scholarly journals Directional selection rather than functional constraints can shape the G matrix in rapidly adapting asexuals

2018 ◽  
Author(s):  
Kevin Gomez ◽  
Jason Bertram ◽  
Joanna Masel
Keyword(s):  
Linkage Disequilibrium ◽  
Population Genetic ◽  
Genetic Variance ◽  
Genetic Models ◽  
Relative Fitness ◽  
Functional Constraints ◽  
Selective Sweeps ◽  
Genetic Covariance ◽  
Wave Models ◽  
Genetic Covariances

ABSTRACTGenetic covariances represent a combination of pleiotropy and linkage disequilibrium, shaped by the population’s history. Observed genetic covariance is most often interpreted in pleiotropic terms. In particular, functional constraints restricting which phenotypes are physically possible can lead to a stable G matrix with high genetic variance in fitness-associated traits and high pleiotropic negative covariance along the phenotypic curve of constraint. In contrast, population genetic models of relative fitness assume endless adaptation without constraint, through a series of selective sweeps that are well described by recent traveling wave models. We describe the implications of such population genetic models for the G matrix when pleiotropy is excluded by design, such that all covariance comes from linkage disequilibrium. The G matrix is far less stable than has previously been found, fluctuating over the timescale of selective sweeps. However, its orientation is relatively stable, corresponding to high genetic variance in fitness-associated traits and strong negative covariance - the same pattern often interpreted in terms of pleiotropic constraints but caused instead by linkage disequilibrium. We find that different mechanisms drive the instabilities along versus perpendicular to the fitness gradient. The origin of linkage disequilibrium is not drift, but small amounts of linkage disequilibrium are instead introduced by mutation and then amplified during competing selective sweeps. This illustrates the need to integrate a broader range of population genetic phenomena into quantitative genetics.

scholarly journals Genetic variance in fitness and its cross-sex covariance predict adaptation during experimental evolution

2020 ◽  
Author(s):  
Eva L. Koch ◽  
Sonja H. Sbilordo ◽  
Frédéric Guillaume
Keyword(s):  
Experimental Evolution ◽  
Genetic Variance ◽  
Environmental Changes ◽  
Additive Genetic Variance ◽  
Relative Fitness ◽  
Male Fitness ◽  
Adaptive Potential ◽  
Genetic Covariance ◽  
Flour Beetles ◽  
Single Stress

AbstractIn presence of rapid environmental changes, it is of particular importance to assess the adaptive potential of populations, which is mostly determined by the additive genetic variation (VA) in fitness. In this study we used Tribolium castaneum (red flour beetles) to investigate its adaptive potential in three new environmental conditions (Dry, Hot, Hot-Dry). We tested for potential constraints that might limit adaptation, including negative genetic covariance between female and male fitness. Based on VA estimates for fitness, we expected the highest relative fitness increase in the most stressful condition Hot-Dry and similar increases in single stress conditions Dry and Hot. High adaptive potential in females in Hot was reduced by a negative covariance with male fitness. We tested adaptation to the three conditions after 20 generations of experimental evolution and found that observed adaptation mainly matched our predictions. Given that body size is commonly used as a proxy for fitness, we also tested how this trait and its genetic variance (including non-additive genetic variance) were impacted by environmental stress. In both traits, variances were sex and condition dependent, but they differed in their variance composition, cross-sex and cross-environment genetic covariances, as well as in the environmental impact on VA.

scholarly journals On the unfounded enthusiasm for soft selective sweeps

2014 ◽  
Author(s):  
Jeffrey D. Jensen
Keyword(s):  
Experimental Evidence ◽  
Population Genetic ◽  
Natural Populations ◽  
Genetic Models ◽  
Relative Importance ◽  
Selective Sweeps ◽  
Beneficial Mutations ◽  
Adaptive Process ◽  
Soft Selective Sweeps

Underlying any understanding of the mode, tempo, and relative importance of the adaptive process in the evolution of natural populations is the notion of whether adaptation is mutation-limited. Two very different population genetic models have recently been proposed in which the rate of adaptation is not strongly limited by the rate at which newly arising beneficial mutations enter the population. This review discusses the theoretical underpinnings and requirements of these models, as well as the experimental insights on the parameters of relevance. Importantly, empirical and experimental evidence to date challenges the recent enthusiasm for invoking these models to explain observed patterns of variation in humans and Drosophila.

scholarly journals Linkage Disequilibrium, Gene Trees and Selfing: An Ancestral Recombination Graph With Partial Self-Fertilization

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 923-929 ◽  
Author(s):  
Magnus Nordborg
Keyword(s):  
Linkage Disequilibrium ◽  
Computational Methods ◽  
Population Genetic ◽  
Random Mating ◽  
Genetic Models ◽  
Gene Trees ◽  
Ancestral Recombination Graph ◽  
Self Fertilization ◽  
Simple Change ◽  
Selfing Species

Abstract It is shown that partial self-fertilization can be introduced into neutral population genetic models with recombination as a simple change in the scaling of the parameters. This means that statistical and computational methods that have been developed under the assumption of random mating can be used without modification, provided the appropriate parameter changes are made. An important prediction is that all forms of linkage disequilibrium will be more extensive in selfing species. The implications of this are discussed.

scholarly journals Linkage disequilibrium and genetic variances under mutation-selection balance.

Genetics ◽  
1989 ◽  
Vol 121 (4) ◽  
pp. 857-860 ◽  
Author(s):  
A Hastings
Keyword(s):  
Linkage Disequilibrium ◽  
Mutation Rate ◽  
Genetic Variance ◽  
Harmonic Mean ◽  
Recombination Rates ◽  
Genetic Variances ◽  
Locus Selection

Abstract I determine the contribution of linkage disequilibrium to genetic variances using results for two loci and for induced or marginal systems. The analysis allows epistasis and dominance, but assumes that mutation is weak relative to selection. The linkage disequilibrium component of genetic variance is shown to be unimportant for unlinked loci if the gametic mutation rate divided by the harmonic mean of the pairwise recombination rates is much less than one. For tightly linked loci, linkage disequilibrium is unimportant if the gametic mutation rate divided by the (induced) per locus selection is much less than one.

scholarly journals Selection Response in Finite Populations

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1961-1974 ◽  
Author(s):  
Ming Wei ◽  
Armando Caballero ◽  
William G Hill
Keyword(s):  
Linkage Disequilibrium ◽  
Inbreeding Depression ◽  
Genetic Variance ◽  
Relative Rate ◽  
Selection Response ◽  
Rate Of Change ◽  
Effective Population ◽  
Short Term ◽  
Model Account

Formulae were derived to predict genetic response under various selection schemes assuming an infinitesimal model. Account was taken of genetic drift, gametic (linkage) disequilibrium (Bulmer effect), inbreeding depression, common environmental variance, and both initial segregating variance within families (σAW02) and mutational (σM2) variance. The cumulative response to selection until generation t(CRt) can be approximated asCRt≈R0[t−β(1−σAW∞2σAW02)t24Ne]−Dt2Ne,where Ne is the effective population size, σAW∞2=NeσM2 is the genetic variance within families at the steady state (or one-half the genic variance, which is unaffected by selection), and D is the inbreeding depression per unit of inbreeding. R  0 is the selection response at generation 0 assuming preselection so that the linkage disequilibrium effect has stabilized. β is the derivative of the logarithm of the asymptotic response with respect to the logarithm of the within-family genetic variance, i.e., their relative rate of change. R  0 is the major determinant of the short term selection response, but σM2, Ne and β are also important for the long term. A selection method of high accuracy using family information gives a small Ne and will lead to a larger response in the short term and a smaller response in the long term, utilizing mutation less efficiently.

Effects of Selection at Linked Sites on Patterns of Genetic Variability

2021 ◽  
Vol 52 (1) ◽  
pp. 177-197
Author(s):  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Frequency Distributions ◽  
A Genome ◽  
Demographic Processes ◽  
Dna Sequence Variants ◽  
Genomic Regions ◽  
Functional Components

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

Population Genetic Models

2004 ◽  
Author(s):  
John Buckleton
Keyword(s):  
Population Genetic ◽  
Genetic Models

scholarly journals Linking Dynamical and Population Genetic Models of Persistent Viral Infection

2003 ◽  
Vol 162 (1) ◽  
pp. 14-28 ◽  
Author(s):  
John K. Kelly ◽  
Scott Williamson ◽  
Maria E. Orive ◽  
Marilyn S. Smith ◽  
Robert D. Holt
Keyword(s):  
Viral Infection ◽  
Population Genetic ◽  
Genetic Models ◽  
Persistent Viral Infection

scholarly journals Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences

2008 ◽  
Vol 363 (1512) ◽  
pp. 3931-3939 ◽  
Author(s):  
Sang Chul Choi ◽  
Benjamin D Redelings ◽  
Jeffrey L Thorne
Keyword(s):  
Molecular Evolution ◽  
Markov Model ◽  
Stationary Distribution ◽  
Population Genetic ◽  
Amino Acid Level ◽  
Protein Sequences ◽  
Relative Fitness ◽  
Evolutionary Models ◽  
Effective Population ◽  
Stationary Distributions

Models of molecular evolution tend to be overly simplistic caricatures of biology that are prone to assigning high probabilities to biologically implausible DNA or protein sequences. Here, we explore how to construct time-reversible evolutionary models that yield stationary distributions of sequences that match given target distributions. By adopting comparatively realistic target distributions, evolutionary models can be improved. Instead of focusing on estimating parameters, we concentrate on the population genetic implications of these models. Specifically, we obtain estimates of the product of effective population size and relative fitness difference of alleles. The approach is illustrated with two applications to protein-coding DNA. In the first, a codon-based evolutionary model yields a stationary distribution of sequences, which, when the sequences are translated, matches a variable-length Markov model trained on human proteins. In the second, we introduce an insertion–deletion model that describes selectively neutral evolutionary changes to DNA. We then show how to modify the neutral model so that its stationary distribution at the amino acid level can match a profile hidden Markov model, such as the one associated with the Pfam database.

scholarly journals On the relevance of three genetic models for the description of genetic variance in small populations undergoing selection

1998 ◽  
Vol 30 (1) ◽  
pp. 59 ◽  
Author(s):  
Florence Fournet-Hanocq ◽  
Jean-Michel Elsen
Keyword(s):  
Genetic Variance ◽  
Genetic Models ◽  
Small Populations
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