scholarly journals Competition between continuously evolving lineages in asexual populations

2016 ◽  
Author(s):  
Noah Ribeck ◽  
Joseph S. Mulka ◽  
Luis Zaman ◽  
Brian D. Connelly ◽  
Richard E. Lenski
Keyword(s):  
Large Population ◽  
Current Theory ◽  
Simple Expression ◽  
Critical Threshold ◽  
Beneficial Mutation ◽  
Asexual Population ◽  
Simplifying Assumptions ◽  
Population Sizes ◽  
Asexual Populations

ABSTRACTIn an asexual population, the fate of a beneficial mutation depends on how its lineage competes against other mutant lineages in the population. With high beneficial mutation rates or large population sizes, competition between contending mutations is strong, and successful lineages can accumulate multiple mutations before any single one achieves fixation. Most current theory about asexual population dynamics either neglects this multiple-mutations regime or introduces simplifying assumptions that may not apply. Here, we develop a theoretical framework that describes the dynamics of adaptation and substitution over all mutation-rate regimes by conceptualizing the population as a collection of continuously adapting lineages. This model of “lineage interference” shows that each new mutant’s advantage over the rest of the population must be above a critical threshold in order to likely achieve fixation, and we derive a simple expression for that threshold. We apply this framework to examine the role of beneficial mutations with different effect sizes across the transition to the multiple-mutations regime.

scholarly journals The advance of Muller's ratchet in a haploid asexual population: approximate solutions based on diffusion theory

1993 ◽  
Vol 61 (3) ◽  
pp. 225-231 ◽  
Author(s):  
Wolfgang Stephan ◽  
Lin Chao ◽  
Joanne Guna Smale
Keyword(s):  
Diffusion Theory ◽  
Large Population ◽  
Approximate Solutions ◽  
Diffusion Approximations ◽  
Asexual Population ◽  
Muller's Ratchet ◽  
Expected Time ◽  
Equilibrium Size ◽  
Muller’S Ratchet ◽  
Asexual Populations

SummaryAsexual populations experiencing random genetic drift can accumulate an increasing number of deleterious mutations, a process called Muller's ratchet. We present here diffusion approximations for the rate at which Muller's ratchet advances in asexual haploid populations. The most important parameter of this process is n0 = N e−U/s, where N is population size, U the genomic mutation rate and s the selection coefficient. In a very large population, n0 is the equilibrium size of the mutation-free class. We examined the case n0 > 1 and developed one approximation for intermediate values of N and s and one for large values of N and s. For intermediate values, the expected time at which the ratchet advances increases linearly with n0. For large values, the time increases in a more or less exponential fashion with n0. In addition to n0, s is also an important determinant of the speed of the ratchet. If N and s are intermediate and n0 is fixed, we find that increasing s accelerates the ratchet. In contrast, for a given n0, but large N and s, increasing s slows the ratchet. Except when s is small, results based on our approximations fit well those from computer simulations.

scholarly journals Martingales and fixation probabilities of evolutionary graphs

2014 ◽  
Vol 470 (2165) ◽  
pp. 20130730 ◽  
Author(s):  
T. Monk ◽  
P. Green ◽  
M. Paulin
Keyword(s):  
Graph Theory ◽  
Random Walk ◽  
Large Population ◽  
Initial Population ◽  
Weak Selection ◽  
Simplifying Assumptions ◽  
Population Sizes ◽  
Fixation Probabilities ◽  
Evolutionary Graph Theory ◽  
Complete Bipartite Graphs

Evolutionary graph theory is the study of birth–death processes that are constrained by population structure. A principal problem in evolutionary graph theory is to obtain the probability that some initial population of mutants will fixate on a graph, and to determine how that fixation probability depends on the structure of that graph. A fluctuating mutant population on a graph can be considered as a random walk. Martingales exploit symmetry in the steps of a random walk to yield exact analytical expressions for fixation probabilities. They do not require simplifying assumptions such as large population sizes or weak selection. In this paper, we show how martingales can be used to obtain fixation probabilities for symmetric evolutionary graphs. We obtain simpler expressions for the fixation probabilities of star graphs and complete bipartite graphs than have been previously reported and show that these graphs do not amplify selection for advantageous mutations under all conditions.

scholarly journals Predictions of response to artificial selection from new mutations

1982 ◽  
Vol 40 (3) ◽  
pp. 255-278 ◽  
Author(s):  
William G. Hill
Keyword(s):  
Large Population ◽  
Mutant Gene ◽  
Gene Effects ◽  
Bristle Number ◽  
Large Populations ◽  
Breeding Programmes ◽  
Population Sizes ◽  
The Difference ◽  
Mutant Genes

SUMMARYThe pattern of response expected from fixation of mutant genes for quantitative traits in finite populations is investigated for a range of distributions of mutant gene effects. The eventual rate depends on the total variance of mutant effects per generation, but the initial rate and the variance of response is higher if the distribution of mutant effects has a large standard deviation or is leptokurtic. The difference between initial and eventual rates of response is greater with large population sizes.For a range of assumptions, new mutants are unlikely to have much influence on response for 20 or so generations, but then may contribute substantially, such that no plateaux are obtained. However, information on the variance contributed by mutants is almost entirely on bristle number in Drosophila.It is argued that the role of new mutants should be considered in designing breeding programmes, in particular in utilizing large populations.

scholarly journals Evolutionary contribution to coexistence of competitors in microbial food webs

2017 ◽  
Vol 284 (1864) ◽  
pp. 20170415 ◽  
Author(s):  
Teppo Hiltunen ◽  
Veijo Kaitala ◽  
Jouni Laakso ◽  
Lutz Becks
Keyword(s):  
Time Scales ◽  
Species Interactions ◽  
Species Coexistence ◽  
Large Population ◽  
Rapid Evolution ◽  
Microbial Food Webs ◽  
Generation Times ◽  
Population Sizes ◽  
Over Time

The theory of species coexistence is a key concept in ecology that has received much attention. The role of rapid evolution for determining species coexistence is still poorly understood although evolutionary change on ecological time-scales has the potential to change almost any ecological process. The influence of evolution on coexistence can be especially pronounced in microbial communities where organisms often have large population sizes and short generation times. Previous work on coexistence has assumed that traits involved in resource use and species interactions are constant or change very slowly in terms of ecological time-scales. However, recent work suggests that these traits can evolve rapidly. Nevertheless, the importance of rapid evolution to coexistence has not been tested experimentally. Here, we show how rapid evolution alters the frequency of two bacterial competitors over time when grown together with specialist consumers (bacteriophages), a generalist consumer (protozoan) and all in combination. We find that consumers facilitate coexistence in a manner consistent with classic ecological theory. However, through disentangling the relative contributions of ecology (changes in consumer abundance) and evolution (changes in traits mediating species interactions) on the frequency of the two competitors over time, we find differences between the consumer types and combinations. Overall, our results indicate that the influence of evolution on species coexistence strongly depends on the traits and species interactions considered.

scholarly journals The Effect of Deleterious Alleles on Adaptation in Asexual Populations

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 395-411 ◽  
Author(s):  
Toby Johnson ◽  
Nick H Barton
Keyword(s):  
Selective Sweep ◽  
Deleterious Mutation ◽  
Short Interval ◽  
Selective Advantage ◽  
Asexual Population ◽  
Restrictive Assumption ◽  
Deleterious Alleles ◽  
Fixation Probabilities ◽  
Asexual Populations ◽  
Beneficial Allele

Abstract We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.

scholarly journals Molecular Analysis of Prothrombotic Gene Variants in Patients with Acute Ischemic Stroke and with Transient Ischemic Attack

Medicina ◽  
2021 ◽  
Vol 57 (7) ◽  
pp. 723
Author(s):  
Gustavo Cernera ◽  
Marika Comegna ◽  
Monica Gelzo ◽  
Marcella Savoia ◽  
Dario Bruzzese ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Causes Of Death ◽  
Southern Italy ◽  
Large Population ◽  
Mthfr C677t ◽  
Geographic Area ◽  
Gene Variants ◽  
Interesting Possibility ◽  
Ischemic Attack

Background and objectives: ischemic stroke (IS) is among the most frequent causes of death worldwide; thus, it is of paramount relevance to know predisposing factors that may help to identify and treat the high-risk subjects. Materials and Methods:we tested nine variants in genes involved in thrombotic pathway in 282 patients that experienced IS and 87 that had transient ischemic attacks (TIA) in comparison to 430 subjects from the general population (GP) of the same geographic area (southern Italy). We included cases of young and child IS to evaluate the eventual differences in the role of the analyzed variants. Results: we did not observe significant differences between TIA and the GP for any of the variants, while the allele frequencies of methylene-tetrahydrofolate reductase (MTHFR) C677T, beta-fibrinogen -455G>A and factor (FXIII) V34L were significantly higher in patients with IS than in the subjects from the GP. No significant interaction was observed with sex. Conclusions: the present data argue that some gene variants have a role in IS and this appears to be an interesting possibility to be pursued in large population studies to help design specific strategies for IS prevention.

scholarly journals Accumulation of mutations in sexual and asexual populations

1987 ◽  
Vol 49 (2) ◽  
pp. 135-146 ◽  
Author(s):  
Pekka Pamilo ◽  
Masatoshi Nei ◽  
Wen-Hsiung Li
Keyword(s):  
Weak Selection ◽  
Population Variance ◽  
Asexual Population ◽  
Term Evolution ◽  
A Genome ◽  
Analytical Formulae ◽  
The Mean ◽  
Asexual Populations ◽  
Mutant Genes

SummaryThe accumulation of beneficial and harmful mutations in a genome is studied by using analytical methods as well as computer simulation for different modes of reproduction. The modes of reproduction examined are biparental (bisexual, hermaphroditic), uniparental (selfing, automictic, asexual) and mixed (partial selfing, mixture of hermaphroditism and parthenogenesis). It is shown that the rates of accumulation of both beneficial and harmful mutations with weak selection depend on the within-population variance of the number of mutant genes per genome. Analytical formulae for this variance are derived for neutral mutant genes for hermaphroditic, selfing and asexual populations; the neutral variance is largest in a selfing population and smallest in an asexual population. Directional selection reduces the population variance in most cases, whereas recombination partially restores the reduced variance. Therefore, biparental organisms accumulate beneficial mutations at the highest rate and harmful mutations at the lowest rate. Selfing organisms are intermediate between biparental and asexual organisms. Even a limited amount of outcrossing in largely selfing and parthenogenetic organisms markedly affects the accumulation rates. The accumulation of mutations is likely to affect the mean population fitness only in long-term evolution.

scholarly journals Bub1 mediates cell death in response to chromosome missegregation and acts to suppress spontaneous tumorigenesis

2007 ◽  
Vol 179 (2) ◽  
pp. 255-267 ◽  
Author(s):  
Karthik Jeganathan ◽  
Liviu Malureanu ◽  
Darren J. Baker ◽  
Susan C. Abraham ◽  
Jan M. van Deursen
Keyword(s):  
Cell Death ◽  
Chromosome Segregation ◽  
Physiological Role ◽  
Mitotic Checkpoint ◽  
Critical Threshold ◽  
Wild Type ◽  
Checkpoint Protein ◽  
Chromosome Missegregation ◽  
Mitotic Checkpoint Protein

The physiological role of the mitotic checkpoint protein Bub1 is unknown. To study this role, we generated a series of mutant mice with a gradient of reduced Bub1 expression using wild-type, hypomorphic, and knockout alleles. Bub1 hypomorphic mice are viable, fertile, and overtly normal despite weakened mitotic checkpoint activity and high percentages of aneuploid cells. Bub1 haploinsufficient mice, which have a milder reduction in Bub1 protein than Bub1 hypomorphic mice, also exhibit reduced checkpoint activity and increased aneuploidy, but to a lesser extent. Although cells from Bub1 hypomorphic and haploinsufficient mice have similar rates of chromosome missegregation, cell death after an aberrant separation decreases dramatically with declining Bub1 levels. Importantly, Bub1 hypomorphic mice are highly susceptible to spontaneous tumors, whereas Bub1 haploinsufficient mice are not. These findings demonstrate that loss of Bub1 below a critical threshold drives spontaneous tumorigenesis and suggest that in addition to ensuring proper chromosome segregation, Bub1 is important for mediating cell death when chromosomes missegregate.

scholarly journals Determining asymptotically large population sizes in insect swarms

2014 ◽  
Vol 11 (99) ◽  
pp. 20140710 ◽  
Author(s):  
James G. Puckett ◽  
Nicholas T. Ouellette
Keyword(s):  
Group Dynamics ◽  
Large Population ◽  
Environmental Cues ◽  
Multi Agent Systems ◽  
Strong Constraint ◽  
Agent Systems ◽  
Self Organized ◽  
Large Numbers ◽  
Population Sizes ◽  
Multi Agent

Social animals commonly form aggregates that exhibit emergent collective behaviour, with group dynamics that are distinct from the behaviour of individuals. Simple models can qualitatively reproduce such behaviour, but only with large numbers of individuals. But how rapidly do the collective properties of animal aggregations in nature emerge with group size? Here, we study swarms of Chironomus riparius midges and measure how their statistical properties change as a function of the number of participating individuals. Once the swarms contain order 10 individuals, we find that all statistics saturate and the swarms enter an asymptotic regime. The influence of environmental cues on the swarm morphology decays on a similar scale. Our results provide a strong constraint on how rapidly swarm models must produce collective states. But our findings support the feasibility of using swarms as a design template for multi-agent systems, because self-organized states are possible even with few agents.

scholarly journals The Role of Movement Patterns in Epidemic Models on Complex Networks

2021 ◽  
Vol 83 (10) ◽  
Author(s):  
Alfonso Ruiz-Herrera ◽  
Pedro J. Torres
Keyword(s):  
Complex Networks ◽  
Network Theory ◽  
Diffusion Rate ◽  
Critical Role ◽  
Movement Patterns ◽  
Epidemic Models ◽  
Simplifying Assumptions ◽  
The Common

AbstractIn this paper, we analyze the influence of the usual movement variables on the spread of an epidemic. Specifically, given two spatial topologies, we can deduce which topology produces less infected individuals. In particular, we determine the topology that minimizes the overall number of infected individuals. It is worth noting that we do not assume any of the common simplifying assumptions in network theory such as all the links have the same diffusion rate or the movement of the individuals is symmetric. Our main conclusion is that the degree of mobility of the population plays a critical role in the spread of a disease. Finally, we derive theoretical insights to management of epidemics.

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