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Uncovering genomic trajectories with heterogeneous genetic and environmental backgrounds across single-cells and populations [article]

Kieran Campbell, Christopher Yau
2017 bioRxiv   pre-print
By applying this model to both single-cell gene expression data and population level cancer studies we show that it uncovers known and novel interaction effects between genetic and enironmental factors  ...  As a solution to this we describe a novel statistical framework that learns pseudotime trajectories in the presence of non-homogeneous genetic, phenotypic, or environmental backgrounds.  ...  We find that 352 the vast majority of the crossover times z * occur towards the end of the trajectory, with a median The condition for the crossover point is that the predicted expression for each phenotype  ... 
doi:10.1101/159913 fatcat:vx26mpad4rfzbakquckuvrdhye

On stability and convergence of the population-dynamics in differential evolution

Sambarta Dasgupta, Swagatam Das, Arijit Biswas, Ajith Abraham
2009 AI Communications  
In this paper we investigate the dynamics of a canonical Differential Evolution (DE) algorithm with DE/rand/1 type mutation and binomial crossover.  ...  itself), with a learning rate parameter that depends on control parameters like scale factor F and crossover rate CR of DE.  ...  Evolution of the population then takes place after the repeated application of the above operators.  ... 
doi:10.3233/aic-2009-0440 fatcat:m5kf67zsk5cgreoytplg3uznai

EOS: a Parallel, Self-Adaptive, Multi-Population Evolutionary Algorithm for Constrained Global Optimization [article]

Lorenzo Federici, Boris Benedikter, Alessandro Zavoli
2020 arXiv   pre-print
method to deal with nonlinear constraints, and a synchronous island-model to handle multiple populations in parallel.  ...  This paper presents the main characteristics of the evolutionary optimization code named EOS, Evolutionary Optimization at Sapienza, and its successful application to challenging, real-world space trajectory  ...  With respect to the previous application, here the constraint handling plays a major role in determining the success or failure of the optimization process.  ... 
arXiv:2007.04681v2 fatcat:7vo3fhpbpzhzjfcr43pgtxvolm

The vitality model: A way to understand population survival and demographic heterogeneity

Ting Li, James J. Anderson
2009 Theoretical Population Biology  
Three temporal scales express the balance of these factors: a time scale of death from senescence, a time scale of accidental mortality and a crossover time between evolving vs. initial heterogeneity.  ...  A four-parameter model describing mortality as the first passage of an abstract measure of survival capacity, vitality, is developed and used to explore four classic problems in demography: (1) medfly  ...  Acknowledgments This work was supported by contract from the Bonneville Power Administration to J. Anderson.  ... 
doi:10.1016/j.tpb.2009.05.004 pmid:19500610 fatcat:bmygj4ro6fcxtp27uz2725uecm

Highly fit ancestors of a partly sexual haploid population

I.M. Rouzine, J.M. Coffin
2007 Theoretical Population Biology  
Evolution of a single site (locus) in a genome, ignoring all others, is readily described mathematically by a model including mutation rate, selective advantage, population size, and other parameters of  ...  We show that, at sufficiently small r, the clones dominating fitness classes, at the moment of their birth, are nearly the best fit in a population.  ...  The work was supported by National Institutes of Health grants K25AI01811 to I.M.R. and R01 CA 089441 to J.M.C.  ... 
doi:10.1016/j.tpb.2006.09.002 pmid:17097121 pmcid:PMC1994660 fatcat:dtsh7jhti5acbkgntqj53lnaly

Rapid adaptation in large populations with very rare sex: Scalings and spontaneous oscillations

Michael T. Pearce, Daniel S. Fisher
2017 Theoretical Population Biology  
Some of the key features may be more broadly applicable for large populations with other types of rare genetic exchange.  ...  The results are potentially applicable to large microbial populations, especially viruses that have a small number of chromosomes.  ...  Natural populations Our model is not directly applicable to any real microbial populations, but it is most natural for the evolution of segmented RNA viruses with genomes divided into a number of segments  ... 
doi:10.1016/j.tpb.2017.11.005 pmid:29246459 fatcat:j5ophiccnnatnldblueyblekey

POPULATION GENETIC PERSPECTIVES ON THE EVOLUTION OF RECOMBINATION

Marcus W. Feldman, Sarah P. Otto, Freddy B. Christiansen
1996 Annual Review of Genetics  
The title of the paper "A genetic model which leads to closer linkage by selection" summarizes his conclusion from this property of his criterion (w) with respect to the rate of recombination R: ∂w/∂ R  ...  When the population is subject to directional selection or to deleterious mutations, increased recombination may be favored under certain conditions, provided that there is negative epistasis among alleles  ...  These studies are consistent with (19) and (4) : directional selection with negative epistasis is a necessary but not sufficient condition for the evolution of increased recombination.  ... 
doi:10.1146/annurev.genet.30.1.261 pmid:8982456 fatcat:j5yyfxw5o5ajhbyqhtavxau3wu

Noise-Induced Stabilization in Population Dynamics

Matthew Parker, Alex Kamenev, Baruch Meerson
2011 Physical Review Letters  
A variety of distinct scaling relations are observed depending on the relative strength of the sub-population noises.  ...  The induced metastable state is vortex-like, and its persistence time grows exponentially with the noise strength.  ...  Having found the conditional probability of y-motion with a given profile of y 2 , we turn now to the xdegree of freedom.  ... 
doi:10.1103/physrevlett.107.180603 pmid:22107619 fatcat:jgsktdyipvdv7p6lf3mge7lrla

Cumulant Dynamics of a Population under Multiplicative Selection, Mutation, and Drift

Magnus Rattray, Jonathan L. Shapiro
2001 Theoretical Population Biology  
Because of the additive nature of cumulants, this reduces to the problem of determining equations of motion for the expected allele distribution cumulants at each locus.  ...  We revisit the classical population genetics model of a population evolving under multiplicative selection, mutation, and drift.  ...  ACKNOWLEDGMENTS We thank Adam Prügel-Bennett and Nick Barton for useful comments on a preliminary version of this paper.  ... 
doi:10.1006/tpbi.2001.1531 pmid:11589636 fatcat:vi74xkzeurdexfkpodekaflau4

Stochastic delocalization of finite populations

Lukas Geyrhofer, Oskar Hallatschek
2013 Journal of Statistical Mechanics: Theory and Experiment  
The typical waiting time to delocalization increases exponentially with both population size and distance to the critical wind speed of the deterministic approximation.  ...  Here, we study the delocalization of a finite population in the presence of number fluctuations. We find that any finite population delocalizes on sufficiently long time scales.  ...  Secondly, one has to determine the mean population density c(x, t) by solving the linear equation (19) , which depends on the previously determined weighting function u * (x).  ... 
doi:10.1088/1742-5468/2013/01/p01007 fatcat:r4yueq7fmzb6ffv7ud55t4bste

Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations [article]

Richard A. Neher, Boris I. Shraiman
2011 arXiv   pre-print
The power law tail in the distribution of the latter makes it impossible to capture the dynamics of draft by an effective neutral model.  ...  Instead, we find that the fixation time of a neutral allele increases only slowly with the population size but depends sensitively on the ratio r/\sigma.  ...  Acknowledgements The authors acknowledge stimulating discussions with Daniel Fisher and Michael Lynch, thank Sally Otto and Nick Barton for a critical reading of the manuscript and thank Jan Albert for  ... 
arXiv:1108.1635v1 fatcat:xsk7nrkgsvbkxpy7b7edykgelu

Convergent evolution to an aptamer observed in small populations on DNA microarrays

W Rowe, M Platt, D C Wedge, P J R Day, D B Kell, J D Knowles
2010 Physical Biology  
Here we use the technique to observe the paths taken through sequence-fitness space by three different evolutionary regimes: asexual reproduction, recombination and model-based evolution.  ...  motif not present in any of the starting populations.  ...  Acknowledgments We acknowledge sponsorship by the Biotechnology and Biological Sciences Research Council PBB/D000203/1.  ... 
doi:10.1088/1478-3975/7/3/036007 pmid:20811084 fatcat:zjx7yjaft5b6piqpxdlvsp762u

Rapid adaptation in large populations with very rare sex: scalings and spontaneous oscillations [article]

Michael T Pearce, Daniel S Fisher
2017 bioRxiv   pre-print
Some of the key features may be more broadly applicable for large populations with other types of rare genetic exchange.  ...  The results are potentially applicable to large microbial populations, especially viruses that have a small number of chromosomes.  ...  Natural populations Our model is not directly applicable to any real microbial populations, but it is most natural for the evolution of segmented RNA viruses with genomes divided into a number of segments  ... 
doi:10.1101/233320 fatcat:3gdpizlzo5hxrh642st7uhtnhe

The Dynamics of Genetic Draft in Rapidly Adapting Populations [article]

Katya Kosheleva, Michael Desai
2013 arXiv   pre-print
We show how this form of draft affects inferences in the McDonald-Kreitman test, and how it relates to recent observations that some aspects of genetic diversity are described by the Bolthausen-Sznitman  ...  evolutionary trajectories.  ...  First, recombination is neglected in this model, which makes our results applicable only to the evolution of microbial populations and tightly linked regions of the genomes of sexually reproducing organisms  ... 
arXiv:1305.7194v1 fatcat:ubo42w7grbaqngreiir642ebny

Cumulant Dynamics of a Population under Multiplicative Selection, Mutation and Drift [article]

Magnus Rattray, Jonathan L. Shapiro
2001 arXiv   pre-print
Because of the additive nature of cumulants, this reduces to the problem of determining equations of motion for the expected allele distribution cumulants at each locus.  ...  We revisit the classical population genetics model of a population evolving under multiplicative selection, mutation and drift.  ...  Acknowledgements We would like to thank Adam Prügel-Bennett and Nick Barton for useful comments on a preliminary version of this paper.  ... 
arXiv:adap-org/9907009v3 fatcat:hhmupfligvaetaaeexzmwacb4e
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