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Miller CL, Sun D, Thornton LH, McGuigan K. The Contribution of Mutation to Variation in Temperature-Dependent Sprint Speed in Zebrafish, Danio rerio. Am Nat 2023; 202:519-533. [PMID: 37792923 DOI: 10.1086/726011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractThe contribution of new mutations to phenotypic variation and the consequences of this variation for individual fitness are fundamental concepts for understanding genetic variation and adaptation. Here, we investigated how mutation influenced variation in a complex trait in zebrafish, Danio rerio. Typical of many ecologically relevant traits in ectotherms, swimming speed in fish is temperature dependent, with evidence of adaptive evolution of thermal performance. We chemically induced novel germline point mutations in males and measured sprint speed in their sons at six temperatures (between 16°C and 34°C). Heterozygous mutational effects on speed were strongly positively correlated among temperatures, resulting in statistical support for only a single axis of mutational variation, reflecting temperature-independent variation in speed (faster-slower mode). These results suggest pleiotropic effects on speed across different temperatures; however, spurious correlations arise via linkage or heterogeneity in mutation number when mutations have consistent directional effects on each trait. Here, mutation did not change mean speed, indicating no directional bias in mutational effects. The results contribute to emerging evidence that mutations may predominantly have synergistic cross-environment effects, in contrast to conditionally neutral or antagonistic effects that underpin thermal adaptation. We discuss several aspects of experimental design that may affect resolution of mutations with nonsynergistic effects.
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The emergence of genotypic divergence and future precision medicine applications. HANDBOOK OF CLINICAL NEUROLOGY 2023; 192:87-99. [PMID: 36796950 DOI: 10.1016/b978-0-323-85538-9.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genotypic divergence is a term adapted from population genetics and intimately linked to evolution. We use divergence here to emphasize the differences that set individuals apart in any cohort. The history of genetics is filled with descriptions of genotypic differences, but causal inference of interindividual biological variation has been scarce. We suggest that the practice of precision medicine requires a divergent approach, an approach dependent on the causal interpretation of previous convergent (and preliminary) knowledge in the field. This knowledge has relied on convergent descriptive syndromology (lumping), which has overemphasized a reductionistic gene determinism on the quest of seeking associations without causal understanding. Regulatory variants with small effect and somatic mutations are some of the modifying factors that lead to incomplete penetrance and intrafamilial variable expressivity often observed in apparently monogenic clinical disorders. A truly divergent approach to precision medicine requires splitting, that is, the consideration of different layers of genetic phenomena that interact causally in a nonlinear fashion. This chapter reviews convergences and divergences in genetics and genomics, aiming to discuss what can be causally understood to approximate the as-yet utopian lands of Precision Medicine for patients with neurodegenerative disorders.
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Bao K, Melde RH, Sharp NP. Are mutations usually deleterious? A perspective on the fitness effects of mutation accumulation. Evol Ecol 2022; 36:753-766. [DOI: 10.1007/s10682-022-10187-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Jonas M, Navarro D. Induced mutations alter patterns of quantitative variation, phenotypic integration, and plasticity to elevated CO 2 in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2019; 132:33-47. [PMID: 30255212 DOI: 10.1007/s10265-018-1064-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
A key step toward predicting responses to climate change is characterizing genetic variation in populations. While short-term responses will likely be shaped by currently available genetic variation, longer-term evolutionary responses will depend on the supply of novel variation by, ultimately, mutation. Studying mutational contributions to phenotypic variation can provide insights into the extent of potential variation on which selection may operate in future human-altered environments. Here we used the chemical mutagen ethyl methanesulfonate (EMS) to explore mutational contributions to phenotypic variation, integration, and plasticity to elevated carbon dioxide (eCO2) in three accessions of Arabidopsis thaliana. We found that (1) mutagenesis increased broad-sense heritabilities and variation in plasticity to eCO2 (genotype by environment interactions); (2) mutational effects varied among the three genetic backgrounds; (3) induced mutations had non-random (biased) effects on patterns of phenotypic integration. To our knowledge, this is the first study to address the effects of chemically induced mutations on phenotypic plasticity to eCO2 in a model plant. We discuss our results in light of emerging insights from theoretical and empirical quantitative genetics, suggest potential avenues of research, and identify approaches that may help advance our understanding of climate-driven evolution in plants.
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Affiliation(s)
- Mark Jonas
- Department of Biology, School of Natural and Social Sciences, State University of New York-Purchase College, 735 Anderson Hill Road, Purchase, NY, 10577, USA.
| | - Dania Navarro
- Department of Biology, School of Natural and Social Sciences, State University of New York-Purchase College, 735 Anderson Hill Road, Purchase, NY, 10577, USA
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Rutter MT, Roles AJ, Fenster CB. Quantifying natural seasonal variation in mutation parameters with mutation accumulation lines. Ecol Evol 2018; 8:5575-5585. [PMID: 29938075 PMCID: PMC6010865 DOI: 10.1002/ece3.4085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 12/13/2022] Open
Abstract
Mutations create novel genetic variants, but their contribution to variation in fitness and other phenotypes may depend on environmental conditions. Furthermore, natural environments may be highly heterogeneous. We assessed phenotypes associated with survival and reproductive success in over 30,000 plants representing 100 mutation accumulation lines of Arabidopsis thaliana across four temporal environments at a single field site. In each of the four assays, environmental variance was substantially larger than mutational variance. For some traits, whether mutational variance was significantly varied between seasons. The founder genotype had mean trait values near the mean of the distribution of the mutation accumulation lines in all field experiments. New mutations also contributed more phenotypic variation than would be predicted, given phenotypic and sequence‐level divergence among natural populations of A. thaliana. The combination of large environmental variance with a mean effect of mutation near zero suggests that mutations could contribute substantially to standing genetic variation.
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Affiliation(s)
- Matthew T Rutter
- Department of Biology College of Charleston Charleston South Carolina
| | | | - Charles B Fenster
- Department of Biology and Microbiology South Dakota State University Brookings South Dakota
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Stearns FW, Fenster CB. The effect of induced mutations on quantitative traits in Arabidopsis thaliana: Natural versus artificial conditions. Ecol Evol 2016; 6:8366-8374. [PMID: 28031789 PMCID: PMC5167040 DOI: 10.1002/ece3.2558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 12/04/2022] Open
Abstract
Mutations are the ultimate source of all genetic variations. New mutations are expected to affect quantitative traits differently depending on the extent to which traits contribute to fitness and the environment in which they are tested. The dogma is that the preponderance of mutations affecting fitness will be skewed toward deleterious while their effects on nonfitness traits will be bidirectionally distributed. There are mixed views on the role of stress in modulating these effects. We quantify mutation effects by inducing mutations in Arabidopsis thaliana (Columbia accession) using the chemical ethylmethane sulfonate. We measured the effects of new mutations relative to a premutation founder for fitness components under both natural (field) and artificial (growth room) conditions. Additionally, we measured three other quantitative traits, not expected to contribute directly to fitness, under artificial conditions. We found that induced mutations were equally as likely to increase as decrease a trait when that trait was not closely related to fitness (traits that were neither survivorship nor reproduction). We also found that new mutations were more likely to decrease fitness or fitness‐related traits under more stressful field conditions than under relatively benign artificial conditions. In the benign condition, the effect of new mutations on fitness components was similar to traits not as closely related to fitness. These results highlight the importance of measuring the effects of new mutations on fitness and other traits under a range of conditions.
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Affiliation(s)
- Frank W Stearns
- Department of Biology Biology-Psychology Building University of Maryland College Park MD USA
| | - Charles B Fenster
- Department of Biology Biology-Psychology Building University of Maryland College Park MD USA
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Roles AJ, Rutter MT, Dworkin I, Fenster CB, Conner JK. Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana. Evolution 2016; 70:1039-50. [PMID: 27061194 DOI: 10.1111/evo.12913] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/24/2016] [Indexed: 12/24/2022]
Abstract
As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations-that is, is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype-environment interaction for spontaneous mutations? We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. At both sites, mean total fitness of mutation accumulation lines exceeded that of the ancestors, contrary to the expected decrease in the mean due to new mutations but in accord with prior work on these MA lines. We observed genotype-environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype-environment interaction would increase the amount of genetic variation maintained by mutation-selection balance.
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Affiliation(s)
- Angela J Roles
- Biology Department, Oberlin College, Oberlin, Ohio, 44074. .,Kellogg Biological Station, Michigan State University, East Lansing, Michigan, 48824. .,Department of Integrative Biology, Michigan State University, East Lansing, Michigan, 48824.
| | - Matthew T Rutter
- Department of Biology, College of Charleston, Charleston, South Carolina, 29401.,Department of Biology, University of Maryland, College Park, Maryland, 20742
| | - Ian Dworkin
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, 48824.,Department of Biology, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Charles B Fenster
- Department of Biology, University of Maryland, College Park, Maryland, 20742
| | - Jeffrey K Conner
- Kellogg Biological Station, Michigan State University, East Lansing, Michigan, 48824.,Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824
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