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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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2
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Duxbury EML, Carlsson H, Sales K, Sultanova Z, Immler S, Chapman T, Maklakov AA. Multigenerational downregulation of insulin/IGF-1 signaling in adulthood improves lineage survival, reproduction, and fitness in Caenorhabditis elegans supporting the developmental theory of ageing. Evolution 2022; 76:2829-2845. [PMID: 36199198 PMCID: PMC10092551 DOI: 10.1111/evo.14640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/18/2022] [Accepted: 09/08/2022] [Indexed: 01/22/2023]
Abstract
Adulthood-only downregulation of insulin/IGF-1 signaling (IIS), an evolutionarily conserved pathway regulating resource allocation between somatic maintenance and reproduction, increases life span without fecundity cost in the nematode, Caenorhabditis elegans. However, long-term multigenerational effects of reduced IIS remain unexplored and are proposed to carry costs for offspring quality. To test this hypothesis, we ran a mutation accumulation (MA) experiment and downregulated IIS in half of the 400 MA lines by silencing daf-2 gene expression using RNA interference (RNAi) across 40 generations. Contrary to the prediction, adulthood-only daf-2 RNAi reduced extinction of MA lines both under UV-induced and spontaneous MA. Fitness of the surviving UV-induced MA lines was higher under daf-2 RNAi. Reduced IIS increased intergenerational F1 offspring fitness under UV stress but had no quantifiable transgenerational effects. Functional hrde-1 was required for the benefits of multigenerational daf-2 RNAi. Overall, we found net benefit to fitness from multigenerational reduction of IIS and the benefits became more apparent under stress. Because reduced daf-2 expression during development carries fitness costs, we suggest that our findings are best explained by the developmental theory of ageing, which maintains that the decline in the force of selection with age results in poorly regulated gene expression in adulthood.
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Affiliation(s)
- Elizabeth M L Duxbury
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Hanne Carlsson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Kris Sales
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Zahida Sultanova
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Alexei A Maklakov
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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3
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Ji CW, Park YS, Cui Y, Wang H, Kwak IS, Chon TS. Analyzing the Response Behavior of Lumbriculus variegatus (Oligochaeta: Lumbriculidae) to Different Concentrations of Copper Sulfate Based on Line Body Shape Detection and a Recurrent Self-Organizing Map. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17082627. [PMID: 32290455 PMCID: PMC7215344 DOI: 10.3390/ijerph17082627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 11/29/2022]
Abstract
Point detection (e.g., the centroid of the body) of species has been conducted in numerous studies. However, line detection (i.e., the line body shape) of elongated species has rarely been investigated under stressful conditions. We analyzed the line movements of an Oligochaeta Lumbriculus variegatus in response to treatments with a toxic chemical, copper sulfate, at low concentrations (0.01 mg/L and 0.1 mg/L). The automatic line-tracking system was devised to identify the movement of body segments (body length) and the movements of segments (i.e., the speed and angles between segments) were recorded before and after treatment. Total body length was shortened from 31.22 (±5.18) mm to 20.91 (±4.65) mm after the 0.1 mg/L treatment. The Shannon entropy index decreased from 0.44 (±0.1) to 0.28 (±0.08) after treatment. On the other hand, the body and movement segments did not significantly change after the 0.01 mg/L treatment. Sequential movements of test organisms were further analyzed with a recurrent self-organizing map (RSOM) to determine the pattern of time-series line movements. The RSOM made it feasible to classify sequential behaviors of indicator organisms and identify various continuous body movements under stressful conditions.
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Affiliation(s)
- Chang Woo Ji
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea; (C.W.J.); (I.-S.K.)
| | - Young-Seuk Park
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
- Correspondence: (Y.-S.P.); (T.-S.C.); Tel.: +82-2-961-0946 (Y.-S.P.); +82-51-512-2262 (T.-S.C.)
| | - Yongde Cui
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.C.); (H.W.)
| | - Hongzhu Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Y.C.); (H.W.)
| | - Ihn-Sil Kwak
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea; (C.W.J.); (I.-S.K.)
| | - Tae-Soo Chon
- Ecology and Future Research Association (EnFRA), Dusil-ro 45 beon-gil 21, Geumjeong-gu, Busan 46228, Korea
- Correspondence: (Y.-S.P.); (T.-S.C.); Tel.: +82-2-961-0946 (Y.-S.P.); +82-51-512-2262 (T.-S.C.)
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4
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Cutter AD, Morran LT, Phillips PC. Males, Outcrossing, and Sexual Selection in Caenorhabditis Nematodes. Genetics 2019; 213:27-57. [PMID: 31488593 PMCID: PMC6727802 DOI: 10.1534/genetics.119.300244] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022] Open
Abstract
Males of Caenorhabditis elegans provide a crucial practical tool in the laboratory, but, as the rarer and more finicky sex, have not enjoyed the same depth of research attention as hermaphrodites. Males, however, have attracted the attention of evolutionary biologists who are exploiting the C. elegans system to test longstanding hypotheses about sexual selection, sexual conflict, transitions in reproductive mode, and genome evolution, as well as to make new discoveries about Caenorhabditis organismal biology. Here, we review the evolutionary concepts and data informed by study of males of C. elegans and other Caenorhabditis We give special attention to the important role of sperm cells as a mediator of inter-male competition and male-female conflict that has led to drastic trait divergence across species, despite exceptional phenotypic conservation in many other morphological features. We discuss the evolutionary forces important in the origins of reproductive mode transitions from males being common (gonochorism: females and males) to rare (androdioecy: hermaphrodites and males) and the factors that modulate male frequency in extant androdioecious populations, including the potential influence of selective interference, host-pathogen coevolution, and mutation accumulation. Further, we summarize the consequences of males being common vs rare for adaptation and for trait divergence, trait degradation, and trait dimorphism between the sexes, as well as for molecular evolution of the genome, at both micro-evolutionary and macro-evolutionary timescales. We conclude that C. elegans male biology remains underexploited and that future studies leveraging its extensive experimental resources are poised to discover novel biology and to inform profound questions about animal function and evolution.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario M5S3B2, Canada
| | - Levi T Morran
- Department of Biology, Emory University, Atlanta, Georgia 30322, and
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
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5
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Abstract
Understanding the context-dependence of spontaneous mutations is crucial to predicting evolutionary trajectories. In this experiment, the impact of genetic background and trait-type on mutational susceptibility was investigated. Mutant and non-mutant lines of six unique genotypes from two populations of Daphnia magna were phenotypically assayed using a common-garden experiment. Morphological, life-history, and behavioral traits were measured and estimates of the mutation parameters were generated. The mutation parameters varied between the populations and among genotypes, suggesting differential susceptibility to mutation depending upon genomic background. Traits also varied in their susceptibility to mutation with behavioral traits evolving more rapidly than life-history and morphological traits. These results may reflect the unique selection histories of these populations.
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6
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Woodruff RC, Balinski MA. Increase in viability due to the accumulation of X chromosome mutations in Drosophila melanogaster males. Genetica 2018; 146:323-328. [PMID: 29744733 DOI: 10.1007/s10709-018-0023-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/05/2018] [Indexed: 10/16/2022]
Abstract
To increase our understanding of the role of new X-chromosome mutations in adaptive evolution, single-X Drosophila melanogaster males were mated with attached-X chromosome females, allowing the male X chromosome to accumulate mutations over 28 generations. Contrary to our hypothesis that male viability would decrease over time, due to the accumulation and expression of X-linked recessive deleterious mutations in hemizygous males, viability significantly increased. This increase may be attributed to germinal selection and to new X-linked beneficial or compensatory mutations, possibly supporting the faster-X hypothesis.
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Affiliation(s)
- Ronny C Woodruff
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Michael A Balinski
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
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7
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Social Epistasis Amplifies the Fitness Costs of Deleterious Mutations, Engendering Rapid Fitness Decline Among Modernized Populations. EVOLUTIONARY PSYCHOLOGICAL SCIENCE 2017. [DOI: 10.1007/s40806-017-0084-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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8
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Abstract
Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.
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9
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Dunkel CS, Nedelec JL, van der Linden D, Marshall RL. Physical Attractiveness and the General Factor of Personality. ADAPTIVE HUMAN BEHAVIOR AND PHYSIOLOGY 2016. [DOI: 10.1007/s40750-016-0055-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Davies SK, Leroi A, Burt A, Bundy JG, Baer CF. The mutational structure of metabolism in Caenorhabditis elegans. Evolution 2016; 70:2239-2246. [PMID: 27465022 PMCID: PMC5050113 DOI: 10.1111/evo.13020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/27/2016] [Accepted: 07/10/2016] [Indexed: 12/14/2022]
Abstract
A properly functioning organism must maintain metabolic homeostasis. Deleterious mutations degrade organismal function, presumably at least in part via effects on metabolic function. Here we present an initial investigation into the mutational structure of the Caenorhabditis elegans metabolome by means of a mutation accumulation experiment. We find that pool sizes of 29 metabolites vary greatly in their vulnerability to mutation, both in terms of the rate of accumulation of genetic variance (the mutational variance, VM) and the rate of change of the trait mean (the mutational bias, ΔM). Strikingly, some metabolites are much more vulnerable to mutation than any other trait previously studied in the same way. Although we cannot statistically assess the strength of mutational correlations between individual metabolites, principal component analysis provides strong evidence that some metabolite pools are genetically correlated, but also that there is substantial scope for independent evolution of different groups of metabolites. Averaged over mutation accumulation lines, PC3 is positively correlated with relative fitness, but a model in which metabolites are uncorrelated with fitness is nearly as good by Akaike's Information Criterion.
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Affiliation(s)
- Sarah K Davies
- Department of Life Sciences, Imperial College London, United Kingdom
- Department of Surgery and Cancer, Imperial College London, United Kingdom
| | - Armand Leroi
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Jacob G Bundy
- Department of Surgery and Cancer, Imperial College London, United Kingdom
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, Florida.
- Genetics Institute, University of Florida, Gainesville, Florida.
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11
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Fitness Effects of Spontaneous Mutations in Picoeukaryotic Marine Green Algae. G3-GENES GENOMES GENETICS 2016; 6:2063-71. [PMID: 27175016 PMCID: PMC4938659 DOI: 10.1534/g3.116.029769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Estimates of the fitness effects of spontaneous mutations are important for understanding the adaptive potential of species. Here, we present the results of mutation accumulation experiments over 265–512 sequential generations in four species of marine unicellular green algae, Ostreococcus tauri RCC4221, Ostreococcus mediterraneus RCC2590, Micromonas pusilla RCC299, and Bathycoccus prasinos RCC1105. Cell division rates, taken as a proxy for fitness, systematically decline over the course of the experiment in O. tauri, but not in the three other species where the MA experiments were carried out over a smaller number of generations. However, evidence of mutation accumulation in 24 MA lines arises when they are exposed to stressful conditions, such as changes in osmolarity or exposure to herbicides. The selection coefficients, estimated from the number of cell divisions/day, varies significantly between the different environmental conditions tested in MA lines, providing evidence for advantageous and deleterious effects of spontaneous mutations. This suggests a common environmental dependence of the fitness effects of mutations and allows the minimum mutation/genome/generation rates to be inferred at 0.0037 in these species.
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12
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Gray JC, Cutter AD. Mainstreaming Caenorhabditis elegans in experimental evolution. Proc Biol Sci 2014; 281:20133055. [PMID: 24430852 DOI: 10.1098/rspb.2013.3055] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host-pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.
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Affiliation(s)
- Jeremy C Gray
- Department of Ecology and Evolutionary Biology, University of Toronto, , 25 Willcocks Street, Toronto, Ontario, Canada , M5S 3B2
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13
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Morran LT, Parrish RC, Gelarden IA, Lively CM. Temporal dynamics of outcrossing and host mortality rates in host-pathogen experimental coevolution. Evolution 2012; 67:1860-8. [PMID: 23815644 DOI: 10.1111/evo.12007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 10/23/2012] [Indexed: 12/13/2022]
Abstract
Cross-fertilization is predicted to facilitate the short-term response and the long-term persistence of host populations engaged in antagonistic coevolutionary interactions. Consistent with this idea, our previous work has shown that coevolving bacterial pathogens (Serratia marcescens) can drive obligately selfing hosts (Caenorhabditis elegans) to extinction, whereas the obligately outcrossing and partially outcrossing populations persisted. We focused the present study on the partially outcrossing (mixed mating) and obligately outcrossing hosts, and analyzed the changes in the host resistance/avoidance (and pathogen infectivity) over time. We found that host mortality rates increased in the mixed mating populations over the first 10 generations of coevolution when outcrossing rates were initially low. However, mortality rates decreased after elevated outcrossing rates evolved during the experiment. In contrast, host mortality rates decreased in the obligately outcrossing populations during the first 10 generations of coevolution, and remained low throughout the experiment. Therefore, predominant selfing reduced the ability of the hosts to respond to coevolving pathogens compared to outcrossing hosts. Thus, we found that host-pathogen coevolution can generate rapid evolutionary change, and that host mating system can influence the outcome of coevolution at a fine temporal scale.
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Affiliation(s)
- Levi T Morran
- Department of Biology, Indiana University, Bloomington, IN, USA.
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14
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Caenorhabditis elegans as a platform for molecular quantitative genetics and the systems biology of natural variation. Genet Res (Camb) 2011; 92:331-48. [PMID: 21429266 DOI: 10.1017/s0016672310000601] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Over the past 30 years, the characteristics that have made the nematode Caenorhabditis elegans one of the premier animal model systems have also allowed it to emerge as a powerful model system for determining the genetic basis of quantitative traits, particularly for the identification of naturally segregating and/or lab-adapted alleles with large phenotypic effects. To better understand the genetic underpinnings of natural variation in other complex phenotypes, C. elegans is uniquely poised in the emerging field of quantitative systems biology because of the extensive knowledge of cellular and neural bases to such traits. However, perturbations in standing genetic variation and patterns of linkage disequilibrium among loci are likely to limit our ability to tie understanding of molecular function to a broader evolutionary context. Coupling the experimental strengths of the C. elegans system with the ecological advantages of closely related nematodes should provide a powerful means of understanding both the molecular and evolutionary genetics of quantitative traits.
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15
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Estes S, Phillips PC, Denver DR. Fitness recovery and compensatory evolution in natural mutant lines of C. elegans. Evolution 2011; 65:2335-44. [PMID: 21790579 DOI: 10.1111/j.1558-5646.2011.01276.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Deleterious mutation accumulation plays a central role in evolutionary genetics, conservation biology, human health, and evolutionary medicine (e.g., methods of viral attenuation for live vaccines). It is therefore important to understand whether and how quickly populations with accumulated deleterious mutational loads can recover fitness through adaptive evolution. We used laboratory experimental evolution with four long-term mutation-accumulation (MA) lines of Caenorhabditis elegans nematodes to study the dynamics of such fitness evolution. We previously showed that when homozygous mutant populations are evolved in large population sizes, they can rapidly achieve wild-type fitness through the accumulation of new beneficial or compensatory epistatic mutations. Here, we expand this approach to demonstrate that when replicate lineages are initiated from the same mutant genotype, phenotypic evolution is only sometimes repeatable. MA genotypes that recovered ancestral fitness in the previous experiment did not always do so here. Further, the pattern of adaptive evolution in independently evolved replicates was contingent upon the MA genotype and varied among fitness-related traits. Our findings suggest that new beneficial mutations can drive rapid fitness evolution, but that the adaptive process is rendered somewhat unpredictable by its susceptibility to chance events and sensitivity to the evolutionary history of the starting population.
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Affiliation(s)
- Suzanne Estes
- Department of Biology, Portland State University, Portland, Oregon 97201, USA.
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16
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Halligan DL, Keightley PD. Spontaneous Mutation Accumulation Studies in Evolutionary Genetics. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2009. [DOI: 10.1146/annurev.ecolsys.39.110707.173437] [Citation(s) in RCA: 320] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel L. Halligan
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom; ,
| | - Peter D. Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom; ,
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17
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Joyner-Matos J, Upadhyay A, Salomon MP, Grigaltchik V, Baer CF. Genetic (Co)variation for life span in rhabditid nematodes: role of mutation, selection, and history. J Gerontol A Biol Sci Med Sci 2009; 64:1134-45. [PMID: 19671885 DOI: 10.1093/gerona/glp112] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The evolutionary mechanisms maintaining genetic variation in life span, particularly post-reproductive life span, are poorly understood. We characterized the effects of spontaneous mutations on life span in the rhabditid nematodes Caenorhabditis elegans and C. briggsae and standing genetic variance for life span and correlation of life span with fitness in C. briggsae. Mutations decreased mean life span, a signature of directional selection. Mutational correlations between life span and fitness were consistently positive. The average selection coefficient against new mutations in C. briggsae was approximately 2% when homozygous. The pattern of phylogeographic variation in life span is inconsistent with global mutation-selection balance (MSB), but MSB appears to hold at the local level. Standing genetic correlations in C. briggsae reflect mutational correlations at a local scale but not at a broad phylogeographic level. At the local scale, results are broadly consistent with predictions of the "mutation accumulation" hypothesis for the evolution of aging.
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Affiliation(s)
- Joanna Joyner-Matos
- Department of Biology, Eastern Washington University, Cheney, WA 99004-2440, USA.
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18
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Cutter AD, Dey A, Murray RL. Evolution of the Caenorhabditis elegans genome. Mol Biol Evol 2009; 26:1199-234. [PMID: 19289596 DOI: 10.1093/molbev/msp048] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology and the Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
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19
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Schwander T, Crespi BJ. Twigs on the tree of life? Neutral and selective models for integrating macroevolutionary patterns with microevolutionary processes in the analysis of asexuality. Mol Ecol 2008; 18:28-42. [PMID: 19067799 DOI: 10.1111/j.1365-294x.2008.03992.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neutral models characterize evolutionary or ecological patterns expected in the absence of specific causal processes, such as natural selection or ecological interactions. In this study, we describe and evaluate three neutral models that can, in principle, help to explain the apparent 'twigginess' of asexual lineages on phylogenetic trees without involving the negative consequences predicted for the absence of recombination and genetic exchange between individuals. Previously, such phylogenetic twiggyness of asexual lineages has been uncritically interpreted as evidence that asexuality is associated with elevated extinction rates and thus represents an evolutionary dead end. Our first model uses simple phylogenetic simulations to illustrate that, with sexual reproduction as the ancestral state, low transition rates to stable asexuality, or low rates of ascertained 'speciation' in asexuals, can generate twiggy distributions of asexuality, in the absence of high extinction rates for asexual lineages. The second model, developed by Janko et al. (2008), shows that a dynamic equilibrium between origins and neutral losses of asexuals can, under some conditions, generate a relatively low mean age of asexual lineages. The third model posits that the risk of extinction for asexual lineages may be higher than that of sexuals simply because asexuals inhabit higher latitudes or altitudes, and not due to effects of their reproductive systems. Such neutral models are useful in that they allow quantitative evaluation of whether empirical data, such as phylogenetic and phylogeographic patterns of sex and asexuality, indeed support the idea that asexually reproducing lineages persist over shorter evolutionary periods than sexual lineages, due to such processes as mutation accumulation, slower rates of adaptive evolution, or relatively lower levels of genetic variability.
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Affiliation(s)
- Tanja Schwander
- Department of Biological Sciences, Simon Fraser University, Burnaby BC, Canada.
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20
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Keightley PD, Halligan DL. Analysis and implications of mutational variation. Genetica 2008; 136:359-69. [PMID: 18663587 DOI: 10.1007/s10709-008-9304-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 07/16/2008] [Indexed: 11/25/2022]
Abstract
Variation from new mutations is important for several questions in quantitative genetics. Key parameters are the genomic mutation rate and the distribution of effects of mutations (DEM), which determine the amount of new quantitative variation that arises per generation from mutation (V(M)). Here, we review methods and empirical results concerning mutation accumulation (MA) experiments that have shed light on properties of mutations affecting quantitative traits. Surprisingly, most data on fitness traits from laboratory assays of MA lines indicate that the DEM is platykurtic in form (i.e., substantially less leptokurtic than an exponential distribution), and imply that most variation is produced by mutations of moderate to large effect. This finding contrasts with results from MA or mutagenesis experiments in which mutational changes to the DNA can be assayed directly, which imply that the vast majority of mutations have very small phenotypic effects, and that the distribution has a leptokurtic form. We compare these findings with recent approaches that attempt to infer the DEM for fitness based on comparing the frequency spectra of segregating nucleotide polymorphisms at putatively neutral and selected sites in population samples. When applied to data for humans and Drosophila, these analyses also indicate that the DEM is strongly leptokurtic. However, by combining the resultant estimates of parameters of the DEM with estimates of the mutation rate per nucleotide, the predicted V(M) for fitness is only a tiny fraction of V(M) observed in MA experiments. This discrepancy can be explained if we postulate that a few deleterious mutations of large effect contribute most of the mutational variation observed in MA experiments and that such mutations segregate at very low frequencies in natural populations, and effectively are never seen in population samples.
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Affiliation(s)
- Peter D Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK.
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21
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Anderson JL, Albergotti L, Proulx S, Peden C, Huey RB, Phillips PC. Thermal preference of Caenorhabditis elegans: a null model and empirical tests. ACTA ACUST UNITED AC 2007; 210:3107-16. [PMID: 17704085 DOI: 10.1242/jeb.007351] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The preferred body temperature of ectotherms is typically inferred from the observed distribution of body temperatures in a laboratory thermal gradient. For very small organisms, however, that observed distribution might misrepresent true thermal preferences. Tiny ectotherms have limited thermal inertia, and so their body temperature and speed of movement will vary with their position along the gradient. In order to separate the direct effects of body temperature on movement from actual preference behaviour on a thermal gradient, we generate a null model (i.e. of non-thermoregulating individuals) of the spatial distribution of ectotherms on a thermal gradient and test the model using parameter values estimated from the movement of nematodes (Caenorhabditis elegans) at fixed temperatures and on a thermal gradient. We show that the standard lab strain N2, which is widely used in thermal gradient studies, avoids high temperature but otherwise does not exhibit a clear thermal preference, whereas the Hawaiian natural isolate CB4856 shows a clear preference for cool temperatures ( approximately 17 degrees C). These differences are not influenced substantially by changes in the starting position of worms in the gradient, the natal temperature of individuals or the presence and physiological state of bacterial food. These results demonstrate the value of an explicit null model of thermal effects and highlight problems in the standard model of C. elegans thermotaxis, showing the value of using natural isolates for tests of complex natural behaviours.
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Affiliation(s)
- Jennifer L Anderson
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97402, USA
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22
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Bégin M, Schoen DJ. Transposable elements, mutational correlations, and population divergence in Caenorhabditis elegans. Evolution 2007; 61:1062-70. [PMID: 17492961 DOI: 10.1111/j.1558-5646.2007.00097.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Transposable element activity is thought to be responsible for a large portion of all mutations, but its influence on the evolution of populations has not been well studied. Using mutation accumulation experiments with the nematode Caenorhabditis elegans, we investigated the impact of transposable element activity on the production of mutational variances and covariances. The experiments involved the use of two mutator strains (RNAi-deficient mutants) that are characterized by high levels of germline transposition, as well as the Bristol N2 strain, which lacks germline transposition. We found that transposition led to an increase in mutational heritabilities, as well as to the intensification of correlation patterns observed in the absence of transposition. No mutational trade-offs were detected and mutations generally had a deleterious effect on components of fitness. We also tested whether the pattern of mutational covariation could be used to predict observed patterns of population divergence in this species. Using 15 natural populations, we found that population divergence of C. elegans in multivariate phenotypic space occurred in directions only partially concordant with mutation, and thus other evolutionary factors, such as natural selection and genetic drift, must be acting to produce divergence within this species. Our results suggest that mutations induced by mobile elements in C. elegans are similar to other spontaneous mutations with respect to their contribution to the microevolution of quantitative traits.
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Affiliation(s)
- Mattieu Bégin
- Department of Biology, McGill University, 1205 Dr. Penfield Avenue, Montréal, Québec, H3A 1B1, Canada
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23
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Manoel D, Carvalho S, Phillips PC, Teotónio H. Selection against males in Caenorhabditis elegans under two mutational treatments. Proc Biol Sci 2007; 274:417-24. [PMID: 17164206 PMCID: PMC1702385 DOI: 10.1098/rspb.2006.3739] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Within populations with mixed mating systems, selfing is expected to be favoured over outcrossing unless a countervailing process such as severe inbreeding depression is present. In this study, we consider the relationship between the expression of deleterious alleles and the maintenance of outcrossing in the nematode species, Caenorhabditis elegans. This species is characterized by an androdioecious breeding system composed of males at low frequency and self-fertilizing hermaphrodites that can only outcross via males. Here, we find that experimentally increasing the mutational load in four different isogenic wild isolates using 10 generations of Ethylmethane sulphonate (EMS) and UV irradiation mutagenesis significantly diminishes the cost of males. Males are maintained at higher frequencies in mutagenized versus non-mutagenized populations. Nevertheless, males still tend to be driven to low frequencies within isolates that are known to be prone to lose males. Further, we determine the viability effects of a single round of mutagen exposure and find that, for EMS, outcrossing overcomes the almost completely recessive and nearly lethal effects generated. We briefly interpret our results in light of current evolutionary theory of outcrossing rates.
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Affiliation(s)
- Diogo Manoel
- Centro de Biologia do Desenvolvimento, Instituto Gulbenkian de CiênciaApartado 14, 2781-901 Oeiras, Portugal
| | - Sara Carvalho
- Centro de Biologia do Desenvolvimento, Instituto Gulbenkian de CiênciaApartado 14, 2781-901 Oeiras, Portugal
| | - Patrick C Phillips
- Centre for Ecology and Evolutionary Biology5289 University of Oregon, Eugene, OR 97403-5289, USA
| | - Henrique Teotónio
- Centro de Biologia do Desenvolvimento, Instituto Gulbenkian de CiênciaApartado 14, 2781-901 Oeiras, Portugal
- Author for correspondence ()
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24
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Griswold CK, Logsdon B, Gomulkiewicz R. Neutral evolution of multiple quantitative characters: a genealogical approach. Genetics 2007; 176:455-66. [PMID: 17339224 PMCID: PMC1893077 DOI: 10.1534/genetics.106.069658] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The G matrix measures the components of phenotypic variation that are genetically heritable. The structure of G, that is, its principal components and their associated variances, determines, in part, the direction and speed of multivariate trait evolution. In this article we present a framework and results that give the structure of G under the assumption of neutrality. We suggest that a neutral expectation of the structure of G is important because it gives a null expectation for the structure of G from which the unique consequences of selection can be determined. We demonstrate how the processes of mutation, recombination, and drift shape the structure of G. Furthermore, we demonstrate how shared common ancestry between segregating alleles shapes the structure of G. Our results show that shared common ancestry, which manifests itself in the form of a gene genealogy, causes the structure of G to be nonuniform in that the variances associated with the principal components of G decline at an approximately exponential rate. Furthermore we show that the extent of the nonuniformity in the structure of G is enhanced with declines in mutation rates, recombination rates, and numbers of loci and is dependent on the pattern and modality of mutation.
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Affiliation(s)
- Cortland K Griswold
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
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25
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Baer CF, Phillips N, Ostrow D, Avalos A, Blanton D, Boggs A, Keller T, Levy L, Mezerhane E. Cumulative effects of spontaneous mutations for fitness in Caenorhabditis: role of genotype, environment and stress. Genetics 2006; 174:1387-95. [PMID: 16888328 PMCID: PMC1667051 DOI: 10.1534/genetics.106.061200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Accepted: 07/25/2006] [Indexed: 01/06/2023] Open
Abstract
It is often assumed that the mutation rate is an evolutionarily optimized property of a taxon. The relevant mutation rate is for mutations that affect fitness, U, but the strength of selection on the mutation rate depends on the average effect of a mutation. Determination of U is complicated by the possibility that mutational effects depend on the particular environmental context in which the organism exists. It has been suggested that the effects of deleterious mutations are typically magnified in stressful environments, but most studies confound genotype with environment, so it is unclear to what extent environmental specificity of mutations is specific to a particular starting genotype. We report a study designed to separate effects of species, genotype, and environment on the degradation of fitness resulting from new mutations. Mutations accumulated for >200 generations at 20 degrees in two strains of two species of nematodes that differ in thermal sensitivity. Caenorhabditis briggsae and C. elegans have similar demography at 20 degrees, but C. elegans suffers markedly reduced fitness at 25 degrees. We find little evidence that mutational properties differ depending on environmental conditions and mutational correlations between environments are close to those expected if effects were identical in both environments.
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Affiliation(s)
- Charles F Baer
- Department of Zoology, University of Florida, Gainesville, FL 32611-8525, USA.
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26
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Bégin M, Schoen DJ. Low impact of germline transposition on the rate of mildly deleterious mutation in Caenorhabditis elegans. Genetics 2006; 174:2129-36. [PMID: 17057249 PMCID: PMC1698647 DOI: 10.1534/genetics.106.065508] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Little is known about the role of transposable element (TE) insertion in the production of mutations with mild effects on fitness, the class of mutations thought to be central to the evolution of many basic features of natural populations. We propagated mutation-accumulation (MA) lines of two RNAi-deficient strains of Caenorhabditis elegans that exhibit germline transposition. We show here that the impact of TE activity was to raise the level of mildly deleterious mutation by 2- to 8.5-fold, as estimated from fecundity, longevity, and body length measurements, compared to that observed in a parallel MA experiment with a control strain characterized by a lack of germline transposition. Despite this increase, the rate of mildly deleterious mutation was between one and two orders of magnitude lower than the rate of TE accumulation, which was approximately two new insertions per genome per generation. This study suggests that high rates of TE activity do not necessarily translate into high rates of detectable nonlethal mutation.
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Affiliation(s)
- Mattieu Bégin
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
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27
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Abstract
Recent studies show that local populations of the nematode Caenorhabditis elegans possess nearly as much genetic variation as that seen in existing worldwide collections. This suggests either wide-ranging migration and intense natural selection or recent dispersal, perhaps by human association. Either way, the effective population size of this ubiquitous model organism is unexpectedly small.
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Affiliation(s)
- Patrick C Phillips
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403-5289, USA.
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28
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Artamonova VS, Makhrov AA. Unintentional genetic processes in artificially maintained populations: Proving the leading role of selection in evolution. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406030021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Estes S, Ajie BC, Lynch M, Phillips PC. Spontaneous mutational correlations for life-history, morphological and behavioral characters in Caenorhabditis elegans. Genetics 2005; 170:645-53. [PMID: 15834140 PMCID: PMC1450393 DOI: 10.1534/genetics.104.040022] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The pattern of mutational covariance among traits plays a central, but largely untested, role in many theories in evolutionary genetics. Here we estimate the pattern of phenotypic, environmental, and mutational correlations for a set of life-history, behavioral, and morphological traits using 67 self-fertilizing lines of Caenorhabditis elegans, each having independently experienced an average of 370 generations of spontaneous mutation accumulation. Bivariate relationships of mutational effects indicate the existence of extensive pleiotropy. We find that mutations may tend to produce manifold effects on suites of functionally related traits; however, our data do not support the idea of completely parcelated pleiotropy, in which functional units are separately affected by mutations. Positive net phenotypic and mutational correlations are common for life-history traits, with environmental correlations being comparatively smaller and of the same sign for most pairs of traits. Observed mutational correlations are shown to be higher than those produced by the chance accumulation of nonpleiotropic mutations in the same lines.
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Affiliation(s)
- Suzanne Estes
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, 97403, USA.
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