1
|
Berdan EL, Blanckaert A, Butlin RK, Bank C. Deleterious mutation accumulation and the long-term fate of chromosomal inversions. PLoS Genet 2021; 17:e1009411. [PMID: 33661924 PMCID: PMC7963061 DOI: 10.1371/journal.pgen.1009411] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 03/16/2021] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Chromosomal inversions contribute widely to adaptation and speciation, yet they present a unique evolutionary puzzle as both their allelic content and frequency evolve in a feedback loop. In this simulation study, we quantified the role of the allelic content in determining the long-term fate of the inversion. Recessive deleterious mutations accumulated on both arrangements with most of them being private to a given arrangement. This led to increasing overdominance, allowing for the maintenance of the inversion polymorphism and generating strong non-adaptive divergence between arrangements. The accumulation of mutations was mitigated by gene conversion but nevertheless led to the fitness decline of at least one homokaryotype under all considered conditions. Surprisingly, this fitness degradation could be permanently halted by the branching of an arrangement into multiple highly divergent haplotypes. Our results highlight the dynamic features of inversions by showing how the non-adaptive evolution of allelic content can play a major role in the fate of the inversion.
Collapse
Affiliation(s)
- Emma L. Berdan
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | | | - Roger K. Butlin
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Institute of Ecology and Evolution, University of Bern, Switzerland
| |
Collapse
|
2
|
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: 53] [Impact Index Per Article: 7.6] [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.
Collapse
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
| |
Collapse
|
3
|
Abstract
Data from several thousand knockout mutations in yeast (Saccharomyces cerevisiae) were used to estimate the distribution of dominance coefficients. We propose a new unbiased likelihood approach to measuring dominance coefficients. On average, deleterious mutations are partially recessive, with a mean dominance coefficient ~0.2. Alleles with large homozygous effects are more likely to be more recessive than are alleles of weaker effect. Our approach allows us to quantify, for the first time, the substantial variance and skew in the distribution of dominance coefficients. This heterogeneity is so great that many population genetic processes analyses based on the mean dominance coefficient alone will be in substantial error. These results are applied to the debate about various mechanisms for the evolution of dominance, and we conclude that they are most consistent with models that depend on indirect selection on homeostatic gene expression or on the ability to perform well under periods of high demand for a protein.
Collapse
|
4
|
Trindade S, Perfeito L, Gordo I. Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli. Philos Trans R Soc Lond B Biol Sci 2010; 365:1177-86. [PMID: 20308092 PMCID: PMC2871818 DOI: 10.1098/rstb.2009.0287] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of the mutational parameters that affect the evolution of organisms is of key importance in understanding the evolution of several characteristics of many natural populations, including recombination and mutation rates. In this study, we estimated the rate and mean effect of spontaneous mutations that affect fitness in a mutator strain of Escherichia coli and review some of the estimation methods associated with mutation accumulation (MA) experiments. We performed an MA experiment where we followed the evolution of 50 independent mutator lines that were subjected to repeated bottlenecks of a single individual for approximately 1150 generations. From the decline in mean fitness and the increase in variance between lines, we estimated a minimum mutation rate to deleterious mutations of 0.005 (+/-0.001 with 95% confidence) and a maximum mean fitness effect per deleterious mutation of 0.03 (+/-0.01 with 95% confidence). We also show that any beneficial mutations that occur during the MA experiment have a small effect on the estimate of the rate and effect of deleterious mutations, unless their rate is extremely large. Extrapolating our results to the wild-type mutation rate, we find that our estimate of the mutational effects is slightly larger and the inferred deleterious mutation rate slightly lower than previous estimates obtained for non-mutator E. coli.
Collapse
Affiliation(s)
- Sandra Trindade
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, No. 6, 2780-156 Oeiras, Portugal
| | - Lilia Perfeito
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, No. 6, 2780-156 Oeiras, Portugal
- Institute for Genetics of the University of Cologne, Zuelpicher Street 47, Cologne 50674, Germany
- Institute for Theoretical Physics of the University of Cologne, Zuelpicher Street 77, Cologne 50937, Germany
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, No. 6, 2780-156 Oeiras, Portugal
| |
Collapse
|
5
|
Xu J. Genotype-environment interactions of spontaneous mutations for vegetative fitness in the human pathogenic fungus Cryptococcus neoformans. Genetics 2005; 168:1177-88. [PMID: 15579678 PMCID: PMC1448770 DOI: 10.1534/genetics.104.030031] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spontaneous mutation is the ultimate source of all genetic variation. By interacting with environmental factors, genetic variation determines the phenotype and fitness of individuals in natural populations. However, except in a few model organisms, relatively little is known about the patterns of genotype-environment interactions of spontaneous mutations. Here I examine the rates of spontaneous mutation and the patterns of genotype-environment interaction of mutations affecting vegetative growth in the human fungal pathogen Cryptococcus neoformans. Eight mutation accumulation (MA) lines were established from a single clone on the nutrient-rich medium YEPD for each of two temperatures, 25 degrees and 37 degrees. Cells from generations 100, 200, 400, and 600 for each of the 16 MA lines were stored and assayed for vegetative growth rates under each of four conditions: (i) 25 degrees on SD (a synthetic dextrose minimal medium); (ii) 25 degrees on YEPD; (iii) 37 degrees on SD; and (iv) 37 degrees on YEPD. Both MA conditions and assay environments for vegetative growth showed significant influence on the estimates of genomic mutation rates, average effect per mutation, and mutational heritability. Significant genotype-environment interactions were detected among the newly accumulated spontaneous mutations. Overall, clones from MA lines maintained at 37 degrees showed less decline in vegetative fitness than those maintained at 25 degrees. The result suggests that a high-temperature environment might be very important for the maintenance of the ability to grow at a high temperature. Results from comparisons between clinical and environmental samples of C. neoformans were consistent with laboratory experimental population analyses. This study calls into question our long-standing view that warm-blooded mammals were only occasional and accidental hosts of this human fungal pathogen.
Collapse
Affiliation(s)
- Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
| |
Collapse
|
6
|
Peters AD, Halligan DL, Whitlock MC, Keightley PD. Dominance and Overdominance of Mildly Deleterious Induced Mutations for Fitness Traits inCaenorhabditis elegans. Genetics 2003; 165:589-99. [PMID: 14573472 PMCID: PMC1462798 DOI: 10.1093/genetics/165.2.589] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractWe estimated the average dominance coefficient of mildly deleterious mutations (h, the proportion by which mutations in the heterozygous state reduce fitness components relative to those in the homozygous state) in the nematode Caenorhabditis elegans. From 56 worm lines that carry mutations induced by the point mutagen ethyl methanesulfonate (EMS), we selected 19 lines that are relatively high in fitness and estimated the viabilities, productivities, and relative fitnesses of heterozygotes and homozygotes compared to the ancestral wild type. There was very little effect of homozygous or heterozygous mutations on egg-to-adult viability. For productivity and relative fitness, we found that the average dominance coefficient, h, was ∼0.1, suggesting that mildly deleterious mutations are on average partially recessive. These estimates were not significantly different from zero (complete recessivity) but were significantly different from 0.5 (additivity). In addition, there was a significant amount of variation in h among lines, and analysis of average dominance coefficients of individual lines suggested that several lines showed overdominance for fitness. Further investigation of two of these lines partially confirmed this finding.
Collapse
Affiliation(s)
- A D Peters
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
| | | | | | | |
Collapse
|
7
|
Abstract
The segregation of alleles disrupts genetic associations at overdominant loci, causing a sexual population to experience a lower mean fitness compared to an asexual population. To investigate whether circumstances promoting increased sex exist within a population with heterozygote advantage, a model is constructed that monitors the frequency of alleles at a modifier locus that changes the relative allocation to sexual and asexual reproduction. The frequency of these modifier alleles changes over time as a correlated response to the dynamics at a fitness locus under overdominant selection. Increased sex can be favored in partially sexual populations that inbreed to some extent. This surprising finding results from the fact that inbred populations have an excess of homozygous individuals, for whom sex is always favorable. The conditions promoting increased levels of sex depend on the selection pressure against the homozygotes, the extent of sex and inbreeding in the population, and the dominance of the invading modifier allele.
Collapse
Affiliation(s)
- Elie S Dolgin
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | | |
Collapse
|
8
|
Abstract
There have been several attempts to estimate the average dominance (ratio of heterozygous to homozygous effects) of spontaneous deleterious mutations in Drosophila melanogaster, but these have given inconsistent results. We investigated whether transposable element (TE) insertions have higher average dominance for egg-to-adult viability than do point mutations, a possibility suggested by the types of fitness-depressing effects that TEs are believed to have. If so, then variation in dominance estimates among strains and crosses would be expected as a consequence of variation in TE activity. As a first test, we estimated the average dominance of all mutations and of copia insertions in a set of lines that had accumulated spontaneous mutations for 33 generations. A traditional regression method gave a dominance estimate for all mutations of 0.17, whereas average dominance of copia insertions was 0.51; the difference between these two estimates approached significance (P = 0.08). As a second test, we reanalyzed Ohnishi 1974 data on dominance of spontaneous and EMS-induced mutations. Because a considerable fraction of spontaneous mutations are caused by TE insertions, whereas EMS induces mainly point mutations, we predicted that average dominance would decline with increasing EMS concentration. This pattern was observed, but again fell short of formal significance (P = 0.07). Taken together, however, the two results give modest support for the hypothesis that TE insertions have greater average dominance in their viability effects than do point mutations, possibly as a result of deleterious effects of expression of TE-encoded genes.
Collapse
Affiliation(s)
- James D Fry
- Department of Biology, University of Rochester, Rochester, New York 14627, USA.
| | | |
Collapse
|
9
|
|
10
|
Spieser OH, Schröder JH. Differential response to irradiation in offspring of freshwater and seawater substrains of Poecilia (Lebistes) reticulata peters in the "guppy male courtship activity test". TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1978; 51:223-232. [PMID: 24317809 DOI: 10.1007/bf00273769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/1977] [Indexed: 06/02/2023]
Abstract
An inbred strain ("Istanbul") of guppies was divided into two substrains, one of which was maintained and bred in seawater. The offspring of irradiated animals of both substrains (1000 R X-rays to spermatogonia and oogonia of neonatal fish) were tested in a new "gruppy male courtship activity test" and compared with control groups. The postirradiation response in the seawater substrain was more intense than in the freshwater substrain.
Collapse
|
11
|
Ohnishi O. Spontaneous and ethyl methanesulfonate-induced mutations controlling viability in Drosophila melanogaster. III. Heterozygous effect of polygenic mutations. Genetics 1977; 87:547-56. [PMID: 200527 PMCID: PMC1213760 DOI: 10.1093/genetics/87.3.547] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Spontaneous and EMS-induced mutations were accumulated for several generations on the second chromosome of Drosophila melanogaster by keeping this chromosome heterozygous under conditions of minimal natural selection. This article reports studies of heterozygous effects of these mutants.--Both lethal and mildly deleterious mutants have a deleterious heterozygous effect. There was no discernible difference between heterozygotes in which all the mutants were on one chromosome and those where the mutants were distributed over both homologs; thus the coupling-repulsion effect of MUKAI and YAMAZAKI (1964, 1968) is not confirmed. The spontaneous polygenic mutants have a dominance of 0.4 to 0.5, and the same value is found at very low EMS doses. However, the value at higher EMS doses is only about half as high. Since the low doses have a large fraction of spontaneous mutants, the dominance of EMS mutants is less, in the range 0.1 to 0.3, but still larger than for lethals.
Collapse
|
12
|
Schröder JH, Holzberg S. Population genetics of Lebistes (Poecilia) reticulatus Peters (Poeciliidae; Pisces). I. Effects of radiation-induced mutations on the segregation ratio in postirradiation F 2 . Genetics 1972; 70:621-30. [PMID: 5034772 PMCID: PMC1212762 DOI: 10.1093/genetics/70.4.621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Wild-type germ cells of the viviparous fish, Lebistes (Poecilia) reticulatus, were irradiated in the stages of oogonia, spermatogonia or spermatozoa with 1000 R of X rays at a dose-rate of 200-220 R/min. The grown-up fish were mated after irradiation or sham treatment to unirradiated mutant fish homozygous for three recessive gene loci, causing albinism, lack of yellow and reddish pigmentation ("blue" constitution), and diminution of the size of melanophores ("blond" constitution). As compared to the control series, the phenotypic segregation ratios in the adult F(2) generation after irradiation was changed significantly in favour of wild-type and blue fish, whereas the proportion of albinotic, blond and "white" (= blond + blue) guppies was lowered. This unidirectional effect in postirradiation F(2) was greatest after exposure of spermatozoa with 2 x 500 R (24 hr apart), followed by single doses of 1000 R to spermatogonia and oogonia. These results were explained in terms of a synergistic interaction of recessive radiation-induced mutations in the heterozygous state with those genotypes of the guppy which affect the formation of melanophoric patterns and the synthesis of melanins.
Collapse
|
13
|
Marinković D, Krunić M, Tucić N, Andjelković M. Recessive genetic variants affecting mating activity of males in natural populations of Drosophila melanogaster. Genetica 1970; 41:581-8. [PMID: 5512358 DOI: 10.1007/bf00958937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
14
|
van Delden W, Beardmore JA. Effects of small increments of genetic variability in inbred populations of Drosophila melanogaster. Mutat Res 1968; 6:117-27. [PMID: 5708065 DOI: 10.1016/0027-5107(68)90108-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
15
|
Mukai T, Yoshikawa I, Sano K. The genetic structure of natural populations of Drosophila melanogaster. IV. Heterozygous effects of radiation-induced mutations on viability in various genetic backgrounds. Genetics 1966; 53:513-27. [PMID: 5919330 PMCID: PMC1211036 DOI: 10.1093/genetics/53.3.513] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
|
16
|
Mukai T, Chigusa S, Yoshikawa I. The genetic structure of natural populations of Drosophila melanogaster. 3. Dominance effect of spontaneous mutant polygenes controlling viability in heterozygous genetic backgrounds. Genetics 1965; 52:493-501. [PMID: 5863900 PMCID: PMC1210915 DOI: 10.1093/genetics/52.3.493] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
|
17
|
MUKAI T, YAMAZAKI T. Position Effect of Spontaneous Mutant Polygenes Controlling Viability in Drosophila melanogaster. ACTA ACUST UNITED AC 1964. [DOI: 10.2183/pjab1945.40.840] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|