scholarly journals A numerical framework for genetic hitchhiking in populations of variable size

2021 ◽  
Author(s):  
Eric Friedlander ◽  
Matthias Steinruecken
Keyword(s):  
Genetic Variation ◽  
Differential Equations ◽  
Population Size ◽  
Transition Density ◽  
Frequency Spectra ◽  
Genetic Hitchhiking ◽  
Deleterious Alleles ◽  
Diffusion Dynamics ◽  
Neutral Variation ◽  
The Impact

Natural selection on beneficial or deleterious alleles results in an increase or decrease, respectively, of its frequency within the population. Due to chromosomal linkage, the dynamics of the selected site affect the genetic variation at nearby neutral loci in a process commonly referred to as genetic hitchhiking. Changes in population size, however, can yield patterns in genomic data that mimic the effects of selection. Accurately modeling these dynamics is thus crucial to understanding how selection and past population size changes impact observed patterns of genetic variation. Here, we model the evolution of haplotype frequencies with the Wright-Fisher diffusion to study the impact of selection on linked neutral variation. Explicit solutions are not known for the dynamics of this diffusion when selection and recombination act simultaneously. Thus, we present a method for numerically evaluating the Wright-Fisher diffusion dynamics of two linked loci separated by a certain recombination distance when selection is acting. We can account for arbitrary population size histories explicitly using this approach. A key step in the method is to express the moments of the associated transition density, or sampling probabilities, as solutions to ordinary differential equations. Numerically solving these differential equations relies on a novel accurate and numerically efficient technique to estimate higher order moments from lower order moments. We demonstrate how this numerical framework can be used to quantify the reduction and recovery of genetic diversity around a selected locus over time and elucidate distortions in the site-frequency-spectra of neutral variation linked to loci under selection in various demographic settings. The method can be readily extended to more general modes of selection and applied in likelihood frameworks to detect loci under selection and infer the strength of the selective pressure.

scholarly journals Transition densities and sample frequency spectra of diffusion processes with selection and variable population size

2015 ◽  
Author(s):  
Daniel Zivkovic ◽  
Matthias Steinrücken ◽  
Yun S. Song ◽  
Wolfgang Stephan
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Diffusion Processes ◽  
Transition Density ◽  
Effective Population ◽  
Frequency Spectra ◽  
Transition Densities ◽  
Population Sizes ◽  
Sample Frequency ◽  
The Impact

Advances in empirical population genetics have made apparent the need for models that simultaneously account for selection and demography. To address this need, we here study the Wright-Fisher diffusion under selection and variable effective population size. In the case of genic selection and piecewise-constant effective population sizes, we obtain the transition density function by extending a recently developed method for computing an accurate spectral representation for a constant population size. Utilizing this extension, we show how to compute the sample frequency spectrum (SFS) in the presence of genic selection and an arbitrary number of instantaneous changes in the effective population size. We also develop an alternate, efficient algorithm for computing the SFS using a method of moments. We apply these methods to answer the following questions: If neutrality is incorrectly assumed when there is selection, what effects does it have on demographic parameter estimation? Can the impact of negative selection be observed in populations that undergo strong exponential growth?

scholarly journals Effects of linked selective sweeps on demographic inference and model selection

2016 ◽  
Author(s):  
Daniel R. Schrider ◽  
Alexander G. Shanku ◽  
Andrew D. Kern
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Positive Selection ◽  
Population Size ◽  
Natural Populations ◽  
Parameter Estimates ◽  
Selective Sweeps ◽  
Recent Positive Selection ◽  
Demographic Inference ◽  
The Impact

AbstractThe availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of datasets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models—often severely. Moreover, we find that selection can lead to incorrect inferences of population size changes when none have occurred. We argue that the amount of recent positive selection required to skew inferences may often be acting in natural populations. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.

scholarly journals Approximate Analytical Analysis of Unsteady MHD Mixed Flow of Non-Newtonian Hybrid Nanofluid over a Stretching Surface

Fluids ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 138
Author(s):  
Ali Rehman ◽  
Zabidin Salleh
Keyword(s):  
Heat Transfer ◽  
Differential Equations ◽  
Base Fluid ◽  
Research Work ◽  
Hybrid Nanofluid ◽  
Stretching Surface ◽  
Optimal Homotopy Analysis Method ◽  
Analytical Analysis ◽  
Transfer Ratio ◽  
The Impact

This paper analyses the two-dimensional unsteady and incompressible flow of a non-Newtonian hybrid nanofluid over a stretching surface. The nanofluid formulated in the present study is TiO2 + Ag + blood, and TiO2 + blood, where in this combination TiO2 + blood is the base fluid and TiO2 + Ag + blood represents the hybrid nanofluid. The aim of the present research work is to improve the heat transfer ratio because the heat transfer ratio of the hybrid nanofluid is higher than that of the base fluid. The novelty of the recent work is the approximate analytical analysis of the magnetohydrodynamics mixed non-Newtonian hybrid nanofluid over a stretching surface. This type of combination, where TiO2+blood is the base fluid and TiO2 + Ag + blood is the hybrid nanofluid, is studied for the first time in the literature. The fundamental partial differential equations are transformed to a set of nonlinear ordinary differential equations with the guide of some appropriate similarity transformations. The analytical approximate method, namely the optimal homotopy analysis method (OHAM), is used for the approximate analytical solution. The convergence of the OHAM for particular problems is also discussed. The impact of the magnetic parameter, dynamic viscosity parameter, stretching surface parameter and Prandtl number is interpreted through graphs. The skin friction coefficient and Nusselt number are explained in table form. The present work is found to be in very good agreement with those published earlier.

Influence of rotating magnetic field on Maxwell saturated ferrofluid flow over a heated stretching sheet with heat generation/absorption

2019 ◽  
Vol 20 (5) ◽  
pp. 502 ◽  
Author(s):  
Aaqib Majeed ◽  
Ahmed Zeeshan ◽  
Farzan Majeed Noori ◽  
Usman Masud
Keyword(s):  
Magnetic Field ◽  
Temperature Field ◽  
Velocity Field ◽  
Differential Equations ◽  
Heat Transport ◽  
Viscous Dissipation ◽  
Heat Generation ◽  
Fluid Motion ◽  
Numerical Procedure ◽  
The Impact

This article is focused on Maxwell ferromagnetic fluid and heat transport characteristics under the impact of magnetic field generated due to dipole field. The viscous dissipation and heat generation/absorption are also taken into account. Flow here is instigated by linearly stretchable surface, which is assumed to be permeable. Also description of magneto-thermo-mechanical (ferrohydrodynamic) interaction elaborates the fluid motion as compared to hydrodynamic case. Problem is modeled using continuity, momentum and heat transport equation. To implement the numerical procedure, firstly we transform the partial differential equations (PDEs) into ordinary differential equations (ODEs) by applying similarity approach, secondly resulting boundary value problem (BVP) is transformed into an initial value problem (IVP). Then resulting set of non-linear differentials equations is solved computationally with the aid of Runge–Kutta scheme with shooting algorithm using MATLAB. The flow situation is carried out by considering the influence of pertinent parameters namely ferro-hydrodynamic interaction parameter, Maxwell parameter, suction/injection and viscous dissipation on flow velocity field, temperature field, friction factor and heat transfer rate are deliberated via graphs. The present numerical values are associated with those available previously in the open literature for Newtonian fluid case (γ 1 = 0) to check the validity of the solution. It is inferred that interaction of magneto-thermo-mechanical is to slow down the fluid motion. We also witnessed that by considering the Maxwell and ferrohydrodynamic parameter there is decrement in velocity field whereas opposite behavior is noted for temperature field.

The impact of founder events and introductions on genetic variation in the muskox Ovibos moschatus in Sweden

2011 ◽  
Vol 56 (4) ◽  
pp. 305-314 ◽  
Author(s):  
Carl-Gustaf Thulin ◽  
Linda Englund ◽  
Göran Ericsson ◽  
Göran Spong
Keyword(s):  
Genetic Variation ◽  
Ovibos Moschatus ◽  
Founder Events ◽  
The Impact

scholarly journals How general are positive relationships between plant population size, fitness and genetic variation?

2006 ◽  
Vol 94 (5) ◽  
pp. 942-952 ◽  
Author(s):  
ROOSA LEIMU ◽  
PIA MUTIKAINEN ◽  
JULIA KORICHEVA ◽  
MARKUS FISCHER
Keyword(s):  
Genetic Variation ◽  
Population Size ◽  
Plant Population ◽  
Positive Relationships ◽  
Plant Population Size

scholarly journals Detecting a Local Signature of Genetic Hitchhiking Along a Recombining Chromosome

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 765-777 ◽  
Author(s):  
Yuseob Kim ◽  
Wolfgang Stephan
Keyword(s):  
Genetic Variation ◽  
Dna Polymorphism ◽  
Nucleotide Diversity ◽  
Sequence Data ◽  
Directional Selection ◽  
Genetic Hitchhiking ◽  
Dna Sequence Data ◽  
Local Reduction ◽  
Polymorphism Data ◽  
Ancestral Recombination Graphs

Abstract The theory of genetic hitchhiking predicts that the level of genetic variation is greatly reduced at the site of strong directional selection and increases as the recombinational distance from the site of selection increases. This characteristic pattern can be used to detect recent directional selection on the basis of DNA polymorphism data. However, the large variance of nucleotide diversity in samples of moderate size imposes difficulties in detecting such patterns. We investigated the patterns of genetic variation along a recombining chromosome by constructing ancestral recombination graphs that are modified to incorporate the effect of genetic hitchhiking. A statistical method is proposed to test the significance of a local reduction of variation and a skew of the frequency spectrum caused by a hitchhiking event. This method also allows us to estimate the strength and the location of directional selection from DNA sequence data.

scholarly journals Numerical Simulation of Heat Mass Transfer Effects on MHD Flow of Williamson Nanofluid by a Stretching Surface with Thermal Conductivity and Variable Thickness

Coatings ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 684
Author(s):  
Saeed Islam ◽  
Haroon Ur Rasheed ◽  
Kottakkaran Sooppy Nisar ◽  
Nawal A. Alshehri ◽  
Mohammed Zakarya
Keyword(s):  
Thermal Conductivity ◽  
Boundary Layer ◽  
Mass Transfer ◽  
Differential Equations ◽  
Variable Thickness ◽  
Heat Mass Transfer ◽  
Mathematical Formulation ◽  
Stretching Surface ◽  
Nanofluid Flow ◽  
The Impact

The current analysis deals with radiative aspects of magnetohydrodynamic boundary layer flow with heat mass transfer features on electrically conductive Williamson nanofluid by a stretching surface. The impact of variable thickness and thermal conductivity characteristics in view of melting heat flow are examined. The mathematical formulation of Williamson nanofluid flow is based on boundary layer theory pioneered by Prandtl. The boundary layer nanofluid flow idea yields a constitutive flow laws of partial differential equations (PDEs) are made dimensionless and then reduce to ordinary nonlinear differential equations (ODEs) versus transformation technique. A built-in numerical algorithm bvp4c in Mathematica software is employed for nonlinear systems computation. Considerable features of dimensionless parameters are reviewed via graphical description. A comparison with another homotopic approach (HAM) as a limiting case and an excellent agreement perceived.

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