Selecting Loci for Genetic Stock Identification Using Maximum Likelihood, and the Connection with Curvature Methods

1991 ◽  
Vol 48 (11) ◽  
pp. 2173-2179 ◽  
Author(s):  
R. B. Millar
Keyword(s):  
Maximum Likelihood ◽  
Sample Size ◽  
Likelihood Function ◽  
Genetic Data ◽  
Stock Identification ◽  
Curvature Measure ◽  
Genetic Stock ◽  
Maximum Likelihood Approach ◽  
Genetic Stock Identification ◽  
Likelihood Approach

Maximum likelihood theory is used to predict the precision of genetic stock identification composition estimators — prior to collection of the mixed fishery sample. It is shown how this allows the researcher to plan the genetic stock identification study, through specification of sample size and choice of genetic data to assay, so as to maximize estimator precision. The curvature methodology used in Gomulkiewicz et al. (1990. Can. J. Fish. Aquat. Sci. 47: 611–619) is shown to be closely related to the maximum likelihood approach. In that study, interpretation of results is complicated by the use of an overparametrized curvature measure. Here it is shown that when applied to an appropriately parametrized likelihood function the curvature methodology reproduces the maximum likelihood theory.

Fatigue Limit Measurement of the Cast Steel for Chinese Railway Rolling Wagon Bogie Frames

2010 ◽  
Vol 118-120 ◽  
pp. 121-125 ◽  
Author(s):  
Lian You Yu ◽  
Yong Xiang Zhao
Keyword(s):  
Maximum Likelihood ◽  
Fatigue Limit ◽  
Likelihood Function ◽  
Fatigue Cracks ◽  
Cast Steel ◽  
Small Sample ◽  
Test Method ◽  
Maximum Likelihood Approach ◽  
Study Results ◽  
Likelihood Approach

Fatigue limit measurement is investigated experimentally on the grade B cast steel for Chinese railway freight car bogie frames. Small sample up-and-down test method was employed for the present study. Results reveal that fatigue cracks initiated mostly from the material cast shrinking cavities. Distinct river-like flowers and second cracks appeared on fracture surface in perpendicular to fatigue crack path. Lots of dimples are distributed in transient fracture district to indicate that present material is ductile. Maximum likelihood approach is applied for measuring the probabilistic fatigue limits, in which the limits are defined as the fatigue strengths following normal distribution at an expected fatigue life. Statistical parameters are then estimated by a likelihood function method. A comparison analysis to the existent conventional, Dixon-Mood and Zhang-Kececioglu approaches indicates that the maximum likelihood approach is the approach meeting the definition.

Maximum Likelihood for Genome Phylogeny on Gene Content

2004 ◽  
Vol 3 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Hongmei Zhang ◽  
Xun Gu
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Likelihood Function ◽  
Probability Model ◽  
Real Data ◽  
Mathematical Structure ◽  
Gene Content ◽  
Entire Genome ◽  
Maximum Likelihood Approach ◽  
Likelihood Approach

With the rapid growth of entire genome data, reconstructing the phylogenetic relationship among different genomes has become a hot topic in comparative genomics. Maximum likelihood approach is one of the various approaches, and has been very successful. However, there is no reported study for any applications in the genome tree-making mainly due to the lack of an analytical form of a probability model and/or the complicated calculation burden. In this paper we studied the mathematical structure of the stochastic model of genome evolution, and then developed a simplified likelihood function for observing a specific phylogenetic pattern under four genome situation using gene content information. We use the maximum likelihood approach to identify phylogenetic trees. Simulation results indicate that the proposed method works well and can identify trees with a high correction rate. Real data application provides satisfied results. The approach developed in this paper can serve as the basis for reconstructing phylogenies of more than four genomes.

Ranking Loci for Genetic Stock Identification by Curvature Methods

1990 ◽  
Vol 47 (3) ◽  
pp. 611-619 ◽  
Author(s):  
Richard Gomulkiewicz ◽  
Jon K. T. Brodziak ◽  
Marc Mangel
Keyword(s):  
General Procedure ◽  
Likelihood Estimation ◽  
Likelihood Method ◽  
Stock Identification ◽  
Curvature Measure ◽  
Genetic Stock ◽  
Multiple Loci ◽  
Genetic Stock Identification ◽  
Genotype Frequencies ◽  
Mixture Sampling

Measures of the utility of loci in genetic stock identification problems are usually not based on the method of maximum likelihood, which is the actual statistical procedure used to estimate stock contributions. We present a general procedure, derived from the likelihood method, for assessing the utility of baseline data. The method depends on the curvatures of potential likelihood surfaces and can be used prior to mixture sampling. We also develop a real time implementation of a curvature measure and apply it to simulated mixture samples. The error in likelihood estimation depends on the amount of variation in genotype frequencies between reference samples as well as the location of the center of that variation. The curvature measure accounts appropriately for both factors and, in addition, is able to quantify the synergistic interaction of multiple loci. The curvature approach and simulation results are also applied to the problem of sampling allocation.

Comprehensive microsatellite baseline for genetic stock identification of Atlantic salmon (Salmo salar L.) in northernmost Europe

2017 ◽  
Vol 74 (8) ◽  
pp. 2159-2169 ◽  
Author(s):  
Mikhail Ozerov ◽  
Juha-Pekka Vähä ◽  
Vidar Wennevik ◽  
Eero Niemelä ◽  
Martin-A. Svenning ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Stock Identification ◽  
Genetic Stock ◽  
Atlantic Salmon Salmo Salar ◽  
Genetic Stock Identification
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