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 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 Soft selective sweeps in evolutionary rescue

2016 ◽  
Author(s):  
Benjamin A. Wilson ◽  
Pleuni S. Pennings ◽  
Dmitri A. Petrov
Keyword(s):  
Drug Resistance ◽  
Population Genetics ◽  
Population Genetic ◽  
Genetic Adaptation ◽  
Selective Sweeps ◽  
Adaptive Mutations ◽  
Evolutionary Rescue ◽  
Large Populations ◽  
Genetic Signatures ◽  
Soft Selective Sweeps

AbstractEvolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics. While most population genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when evolutionary rescue is likely, it is often driven by soft selective sweeps where multiple adaptive mutations spread through the population simultaneously. We give full analytic results for the probability of evolutionary rescue and the probability that evolutionary rescue occurs via soft selective sweeps in our model. We expect that these results will find utility in understanding the genetic signatures associated with various evolutionary rescue scenarios in large populations, such as the evolution of drug resistance in viral, bacterial, or eukaryotic pathogens.

scholarly journals On the unfounded enthusiasm for soft selective sweeps II: examining recent evidence from humans, flies, and viruses

2018 ◽  
Author(s):  
Rebecca B. Harris ◽  
Andrew Sackman ◽  
Jeffrey D. Jensen
Keyword(s):  
Positive Selection ◽  
Large Scale ◽  
Natural Populations ◽  
Population Data ◽  
Population Level ◽  
Selective Sweeps ◽  
Effective Population ◽  
Initial Description ◽  
Neutral Models ◽  
Soft Selective Sweeps

ABSTRACTSince the initial description of the genomic patterns expected under models of positive selection acting on standing genetic variation and on multiple beneficial mutations—so-called soft selective sweeps—researchers have sought to identify these patterns in natural population data. Indeed, over the past two years, large-scale data analyses have argued that soft sweeps are pervasive across organisms of very different effective population size and mutation rate—humans, Drosophila, and HIV. Yet, others have evaluated the relevance of these models to natural populations, as well as the identifiability of the models relative to other known population-level processes, arguing that soft sweeps are likely to be rare. Here, we look to reconcile these opposing results by carefully evaluating three recent studies and their underlying methodologies. Using population genetic theory, as well as extensive simulation, we find that all three examples are prone to extremely high false-positive rates, incorrectly identifying soft sweeps under both hard sweep and neutral models. Furthermore, we demonstrate that well-fit demographic histories combined with rare hard sweeps serve as the more parsimonious explanation. These findings represent a necessary response to the growing tendency of invoking parameter-heavy, assumption-laden models of pervasive positive selection, and neglecting best practices regarding the construction of proper demographic null models.

scholarly journals SFS_CODE: More Efficient and Flexible Forward Simulations

2015 ◽  
Author(s):  
Ryan D. Hernandez ◽  
Lawrence H. Uricchio
Keyword(s):  
Human Genome ◽  
Open Source Software ◽  
General Public ◽  
Population Genetic ◽  
Genome Structure ◽  
Supplementary Information ◽  
Selective Sweeps ◽  
Complex Models ◽  
Soft Selective Sweeps ◽  
General Public License

SUMMARY: Modern implementations of forward population genetic simulations are efficient and flexible, enabling the exploration of complex models that may otherwise be intractable. Here we describe an updated version of SFS_CODE, which has increased efficiency and includes many novel features. Among these features is an arbitrary model of dominance, the ability to simulate partial and soft selective sweeps, as well as track the trajectories of mutations and/or ancestries across multiple populations under complex models that are not possible under a coalescent framework. We also release sfs_coder, a Python wrapper to SFS_CODE allowing the user to easily generate command lines for common models of demography, selection, and human genome structure, as well as parse and simulate phenotypes from SFS_CODE output. Availability and Implementation: Our open source software is written in C and Python, and are available under the GNU General Public License at http://sfscode.sourceforge.net. Contact: [email protected] Supplementary information: Detailed usage information is available from the project website at http://sfscode.sourceforge.net.

Experimental Evidence for the Rapid Evolution of Behavioral Canalization in Natural Populations

2009 ◽  
Vol 174 (3) ◽  
pp. 434
Author(s):  
Edgell ◽  
Lynch ◽  
Trussell ◽  
Palmer
Keyword(s):  
Experimental Evidence ◽  
Rapid Evolution ◽  
Natural Populations

scholarly journals Evolutionary dynamics of spore killers.

Genetics ◽  
1993 ◽  
Vol 135 (3) ◽  
pp. 923-930 ◽  
Author(s):  
M J Nauta ◽  
R F Hoekstra
Keyword(s):  
Life Cycle ◽  
Segregation Distortion ◽  
Population Genetic ◽  
Field Data ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Additional Advantage ◽  
Genetic Modeling ◽  
Spore Killing ◽  
Ascospore Formation

Abstract Spore killing in ascomycetes is a special form of segregation distortion. When a strain with the Killer genotype is crossed to a Sensitive type, spore killing is expressed by asci with only half the number of ascospores as usual, all surviving ascospores being of the Killer type. Using population genetic modeling, this paper explores conditions for invasion of Spore killers and for polymorphism of Killers, Sensitives and Resistants (which neither kill, nor get killed), as found in natural populations. The models show that a population with only Killers and Sensitives can never be stable. The invasion of Killers and stable polymorphism only occur if Killers have some additional advantage during the process of spore killing. This may be due to the effects of local sib competition or some kind of "heterozygous" advantage in the stage of ascospore formation or in the short diploid stage of the life cycle. This form of segregation distortion appears to be essentially different from other, well-investigated forms, and more field data are needed for a better understanding of spore killing.

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 structure and dispersal of Pinus occidentalis in the Dominican Republic by chloroplastic SSR with implications for its conservation, management, and reforestation

2021 ◽  
Author(s):  
Luis E. Rodríguez de Francisco ◽  
Rosanna Carreras-De León ◽  
Rafael M. Navarro Cerrillo ◽  
Liz A. Paulino-Gervacio ◽  
María-Dolores Rey ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Dominican Republic ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Conservation Management ◽  
Natural Populations ◽  
Limited Information ◽  
High Genetic Diversity ◽  
The Impact ◽  
Pinus Occidentalis

<i>Pinus occidentalis</i> is the dominant species of forest ecosystems in the Dominican Republic, located between 200 and 3000 meters above sea level, with extensive and overexploited natural populations. However, over the years, various restoration plans have been performed, which could affect the genetic structure of <i>P. occidentalis</i>. Despite being the species with the highest occurrence in the Dominican forests, there is no existing information on genetic structure and molecular characterization among natural populations with limited information on both phenological and productive characterization. In this study, the genetic structure, diversity, and gene flow of the five <i>P. occidentalis</i> natural populations of the Dominican Republic were determined using microsatellite markers. A total of 145 individuals were genotyped with eight polymorphic chloroplastic microsatellites, producing an average of 41 haplotypes with high genetic diversity across populations (H<sub>E</sub> = 0.90). Significant population genetic structure was found between populations (F<sub>ST</sub> = 0.123). These results reflect the impact of reforestation programs on natural populations and diluting the natural genetic signature. Analysis of population genetic data is, therefore, crucial for the breeding and conservation programs of <i>P. occidentalis</i> in the country.

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
Sign in / Sign up

Export Citation Format

Share Document