scholarly journals On Negative Heritability and Negative Estimates of Heritability

2017 ◽  
Author(s):  
David Steinsaltz ◽  
Andy Dahl ◽  
Kenneth W. Wachter
Keyword(s):  
Genetic Variation ◽  
Maximum Likelihood ◽  
Statistical Models ◽  
Biological Process ◽  
Random Noise ◽  
Statistical Procedure ◽  
Maximum Likelihood Estimates ◽  
Physical Feature ◽  
Additive Genetic Variation ◽  
Heritability Estimates

AbstractWe consider the problem of interpreting negative maximum likelihood estimates of heritability that sometimes arise from popular statistical models of additive genetic variation. These may result from random noise acting on estimates of genuinely positive heritability, but we argue that they may also arise from misspecification of the standard additive mechanism that is supposed to justify the statistical procedure. Researchers should be open to the possibility that negative heritability estimates could reflect a real physical feature of the biological process from which the data were sampled.

scholarly journals On Negative Heritability and Negative Estimates of Heritability

Genetics ◽  
2020 ◽  
Vol 215 (2) ◽  
pp. 343-357 ◽  
Author(s):  
David Steinsaltz ◽  
Andy Dahl ◽  
Kenneth W. Wachter
Keyword(s):  
Genetic Variation ◽  
Maximum Likelihood ◽  
Statistical Models ◽  
Biological Process ◽  
Random Noise ◽  
Statistical Procedure ◽  
Maximum Likelihood Estimates ◽  
Physical Feature ◽  
Additive Genetic Variation ◽  
Heritability Estimates

We consider the problem of interpreting negative maximum likelihood estimates of heritability that sometimes arise from popular statistical models of additive genetic variation. These may result from random noise acting on estimates of genuinely positive heritability, but we argue that they may also arise from misspecification of the standard additive mechanism that is supposed to justify the statistical procedure. Researchers should be open to the possibility that negative heritability estimates could reflect a real physical feature of the biological process from which the data were sampled.

scholarly journals SWALO: scaffolding with assembly likelihood optimization

2016 ◽  
Author(s):  
Atif Rahman ◽  
Lior Pachter
Keyword(s):  
Maximum Likelihood ◽  
Genome Assembly ◽  
Statistical Models ◽  
Substantial Improvement ◽  
Generative Models ◽  
Large Datasets ◽  
Maximum Likelihood Estimates ◽  
Link Type ◽  
Genome Assemblies

AbstractScaffolding i.e. ordering and orienting contigs is an important step in genome assembly. We present a method for scaffolding based on likelihoods of genome assemblies. Generative models for sequencing are used to obtain maximum likelihood estimates of gaps between contigs and to estimate whether linking contigs into scaffolds would lead to an increase in the likelihood of the assembly. We then link contigs if they can be unambiguously joined or if the corresponding increase in likelihood is substantially greater than that of other possible joins of those contigs. The method is implemented in a tool called Swalo with approximations to make it efficient and applicable to large datasets. Analysis on real and simulated datasets reveals that it consistently makes more or similar number of correct joins as other scaffolders while linking very few contigs incorrectly, thus outperforming other scaffolders and demonstrating that substantial improvement in genome assembly may be achieved through the use of statistical models. Swalo is freely available for download at https://atifrahman.github.io/SWALO/.

scholarly journals Phenotypic and Genetic Parameter Estimates for Local Guinea Fowl Production and Some Other Traits

2020 ◽  
pp. 1-12
Author(s):  
Addison Doudu ◽  
Serekye Yaw Annor ◽  
James Kwame Kagya-Agyemang ◽  
Godson Aryee Zagbede ◽  
Clement Gyeabour Kyere
Keyword(s):  
Body Weight ◽  
Genetic Variation ◽  
Weight Gain ◽  
Feed Intake ◽  
Guinea Fowl ◽  
Parameter Estimates ◽  
Egg Weight ◽  
Additive Genetic Variation ◽  
High Heritability ◽  
Heritability Estimates

This study on indigenous Guinea fowls in Ghana was undertaken to estimate genetic variation and heritability of traits in these birds. The study was conducted at the Poultry Section of the Animal farm of the Department of Animal Science Education, University of Education, Winneba, Mampong-Ashanti campus, Ghana, from 2015 to 2018. The data used in the present experiment were collected from six hundred keets (300 males and 300 females) produced from randomly selecting and mating 110 dams and 22 sires and consisted of 780 records collected over a period of 3 years. The genetic parameters were estimated using sire-son, sire-daughter and dam-daughter regression analysis.  Body weight and 8-month weight gain showed the greatest additive genetic variation, with survival, docility, dressing percentage, age at first egg, egg weight, egg number, fertility, hatchability traits, feed intake and FCR showing relatively low additive genetic variation.  Moderate to high heritability estimates were obtained for body weight, weight gain at ages 1day to 2 months, 2-4 months in females, 4-6 months in males, docility, feed intake in females and feed conversion ratio in both males and females. Similarly, moderate to high heritability estimates were also obtained for age at first egg, egg weight and egg numbers. However, all other parameters considered in this study had low heritability estimates. This study concludes that, the results could be used to initiate Guinea fowl selection breeding programmes.

scholarly journals Mixtures and products in two graphical models

2018 ◽  
Vol 9 (1) ◽  
pp. 1-20 ◽  
Author(s):  
Anna Seigal ◽  
Guido Montufar
Keyword(s):  
Maximum Likelihood ◽  
Closed Form ◽  
Graphical Models ◽  
Statistical Models ◽  
The Other ◽  
Maximum Likelihood Estimates ◽  
Boltzmann Machine ◽  
Algebraic Description ◽  
Binary Random Variables ◽  
Probability Simplex

We compare two statistical models of three binary random variables. One is a mixture model and the other is a product of mixtures model called a restricted Boltzmann machine. Although the two models we study look different from their parametrizations, we show that they represent the same set of distributions on the interior of the probability simplex, and are equal up to closure. We give a semi-algebraic description of the model in terms of six binomial inequalities and obtain closed form expressions for the maximum likelihood estimates. We briefly discuss extensions to larger models.

scholarly journals Directional Selection and the Site-Frequency Spectrum

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1779-1788 ◽  
Author(s):  
Carlos D Bustamante ◽  
John Wakeley ◽  
Stanley Sawyer ◽  
Daniel L Hartl
Keyword(s):  
Maximum Likelihood ◽  
High Power ◽  
Negative Selection ◽  
Likelihood Estimation ◽  
Directional Selection ◽  
Likelihood Ratio Tests ◽  
Maximum Likelihood Estimates ◽  
Likelihood Methods ◽  
Ancestral States ◽  
Asymptotic Variances

Abstract In this article we explore statistical properties of the maximum-likelihood estimates (MLEs) of the selection and mutation parameters in a Poisson random field population genetics model of directional selection at DNA sites. We derive the asymptotic variances and covariance of the MLEs and explore the power of the likelihood ratio tests (LRT) of neutrality for varying levels of mutation and selection as well as the robustness of the LRT to deviations from the assumption of free recombination among sites. We also discuss the coverage of confidence intervals on the basis of two standard-likelihood methods. We find that the LRT has high power to detect deviations from neutrality and that the maximum-likelihood estimation performs very well when the ancestral states of all mutations in the sample are known. When the ancestral states are not known, the test has high power to detect deviations from neutrality for negative selection but not for positive selection. We also find that the LRT is not robust to deviations from the assumption of independence among sites.

scholarly journals An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1429-1437
Author(s):  
Oliver G Pybus ◽  
Andrew Rambaut ◽  
Paul H Harvey
Keyword(s):  
Maximum Likelihood ◽  
Sequence Data ◽  
Demographic History ◽  
Population History ◽  
Maximum Likelihood Estimates ◽  
Viral Population ◽  
True Parameter ◽  
Subtype B ◽  
Exponential Growth Model ◽  
Parameter Values

Abstract We describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.

scholarly journals Pleiotropy and multilocus polymorphisms.

Genetics ◽  
1992 ◽  
Vol 130 (1) ◽  
pp. 223-227
Author(s):  
A Gimelfarb
Keyword(s):  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Stabilizing Selection ◽  
Additive Genetic Variation ◽  
Very High

Abstract It is demonstrated that systems of two pleiotropically related characters controlled by additive diallelic loci can maintain under Gaussian stabilizing selection a stable polymorphism in more than two loci. It is also shown that such systems may have multiple stable polymorphic equilibria. Stabilizing selection generates negative linkage disequilibrium, as a result of which the equilibrium phenotypic variances are quite low, even though the level of allelic polymorphisms can be very high. Consequently, large amounts of additive genetic variation can be hidden in populations at equilibrium under stabilizing selection on pleiotropically related characters.

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