scholarly journals Efficient Maximum-Likelihood Inference For The Isolation-With-Initial-Migration Model With Potentially Asymmetric Gene Flow

2016 ◽  
Author(s):  
Rui J. Costa ◽  
Hilde Wilkinson-Herbots
Keyword(s):  
Gene Flow ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Computing Time ◽  
Likelihood Method ◽  
Ancestral Population ◽  
Parameter Estimates ◽  
Fast Method ◽  
Data Set ◽  
Im Model

AbstractThe isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, Becquet and Przeworski (2009) report that the parameter estimates obtained by fitting the IM model are very sensitive to the model's assumptions (including the assumption of constant gene flow until the present). This paper is concerned with the isolation-with-initial-migration (IIM) model of Wilkinson-Herbots (2012), which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to obtaining parameter estimates, our method can also be used to distinguish between alternative models representing different evolutionary scenarios, by means of likelihood ratio tests. We illustrate the procedure on pairs of Drosophila sequences from approximately 30,000 loci. The computing time needed to fit the most complex version of the model to this data set is only a couple of minutes. The R code to fit the IIM model can be found in the supplementary files of this paper.

scholarly journals Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure

2020 ◽  
Vol 12 (2) ◽  
pp. 3977-3995 ◽  
Author(s):  
Hillary Koch ◽  
Michael DeGiorgio
Keyword(s):  
Population Structure ◽  
Maximum Likelihood ◽  
Gene Tree ◽  
Species Tree ◽  
Ease Of Use ◽  
Likelihood Method ◽  
Ancestral Population ◽  
Gene Trees ◽  
Species Trees ◽  
Data Set

Abstract Though large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI (Taxa with Ancestral structure Species Tree Inference), that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI’s performance in the three- and four-taxon settings and demonstrate the application of TASTI on a six-species Afrotropical mosquito data set. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community.

scholarly journals New Lindley Half Cauchy Distribution: Theory and Applications

2020 ◽  
Vol 9 (4) ◽  
pp. 1-7
Keyword(s):  
Maximum Likelihood ◽  
Real Data ◽  
Cauchy Distribution ◽  
Least Square ◽  
Cumulative Distribution ◽  
Likelihood Method ◽  
Estimation Methods ◽  
Model Parameters ◽  
Data Set ◽  
Von Mises

In this paper, we have defined a new two-parameter new Lindley half Cauchy (NLHC) distribution using Lindley-G family of distribution which accommodates increasing, decreasing and a variety of monotone failure rates. The statistical properties of the proposed distribution such as probability density function, cumulative distribution function, quantile, the measure of skewness and kurtosis are presented. We have briefly described the three well-known estimation methods namely maximum likelihood estimators (MLE), least-square (LSE) and Cramer-Von-Mises (CVM) methods. All the computations are performed in R software. By using the maximum likelihood method, we have constructed the asymptotic confidence interval for the model parameters. We verify empirically the potentiality of the new distribution in modeling a real data set.

An application of Bayesian techniques to the genetic evaluation of growth traits in Eucalyptus globulus

1998 ◽  
Vol 28 (9) ◽  
pp. 1286-1294 ◽  
Author(s):  
F Soria ◽  
F Basurco ◽  
G Toval ◽  
L Silió ◽  
M C Rodriguez ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Eucalyptus Globulus ◽  
Maximum Likelihood Estimates ◽  
Breeding Value ◽  
Likelihood Method ◽  
Phenotypic Correlation ◽  
Data Set ◽  
Breeding Values ◽  
Bayesian Techniques ◽  
Self Pollination

A Bayesian procedure coupled with Gibbs sampling was implemented to obtain inferences about genetic parameters and breeding values for height and diameter of 7-year-old Eucalyptus globulus Labill. is described. The data set consisted of 21 708 trees from 260 open-pollinated families taken from 10 different Australian provenances, from one Spanish population, and from two clones. The trees are distributed over eight sites in the south of Spain, with 20 blocks per site. Data were corrected for heterogeneity of phenotypic variances between blocks. In the analysis, a self-pollination rate of 30% for the open-pollinated families is assumed in the relationship matrix. The posterior means (and standard deviations) of the heritabilities of height and diameter and the genetic and phenotypic correlation were 0.217 (0.014), 0.128 (0.084), 0.768 (0.028), and 0.799 (0.003). Results from the standard restricted maximum likelihood method were 0.173, 0.113, 0.759, and 0.798, respectively. Most of the discrepancy in heritability estimates from both methods can be attributed to the adjustement of residual maximum likelihood estimates to the assumed self-pollination rate, which ignores the presence of clones in the trial. The effect of the method of prediction of breeding values (best linear unbiased prediction or Bayesian techniques) on the genetic superiority of the selected trees was not important. Differences in breeding value among provenances and among families were evidenced for both traits.

Fitting The Best–Fit Distribution For The Hourly Rainfall Amount In The Wilayah Persekutuan

2012 ◽  
Author(s):  
Fadhilah Y. ◽  
Zalina Md. ◽  
Nguyen V–T–V. ◽  
Suhaila S. ◽  
Zulkifli Y.
Keyword(s):  
Maximum Likelihood ◽  
Goodness Of Fit ◽  
Rainfall Amount ◽  
Likelihood Method ◽  
Exceedance Probability ◽  
Parameter Estimates ◽  
Goodness Of Fit Test ◽  
Hourly Rainfall ◽  
Best Fit ◽  
Mixed Exponential Distribution

Dalam mengenal pasti model yang terbaik untuk mewakili taburan jumlah hujan bagi data selang masa satu jam di 12 stesen di Wilayah Persekutuan empat taburan digunakan iaitu Taburan Eksponen, Gamma, Weibull dan Gabungan Eksponen. Parameter–parameter dianggar menggunakan kaedah kebolehjadian maksimum. Model yang terbaik dipilih berdasarkan nilai minimum yang diperolehi daripada ujian–ujian kebagusan penyuaian yang digunakan dalam kajian ini. Ujian ini dipertahankan lagi dengan plot kebarangkalian dilampaui. Taburan Gabungan Eksponen di dapati paling baik untuk mewakili taburan jumlah hujan dalam selang masa satu jam. Daripada anggaran parameter bagi taburan Gabungan Eksponen ini, boleh diterjemah bahawa jumlah hujan tertinggi yang direkodkan diperolehi daripada hujan yang dikategorikan sebagai hujan lebat, walaupun hujan renyai–renyai berlaku lebih kerap. Kata kunci: Jumlah hujan dalam selang masa sejam, ujian kebagusan penyuaian, kebolehjadian maksimum In determining the best–fit model for the hourly rainfall amounts for the twelve stations in the Wilayah Persekutuan, four distributions namely, the Exponential, Gamma, Weibull and Mixed–Exponential were used. Parameters for each distribution were estimated using the maximum likelihood method. The best–fit model was chosen based upon the minimum error produced by the goodness–offit tests used in this study. The tests were justified further by the exceedance probability plot. The Mixed–Exponential was found to be the most appropriate distribution in describing the hourly rainfall amounts. From the parameter estimates for the Mixed–Exponential distribution, it could be implied that most of the hourly rainfall amount recorded were received from the heavy rainfall even though there was a high occurrences of light rainfall. Key words: Hourly rainfall amount, goodness-of-fit test, exceedance probability, maximum likelihood

ON THE PROPERTIES AND MLEs OF GENERALIZED ODD GENERALIZED EXPONENTIAL- EXPONENTIAL DISTRIBUTION

2021 ◽  
Vol 4 (4) ◽  
pp. 155-165
Author(s):  
Aminu Suleiman Mohammed ◽  
Badamasi Abba ◽  
Abubakar G. Musa
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Maximum Likelihood ◽  
Exponential Distribution ◽  
Estimation Method ◽  
Likelihood Method ◽  
Parameter Estimates ◽  
Lifetime Data ◽  
Failure Rates ◽  
Simulation Experiments

For proper actualization of the phenomenon contained in some lifetime data sets, a generalization, extension or modification of classical distributions is required. In this paper, we introduce a new generalization of exponential distribution, called the generalized odd generalized exponential-exponential distribution. The proposed distribution can model lifetime data with different failure rates, including the increasing, decreasing, unimodal, bathtub, and decreasing-increasing-decreasing failure rates. Various properties of the model such as quantile function, moment, mean deviations, Renyi entropy, and order statistics.  We provide an approximation for the values of the mean, variance, skewness, kurtosis, and mean deviations using Monte Carlo simulation experiments. Estimating of the distribution parameters is performed using the maximum likelihood method, and Monte Carlo simulation experiments is used to assess the estimation method. The method of maximum likelihood is shown to provide a promising parameter estimates, and hence can be adopted in practice for estimating the parameters of the distribution. An application to real and simulated datasets indicated that the new model is superior to the fits than the other compared distributions

Pollen-mediated gene flow in a small, fragmented natural population of Fagus crenata

2007 ◽  
Vol 85 (4) ◽  
pp. 404-413 ◽  
Author(s):  
So Hanaoka ◽  
Jungo Yuzurihara ◽  
Yamashita Asuka ◽  
Nobuhiro Tomaru ◽  
Yoshihiko Tsumura ◽  
...  
Keyword(s):  
Gene Flow ◽  
Maximum Likelihood ◽  
Natural Population ◽  
Maximum Likelihood Method ◽  
Pollen Dispersal ◽  
Fagus Crenata ◽  
Likelihood Method ◽  
Dispersal Patterns ◽  
Breast Height ◽  
Fagus Crenata Blume

Pollen-mediated gene flow was analyzed in a small, fragmented, natural population of Fagus crenata Blume by surveying five microsatellite markers in seedlings derived from open-pollinated crosses. Paternity of 162 seedlings derived from two maternal trees was assigned by the maximum-likelihood method using CERVUS 2.0, and pollen dispersal patterns within the study site were determined. Most of the trees within the site sired seeds, although we found evidence of limited pollen-mediated gene flow from outside the stand; 92% of the matings that generated the seedlings occurred between trees within the population, and 8% of the matings were mediated by pollen derived from trees located outside the study site. Although the pollen-mediated gene flow within the site was not strongly limited, mating frequencies of paternal trees were found to be weakly negatively correlated with their distance from the mother trees, positively correlated with their stem diameter at breast height, and uncorrelated with their relatedness to the mother trees.

scholarly journals A New Kumaraswamy Generalized Family of Distributions with Properties, Applications and Bivariate Extension

2020 ◽  
Author(s):  
Muhammad H. Tahir ◽  
Muhammad Adnan Hussain ◽  
Gauss Cordeiro ◽  
Mahmoud El-Morshedy ◽  
Mohammed S. Eliwa
Keyword(s):  
Maximum Likelihood ◽  
Real Life ◽  
Unit Interval ◽  
Likelihood Method ◽  
Data Sets ◽  
Data Set ◽  
Life Data ◽  
Real Life Data ◽  
The Family ◽  
Family Of Distributions

For bounded unit interval, we propose a new Kumaraswamy generalized (G) family of distributions from a new generator which could be an alternate to the Kumaraswamy-G family proposed earlier by Cordeiro and de-Castro in 2011. This new generator can also be used to develop alternate G-classes such as beta-G, McDonald-G, Topp-Leone-G, Marshall-Olkin-G and Transmuted-G for bounded unit interval. Some mathematical properties of this new family are obtained and maximum likelihood method is used for estimating the family parameters. We investigate the properties of one special model called a new Kumaraswamy-Weibull (NKwW) distribution. Parameter estimation is dealt and maximum likelihood estimators are assessed through simulation study. Two real life data sets are analyzed to illustrate the importance and flexibility of this distribution. In fact, this model outperforms some generalized Weibull models such as the Kumaraswamy-Weibull, McDonald-Weibull, beta-Weibull, exponentiated-generalized Weibull, gamma-Weibull, odd log-logistic-Weibull, Marshall-Olkin-Weibull, transmuted-Weibull, exponentiated-Weibull and Weibull distributions when applied to these data sets. The bivariate extension of the family is proposed and the estimation of parameters is given. The usefulness of the bivariate NKwW model is illustrated empirically by means of a real-life data set.

scholarly journals Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure

2019 ◽  
Author(s):  
Hillary Koch ◽  
Michael DeGiorgio
Keyword(s):  
Population Structure ◽  
Maximum Likelihood ◽  
Gene Tree ◽  
Likelihood Estimation ◽  
Ease Of Use ◽  
Likelihood Method ◽  
Ancestral Population ◽  
Gene Trees ◽  
Species Trees ◽  
Open Source Software Package

AbstractThough large multilocus genomic datasets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI, that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI’s performance in the four-taxon setting, and demonstrate the application of TASTI on a six-species Afrotropical mosquito dataset. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community.

scholarly journals Distribution of gene tree histories under the coalescent model with gene flow

2015 ◽  
Author(s):  
Yuan Tian ◽  
Laura Kubatko
Keyword(s):  
Gene Flow ◽  
Maximum Likelihood ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Topology ◽  
Effective Population ◽  
Sequence Alignments ◽  
Data Set ◽  
Coalescent Model ◽  
Population Sizes

We propose a coalescent model for three species that allows gene flow between both pairs of sister populations. The model is designed to analyze multilocus genomic sequence alignments, with one sequence sampled from each of the three species. The model is formulated using a Markov chain representation, which allows use of matrix exponentiation to compute analytical expressions for the probability density of gene tree genealogies. The gene tree history distribution as well as the gene tree topology distribution under this coalescent model with gene flow are then calculated via numerical integration. We analyze the model to compare the distributions of gene tree topologies and gene tree histories for species trees with differing effective population sizes and gene flow rates. Our results suggest conditions under which the species tree and associated parameters are not identifiable from the gene tree topology distribution when gene flow is present, but indicate that the gene tree history distribution may identify the species tree and associated parameters. Thus, the gene tree history distribution can be used to infer parameters such as the ancestral effective population sizes and the rates of gene flow in a maximum likelihood (ML) framework. We conduct computer simulations to evaluate the performance of our method in estimating these parameters, and we apply our method to an Afrotropical mosquito data set (Fontaine et al., 2015) to demonstrate the usefulness of our method for the analysis of empirical data. Key words: coalescent, gene flow, migration, hybridization, gene tree, topology, history, maximum likelihood, speciation.

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