A Steige
- CEPLAS, University of Cologne, Cologne, Germany
| | - V Kovacova
- CECAD, University of Cologne, Cologne, Germany
| | - U Göbel
- CEPLAS, University of Cologne, Cologne, Germany
| | - M Bouzid
- CEPLAS, University of Cologne, Cologne, Germany
| | - P D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - A Beyer
- CEPLAS, University of Cologne, Cologne, Germany
| | - J de Meaux
- CEPLAS, University of Cologne, Cologne, Germany.
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14
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O’Connor CH, Sikkink KL, Nelson TC, Fierst JL, Cresko WA, Phillips PC. Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei. G3 (BETHESDA, MD.) 2021; 11:jkab045. [PMID: 33605401 PMCID: PMC8049431 DOI: 10.1093/g3journal/jkab045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/01/2021] [Indexed: 12/04/2022]
Abstract
The adaptation of complex organisms to changing environments has been a central question in evolutionary quantitative genetics since its inception. The structure of the genotype-phenotype maps is critical because pleiotropic effects can generate widespread correlated responses to selection and potentially restrict the extent of evolutionary change. In this study, we use experimental evolution to dissect the genetic architecture of natural variation for acute heat stress and oxidative stress response in the nematode Caenorhabiditis remanei. Previous work in the classic model nematode Caenorhabiditis elegans has found that abiotic stress response is controlled by a handful of genes of major effect and that mutations in any one of these genes can have widespread pleiotropic effects on multiple stress response traits. Here, we find that acute heat stress response and acute oxidative response in C. remanei are polygenic, complex traits, with hundreds of genomic regions responding to selection. In contrast to expectation from mutation studies, we find that evolved acute heat stress and acute oxidative stress response for the most part display independent genetic bases. This lack of correlation is reflected at the levels of phenotype, gene expression, and in the genomic response to selection. Thus, while these findings support the general view that rapid adaptation can be generated by changes at hundreds to thousands of sites in the genome, the architecture of segregating variation is likely to be determined by the pleiotropic structure of the underlying genetic networks.
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Affiliation(s)
- Christine H O’Connor
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Kristin L Sikkink
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas C Nelson
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Janna L Fierst
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - William A Cresko
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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15
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Rivera HE, Aichelman HE, Fifer JE, Kriefall NG, Wuitchik DM, Wuitchik SJS, Davies SW. A framework for understanding gene expression plasticity and its influence on stress tolerance. Mol Ecol 2021; 30:1381-1397. [PMID: 33503298 DOI: 10.1111/mec.15820] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/10/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
Phenotypic plasticity can serve as a stepping stone towards adaptation. Recently, studies have shown that gene expression contributes to emergent stress responses such as thermal tolerance, with tolerant and susceptible populations showing distinct transcriptional profiles. However, given the dynamic nature of gene expression, interpreting transcriptomic results in a way that elucidates the functional connection between gene expression and the observed stress response is challenging. Here, we present a conceptual framework to guide interpretation of gene expression reaction norms in the context of stress tolerance. We consider the evolutionary and adaptive potential of gene expression reaction norms and discuss the influence of sampling timing, transcriptomic resilience, as well as complexities related to life history when interpreting gene expression dynamics and how these patterns relate to host tolerance. We highlight corals as a case study to demonstrate the value of this framework for non-model systems. As species face rapidly changing environmental conditions, modulating gene expression can serve as a mechanistic link from genetic and cellular processes to the physiological responses that allow organisms to thrive under novel conditions. Interpreting how or whether a species can employ gene expression plasticity to ensure short-term survival will be critical for understanding the global impacts of climate change across diverse taxa.
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Affiliation(s)
- Hanny E Rivera
- Department of Biology, Boston University, Boston, MA, USA
| | | | - James E Fifer
- Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Sara J S Wuitchik
- Department of Biology, Boston University, Boston, MA, USA.,FAS Informatics, Harvard University, Cambridge, MA, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA
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16
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Nijhout HF, Kudla AM, Hazelwood CC. Genetic assimilation and accommodation: Models and mechanisms. Curr Top Dev Biol 2020; 141:337-369. [PMID: 33602492 DOI: 10.1016/bs.ctdb.2020.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic assimilation and genetic accommodation are mechanisms by which novel phenotypes are produced and become established in a population. Novel characters may be fixed and canalized so they are insensitive to environmental variation, or can be plastic and adaptively responsive to environmental variation. In this review we explore the various theories that have been proposed to explain the developmental origin and evolution of novel phenotypes and the mechanisms by which canalization and phenotypic plasticity evolve. These theories and models range from conceptual to mathematical and have taken different views of how genes and environment contribute to the development and evolution of the properties of phenotypes. We will argue that a deeper and more nuanced understanding of genetic accommodation requires a recognition that phenotypes are not static entities but are dynamic system properties with no fixed deterministic relationship between genotype and phenotype. We suggest a mechanistic systems-view of development that allows one to incorporate both genes and environment in a common model, and that enables both quantitative analysis and visualization of the evolution of canalization and phenotypic plasticity.
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Affiliation(s)
| | - Anna M Kudla
- Department of Biology, Duke University, Durham, NC, United States
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17
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Koch EL, Guillaume F. Restoring ancestral phenotypes is a general pattern in gene expression evolution during adaptation to new environments in Tribolium castaneum. Mol Ecol 2020; 29:3938-3953. [PMID: 32844494 DOI: 10.1111/mec.15607] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 06/19/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]
Abstract
Plasticity and evolution are two processes allowing populations to respond to environmental changes, but how both are related and impact each other remains controversial. We studied plastic and evolutionary responses in gene expression of Tribolium castaneum after exposure of the beetles to new environments that differed from ancestral conditions in temperature, humidity or both. Using experimental evolution with 10 replicated lines per condition, we were able to demonstrate adaptation after 20 generations. We measured whole-transcriptome gene expression with RNA-sequencing to infer evolutionary and plastic changes. We found more evidence for changes in mean expression (shift in the intercept of reaction norms) in adapted lines than for changes in plasticity (shifts in slopes). Plasticity was mainly preserved in selected lines and was responsible for a large part of the phenotypic divergence in expression between ancestral and new conditions. However, we found that genes with the largest evolutionary changes in expression also evolved reduced plasticity and often showed expression levels closer to the ancestral stage. Results obtained in the three different conditions were similar, suggesting that restoration of ancestral expression levels during adaptation is a general evolutionary pattern. With a larger sample in the most stressful condition, we were able to detect a positive correlation between the proportion of genes with reversion of the ancestral plastic response and mean fitness per selection line.
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Affiliation(s)
- Eva L Koch
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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18
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Casasa S, Zattara EE, Moczek AP. Nutrition-responsive gene expression and the developmental evolution of insect polyphenism. Nat Ecol Evol 2020; 4:970-978. [PMID: 32424280 DOI: 10.1038/s41559-020-1202-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/09/2020] [Indexed: 01/05/2023]
Abstract
Nutrition-responsive development is a ubiquitous and highly diversified example of phenotypic plasticity, yet its underlying molecular and developmental mechanisms and modes of evolutionary diversification remain poorly understood. We measured genome-wide transcription in three closely related species of horned beetles exhibiting strikingly diverse degrees of nutrition responsiveness in the development of male weaponry. We show that (1) counts of differentially expressed genes between low- and high-nutritional backgrounds mirror species-specific degrees of morphological nutrition responsiveness; (2) evolutionary exaggeration of morphological responsiveness is underlain by both amplification of ancestral nutrition-responsive gene expression and recruitment of formerly low nutritionally responsive genes; and (3) secondary loss of morphological responsiveness to nutrition coincides with a dramatic reduction in gene expression plasticity. Our results further implicate genetic accommodation of ancestrally high variability of gene expression plasticity in both exaggeration and loss of nutritional plasticity, yet reject a major role of taxon-restricted genes in the developmental regulation and evolution of nutritional plasticity.
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Affiliation(s)
- Sofia Casasa
- Department of Biology, Indiana University, Bloomington, IN, USA.
| | - Eduardo E Zattara
- Department of Biology, Indiana University, Bloomington, IN, USA. .,INIBIOMA, Universidad Nacional del Comahue - CONICET, Bariloche, Argentina.
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, IN, USA
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19
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Teterina AA, Willis JH, Phillips PC. Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization. Genetics 2020; 214:769-780. [PMID: 32111628 PMCID: PMC7153949 DOI: 10.1534/genetics.119.303018] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 12/23/2022] Open
Abstract
The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of interchromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.
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Affiliation(s)
- Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
- Center of Parasitology, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow 117071, Russia
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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20
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Kelly M. Adaptation to climate change through genetic accommodation and assimilation of plastic phenotypes. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180176. [PMID: 30966963 DOI: 10.1098/rstb.2018.0176] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Theory suggests that evolutionary changes in phenotypic plasticity could either hinder or facilitate evolutionary rescue in a changing climate. Nevertheless, the actual role of evolving plasticity in the responses of natural populations to climate change remains unresolved. Direct observations of evolutionary change in nature are rare, making it difficult to assess the relative contributions of changes in trait means versus changes in plasticity to climate change responses. To address this gap, this review explores several proxies that can be used to understand evolving plasticity in the context of climate change, including space for time substitutions, experimental evolution and tests for genomic divergence at environmentally responsive loci. Comparisons among populations indicate a prominent role for divergence in environmentally responsive traits in local adaptation to climatic gradients. Moreover, genomic comparisons among such populations have identified pervasive divergence in the regulatory regions of environmentally responsive loci. Taken together, these lines of evidence suggest that divergence in plasticity plays a prominent role in adaptation to climatic gradients over space, indicating that evolving plasticity is also likely to play a key role in adaptive responses to climate change through time. This suggests that genetic variation in plastic responses to the environment (G × E) might be an important predictor of species' vulnerabilities to climate-driven decline or extinction. This article is part of the theme issue 'The role of plasticity in phenotypic adaptation to rapid environmental change'.
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Affiliation(s)
- Morgan Kelly
- Biological Sciences, Louisiana State University , Baton Rouge, LA 70808 , USA
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21
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Ecological genomics of adaptation to unpredictability in experimental rotifer populations. Sci Rep 2019; 9:19646. [PMID: 31873145 PMCID: PMC6927961 DOI: 10.1038/s41598-019-56100-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 12/02/2019] [Indexed: 12/29/2022] Open
Abstract
Elucidating the genetic basis of phenotypic variation in response to different environments is key to understanding how populations evolve. Facultatively sexual rotifers can develop adaptive responses to fluctuating environments. In a previous evolution experiment, diapause-related traits changed rapidly in response to two selective regimes (predictable vs unpredictable) in laboratory populations of the rotifer Brachionus plicatilis. Here, we investigate the genomic basis of adaptation to environmental unpredictability in these experimental populations. We identified and genotyped genome-wide polymorphisms in 169 clones from both selective regimes after seven cycles of selection using genotyping by sequencing (GBS). Additionally, we used GBS data from the 270 field clones from which the laboratory populations were established. This GBS dataset was used to identify candidate SNPs under selection. A total of 76 SNPs showed divergent selection, three of which are candidates for being under selection in the particular unpredictable fluctuation pattern studied. Most of the remaining SNPs showed strong signals of adaptation to laboratory conditions. Furthermore, a genotype-phenotype association approach revealed five SNPs associated with two key life-history traits in the adaptation to unpredictability. Our results contribute to elucidating the genomic basis for adaptation to unpredictable environments and lay the groundwork for future evolution studies in rotifers.
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22
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Hu Y, Linz DM, Parker ES, Schwab DB, Casasa S, Macagno ALM, Moczek AP. Developmental bias in horned dung beetles and its contributions to innovation, adaptation, and resilience. Evol Dev 2019; 22:165-180. [PMID: 31475451 DOI: 10.1111/ede.12310] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Developmental processes transduce diverse influences during phenotype formation, thereby biasing and structuring amount and type of phenotypic variation available for evolutionary processes to act on. The causes, extent, and consequences of this bias are subject to significant debate. Here we explore the role of developmental bias in contributing to organisms' ability to innovate, to adapt to novel or stressful conditions, and to generate well integrated, resilient phenotypes in the face of perturbations. We focus our inquiry on one taxon, the horned dung beetle genus Onthophagus, and review the role developmental bias might play across several levels of biological organization: (a) gene regulatory networks that pattern specific body regions; (b) plastic developmental mechanisms that coordinate body wide responses to changing environments and; (c) developmental symbioses and niche construction that enable organisms to build teams and to actively modify their own selective environments. We posit that across all these levels developmental bias shapes the way living systems innovate, adapt, and withstand stress, in ways that can alternately limit, bias, or facilitate developmental evolution. We conclude that the structuring contribution of developmental bias in evolution deserves further study to better understand why and how developmental evolution unfolds the way it does.
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Affiliation(s)
- Yonggang Hu
- Department of Biology, Indiana University, Bloomington, Indiana
| | - David M Linz
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Erik S Parker
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Daniel B Schwab
- Department of Biology, Indiana University, Bloomington, Indiana
| | - Sofia Casasa
- Department of Biology, Indiana University, Bloomington, Indiana
| | | | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana
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23
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Levis NA, Pfennig DW. Plasticity‐led evolution: A survey of developmental mechanisms and empirical tests. Evol Dev 2019; 22:71-87. [DOI: 10.1111/ede.12309] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Nicholas A. Levis
- Department of Biology University of North Carolina Chapel Hill North Carolina
| | - David W. Pfennig
- Department of Biology University of North Carolina Chapel Hill North Carolina
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24
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Lafuente E, Beldade P. Genomics of Developmental Plasticity in Animals. Front Genet 2019; 10:720. [PMID: 31481970 PMCID: PMC6709652 DOI: 10.3389/fgene.2019.00720] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022] Open
Abstract
Developmental plasticity refers to the property by which the same genotype produces distinct phenotypes depending on the environmental conditions under which development takes place. By allowing organisms to produce phenotypes adjusted to the conditions that adults will experience, developmental plasticity can provide the means to cope with environmental heterogeneity. Developmental plasticity can be adaptive and its evolution can be shaped by natural selection. It has also been suggested that developmental plasticity can facilitate adaptation and promote diversification. Here, we summarize current knowledge on the evolution of plasticity and on the impact of plasticity on adaptive evolution, and we identify recent advances and important open questions about the genomics of developmental plasticity in animals. We give special attention to studies using transcriptomics to identify genes whose expression changes across developmental environments and studies using genetic mapping to identify loci that contribute to variation in plasticity and can fuel its evolution.
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Affiliation(s)
| | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- CNRS-UMR5174, Université Paul Sabatier, Toulouse, France
- Centre for Ecology, Evolution, and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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25
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Evolutionary transitions in controls reconcile adaptation with continuity of evolution. Semin Cell Dev Biol 2019; 88:36-45. [DOI: 10.1016/j.semcdb.2018.05.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/19/2018] [Accepted: 05/15/2018] [Indexed: 12/14/2022]
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26
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Sikkink KL, Reynolds RM, Ituarte CM, Cresko WA, Phillips PC. Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the Nematode Caenorhabditis remanei. G3 (BETHESDA, MD.) 2019; 9:969-982. [PMID: 30679247 PMCID: PMC6404610 DOI: 10.1534/g3.118.200017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/23/2019] [Indexed: 11/18/2022]
Abstract
Organisms can cope with stressful environments via a combination of phenotypic plasticity at the individual level and adaptation at the population level. Changes in gene expression can play an important role in both. Significant advances in our understanding of gene regulatory plasticity and evolution have come from comparative studies in the field and laboratory. Experimental evolution provides another powerful path by which to learn about how differential regulation of genes and pathways contributes to both acclimation and adaptation. Here we present results from one such study using the nematode Caenorhabditis remanei We selected one set of lines to withstand heat stress and another oxidative stress. We then compared transcriptional responses to acute heat stress of both and an unselected control to the ancestral population using a weighted gene coexpression network analysis, finding that the transcriptional response is primarily dominated by a plastic response that is shared in the ancestor and all evolved populations. In addition, we identified several modules that respond to artificial selection by (1) changing the baseline level of expression, (2) altering the magnitude of the plastic response, or (3) a combination of the two. Our findings therefore reveal that while patterns of transcriptional response can be perturbed with short bouts of intense selection, the overall ancestral structure of transcriptional plasticity is largely maintained over time.
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Affiliation(s)
- Kristin L Sikkink
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Rose M Reynolds
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
- Department of Biology, William Jewell College, Liberty, Missouri 64068
| | - Catherine M Ituarte
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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27
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Levis NA, Pfennig DW. Plasticity-led evolution: evaluating the key prediction of frequency-dependent adaptation. Proc Biol Sci 2019; 286:20182754. [PMID: 30963848 PMCID: PMC6408876 DOI: 10.1098/rspb.2018.2754] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/05/2019] [Indexed: 01/20/2023] Open
Abstract
Plasticity-led evolution occurs when a change in the environment triggers a change in phenotype via phenotypic plasticity, and this pre-existing plasticity is subsequently refined by selection into an adaptive phenotype. A critical, but largely untested prediction of plasticity-led evolution (and evolution by natural selection generally) is that the rate and magnitude of evolutionary change should be positively associated with a phenotype's frequency of expression in a population. Essentially, the more often a phenotype is expressed and exposed to selection, the greater its opportunity for adaptive refinement. We tested this prediction by competing against each other spadefoot toad tadpoles from different natural populations that vary in how frequently they express a novel, environmentally induced carnivore ecomorph. As expected, laboratory-reared tadpoles whose parents were derived from populations that express the carnivore ecomorph more frequently were superior competitors for the resource for which this ecomorph is specialized-fairy shrimp. These tadpoles were better at using this resource both because they were more efficient at capturing and consuming shrimp and because they produced more exaggerated carnivore traits. Moreover, they exhibited these more carnivore-like features even without experiencing the inducing cue, suggesting that this ecomorph has undergone an extreme form of plasticity-led evolution-genetic assimilation. Thus, our findings provide evidence that the frequency of trait expression drives the magnitude of adaptive refinement, thereby validating a key prediction of plasticity-led evolution specifically and adaptive evolution generally.
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Affiliation(s)
- Nicholas A. Levis
- Department of Biology, University of North Carolina, CB no. 3280, Chapel Hill, NC 27599, USA
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28
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Limited social plasticity in the socially polymorphic sweat bee Lasioglossum calceatum. Behav Ecol Sociobiol 2018; 72:56. [PMID: 29568150 PMCID: PMC5845590 DOI: 10.1007/s00265-018-2475-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/02/2018] [Accepted: 03/02/2018] [Indexed: 11/12/2022]
Abstract
Abstract Eusociality is characterised by a reproductive division of labour, where some individuals forgo direct reproduction to instead help raise kin. Socially polymorphic sweat bees are ideal models for addressing the mechanisms underlying the transition from solitary living to eusociality, because different individuals in the same species can express either eusocial or solitary behaviour. A key question is whether alternative social phenotypes represent environmentally induced plasticity or predominantly genetic differentiation between populations. In this paper, we focus on the sweat bee Lasioglossum calceatum, in which northern or high-altitude populations are solitary, whereas more southern or low-altitude populations are typically eusocial. To test whether social phenotype responds to local environmental cues, we transplanted adult females from a solitary, northern population, to a southern site where native bees are typically eusocial. Nearly all native nests were eusocial, with foundresses producing small first brood (B1) females that became workers. In contrast, nine out of ten nests initiated by transplanted bees were solitary, producing female offspring that were the same size as the foundress and entered directly into hibernation. Only one of these ten nests became eusocial. Social phenotype was unlikely to be related to temperature experienced by nest foundresses when provisioning B1 offspring, or by B1 emergence time, both previously implicated in social plasticity seen in two other socially polymorphic sweat bees. Our results suggest that social polymorphism in L. calceatum predominantly reflects genetic differentiation between populations, and that plasticity is in the process of being lost by bees in northern populations. Significance statement Phenotypic plasticity is thought to play a key role in the early stages of the transition from solitary to eusocial behaviour, but may then be lost if environmental conditions become less variable. Socially polymorphic sweat bees exhibit either solitary or eusocial behaviour in different geographic populations, depending on the length of the nesting season. We tested for plasticity in the socially polymorphic sweat bee Lasioglossum calceatum by transplanting nest foundresses from a northern, non-eusocial population to a southern, eusocial population. Plasticity would be detected if transplanted bees exhibited eusocial behaviour. We found that while native bees were eusocial, 90% of transplanted bees and their offspring did not exhibit traits associated with eusociality. Environmental variables such as time of offspring emergence or temperatures experienced by foundresses during provisioning could not explain these differences. Our results suggest that the ability of transplanted bees to express eusociality is being lost, and that social polymorphism predominantly reflects genetic differences between populations. Electronic supplementary material The online version of this article (10.1007/s00265-018-2475-9) contains supplementary material, which is available to authorized users.
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29
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The role of ancestral phenotypic plasticity in evolutionary diversification: population density effects in horned beetles. Anim Behav 2018. [DOI: 10.1016/j.anbehav.2018.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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30
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Mäkinen H, Sävilammi T, Papakostas S, Leder E, Vøllestad LA, Primmer CR. Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence. Genome Biol Evol 2018; 10:77-93. [PMID: 29293993 PMCID: PMC5758911 DOI: 10.1093/gbe/evx278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.
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Affiliation(s)
| | | | | | - Erica Leder
- Department of Biology, University of Turku, Finland
- Natural History Museum, University of Oslo, Norway
| | - Leif A Vøllestad
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Craig R Primmer
- Department of Biosciences, University of Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Finland
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31
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Bailey NW, Marie-Orleach L, Moore AJ. Indirect genetic effects in behavioral ecology: does behavior play a special role in evolution? Behav Ecol 2017. [DOI: 10.1093/beheco/arx127] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Nathan W Bailey
- School of Biology, University of St Andrews, St Andrews, Fife, UK
| | | | - Allen J Moore
- Department of Genetics, University of Georgia, Athens, GA USA
- Department of Entomology, University of Georgia, Athens, GA USA
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32
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Scheiner SM, Barfield M, Holt RD. The genetics of phenotypic plasticity. XV. Genetic assimilation, the Baldwin effect, and evolutionary rescue. Ecol Evol 2017; 7:8788-8803. [PMID: 29152178 PMCID: PMC5677470 DOI: 10.1002/ece3.3429] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/14/2017] [Accepted: 08/03/2017] [Indexed: 02/06/2023] Open
Abstract
We used an individual-based simulation model to examine the role of phenotypic plasticity on persistence and adaptation to two patterns of environmental variation, a single, abrupt step change and continual, linear change. Our model tested the assumptions and predictions of the theory of genetic assimilation, explored the evolutionary dynamics of the Baldwin effect, and provided expectations for the evolutionary response to climate change. We found that genetic assimilation as originally postulated is not likely to occur because the replacement of plasticity by fixed genetic effects takes much longer than the environment is likely to remain stable. On the other hand, trait plasticity as an enhancement to continual evolutionary change may be an important evolutionary mechanism as long as plasticity has little or no costs. Whether or not plasticity helps or hinders evolutionary rescue following a step change in the environment depends on whether plasticity is costly. For linear environmental change, noncostly plasticity always decreases extinction rates, while costly plasticity can create a fitness drag and increase the chance of extinction. Thus, with changing climates plasticity can enhance adaptation and prevent extinction under some conditions, but not others.
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Affiliation(s)
- Samuel M. Scheiner
- Division of Environmental BiologyNational Science FoundationArlingtonVAUSA
| | | | - Robert D. Holt
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
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33
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Werner MS, Sieriebriennikov B, Loschko T, Namdeo S, Lenuzzi M, Dardiry M, Renahan T, Sharma DR, Sommer RJ. Environmental influence on Pristionchus pacificus mouth form through different culture methods. Sci Rep 2017; 7:7207. [PMID: 28775277 PMCID: PMC5543044 DOI: 10.1038/s41598-017-07455-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 06/28/2017] [Indexed: 12/29/2022] Open
Abstract
Environmental cues can impact development to elicit distinct phenotypes in the adult. The consequences of phenotypic plasticity can have profound effects on morphology, life cycle, and behavior to increase the fitness of the organism. The molecular mechanisms governing these interactions are beginning to be elucidated in a few cases, such as social insects. Nevertheless, there is a paucity of systems that are amenable to rigorous experimentation, preventing both detailed mechanistic insight and the establishment of a generalizable conceptual framework. The mouth dimorphism of the model nematode Pristionchus pacificus offers the rare opportunity to examine the genetics, genomics, and epigenetics of environmental influence on developmental plasticity. Yet there are currently no easily tunable environmental factors that affect mouth-form ratios and are scalable to large cultures required for molecular biology. Here we present a suite of culture conditions to toggle the mouth-form phenotype of P. pacificus. The effects are reversible, do not require the costly or labor-intensive synthesis of chemicals, and proceed through the same pathways previously examined from forward genetic screens. Different species of Pristionchus exhibit different responses to culture conditions, demonstrating unique gene-environment interactions, and providing an opportunity to study environmental influence on a macroevolutionary scale.
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Affiliation(s)
- Michael S Werner
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Tobias Loschko
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Suryesh Namdeo
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Masa Lenuzzi
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Mohannad Dardiry
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Tess Renahan
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Devansh Raj Sharma
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
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34
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Levis NA, Serrato‐Capuchina A, Pfennig DW. Genetic accommodation in the wild: evolution of gene expression plasticity during character displacement. J Evol Biol 2017; 30:1712-1723. [DOI: 10.1111/jeb.13133] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- N. A. Levis
- Department of Biology University of North Carolina Chapel Hill NC USA
| | | | - D. W. Pfennig
- Department of Biology University of North Carolina Chapel Hill NC USA
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35
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Assessing elements of an extended evolutionary synthesis for plant domestication and agricultural origin research. Proc Natl Acad Sci U S A 2017; 114:6429-6437. [PMID: 28576881 DOI: 10.1073/pnas.1703658114] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The development of agricultural societies, one of the most transformative events in human and ecological history, was made possible by plant and animal domestication. Plant domestication began 12,000-10,000 y ago in a number of major world areas, including the New World tropics, Southwest Asia, and China, during a period of profound global environmental perturbations as the Pleistocene epoch ended and transitioned into the Holocene. Domestication is at its heart an evolutionary process, and for many prehistorians evolutionary theory has been foundational in investigating agricultural origins. Similarly, geneticists working largely with modern crops and their living wild progenitors have documented some of the mechanisms that underwrote phenotypic transformations from wild to domesticated species. Ever-improving analytic methods for retrieval of empirical data from archaeological sites, together with advances in genetic, genomic, epigenetic, and experimental research on living crop plants and wild progenitors, suggest that three fields of study currently little applied to plant domestication processes may be necessary to understand these transformations across a range of species important in early prehistoric agriculture. These fields are phenotypic (developmental) plasticity, niche construction theory, and epigenetics with transgenerational epigenetic inheritance. All are central in a controversy about whether an Extended Evolutionary Synthesis is needed to reconceptualize how evolutionary change occurs. An exploration of their present and potential utility in domestication study shows that all three fields have considerable promise in elucidating important issues in plant domestication and in agricultural origin and dispersal research and should be increasingly applied to these issues.
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36
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Teotónio H, Estes S, Phillips PC, Baer CF. Experimental Evolution with Caenorhabditis Nematodes. Genetics 2017; 206:691-716. [PMID: 28592504 PMCID: PMC5499180 DOI: 10.1534/genetics.115.186288] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 03/07/2017] [Indexed: 12/17/2022] Open
Abstract
The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host-pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative.
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Affiliation(s)
- Henrique Teotónio
- Institut de Biologie de l´École Normale Supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre Nationnal de la Recherche Scientifique Unité Mixte de Recherche 8197, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Suzanne Estes
- Department of Biology, Portland State University, Oregon 97201
| | - Patrick C Phillips
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, Oregon 97403, and
| | - Charles F Baer
- Department of Biology, and
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida 32611
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37
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Schneider RF, Meyer A. How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations. Mol Ecol 2016; 26:330-350. [PMID: 27747962 DOI: 10.1111/mec.13880] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/30/2016] [Accepted: 10/07/2016] [Indexed: 12/13/2022]
Abstract
There is increasing evidence that phenotypic plasticity can promote population divergence by facilitating phenotypic diversification and, eventually, genetic divergence. When a 'plastic' population colonizes a new habitat, it has the possibility to occupy multiple niches by expressing several distinct phenotypes. These initially reflect the population's plastic range but may later become genetically fixed by selection via the process of 'genetic assimilation' (GA). Through this process multiple specialized sister lineages can arise that share a common plastic ancestor - the 'flexible stem'. Here, we review possible molecular mechanisms through which natural selection could fix an initially plastic trait during GA. These mechanisms could also explain how GA may contribute to cryptic genetic variation that can subsequently be coopted into other phenotypes or traits, but also lead to nonadaptive responses. We outline the predicted patterns of genetic and transcriptional divergence accompanying flexible stem radiations. The analysis of such patterns of (retained) adaptive and nonadaptive plastic responses within and across radiating lineages can inform on the state of ongoing GA. We conclude that, depending on the stability of the environment, the molecular architecture underlying plastic traits can facilitate diversification, followed by fixation and consolidation of an adaptive phenotype and degeneration of nonadaptive ones. Additionally, the process of GA may increase the cryptic genetic variation of populations, which on one hand may serve as substrate for evolution, but on another may be responsible for nonadaptive responses that consolidate local allopatry and thus reproductive isolation.
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Affiliation(s)
- Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitaetstrasse 10, 78457, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitaetstrasse 10, 78457, Konstanz, Germany
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38
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Kelly MW, Pankey MS, DeBiasse MB, Plachetzki DC. Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12725] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Morgan W. Kelly
- Department of Biological Sciences Louisiana State University Baton Rouge LA70803 USA
| | - M. Sabrina Pankey
- Molecular, Cellular, & Biomedical Sciences University of New Hampshire Rudman Hall 46 College Rd. Durham NH03824‐2618 USA
| | - Melissa B. DeBiasse
- Department of Biological Sciences Louisiana State University Baton Rouge LA70803 USA
| | - David C. Plachetzki
- Molecular, Cellular, & Biomedical Sciences University of New Hampshire Rudman Hall 46 College Rd. Durham NH03824‐2618 USA
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Jakšić AM, Schlötterer C. The Interplay of Temperature and Genotype on Patterns of Alternative Splicing in Drosophila melanogaster. Genetics 2016; 204:315-25. [PMID: 27440867 PMCID: PMC5012396 DOI: 10.1534/genetics.116.192310] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/08/2016] [Indexed: 01/02/2023] Open
Abstract
Alternative splicing is the highly regulated process of variation in the removal of introns from premessenger-RNA transcripts. The consequences of alternative splicing on the phenotype are well documented, but the impact of the environment on alternative splicing is not yet clear. We studied variation in alternative splicing among four different temperatures, 13, 18, 23, and 29°, in two Drosophila melanogaster genotypes. We show plasticity of alternative splicing with up to 10% of the expressed genes being differentially spliced between the most extreme temperatures for a given genotype. Comparing the two genotypes at different temperatures, we found <1% of the genes being differentially spliced at 18°. At extreme temperatures, however, we detected substantial differences in alternative splicing-with almost 10% of the genes having differential splicing between the genotypes: a magnitude similar to between species differences. Genes with differential alternative splicing between genotypes frequently exhibit dominant inheritance. Remarkably, the pattern of surplus of differences in alternative splicing at extreme temperatures resembled the pattern seen for gene expression intensity. Since different sets of genes were involved for the two phenotypes, we propose that purifying selection results in the reduction of differences at benign temperatures. Relaxed purifying selection at temperature extremes, on the other hand, may cause the divergence in gene expression and alternative splicing between the two strains in rarely encountered environments.
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Affiliation(s)
- Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria
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40
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Rundle SD, Spicer JI. Heterokairy: a significant form of developmental plasticity? Biol Lett 2016; 12:20160509. [PMID: 27624796 PMCID: PMC5046929 DOI: 10.1098/rsbl.2016.0509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/24/2016] [Indexed: 12/15/2022] Open
Abstract
There is a current surge of research interest in the potential role of developmental plasticity in adaptation and evolution. Here we make a case that some of this research effort should explore the adaptive significance of heterokairy, a specific type of plasticity that describes environmentally driven, altered timing of development within a species. This emphasis seems warranted given the pervasive occurrence of heterochrony, altered developmental timing between species, in evolution. We briefly review studies investigating heterochrony within an adaptive context across animal taxa, including examples that explore links between heterokairy and heterochrony. We then outline how sequence heterokairy could be included within the research agenda for developmental plasticity. We suggest that the study of heterokairy may be particularly pertinent in (i) determining the importance of non-adaptive plasticity, and (ii) embedding concepts from comparative embryology such as developmental modularity and disassociation within a developmental plasticity framework.
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Affiliation(s)
- S D Rundle
- Marine Biology and Ecology Research Centre, Plymouth University, Plymouth, UK
| | - J I Spicer
- Marine Biology and Ecology Research Centre, Plymouth University, Plymouth, UK
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41
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Evaluating ‘Plasticity-First’ Evolution in Nature: Key Criteria and Empirical Approaches. Trends Ecol Evol 2016; 31:563-574. [DOI: 10.1016/j.tree.2016.03.012] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 01/19/2023]
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42
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Preston JL, Royall AE, Randel MA, Sikkink KL, Phillips PC, Johnson EA. High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq). BMC Genomics 2016; 17:464. [PMID: 27301885 PMCID: PMC4908710 DOI: 10.1186/s12864-016-2669-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 04/25/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Polymorphic loci exist throughout the genomes of a population and provide the raw genetic material needed for a species to adapt to changes in the environment. The minor allele frequencies of rare Single Nucleotide Polymorphisms (SNPs) within a population have been difficult to track with Next-Generation Sequencing (NGS), due to the high error rate of standard methods such as Illumina sequencing. RESULTS We have developed a wet-lab protocol and variant-calling method that identifies both sequencing and PCR errors, called Paired-End Low Error Sequencing (PELE-Seq). To test the specificity and sensitivity of the PELE-Seq method, we sequenced control E. coli DNA libraries containing known rare alleles present at frequencies ranging from 0.2-0.4 % of the total reads. PELE-Seq had higher specificity and sensitivity than standard libraries. We then used PELE-Seq to characterize rare alleles in a Caenorhabditis remanei nematode worm population before and after laboratory adaptation, and found that minor and rare alleles can undergo large changes in frequency during lab-adaptation. CONCLUSION We have developed a method of rare allele detection that mitigates both sequencing and PCR errors, called PELE-Seq. PELE-Seq was evaluated using control E. coli populations and was then used to compare a wild C. remanei population to a lab-adapted population. The PELE-Seq method is ideal for investigating the dynamics of rare alleles in a broad range of reduced-representation sequencing methods, including targeted amplicon sequencing, RAD-Seq, ddRAD, and GBS. PELE-Seq is also well-suited for whole genome sequencing of mitochondria and viruses, and for high-throughput rare mutation screens.
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Affiliation(s)
- Jessica L Preston
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
| | - Ariel E Royall
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Melissa A Randel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Kristin L Sikkink
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
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43
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Stanton-Geddes J, Nguyen A, Chick L, Vincent J, Vangala M, Dunn RR, Ellison AM, Sanders NJ, Gotelli NJ, Cahan SH. Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species. BMC Genomics 2016; 17:171. [PMID: 26934985 PMCID: PMC4776372 DOI: 10.1186/s12864-016-2466-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/12/2016] [Indexed: 12/03/2022] Open
Abstract
Background The distributions of species and their responses to climate change are in part determined by their thermal tolerances. However, little is known about how thermal tolerance evolves. To test whether evolutionary extension of thermal limits is accomplished through enhanced cellular stress response (enhanced response), constitutively elevated expression of protective genes (genetic assimilation) or a shift from damage resistance to passive mechanisms of thermal stability (tolerance), we conducted an analysis of the reactionome: the reaction norm for all genes in an organism’s transcriptome measured across an experimental gradient. We characterized thermal reactionomes of two common ant species in the eastern U.S, the northern cool-climate Aphaenogaster picea and the southern warm-climate Aphaenogaster carolinensis, across 12 temperatures that spanned their entire thermal breadth. Results We found that at least 2 % of all genes changed expression with temperature. The majority of upregulation was specific to exposure to low temperatures. The cool-adapted A. picea induced expression of more genes in response to extreme temperatures than did A. carolinensis, consistent with the enhanced response hypothesis. In contrast, under high temperatures the warm-adapted A. carolinensis downregulated many of the genes upregulated in A. picea, and required more extreme temperatures to induce down-regulation in gene expression, consistent with the tolerance hypothesis. We found no evidence for a trade-off between constitutive and inducible gene expression as predicted by the genetic assimilation hypothesis. Conclusions These results suggest that increases in upper thermal limits may require an evolutionary shift in response mechanism away from damage repair toward tolerance and prevention. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2466-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John Stanton-Geddes
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA. .,Data Scientist, Dealer.com, 1 Howard St, Burlington, VT, 05401, USA.
| | - Andrew Nguyen
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Lacy Chick
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - James Vincent
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA
| | - Mahesh Vangala
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA
| | - Robert R Dunn
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Aaron M Ellison
- Harvard Forest, Harvard University, Petersham, MA, 01336, USA
| | - Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.,Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Nicholas J Gotelli
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Sara Helms Cahan
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
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44
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Ebel ER, Phillips PC. Intrinsic differences between males and females determine sex-specific consequences of inbreeding. BMC Evol Biol 2016; 16:36. [PMID: 26860745 PMCID: PMC4748534 DOI: 10.1186/s12862-016-0604-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inbreeding increases homozygosity and exposes deleterious recessive alleles, generally decreasing the fitness of inbred individuals. Interestingly, males and females are usually affected differently by inbreeding, though the more vulnerable sex depends on the species and trait measured. RESULTS We used the soil-dwelling nematode Caenorhabditis remanei to examine sex-specific inbreeding depression across nine lineages, five levels of inbreeding, and hundreds of thousands of progeny. Female nematodes consistently suffered greater fitness losses than their male counterparts, especially at high levels of inbreeding. CONCLUSIONS These results suggest that females experience stronger selection on genes contributing to reproductive traits. Inbreeding depression in males may be further reduced by sex chromosome hemizygosity, which affects the dominance of some mutations, as well as by the absence of sexual selection. Determining the relative contributions of sex-specific expression, genes on the sex chromosomes, and the environment they are filtered through-including opportunities for sexual selection-may explain the frequent though inconsistent records of sex differences in inbreeding depression, along with their implications for conservation and the evolution of mating systems.
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Affiliation(s)
- Emily R Ebel
- Institute of Ecology and Evolution and Department of Biology, 5289 University of Oregon, 97403, Eugene, Oregon, USA.,Present address: Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution and Department of Biology, 5289 University of Oregon, 97403, Eugene, Oregon, USA.
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45
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Dey S, Proulx SR, Teotónio H. Adaptation to Temporally Fluctuating Environments by the Evolution of Maternal Effects. PLoS Biol 2016; 14:e1002388. [PMID: 26910440 PMCID: PMC4766184 DOI: 10.1371/journal.pbio.1002388] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/21/2016] [Indexed: 01/27/2023] Open
Abstract
All organisms live in temporally fluctuating environments. Theory predicts that the evolution of deterministic maternal effects (i.e., anticipatory maternal effects or transgenerational phenotypic plasticity) underlies adaptation to environments that fluctuate in a predictably alternating fashion over maternal-offspring generations. In contrast, randomizing maternal effects (i.e., diversifying and conservative bet-hedging), are expected to evolve in response to unpredictably fluctuating environments. Although maternal effects are common, evidence for their adaptive significance is equivocal since they can easily evolve as a correlated response to maternal selection and may or may not increase the future fitness of offspring. Using the hermaphroditic nematode Caenorhabditis elegans, we here show that the experimental evolution of maternal glycogen provisioning underlies adaptation to a fluctuating normoxia-anoxia hatching environment by increasing embryo survival under anoxia. In strictly alternating environments, we found that hermaphrodites evolved the ability to increase embryo glycogen provisioning when they experienced normoxia and to decrease embryo glycogen provisioning when they experienced anoxia. At odds with existing theory, however, populations facing irregularly fluctuating normoxia-anoxia hatching environments failed to evolve randomizing maternal effects. Instead, adaptation in these populations may have occurred through the evolution of fitness effects that percolate over multiple generations, as they maintained considerably high expected growth rates during experimental evolution despite evolving reduced fecundity and reduced embryo survival under one or two generations of anoxia. We develop theoretical models that explain why adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that such deterministic maternal effects are more likely to contribute to adaptation than randomizing maternal effects.
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Affiliation(s)
- Snigdhadip Dey
- Institut de Biologie de l´École Normale Supérieure, INSERM U1024, CNRS UMR 8197, Paris, France
| | - Stephen R. Proulx
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Henrique Teotónio
- Institut de Biologie de l´École Normale Supérieure, INSERM U1024, CNRS UMR 8197, Paris, France
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46
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Gouvêa DY, Aprison EZ, Ruvinsky I. Experience Modulates the Reproductive Response to Heat Stress in C. elegans via Multiple Physiological Processes. PLoS One 2015; 10:e0145925. [PMID: 26713620 PMCID: PMC4699941 DOI: 10.1371/journal.pone.0145925] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/10/2015] [Indexed: 11/29/2022] Open
Abstract
Natural environments are considerably more variable than laboratory settings and often involve transient exposure to stressful conditions. To fully understand how organisms have evolved to respond to any given stress, prior experience must therefore be considered. We investigated the effects of individual and ancestral experience on C. elegans reproduction. We documented ways in which cultivation at 15°C or 25°C affects developmental time, lifetime fecundity, and reproductive performance after severe heat stress that exceeds the fertile range of the organism but is compatible with survival and future fecundity. We found that experience modulates multiple aspects of reproductive physiology, including the male and female germ lines and the interaction between them. These responses vary in their environmental sensitivity, suggesting the existence of complex mechanisms for coping with unpredictable and stressful environments.
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Affiliation(s)
- Devin Y. Gouvêa
- Committee on Conceptual and Historical Studies of Science, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Evolutionary Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Erin Z. Aprison
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Ilya Ruvinsky
- Committee on Evolutionary Biology, The University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America
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47
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Chen J, Nolte V, Schlötterer C. Temperature-Related Reaction Norms of Gene Expression: Regulatory Architecture and Functional Implications. Mol Biol Evol 2015; 32:2393-402. [PMID: 25976350 PMCID: PMC4540970 DOI: 10.1093/molbev/msv120] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The environment has profound effects on the expression of many traits and reaction norms describe the expression dynamics of a trait across a broad range of environmental conditions. Here, we analyze gene expression in Drosophila melanogaster across four different developmental temperatures (13-29 °C). Gene expression is highly plastic with 83.3% of the genes being differentially expressed. We distinguished three components of plasticity: 1) Dynamics of gene expression intensity (sum of change), 2) direction of change, and 3) curvature of the reaction norm (linear vs. quadratic). Studying their regulatory architecture we found that all three plasticity components were most strongly affected by the number of different transcription factors (TFs) binding to the target gene. More TFs were found in genes with less expression changes across temperatures. Although the effect of microRNAs was weaker, we consistently noted a trend in the opposite direction. The most plastic genes were regulated by fewer TFs and more microRNAs than less plastic genes. Different patterns of plasticity were also reflected by their functional characterization based on gene ontology. Our results suggest that reaction norms provide an important key to understand the functional requirements of natural populations exposed to variable environmental conditions.
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Affiliation(s)
- Jun Chen
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria/Europe
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria/Europe
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48
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Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, Cutter AD, Phillips PC. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet 2015; 11:e1005323. [PMID: 26114425 PMCID: PMC4482642 DOI: 10.1371/journal.pgen.1005323] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 05/31/2015] [Indexed: 11/18/2022] Open
Abstract
The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.
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Affiliation(s)
- Janna L. Fierst
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Cristel G. Thomas
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Wei Wang
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Rose M. Reynolds
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Timothy E. Ahearne
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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49
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Sikkink KL, Reynolds RM, Cresko WA, Phillips PC. Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network. Evolution 2015; 69:1128-42. [PMID: 25809411 PMCID: PMC5523853 DOI: 10.1111/evo.12651] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 03/06/2015] [Indexed: 12/28/2022]
Abstract
Selection in novel environments can lead to a coordinated evolutionary response across a suite of characters. Environmental conditions can also potentially induce changes in the genetic architecture of complex traits, which in turn could alter the pattern of the multivariate response to selection. We describe a factorial selection experiment using the nematode Caenorhabditis remanei in which two different stress-related phenotypes (heat and oxidative stress resistance) were selected under three different environmental conditions. The pattern of covariation in the evolutionary response between phenotypes or across environments differed depending on the environment in which selection occurred, including asymmetrical responses to selection in some cases. These results indicate that variation in pleiotropy across the stress response network is highly sensitive to the external environment. Our findings highlight the complexity of the interaction between genes and environment that influences the ability of organisms to acclimate to novel environments. They also make clear the need to identify the underlying genetic basis of genetic correlations in order understand how patterns of pleiotropy are distributed across complex genetic networks.
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Affiliation(s)
- Kristin L Sikkink
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, Minnesota, 55108
| | - Rose M Reynolds
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
- Department of Biology, William Jewell College, Liberty, Missouri, 64068
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403.
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403.
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50
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Singh RS. Darwin's legacy II: why biology is not physics, or why it has taken a century to see the dependence of genes on the environment. Genome 2015; 58:55-62. [PMID: 25985891 DOI: 10.1139/gen-2015-0012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genes and environment make the organism. Darwin stood firm in his denial of any direct role of environment in the modification of heredity. His theory of evolution heralded two debates: one about the importance and adequacy of natural selection as the main mechanism of evolution, and the other about the role of genes versus environment in the modification of phenotype and evolution. Here, I provide an overview of the second debate and show that the reasons for the gene versus environment battle were twofold: first, there was confusion about the role of environment in modifying the inheritance of a trait versus the evolution of that trait, and second, there was misunderstanding about the meaning of environment and its interaction with genes in the production of phenotypes. It took nearly a century to see that environment does not directly affect the inheritance of a phenotype (i.e., its heredity), but it is nevertheless the primary mover of phenotypic evolution. Effects of genes and environment are not separate but interdependent. One cannot separate the effect of genes from that of environment, or nature from nurture. To answer the question posed in the title, it is partly because the 20th century has been a century of unending progress in genetics. But also because unlike physics, biology is not colorblind; progress in biology has often been delayed beyond the Kuhnian paradigm change due to built-in interest in negating the influence of environment. Those who are against evolution, of course, cannot be expected to understand the role of environment in evolution. Those for it, many biologists included, believing in the supremacy of genes empowers them by giving adaptation a solely gene-directed (self-driven) "teleological" interpretation.
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Affiliation(s)
- Rama S Singh
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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