Maximum Likelihood Estimation of Recombination Rates From Population Data

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1393-1401 ◽  
Author(s):  
Mary K Kuhner ◽  
Jon Yamato ◽  
Joseph Felsenstein
Keyword(s):  
Population Sample ◽  
Likelihood Estimation ◽  
Population Data ◽  
Molecular Data ◽  
Effective Population ◽  
Recombination Rates ◽  
Wide Range ◽  
Estimate Rate ◽  
Parameter Values ◽  
Neutral Mutation Rate

AbstractWe describe a method for co-estimating r = C/μ (where C is the per-site recombination rate and μ is the per-site neutral mutation rate) and Θ = 4Neμ (where Ne is the effective population size) from a population sample of molecular data. The technique is Metropolis-Hastings sampling: we explore a large number of possible reconstructions of the recombinant genealogy, weighting according to their posterior probability with regard to the data and working values of the parameters. Different relative rates of recombination at different locations can be accommodated if they are known from external evidence, but the algorithm cannot itself estimate rate differences. The estimates of Θ are accurate and apparently unbiased for a wide range of parameter values. However, when both Θ and r are relatively low, very long sequences are needed to estimate r accurately, and the estimates tend to be biased upward. We apply this method to data from the human lipoprotein lipase locus.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

Maximum Likelihood Estimation of Population Growth Rates Based on the Coalescent

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 429-434 ◽  
Author(s):  
Mary K Kuhner ◽  
Jon Yamato ◽  
Joseph Felsenstein
Keyword(s):  
Growth Rate ◽  
Maximum Likelihood ◽  
Maximum Likelihood Estimation ◽  
Population Growth ◽  
Growth Rates ◽  
Population Growth Rate ◽  
Likelihood Estimation ◽  
Effective Population ◽  
Population Growth Rates ◽  
Neutral Mutation Rate

Abstract We describe a method for co-estimating 4Neμ (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling. Population growth (or decline) is assumed to be exponential. The estimates of growth rate are biased upwards, especially when 4Neμ is low; there is also a slight upwards bias in the estimate of 4Neμ itself due to correlation between the parameters. This bias cannot be attributed solely to Metropolis-Hastings sampling but appears to be an inherent property of the estimator and is expected to appear in any approach which estimates growth rate from genealogy structure. Sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus.

scholarly journals Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium

2020 ◽  
Vol 37 (12) ◽  
pp. 3642-3653
Author(s):  
Enrique Santiago ◽  
Irene Novo ◽  
Antonio F Pardiñas ◽  
María Saura ◽  
Jinliang Wang ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Demographic History ◽  
Sequencing Data ◽  
Effective Population ◽  
Recombination Rates ◽  
Animal Populations ◽  
Wide Range ◽  
Demographic Trajectories ◽  
Model Computer ◽  
Conservation Of Endangered Species

Abstract Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.

scholarly journals β-Lactoglobulin Adsorption Layers at the Water/Air Surface: 5. Adsorption Isotherm and Equation of State Revisited, Impact of pH

2021 ◽  
Vol 5 (1) ◽  
pp. 14
Author(s):  
Georgi G. Gochev ◽  
Volodymyr I. Kovalchuk ◽  
Eugene V. Aksenenko ◽  
Valentin B. Fainerman ◽  
Reinhard Miller
Keyword(s):  
Theoretical Description ◽  
Fluid Interfaces ◽  
Interfacial Behavior ◽  
Current State ◽  
Air Interface ◽  
Direct Measurements ◽  
Wide Range ◽  
Dilational Viscoelasticity ◽  
Parameter Values ◽  
Β Lactoglobulin

The theoretical description of the adsorption of proteins at liquid/fluid interfaces suffers from the inapplicability of classical formalisms, which soundly calls for the development of more complicated adsorption models. A Frumkin-type thermodynamic 2-d solution model that accounts for nonidealities of interface enthalpy and entropy was proposed about two decades ago and has been continuously developed in the course of comparisons with experimental data. In a previous paper we investigated the adsorption of the globular protein β-lactoglobulin at the water/air interface and used such a model to analyze the experimental isotherms of the surface pressure, Π(c), and the frequency-, f-, dependent surface dilational viscoelasticity modulus, E(c)f, in a wide range of protein concentrations, c, and at pH 7. However, the best fit between theory and experiment proposed in that paper appeared incompatible with new data on the surface excess, Γ, obtained from direct measurements with neutron reflectometry. Therefore, in this work, the same model is simultaneously applied to a larger set of experimental dependences, e.g., Π(c), Γ(c), E(Π)f, etc., with E-values measured strictly in the linear viscoelasticity regime. Despite this ambitious complication, a best global fit was elaborated using a single set of parameter values, which well describes all experimental dependencies, thus corroborating the validity of the chosen thermodynamic model. Furthermore, we applied the model in the same manner to experimental results obtained at pH 3 and pH 5 in order to explain the well-pronounced effect of pH on the interfacial behavior of β-lactoglobulin. The results revealed that the propensity of β-lactoglobulin globules to unfold upon adsorption and stretch at the interface decreases in the order pH 3 > pH 7 > pH 5, i.e., with decreasing protein net charge. Finally, we discuss advantages and limitations in the current state of the model.

scholarly journals Wolbachia: endosymbiont of onchocercid nematodes and their vectors

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ranju Ravindran Santhakumari Manoj ◽  
Maria Stefania Latrofa ◽  
Sara Epis ◽  
Domenico Otranto
Keyword(s):  
Control Strategies ◽  
Molecular Data ◽  
Scientific Data ◽  
Growth And Survival ◽  
Vector Borne Diseases ◽  
Wide Range ◽  
Veterinary Importance ◽  
Wolbachia Endosymbiont ◽  
Vector Borne ◽  
And Control

Abstract Background Wolbachia is an obligate intracellular maternally transmitted, gram-negative bacterium which forms a spectrum of endosymbiotic relationships from parasitism to obligatory mutualism in a wide range of arthropods and onchocercid nematodes, respectively. In arthropods Wolbachia produces reproductive manipulations such as male killing, feminization, parthenogenesis and cytoplasmic incompatibility for its propagation and provides an additional fitness benefit for the host to protect against pathogens, whilst in onchocercid nematodes, apart from the mutual metabolic dependence, this bacterium is involved in moulting, embryogenesis, growth and survival of the host. Methods This review details the molecular data of Wolbachia and its effect on host biology, immunity, ecology and evolution, reproduction, endosymbiont-based treatment and control strategies exploited for filariasis. Relevant peer-reviewed scientic papers available in various authenticated scientific data bases were considered while writing the review. Conclusions The information presented provides an overview on Wolbachia biology and its use in the control and/or treatment of vectors, onchocercid nematodes and viral diseases of medical and veterinary importance. This offers the development of new approaches for the control of a variety of vector-borne diseases. Graphic Abstract

scholarly journals A New Statistic for Detecting Genetic Differentiation

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 2011-2014 ◽  
Author(s):  
Richard R Hudson
Keyword(s):  
Genetic Differentiation ◽  
Dna Sequences ◽  
Genetic Data ◽  
Island Model ◽  
Wide Range ◽  
Infinite Sites Model ◽  
Parameter Values

Abstract A new statistic for detecting genetic differentiation of subpopulations is described. The statistic can be calculated when genetic data are collected on individuals sampled from two or more localities. It is assumed that haplotypic data are obtained, either in the form of DNA sequences or data on many tightly linked markers. Using a symmetric island model, and assuming an infinite-sites model of mutation, it is found that the new statistic is as powerful or more powerful than previously proposed statistics for a wide range of parameter values.

scholarly journals Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST

2020 ◽  
Vol 70 (1) ◽  
pp. 181-189
Author(s):  
Guy Baele ◽  
Mandev S Gill ◽  
Paul Bastide ◽  
Philippe Lemey ◽  
Marc A Suchard
Keyword(s):  
High Performance ◽  
Markov Models ◽  
Marginal Likelihood ◽  
Likelihood Estimation ◽  
Phylogenetic Inference ◽  
Time Variability ◽  
Substitution Process ◽  
Wide Range ◽  
Markov Modulated ◽  
Over Time

Abstract Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are highly variable, subjecting different sites to different selective constraints over time, impacting their substitution behavior. We propose incorporating time variability through Markov-modulated models (MMMs), which extend covarion-like models and allow the substitution process (including relative character exchange rates as well as the overall substitution rate) at individual sites to vary across lineages. We implement a general MMM framework in BEAST, a popular Bayesian phylogenetic inference software package, allowing researchers to compose a wide range of MMMs through flexible XML specification. Using examples from bacterial, viral, and plastid genome evolution, we show that MMMs impact phylogenetic tree estimation and can substantially improve model fit compared to standard substitution models. Through simulations, we show that marginal likelihood estimation accurately identifies the generative model and does not systematically prefer the more parameter-rich MMMs. To mitigate the increased computational demands associated with MMMs, our implementation exploits recent developments in BEAGLE, a high-performance computational library for phylogenetic inference. [Bayesian inference; BEAGLE; BEAST; covarion, heterotachy; Markov-modulated models; phylogenetics.]

scholarly journals Testing temporal changes in allele frequencies: a simulation approach

2010 ◽  
Vol 92 (4) ◽  
pp. 309-320 ◽  
Author(s):  
EDSON SANDOVAL-CASTELLANOS
Keyword(s):  
Molecular Data ◽  
Temporal Changes ◽  
Allele Frequencies ◽  
Small Populations ◽  
Simulation Approach ◽  
Simulation Test ◽  
Agent Based ◽  
Binomial Sampling ◽  
Molecular Databases ◽  
Parameter Values

SummaryAnalysis of the temporal variation in allele frequencies is useful for studying microevolutionary processes. However, many statistical methods routinely used to test temporal changes in allele frequencies fail to establish a proper hypothesis or have theoretical or practical limitations. Here, a Bayesian statistical test is proposed in which the distribution of the distances among sampling frequencies is approached with computer simulations, and hypergeometric sampling is considered instead of binomial sampling. To validate the test and compare its performance with other tests, agent-based model simulations were run for a variety of scenarios, and two real molecular databases were analysed. The results showed that the simulation test (ST) maintained the significance value used (α=0·05) for a vast combination of parameter values, whereas other tests were sensitive to the effect of genetic drift or binomial sampling. The differences between binomial and hypergeometric sampling were more complex than expected, and a novel effect was described. This study suggests that the ST is especially useful for studies with small populations and many alleles, as in microsatellite or sequencing molecular data.

Motion of slender bodies in unsteady Stokes flow

2011 ◽  
Vol 688 ◽  
pp. 66-87 ◽  
Author(s):  
Efrath Barta
Keyword(s):  
Stokes Flow ◽  
Slenderness Ratio ◽  
Creeping Flow ◽  
Slender Body Theory ◽  
Wide Range ◽  
Unsteady Stokes Flow ◽  
Slender Bodies ◽  
Set Up ◽  
Micro Organisms ◽  
Parameter Values

AbstractThe flow regime in the vicinity of oscillatory slender bodies, either an isolated one or a row of many bodies, immersed in viscous fluid (i.e. under creeping flow conditions) is studied. Applying the slender-body theory by distributing proper singularities on the bodies’ major axes yields reasonably accurate and easily computed solutions. The effect of the oscillations is revealed by comparisons with known Stokes flow solutions and is found to be most significant for motion along the normal direction. Streamline patterns associated with motion of a single body are characterized by formation and evolution of eddies. The motion of adjacent bodies results, with a reduction or an increase of the drag force exerted by each body depending on the direction of motion and the specific geometrical set-up. This dependence is demonstrated by parametric results for frequency of oscillations, number of bodies, their slenderness ratio and the spacing between them. Our method, being valid for a wide range of parameter values and for densely packed arrays of rods, enables simulation of realistic flapping of bristled wings of some tiny insects and of locomotion of flagella and ciliated micro-organisms, and might serve as an efficient tool in the design of minuscule vehicles. Its potency is demonstrated by a solution for the flapping of thrips.

Convective and turbulent motions in non-precipitating Cu. Part 1: Method of separation of convective and turbulent motions

2021 ◽  
Author(s):  
Mark Pinsky ◽  
Eshkol Eytan ◽  
Ilan Koren ◽  
Orit Altaratz ◽  
Alexander Khain
Keyword(s):  
Velocity Field ◽  
Vertical Velocity ◽  
Isotropic Turbulence ◽  
Convective Velocity ◽  
Cloud Dynamics ◽  
Wide Range ◽  
Homogeneous And Isotropic Turbulence ◽  
Microphysical Processes ◽  
Bin Microphysics ◽  
Parameter Values

AbstractAtmospheric motions in clouds and cloud surrounding have a wide range of scales, from several kilometers to centimeters. These motions have different impacts on cloud dynamics and microphysics. Larger-scale motions (hereafter referred to as convective motions) are responsible for mass transport over distances comparable with cloud scale, while motions of smaller scales (hereafter referred to as turbulent motions) are stochastic and responsible for mixing and cloud dilution. This distinction substantially simplifies the analysis of dynamic and microphysical processes in clouds. The present research is Part 1 of the study aimed at describing the method for separating the motion scale into a convective component and a turbulent component. An idealized flow is constructed, which is a sum of an initially prescribed field of the convective velocity with updrafts in the cloud core and downdrafts outside the core, and a stochastic turbulent velocity field obeying the turbulent properties, including the -5/3 law and the 2/3 structure function law. A wavelet method is developed allowing separation of the velocity field into the convective and turbulent components, with parameter values being in a good agreement with those prescribed initially. The efficiency of the method is demonstrated by an example of a vertical velocity field of a cumulus cloud simulated using SAM with bin-microphysics and resolution of 10 m. It is shown that vertical velocity in clouds indeed can be represented as a sum of convective velocity (forming zone of cloud updrafts and subsiding shell) and a stochastic velocity obeying laws of homogeneous and isotropic turbulence.

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