1
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McDonald TK, Yeaman S. Effect of migration and environmental heterogeneity on the maintenance of quantitative genetic variation: a simulation study. J Evol Biol 2018; 31:1386-1399. [PMID: 29938863 DOI: 10.1111/jeb.13341] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 01/15/2023]
Abstract
The paradox of high genetic variation observed in traits under stabilizing selection is a long-standing problem in evolutionary theory, as mutation rates appear too low to explain observed levels of standing genetic variation under classic models of mutation-selection balance. Spatially or temporally heterogeneous environments can maintain more standing genetic variation within populations than homogeneous environments, but it is unclear whether such conditions can resolve the above discrepancy between theory and observation. Here, we use individual-based simulations to explore the effect of various types of environmental heterogeneity on the maintenance of genetic variation (VA ) for a quantitative trait under stabilizing selection. We find that VA is maximized at intermediate migration rates in spatially heterogeneous environments and that the observed patterns are robust to changes in population size. Spatial environmental heterogeneity increased variation by as much as 10-fold over mutation-selection balance alone, whereas pure temporal environmental heterogeneity increased variance by only 45% at max. Our results show that some combinations of spatial heterogeneity and migration can maintain considerably more variation than mutation-selection balance, potentially reconciling the discrepancy between theoretical predictions and empirical observations. However, given the narrow regions of parameter space required for this effect, this is unlikely to provide a general explanation for the maintenance of variation. Nonetheless, our results suggest that habitat fragmentation may affect the maintenance of VA and thereby reduce the adaptive capacity of populations.
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Affiliation(s)
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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2
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Huang W, Lyman RF, Lyman RA, Carbone MA, Harbison ST, Magwire MM, Mackay TF. Spontaneous mutations and the origin and maintenance of quantitative genetic variation. eLife 2016; 5. [PMID: 27213517 PMCID: PMC4929002 DOI: 10.7554/elife.14625] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/21/2016] [Indexed: 11/30/2022] Open
Abstract
Mutation and natural selection shape the genetic variation in natural populations. Here, we directly estimated the spontaneous mutation rate by sequencing new Drosophila mutation accumulation lines maintained with minimal natural selection. We inferred strong stabilizing natural selection on quantitative traits because genetic variation among wild-derived inbred lines was much lower than predicted from a neutral model and the mutational effects were much larger than allelic effects of standing polymorphisms. Stabilizing selection could act directly on the traits, or indirectly from pleiotropic effects on fitness. However, our data are not consistent with simple models of mutation-stabilizing selection balance; therefore, further empirical work is needed to assess the balance of evolutionary forces responsible for quantitative genetic variation. DOI:http://dx.doi.org/10.7554/eLife.14625.001 A key challenge in evolutionary biology is to understand how genetic variation – differences in the DNA of individuals in a population – is generated and maintained to create the enormous diversity that exists in nature. Mutations to the DNA introduce new variation, but these are constantly removed from populations by two other evolutionary forces: natural selection and genetic drift. Natural selection removes harmful genetic mutations that affect an organism’s fitness and reproduction, and genetic drift is the random increase in, or loss of, a genetic variant from a population over time. However, disentangling the effects of these evolutionary forces is challenging because the genetic variation we observe is often the final product of a long history of interaction between them. Huang et al. have now investigated genetic variation by breeding fruit flies in the laboratory. Natural selection was minimized for these flies; genetic drift was therefore the main force that removed variation. Huang et al. then sequenced the DNA of the flies to estimate the rate at which genetic mutations spontaneously occur. The sequences contained many more “high-impact” mutations (which directly affect how proteins in the fly’s cells work) than seen in sequences taken from a natural fly population. Traits that are produced by the cumulative actions of many genes and the environment are known as quantitative traits. By examining how much variation genetic mutations introduced into the quantitative traits of each generation of the laboratory-grown flies, Huang et al. estimated how much variation should occur in a natural population whose quantitative traits evolved without natural selection. This estimate was much higher than the levels of genetic variation seen in nature, suggesting that natural selection acts to eliminate mutations that significantly affect quantitative traits. Simple theoretical models cannot explain the relatively high spontaneous mutation rate and low genetic variation seen in the quantitative traits of natural populations. Therefore, further work is now required to understand more about the balance of evolutionary forces that maintain quantitative genetic variation. DOI:http://dx.doi.org/10.7554/eLife.14625.002
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Affiliation(s)
- Wen Huang
- Program in Genetics, North Carolina State University, Raleigh, United States.,W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, United States
| | - Richard F Lyman
- Program in Genetics, North Carolina State University, Raleigh, United States.,W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, United States
| | - Rachel A Lyman
- Program in Genetics, North Carolina State University, Raleigh, United States.,W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, United States.,Department of Biology, Knox College, Galesburg, United States
| | - Mary Anna Carbone
- Program in Genetics, North Carolina State University, Raleigh, United States.,W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, United States
| | - Susan T Harbison
- Program in Genetics, North Carolina State University, Raleigh, United States.,W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, United States
| | - Michael M Magwire
- Program in Genetics, North Carolina State University, Raleigh, United States.,W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, United States
| | - Trudy Fc Mackay
- Program in Genetics, North Carolina State University, Raleigh, United States.,W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, United States
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3
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Fu YB. Understanding crop genetic diversity under modern plant breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2131-42. [PMID: 26246331 PMCID: PMC4624815 DOI: 10.1007/s00122-015-2585-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/16/2015] [Indexed: 05/18/2023]
Abstract
Maximizing crop yield while at the same time minimizing crop failure for sustainable agriculture requires a better understanding of the impacts of plant breeding on crop genetic diversity. This review identifies knowledge gaps and shows the need for more research into genetic diversity changes under plant breeding. Modern plant breeding has made a profound impact on food production and will continue to play a vital role in world food security. For sustainable agriculture, a compromise should be sought between maximizing crop yield under changing climate and minimizing crop failure under unfavorable conditions. Such a compromise requires better understanding of the impacts of plant breeding on crop genetic diversity. Efforts have been made over the last three decades to assess crop genetic diversity using molecular marker technologies. However, these assessments have revealed some temporal diversity patterns that are largely inconsistent with our perception that modern plant breeding reduces crop genetic diversity. An attempt was made in this review to explain such discrepancies by examining empirical assessments of crop genetic diversity and theoretical investigations of genetic diversity changes over time under artificial selection. It was found that many crop genetic diversity assessments were not designed to assess diversity impacts from specific plant breeding programs, while others were experimentally inadequate and contained technical biases from the sampling of cultivars and genomes. Little attention has been paid to theoretical investigations on crop genetic diversity changes from plant breeding. A computer simulation of five simplified breeding schemes showed the substantial effects of plant breeding on the retention of heterozygosity over generations. It is clear that more efforts are needed to investigate crop genetic diversity in space and time under plant breeding to achieve sustainable crop production.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, AAFC Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, S7N0X2, Canada.
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4
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Complex trait architecture: the pleiotropic model revisited. Sci Rep 2015; 5:9351. [PMID: 25792462 PMCID: PMC4366851 DOI: 10.1038/srep09351] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/20/2015] [Indexed: 01/30/2023] Open
Abstract
There is currently much debate about how much the genetic heritability of complex traits is due to very rare alleles. This issue is important because it determines sampling strategies for genetic association studies. Several recent theoretical papers based on a pleiotropic model for trait evolution suggest that it is possible that a large proportion of the genetic variance could be explained by rare alleles. This model assumes that mutations with a large effect on fitness also tend to have large positive or negative effects on phenotypic traits. We show that conclusions based on standard diffusion results are generally applicable to simulations of whole genomes with overlapping generations in a finite population, although the variance contribution of rare alleles is somewhat smaller than theoretical predictions. We show that under many scenarios the pleiotropic model predicts trait distributions that are unrealistically leptokurtic. We argue that this imposes a limit on the relationship between fitness and trait effects.
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5
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Gianola D, Hospital F, Verrier E. Contribution of an additive locus to genetic variance when inheritance is multi-factorial with implications on interpretation of GWAS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1457-1472. [PMID: 23508282 DOI: 10.1007/s00122-013-2064-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 02/08/2013] [Indexed: 06/01/2023]
Abstract
Although the effects of linkage disequilibrium (LD) on partition of genetic variance have received attention in quantitative genetics, there has been little discussion on how this phenomenon affects attribution of variance to a given locus. This paper reinforces the point that standard metrics used for assessing the contribution of a locus to variance can be misleading when there is linkage LD and that factors such as distribution of effects and of allelic frequencies over loci, or existence of frequency-dependent effects, play a role as well. An apparently new metric is proposed for measuring how much of the variability is contributed by a locus when LD exists. Effects of intervening factors, such as type and extent of LD, number of loci, distribution of effects, and of allelic frequencies over loci, as well as a model for generating frequency-dependent effects, are illustrated via hypothetical simulation scenarios. Implications on the interpretation of genome-wide association studies (GWAS), as typically carried out in human genetics, where single marker regression and the assumption of a sole quantitative trait locus (QTL) are common, are discussed. It is concluded that the standard attributions to variance contributed by a single QTL from a GWAS analysis may be misleading, conceptually and statistically, when a trait is complex and affected by sets of many genes in linkage disequilibrium. Yet another factor to consider in the "missing heritability" saga?.
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Affiliation(s)
- Daniel Gianola
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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6
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Zhang XS. Fisher's geometrical model of fitness landscape and variance in fitness within a changing environment. Evolution 2012; 66:2350-68. [PMID: 22834737 DOI: 10.1111/j.1558-5646.2012.01610.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The fitness of an individual can be simply defined as the number of its offspring in the next generation. However, it is not well understood how selection on the phenotype determines fitness. In accordance with Fisher's fundamental theorem, fitness should have no or very little genetic variance, whereas empirical data suggest that is not the case. To bridge these knowledge gaps, we follow Fisher's geometrical model and assume that fitness is determined by multivariate stabilizing selection toward an optimum that may vary among generations. We assume random mating, free recombination, additive genes, and uncorrelated stabilizing selection and mutational effects on traits. In a constant environment, we find that genetic variance in fitness under mutation-selection balance is a U-shaped function of the number of traits (i.e., of the so-called "organismal complexity"). Because the variance can be high if the organism is of either low or high complexity, this suggests that complexity has little direct costs. Under a temporally varying optimum, genetic variance increases relative to a constant optimum and increasingly so when the mutation rate is small. Therefore, mutation and changing environment together can maintain high genetic variance. These results therefore lend support to Fisher's geometric model of a fitness landscape.
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Affiliation(s)
- Xu-Sheng Zhang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
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7
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Loiseau C, Zoorob R, Robert A, Chastel O, Julliard R, Sorci G. Plasmodium relictum infection and MHC diversity in the house sparrow (Passer domesticus). Proc Biol Sci 2011; 278:1264-72. [PMID: 20943698 PMCID: PMC3049082 DOI: 10.1098/rspb.2010.1968] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 09/22/2010] [Indexed: 01/22/2023] Open
Abstract
Antagonistic coevolution between hosts and parasites has been proposed as a mechanism maintaining genetic diversity in both host and parasite populations. In particular, the high level of genetic diversity usually observed at the major histocompatibility complex (MHC) is generally thought to be maintained by parasite-driven selection. Among the possible ways through which parasites can maintain MHC diversity, diversifying selection has received relatively less attention. This hypothesis is based on the idea that parasites exert spatially variable selection pressures because of heterogeneity in parasite genetic structure, abundance or virulence. Variable selection pressures should select for different host allelic lineages resulting in population-specific associations between MHC alleles and risk of infection. In this study, we took advantage of a large survey of avian malaria in 13 populations of the house sparrow (Passer domesticus) to test this hypothesis. We found that (i) several MHC alleles were either associated with increased or decreased risk to be infected with Plasmodium relictum, (ii) the effects were population specific, and (iii) some alleles had antagonistic effects across populations. Overall, these results support the hypothesis that diversifying selection in space can maintain MHC variation and suggest a pattern of local adaptation where MHC alleles are selected at the local host population level.
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Affiliation(s)
- Claire Loiseau
- Laboratoire Parasitologie Evolutive, Université Pierre et Marie Curie, CNRS UMR 7103, 7, quai St Bernard, Case 237, 75252 Paris Cedex 05, France
| | - Rima Zoorob
- Laboratoire de Génétique Moléculaire et Intégration des Fonctions Cellulaires, CNRS FRE 2937, 7 rue Guy Mocquet, 94801 Villejuif Cedex, France
| | - Alexandre Robert
- Laboratoire Conservation des Espèces, Restauration et Suivi des Populations, Muséum National d'Histoire Naturelle, UMR 5173 CNRS-MNHN-UPMC 55 rue Buffon, 75005 Paris, France
| | - Olivier Chastel
- Centre d'Etudes Biologique de Chizé, CNRS UPR 1934, 79360 Beauvoir-sur-Niort, France
| | - Romain Julliard
- Laboratoire Conservation des Espèces, Restauration et Suivi des Populations, Muséum National d'Histoire Naturelle, UMR 5173 CNRS-MNHN-UPMC 55 rue Buffon, 75005 Paris, France
| | - Gabriele Sorci
- BioGéoSciences, Université de Bourgogne, CNRS UMR 5561, 6 Boulevard Gabriel, 21000 Dijon, France
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8
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Mackay TFC. Mutations and quantitative genetic variation: lessons from Drosophila. Philos Trans R Soc Lond B Biol Sci 2010; 365:1229-39. [PMID: 20308098 DOI: 10.1098/rstb.2009.0315] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A central issue in evolutionary quantitative genetics is to understand how genetic variation for quantitative traits is maintained in natural populations. Estimates of genetic variation and of genetic correlations and pleiotropy among multiple traits, inbreeding depression, mutation rates for fitness and quantitative traits and of the strength and nature of selection are all required to evaluate theoretical models of the maintenance of genetic variation. Studies in Drosophila melanogaster have shown that a substantial fraction of segregating variation for fitness-related traits in Drosophila is due to rare deleterious alleles maintained by mutation-selection balance, with a smaller but significant fraction attributable to intermediate frequency alleles maintained by alleles with antagonistic pleiotropic effects, and late-age-specific effects. However, the nature of segregating variation for traits under stabilizing selection is less clear and requires more detailed knowledge of the loci, mutation rates, allelic effects and frequencies of molecular polymorphisms affecting variation in suites of pleiotropically connected traits. Recent studies in D. melanogaster have revealed unexpectedly complex genetic architectures of many quantitative traits, with large numbers of pleiotropic genes and alleles with sex-, environment- and genetic background-specific effects. Future genome wide association analyses of many quantitative traits on a common panel of fully sequenced Drosophila strains will provide much needed empirical data on the molecular genetic basis of quantitative traits.
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Affiliation(s)
- Trudy F C Mackay
- Department of Genetics, W. M. Keck Center for Behavioral Biology, North Carolina State University, , Campus Box 7614, Raleigh, NC 27697, USA.
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9
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Tanaka Y. Apparent directional selection by biased pleiotropic mutation. Genetica 2010; 138:717-23. [DOI: 10.1007/s10709-010-9451-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 02/26/2010] [Indexed: 11/30/2022]
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10
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Walsh B, Blows MW. Abundant Genetic Variation + Strong Selection = Multivariate Genetic Constraints: A Geometric View of Adaptation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2009. [DOI: 10.1146/annurev.ecolsys.110308.120232] [Citation(s) in RCA: 438] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bruce Walsh
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072 Australia;
- Permanent address: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721;
| | - Mark W. Blows
- School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072 Australia;
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11
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Zhang XS, Hill WG. Change and maintenance of variation in quantitative traits in the context of the Price equation. Theor Popul Biol 2009; 77:14-22. [PMID: 19836408 DOI: 10.1016/j.tpb.2009.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 10/06/2009] [Accepted: 10/12/2009] [Indexed: 11/30/2022]
Abstract
The Price equation is a general description of evolutionary change in any character from one generation to the next due to natural selection and other forces such as mutation and recombination. Recently it has been widely utilised in many fields including quantitative genetics, but these applications have focused mainly on the response to selection in the mean of characters. Many different and, in some cases, conflicting models have been investigated by quantitative geneticists to examine the change and maintenance of both genetic and environmental variance of quantitative traits under selection and other forces. In this study, we use the Price equation to derive many such well-known results for the dynamics and equilibria of variances in a straightforward way and to develop them further.
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Affiliation(s)
- Xu-Sheng Zhang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
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12
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Patterns of quantitative genetic variation in multiple dimensions. Genetica 2008; 136:271-84. [PMID: 18695991 DOI: 10.1007/s10709-008-9302-6] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 07/16/2008] [Indexed: 10/21/2022]
Abstract
A fundamental question for both evolutionary biologists and breeders is the extent to which genetic correlations limit the ability of populations to respond to selection. Here I view this topic from three perspectives. First, I propose several nondimensional statistics to quantify the genetic variation present in a suite of traits and to describe the extent to which correlations limit their selection response. A review of five data sets suggests that the total variation differs substantially between populations. In all cases analyzed, however, the "effective number of dimensions" is less than two: more than half of the total genetic variation is explained by a single combination of traits. Second, I consider how patterns of variation affect the average evolutionary response to selection in a random direction. When genetic variation lies in a small number of dimensions but there are a large number of traits under selection, then the average selection response will be reduced substantially from its potential maximum. Third, I discuss how a low genetic correlation between male fitness and female fitness limits the ability of populations to adapt. Data from two recent studies of natural populations suggest this correlation can diminish or even erase any genetic benefit to mate choice. Together these results suggest that adaptation (in natural populations) and genetic improvement (in domesticated populations) may often be as much constrained by patterns of genetic correlation as by the overall amount of genetic variation.
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13
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Loiseau C, Zoorob R, Garnier S, Birard J, Federici P, Julliard R, Sorci G. Antagonistic effects of a Mhc class I allele on malaria-infected house sparrows. Ecol Lett 2008; 11:258-65. [DOI: 10.1111/j.1461-0248.2007.01141.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Kelly JK. Testing the rare-alleles model of quantitative variation by artificial selection. Genetica 2008; 132:187-98. [PMID: 17607507 PMCID: PMC2682333 DOI: 10.1007/s10709-007-9163-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 06/09/2007] [Indexed: 10/23/2022]
Abstract
The rare-alleles model of quantitative variation posits that a common allele (the 'wild-type') and one or more rare alleles segregate at each locus affecting a quantitative trait; a scenario predicted by several distinct evolutionary hypotheses. Single locus arguments suggest that artificial selection should substantially increase the genetic variance (Vg) if the rare-alleles model is accurate. This paper tests the 'DeltaVg prediction' using a large artificial selection experiment on flower size of Mimulus guttatus. Vg for flower size does evolve, increasing with selection for larger flower while decreasing in the other direction. These data are consistent with a model in which flower size variation is caused by rare, partially dominant alleles. However, this explanation becomes increasingly tenuous when considered with other data (correlated responses to selection and the effects of inbreeding). A combination of modern (marker-based mapping) and classical (biometric) techniques will likely to be required to determine the distribution of allele frequencies at loci influencing quantitative traits.
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Affiliation(s)
- John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS, 66045-7534, USA.
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15
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Hunt J, Blows MW, Zajitschek F, Jennions MD, Brooks R. Reconciling strong stabilizing selection with the maintenance of genetic variation in a natural population of black field crickets (Teleogryllus commodus). Genetics 2007; 177:875-80. [PMID: 17660544 PMCID: PMC2034650 DOI: 10.1534/genetics.107.077057] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Genetic variation in single traits, including those closely related to fitness, is pervasive and generally high. By contrast, theory predicts that several forms of selection, including stabilizing selection, will eliminate genetic variation. Stabilizing selection in natural populations tends to be stronger than that assumed in theoretical models of the maintenance of genetic variation. The widespread presence of genetic variation in the presence of strong stabilizing selection is a persistent problem in evolutionary genetics that currently has no compelling explanation. The recent insight that stabilizing selection often acts most strongly on trait combinations via correlational selection may reconcile this problem. Here we show that for a set of male call properties in the cricket Teleogryllus commodus, the pattern of multivariate stabilizing sexual selection is closely associated with the degree of additive genetic variance. The multivariate trait combinations experiencing the strongest stabilizing selection harbored very little genetic variation while combinations under weak selection contained most of the genetic variation. Our experiment provides empirical support for the prediction that a small number of trait combinations experiencing strong stabilizing selection will have reduced genetic variance and that genetically independent trait combinations experiencing weak selection can simultaneously harbor much higher levels of genetic variance.
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Affiliation(s)
- John Hunt
- Evolution and Ecology Research Centre, University of New South Wales, Kensington, Sydney 2052, Australia.
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16
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Griswold CK. The relationship between the pleiotropic phenotypic effects of a mutation fixed by selection. Heredity (Edinb) 2007; 98:232-42. [PMID: 17228334 DOI: 10.1038/sj.hdy.6800933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A pleiotropic model of mutation is presented that allows for correlations between the effects of a new mutation and for the distribution of mutational effects to vary from being leptokurtic to normally distributed. Using this model I quantify how selection transforms the correlation between the effects of a new (random) mutation into the correlation between the effects of a mutation that is fixed by selection and contributes to an adaptation. Results suggest that under most conditions the correlation between the effects of a fixed mutation is less than the correlation between the effects of a new mutation. I also generalize previous results that quantified the expected size of a fixed mutation's effect on a character given an observed effect of that mutation on another character. In agreement with previous results, work here suggests that as the observed effect becomes large and beneficial the expected effect on another character approaches the expected effect of a new (random) mutation given the observed effect. Lastly, these theoretical results are related to recent empirical work that found beneficial mutations had a positive correlation in their pleiotropic effects.
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Affiliation(s)
- C K Griswold
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada.
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17
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Shaw RG, Chang SM. Gene action of new mutations in Arabidopsis thaliana. Genetics 2006; 172:1855-65. [PMID: 16361233 PMCID: PMC1456307 DOI: 10.1534/genetics.105.050971] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 11/28/2005] [Indexed: 11/18/2022] Open
Abstract
For a newly arising mutation affecting a trait under selection, its degree of dominance relative to the preexisting allele(s) strongly influences its evolutionary impact. We have estimated dominance parameters for spontaneous mutations in a subset of lines derived from a highly inbred founder of Arabidopsis thaliana by at least 17 generations of mutation accumulation (MA). The labor-intensive nature of the crosses and the anticipated subtlety of effects limited the number of MA lines included in this study to 8. Each MA line was selfed and reciprocally crossed to plants representing the founder genotype, and progeny were assayed in the greenhouse. Significant mutational effects on reproductive fitness included a recessive fitness-enhancing effect in one line and fitness-reducing effects, one additive and the other slightly recessive. Mutations conferring earlier phenology or smaller leaves were significantly recessive. For effects increasing leaf number and reducing height at flowering, additive gene action accounted for the expression of the traits. The sole example of a significantly dominant mutational effect delayed phenology. Our findings of recessive action of a fitness-enhancing mutational effect and additive action of a deleterious effect counter a common expectation of (partial) dominance of alleles that increase fitness, but the frequency of occurrence of such mutations is unknown.
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Affiliation(s)
- Ruth G Shaw
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul 55108-6097, USA.
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18
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Brotherstone S, Goddard M. Artificial selection and maintenance of genetic variance in the global dairy cow population. Philos Trans R Soc Lond B Biol Sci 2005; 360:1479-88. [PMID: 16048790 PMCID: PMC1569519 DOI: 10.1098/rstb.2005.1668] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic improvement of dairy cows, which has increased the milk yield of cows in the UK by 1200 kg per lactation in 12 years, is an excellent example of the application of quantitative genetics to agriculture. The most important traits of dairy cattle are expressed only in females, but the main opportunity for selection is in males. Despite this, genetic improvement was achieved by the invention of a new statistical methodology, called 'best linear unbiased prediction' to estimate the breeding value of bulls. Intense selection of the best bulls, combined with the worldwide use of these bulls through artificial insemination and frozen semen, has created a global population and caused concern that the genetic variation available in the future will be reduced. Maintenance of genetic variation and long-term genetic gains would be aided by rational payment systems, use of crossbreeding where profitable, inclusion of all economically important traits in the breeding objective, recognition of genotype by environment interactions and the use of selection algorithms that balance estimated breeding value against the average relationship among the selected animals. Fortunately, all of these things are happening to some degree.
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Affiliation(s)
- S Brotherstone
- School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK.
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19
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Nuismer SL, Doebeli M, Browning D. THE COEVOLUTIONARY DYNAMICS OF ANTAGONISTIC INTERACTIONS MEDIATED BY QUANTITATIVE TRAITS WITH EVOLVING VARIANCES. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb00918.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Tanaka Y. Constrained evolution of a quantitative character by pleiotropic mutation. Theor Popul Biol 2005; 68:243-51. [PMID: 16054182 DOI: 10.1016/j.tpb.2005.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Revised: 05/17/2005] [Accepted: 06/03/2005] [Indexed: 10/25/2022]
Abstract
The long-term response to directional selection and its selection limit are derived for a quantitative character that is controlled by pleiotropic mutations with direct deleterious effect on fitness. Directional selection is assumed to be weaker than the selection acting directly on mutations via deleterious effects (purging selection), which renders all mutations to eventual elimination. The analysis embedding this restrictive assumption indicates that the evolutionary response of the character starting from an equilibrium state, in which mutation and purging selection balance but no directional selection is operating, decreases monotonically with time at an exponential rate. And the fading rate of responses is mostly determined by the direct deleterious effect. Contrary to the expectation by the standard selection limit theory based on fixation of extant genetic variation, the present model predicts that the selection limit depends on the intensity of directional selection, the limit being proportional to the ratio of the directional selection intensity to the direct deleterious effect. A slightly larger genetic variance is maintained at the selection limit than would be without directional selection.
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Affiliation(s)
- Y Tanaka
- Faculty of Economics, Chuo University, Higashinakano 742-1, Hachioji, Tokyo 192-0393, Japan.
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21
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Johnson T, Barton N. Theoretical models of selection and mutation on quantitative traits. Philos Trans R Soc Lond B Biol Sci 2005; 360:1411-25. [PMID: 16048784 PMCID: PMC1569515 DOI: 10.1098/rstb.2005.1667] [Citation(s) in RCA: 235] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Empirical studies of quantitative genetic variation have revealed robust patterns that are observed both across traits and across species. However, these patterns have no compelling explanation, and some of the observations even appear to be mutually incompatible. We review and extend a major class of theoretical models, 'mutation-selection models', that have been proposed to explain quantitative genetic variation. We also briefly review an alternative class of 'balancing selection models'. We consider to what extent the models are compatible with the general observations, and argue that a key issue is understanding and modelling pleiotropy. We discuss some of the thorny issues that arise when formulating models that describe many traits simultaneously.
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Affiliation(s)
- Toby Johnson
- Rothamsted Research, Harpenden, Hertfordshire AL5 2FQ, UK.
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22
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Brooks R, Hunt J, Blows MW, Smith MJ, Bussiére LF, Jennions MD. EXPERIMENTAL EVIDENCE FOR MULTIVARIATE STABILIZING SEXUAL SELECTION. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb01760.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Brooks R, Hunt J, Blows MW, Smith MJ, Bussière LF, Jennions MD. EXPERIMENTAL EVIDENCE FOR MULTIVARIATE STABILIZING SEXUAL SELECTION. Evolution 2005. [DOI: 10.1554/04-662] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Nuismer SL, Doebeli M, Browning D. THE COEVOLUTIONARY DYNAMICS OF ANTAGONISTIC INTERACTIONS MEDIATED BY QUANTITATIVE TRAITS WITH EVOLVING VARIANCES. Evolution 2005. [DOI: 10.1554/05-141.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Zhang XS, Wang J, Hill WG. Influence of dominance, leptokurtosis and pleiotropy of deleterious mutations on quantitative genetic variation at mutation-selection balance. Genetics 2004; 166:597-610. [PMID: 15020447 PMCID: PMC1470700 DOI: 10.1534/genetics.166.1.597] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In models of maintenance of genetic variance (V (G)) it has often been assumed that mutant alleles act additively. However, experimental data show that the dominance coefficient varies among mutant alleles and those of large effect tend to be recessive. On the basis of empirical knowledge of mutations, a joint-effect model of pleiotropic and real stabilizing selection that includes dominance is constructed and analyzed. It is shown that dominance can dramatically alter the prediction of equilibrium V (G). Analysis indicates that for the situations where mutations are more recessive for fitness than for a quantitative trait, as supported by the available data, the joint-effect model predicts a significantly higher V (G) than does an additive model. Importantly, for what seem to be realistic distributions of mutational effects (i.e., many mutants may not affect the quantitative trait substantially but are likely to affect fitness), the observed high levels of genetic variation in the quantitative trait under strong apparent stabilizing selection can be generated. This investigation supports the hypothesis that most V (G) comes from the alleles nearly neutral for fitness in heterozygotes while apparent stabilizing selection is contributed mainly by the alleles of large effect on the quantitative trait. Thus considerations of dominance coefficients of mutations lend further support to our previous conclusion that mutation-selection balance is a plausible mechanism of the maintenance of the genetic variance in natural populations.
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Affiliation(s)
- Xu-Sheng Zhang
- Institute of Cell, Animal and Population Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom.
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26
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Abstract
Pleiotropy is one of the most commonly observed attributes of genes. Yet the extent and influence of pleiotropy have been underexplored in population genetics models. In this paper, I quantify the extent to which pleiotropy inhibits the spread of alleles in response to directional selection on a focal trait. Under the assumption that pleiotropic effects are extensive and deleterious, the fraction of alleles that are beneficial overall is severely limited by pleiotropy and rises nearly linearly with the strength of directional selection on the focal trait. Over a broad class of distribution of pleiotropic effects, the mean selective effect of those alleles that are beneficial overall is halved, on average, by pleiotropy. The fraction of new mutant alleles that are beneficial overall and that succeed in fixing within a population is even more severely limited when directional selection is weak, but it rises quadratically with the strength of directional selection. Finally, the mean selective effect of mutant alleles that are beneficial and succeed in fixing is reduced by one-third, on average, by pleiotropy. These results help to shape our understanding of the evolutionary inertia caused by pleiotropy.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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27
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Zhang XS, Hill WG. Multivariate stabilizing selection and pleiotropy in the maintenance of quantitative genetic variation. Evolution 2004; 57:1761-75. [PMID: 14503618 DOI: 10.1111/j.0014-3820.2003.tb00584.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate maintenance of quantitative genetic variation at mutation-selection balance for multiple traits. The intrinsic strength of real stabilizing selection on one of these traits denoted the "target trait" and the observed strength of apparent stabilizing selection on the target trait can be quite different: the latter, which is estimable, is much smaller (i.e., implying stronger selection) than the former. Distinguishing them may enable the mutation load to be relaxed when considering multivariate stabilizing selection. It is shown that both correlations among mutational effects and among strengths of real stabilizing selection on the traits are not important unless they are high. The analysis for independent situations thus provides a good approximation to the case where mutant and stabilizing selection effects are correlated. Multivariate stabilizing selection can be regarded as a combination of stabilizing selection on the target trait and the pleiotropic direct selection on fitness that is solely due to the effects of real stabilizing selection on the hidden traits. As the overall fitness approaches a constant value as the number of traits increases, multivariate stabilizing selection can maintain abundant genetic variance only under quite weak selection. The common observations of high polygenic variance and strong stabilizing selection thus imply that if the mutation-selection balance is the true mechanism of maintenance of genetic variation, the apparent stabilizing selection cannot arise solely by real stabilizing selection simultaneously on many metric traits.
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Affiliation(s)
- Xu-Sheng Zhang
- Institute of Cell, Animal and Population Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
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28
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Blows MW, Brooks R. Measuring Nonlinear Selection. Am Nat 2003; 162:815-20. [PMID: 14737718 DOI: 10.1086/378905] [Citation(s) in RCA: 245] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2003] [Accepted: 06/02/2003] [Indexed: 11/03/2022]
Affiliation(s)
- Mark W Blows
- Department of Zoology and Entomology, University of Queensland, Brisbane 4072, Australia.
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29
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Kelly JK. Deleterious mutations and the genetic variance of male fitness components in Mimulus guttatus. Genetics 2003; 164:1071-85. [PMID: 12871916 PMCID: PMC1462635 DOI: 10.1093/genetics/164.3.1071] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deleterious mutations are relevant to a broad range of questions in genetics and evolutionary biology. I present an application of the "biometric method" for estimating mutational parameters for male fitness characters of the yellow monkeyflower, Mimulus guttatus. The biometric method rests on two critical assumptions. The first is that experimental inbreeding changes genotype frequencies without changing allele frequencies; i.e., there is no genetic purging during the experiment. I satisfy this condition by employing a breeding design in which the parents are randomly extracted, fully homozygous inbred lines. The second is that all genetic variation is attributable to deleterious mutations maintained in mutation-selection balance. I explicitly test this hypothesis using likelihood ratios. Of the three deleterious mutation models tested, the first two are rejected for all characters. The failure of these models is due to an excess of additive genetic variation relative to the expectation under mutation-selection balance. The third model is not rejected for either of two log-transformed male fitness traits. However, this model imposes only "weak conditions" and is not sufficiently detailed to provide estimates for mutational parameters. The implication is that, if biometric methods are going to yield useful parameter estimates, they will need to consider mutational models more complicated than those typically employed in experimental studies.
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Affiliation(s)
- John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA.
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30
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Abstract
Mutation-selection models provide a framework to relate the parameters of microevolution to properties of populations. Like all models, these must be subject to test and refinement in light of experiments. The standard mutation-selection model assumes that the effects of a pleiotropic mutation on different characters are uncorrelated. As a consequence of this assumption, mutations of small overall effect are suppressed. For strong enough pleiotropy, the result is a nonvanishing fraction of a population with the "perfect" phenotype. However, experiments on microorganisms and experiments on protein structure and function contradict the assumptions of the standard model, and Kimura's observations of heterogeneity within populations contradict its conclusions. Guided by these observations, we present an alternative model for pleiotropic mutations. The new model allows mutations of small overall effect and thus eliminates the finite fraction of the population with the perfect phenotype.
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Affiliation(s)
- Ned S Wingreen
- NEC Laboratories America, Princeton, New Jersey 08540, USA.
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31
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Zhang XS, Hill WG. MULTIVARIATE STABILIZING SELECTION AND PLEIOTROPY IN THE MAINTENANCE OF QUANTITATIVE GENETIC VARIATION. Evolution 2003. [DOI: 10.1554/02-587] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Zhang XS, Hill WG. Joint Effects of Pleiotropic Selection and Stabilizing Selection on the Maintenance of Quantitative Genetic Variation at Mutation-Selection Balance. Genetics 2002; 162:459-71. [PMID: 12242254 PMCID: PMC1462254 DOI: 10.1093/genetics/162.1.459] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractIn quantitative genetics, there are two basic “conflicting” observations: abundant polygenic variation and strong stabilizing selection that should rapidly deplete that variation. This conflict, although having attracted much theoretical attention, still stands open. Two classes of model have been proposed: real stabilizing selection directly on the metric trait under study and apparent stabilizing selection caused solely by the deleterious pleiotropic side effects of mutations on fitness. Here these models are combined and the total stabilizing selection observed is assumed to derive simultaneously through these two different mechanisms. Mutations have effects on a metric trait and on fitness, and both effects vary continuously. The genetic variance (VG) and the observed strength of total stabilizing selection (Vs,t) are analyzed with a rare-alleles model. Both kinds of selection reduce VG but their roles in depleting it are not independent: The magnitude of pleiotropic selection depends on real stabilizing selection and such dependence is subject to the shape of the distributions of mutational effects. The genetic variation maintained thus depends on the kurtosis as well as the variance of mutational effects: All else being equal, VG increases with increasing leptokurtosis of mutational effects on fitness, while for a given distribution of mutational effects on fitness, VG decreases with increasing leptokurtosis of mutational effects on the trait. The VG and Vs,t are determined primarily by real stabilizing selection while pleiotropic effects, which can be large, have only a limited impact. This finding provides some promise that a high heritability can be explained under strong total stabilizing selection for what are regarded as typical values of mutation and selection parameters.
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Affiliation(s)
- Xu-Sheng Zhang
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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