scholarly journals Mutation bias can shape adaptation in large asexual populations experiencing clonal interference

2020 ◽  
Vol 287 (1937) ◽  
pp. 20201503
Author(s):  
Kevin Gomez ◽  
Jason Bertram ◽  
Joanna Masel
Keyword(s):  
Population Genetics ◽  
Travelling Wave ◽  
The Other ◽  
Clonal Interference ◽  
Mutation Bias ◽  
Extended Evolutionary Synthesis ◽  
Shape Adaptation ◽  
Sensitivity Ratio ◽  
Wave Models ◽  
Asexual Populations

The extended evolutionary synthesis invokes a role for development in shaping adaptive evolution, which in population genetics terms corresponds to mutation-biased adaptation. Critics have claimed that clonal interference makes mutation-biased adaptation rare. We consider the behaviour of two simultaneously adapting traits, one with larger mutation rate U , the other with larger selection coefficient s , using asexual travelling wave models. We find that adaptation is dominated by whichever trait has the faster rate of adaptation v in isolation, with the other trait subject to evolutionary stalling. Reviewing empirical claims for mutation-biased adaptation, we find that not all occur in the ‘origin-fixation’ regime of population genetics where v is only twice as sensitive to s as to U . In some cases, differences in U are at least ten to twelve times larger than differences in s , as needed to cause mutation-biased adaptation even in the ‘multiple mutations’ regime. Surprisingly, when U > s in the ‘diffusive-mutation’ regime, the required sensitivity ratio is also only two, despite pervasive clonal interference. Given two traits with identical v , the benefit of having higher s is surprisingly small, occurring largely when one trait is at the boundary between the origin-fixation and multiple mutations regimes.

scholarly journals Mutation bias can shape adaptation in large asexual populations experiencing clonal interference

2020 ◽  
Author(s):  
Kevin Gomez ◽  
Jason Bertram ◽  
Joanna Masel
Keyword(s):  
Population Genetics ◽  
The Other ◽  
Selection Coefficient ◽  
Clonal Interference ◽  
Mutation Bias ◽  
Extended Evolutionary Synthesis ◽  
Shape Adaptation ◽  
Sensitivity Ratio ◽  
Wave Models ◽  
Asexual Populations

AbstractThe Extended Evolutionary Synthesis invokes a role for development in shaping adaptive evolution, which in population genetics terms corresponds to mutation-biased adaptation. Critics have claimed that clonal interference makes mutation-biased adaptation rare. We consider the behavior of two simultaneously adapting traits, one with larger mutation rate U, the other with larger selection coefficient s, using asexual traveling wave models. We find that adaptation is dominated by whichever trait has the faster rate of adaptation v in isolation, with the other trait subject to evolutionary stalling. Reviewing empirical claims for mutation-biased adaptation, we find that not all occur in the “origin-fixation” regime of population genetics where v is only twice as sensitive to s as to U. In some cases, differences in U are at least ten to twelve times larger than differences in s, as needed to cause mutation-biased adaptation even in the “multiple mutations” regime. Surprisingly, when U > s in the “diffusive-mutation” regime, the required sensitivity ratio is also only two, despite pervasive clonal interference. Given two traits with identical v, the benefit of having higher s is surprisingly small, occurring largely when one trait is at the boundary between the origin-fixation and multiple mutations regimes.

scholarly journals The Evolution of Isochores: Evidence From SNP Frequency Distributions

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1805-1810 ◽  
Author(s):  
Martin J Lercher ◽  
Nick G C Smith ◽  
Adam Eyre-Walker ◽  
Laurence D Hurst
Keyword(s):  
Population Genetics ◽  
Large Scale ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Compositional Variation ◽  
Mutation Bias ◽  
Single Nucleotide ◽  
Frequency Distributions ◽  
Noncoding Regions ◽  
Standard Population

AbstractThe large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.

scholarly journals Intragenomic variation in mutation biases causes underestimation of selection on synonymous codon usage

2021 ◽  
Author(s):  
Alexander L Cope ◽  
Premal Shah
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mutation Bias ◽  
Biased Gene Conversion ◽  
Intragenomic Variation ◽  
The Impact

Patterns of non-uniform usage of synonymous codons (codon bias) varies across genes in an organism and across species from all domains of life. The bias in codon usage is due to a combination of both non-adaptive (e.g. mutation biases) and adaptive (e.g. natural selection for translation efficiency/accuracy) evolutionary forces. Most population genetics models quantify the effects of mutation bias and selection on shaping codon usage patterns assuming a uniform mutation bias across the genome. However, mutation biases can vary both along and across chromosomes due to processes such as biased gene conversion, potentially obfuscating signals of translational selection. Moreover, estimates of variation in genomic mutation biases are often lacking for non-model organisms. Here, we combine an unsupervised learning method with a population genetics model of synonymous codon bias evolution to assess the impact of intragenomic variation in mutation bias on the strength and direction of natural selection on synonymous codon usage across 49 Saccharomycotina budding yeasts. We find that in the absence of a priori information, unsupervised learning approaches can be used to identify regions evolving under different mutation biases. We find that the impact of intragenomic variation in mutation bias varies widely, even among closely-related species. We show that the overall strength and direction of selection on codon usage can be underestimated by failing to account for intragenomic variation in mutation biases. Interestingly, genes falling into clusters identified by machine learning are also often physically clustered across chromosomes, consistent with processes such as biased gene conversion. Our results indicate the need for more nuanced models of sequence evolution that systematically incorporate the effects of variable mutation biases on codon frequencies.

Biometric and chromosome algebras

1992 ◽  
Vol 29 (02) ◽  
pp. 247-254
Author(s):  
Philip Holgate
Keyword(s):  
Population Genetics ◽  
Quantitative Characteristic ◽  
The Other ◽  
Infinite Dimensional ◽  
Algebra Approach

This note continues the development of the infinite-dimensional genetic algebra approach to problems of population genetics. Two algebras are studied. One describes the familiar problem of a quantitative characteristic, and the other provides a way of treating the whole chromosome as an entity.

scholarly journals Genetic Diversity and Population Genetics of Mosquitoes (Diptera: Culicidae:Culexspp.) from the Sonoran Desert of North America

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Edward Pfeiler ◽  
Carlos A. Flores-López ◽  
Jesús Gerardo Mada-Vélez ◽  
Juan Escalante-Verdugo ◽  
Therese A. Markow
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
North America ◽  
Sonoran Desert ◽  
Phylogenetic Analyses ◽  
Gene Segment ◽  
Population Expansion ◽  
The Other ◽  
Coi Gene ◽  
Unidentified Species

The population genetics and phylogenetic relationships ofCulexmosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochromecoxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding toCx. quinquefasciatus, Cx. tarsalis,and two unidentified species,Culexsp. 1 and sp. 2.Culex quinquefasciatuswas found at all localities and was the most abundant species collected.Culex tarsaliswas collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species ofCulexwere most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower inCx. quinquefasciatuscompared with the other three species. Analysis of molecular variance revealed little structure among seven populations ofCx. quinquefasciatus, whereas significant structure was found between the two populations ofCx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found forCx. tarsalis. Possible explanations for the large differences in genetic diversity betweenCx. quinquefasciatusand the other species ofCulexare presented.

scholarly journals Fierce selection and interference in B-cell repertoire response to chronic HIV-1

2018 ◽  
Author(s):  
Armita Nourmohammad ◽  
Jakub Otwinowski ◽  
Marta Łuksza ◽  
Thierry Mora ◽  
Aleksandra M Walczak
Keyword(s):  
Immune Response ◽  
Population Genetics ◽  
Immune System ◽  
B Cell ◽  
Adaptive Immune System ◽  
Clonal Interference ◽  
Cell Repertoire ◽  
Beneficial Mutations ◽  
Adaptive Immune ◽  
Hiv 1

AbstractDuring chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host’s adaptive immune system. While it is clear that HIV exerts strong selection on the adaptive immune system, the characteristics of the somatic evolution that shape the immune response are still unknown. Traditional population genetics methods fail to distinguish chronic immune response from healthy repertoire evolution. Here, we infer the evolutionary modes of B-cell repertoires and identify complex dynamics with a constant production of better B-cell receptor mutants that compete, maintaining large clonal diversity and potentially slowing down adaptation. A substantial fraction of mutations that rise to high frequencies in pathogen engaging CDRs of B-cell receptors (BCRs) are beneficial, in contrast to many such changes in structurally relevant frameworks that are deleterious and circulate by hitchhiking. We identify a pattern where BCRs in patients who experience larger viral expansions undergo stronger selection with a rapid turnover of beneficial mutations due to clonal interference in their CDR3 regions. Using population genetics modeling, we show that the extinction of these beneficial mutations can be attributed to the rise of competing beneficial alleles and clonal interference. The picture is of a dynamic repertoire, where better clones may be outcompeted by new mutants before they fix.

scholarly journals POPULATION DYNAMICS OF THE SEGREGATION DISTORTER POLYMORPHISM OF DROSOPHILA MELANOGASTER

Genetics ◽  
1978 ◽  
Vol 89 (1) ◽  
pp. 171-192 ◽  
Author(s):  
Brian Charlesworth ◽  
Daniel L Hartl
Keyword(s):  
Population Genetics ◽  
Population Dynamics ◽  
Drosophila Melanogaster ◽  
The Other ◽  
The Core ◽  
Segregation Distorter ◽  
Tight Linkage ◽  
Highly Oscillatory ◽  
Approximate Treatment ◽  
Special Case

ABSTRACT Two two-locus models of the population dynamics of the segregation distortion (SD) polymorphism of Drosophila melanogaster are described. One model is appropriate for understanding the population genetics of SD in nature, whereas the other is a special case appropriate for understanding an artificial population that has been extensively analysed. The models incorporate the general features of the Sd and Rsp loci which form the core of the SD system. It is shown that the SD polymorphism can be established only when there is sufficiently tight linkage between Sd and Rsp. An approximate treatment, valid for tight linkage, is given of all the equilibria of the system and their stabilities. It is shown that the observed composition of natural and artificial populations with respect to the Sd and Rsp loci is predicted well by the model, provided that restrictions are imposed on the fertilities of certain genotypes. Highly oscillatory paths towards equilibrium are usually to be expected on the basis of this model. The selection pressures on inversions introduced into this system are also investigated.

scholarly journals Clonal Interference, Multiple Mutations and Adaptation in Large Asexual Populations

Genetics ◽  
2008 ◽  
Vol 180 (4) ◽  
pp. 2163-2173 ◽  
Author(s):  
Craig A. Fogle ◽  
James L. Nagle ◽  
Michael M. Desai
Keyword(s):  
Clonal Interference ◽  
Asexual Populations

Growth patterns of the ladybird (Harmonia axyridis Pallas) relative to variations in population genetics

1995 ◽  
Vol 16 (1) ◽  
pp. 35-38 ◽  
Author(s):  
R. P. Kuang ◽  
N. N. Xiao
Keyword(s):  
Population Genetics ◽  
Population Growth ◽  
Growth Rates ◽  
Harmonia Axyridis ◽  
Growth Parameters ◽  
Growth Patterns ◽  
The Other ◽  
Ladybird Beetle ◽  
Harmonia Axyridis Pallas

AbstractDifferences in population growth among four variation types of the ladybird beetle, Harmonia axyridis Pallas, namely succinea, conspicua, spectabilis and aulica, were investigated using various growth parameters. The variation types showed three growth patterns from the intrinsic growth rates (rm), with rates of 0.093–0.099 (for conspicua and aulica), 0.073 (for succinea) and 0.040 (for spectabilis). The growth rates of these patterns were realised in different ways. Spectabilis differed from the other three types in the age and per cent distribution of the specific period to the rm values.

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