scholarly journals Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population

2015 ◽  
Author(s):  
Benjamin D Redelings ◽  
Seiji Kumagai ◽  
Liuyang Wang ◽  
Andrey Tatarenkov ◽  
Ann K. Sakai ◽  
...  
Keyword(s):  
Mating System ◽  
Dirichlet Process ◽  
Mutation Rates ◽  
Common Mutation ◽  
Dirichlet Process Prior ◽  
Coalescence Model ◽  
Specific Mutation ◽  
Sampling Formula ◽  
Self Fertilization ◽  
Infinite Alleles Model

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens Sampling Formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet Process Prior model. Among the parameters jointly inferred are the population-wide rate of self-fertilization, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual.

scholarly journals Likelihoods and Simulation Methods for a Class of Nonneutral Population Genetics Models

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 853-867 ◽  
Author(s):  
Peter Donnelly ◽  
Magnus Nordborg ◽  
Paul Joyce
Keyword(s):  
Population Genetics ◽  
Population Size ◽  
Mutant Allele ◽  
Mutation Rates ◽  
Simulation Methods ◽  
Large Populations ◽  
Selection Intensities ◽  
Infinite Alleles Model

Abstract Methods for simulating samples and sample statistics, under mutation-selection-drift equilibrium for a class of nonneutral population genetics models, and for evaluating the likelihood surface, in selection and mutation parameters, are developed and applied for observed data. The methods apply to large populations in settings in which selection is weak, in the sense that selection intensities, like mutation rates, are of the order of the inverse of the population size. General diploid selection is allowed, but the approach is currently restricted to models, such as the infinite alleles model and certain K-models, in which the type of a mutant allele does not depend on the type of its progenitor allele. The simulation methods have considerable advantages over available alternatives. No other methods currently seem practicable for approximating likelihood surfaces.

Sex-Specific Mutation Rates in Salmonid Fish

2003 ◽  
Vol 56 (4) ◽  
pp. 458-463 ◽  
Author(s):  
Hans Ellegren ◽  
Anna-Karin Fridolfsson
Keyword(s):  
Salmonid Fish ◽  
Mutation Rates ◽  
Specific Mutation

scholarly journals Mating System and Hybridity in Eucalyptus pauciflora

1977 ◽  
Vol 30 (4) ◽  
pp. 337 ◽  
Author(s):  
MA Phillips ◽  
AHD Brown
Keyword(s):  
Mating System ◽  
Outcrossing Rate ◽  
Seedling Stage ◽  
Average Heterozygosity ◽  
Evolutionary Advantage ◽  
Allozyme Polymorphisms ◽  
Self Fertilization

Allozyme polymorphisms at four loci expressed in seeds, and three other loci expressed in seedlings, were used to determine the outcrossing rate in three natural subalpine populations of snow gum (E. paucijlora). Based on the seed loci data, an estimated 37 % of seed was derived from self-fertilization and 63 % from random outcrossing. In the most elevated population the estimate after germination was similar. However, at lower elevations the frequency of effective self-fertilization estimated at the seedling stage was only 16 %. The less elevated populations also showed a greater average heterozygosity and a larger increase in heterozygosity in the adult over the progeny stages. Heterosis apparently operated differentially in these populations-it was more intense at the lower altitudes. Selection in favour of outcrossed individuals may be an important factor in checking the spread through the population of genes which promote self-fertilization, and which would otherwise enjoy an evolutionary advantage.

scholarly journals Risk, Return and Volatility Feedback: A Bayesian Nonparametric Analysis

2018 ◽  
Vol 11 (3) ◽  
pp. 52 ◽  
Author(s):  
Mark Jensen ◽  
John Maheu
Keyword(s):  
Dirichlet Process ◽  
Joint Distribution ◽  
Nonparametric Model ◽  
Bayesian Nonparametric ◽  
Excess Returns ◽  
Dirichlet Process Prior ◽  
Stock Market Returns ◽  
Conditional Mean ◽  
Risk Return ◽  
Volatility Feedback

In this paper, we let the data speak for itself about the existence of volatility feedback and the often debated risk–return relationship. We do this by modeling the contemporaneous relationship between market excess returns and log-realized variances with a nonparametric, infinitely-ordered, mixture representation of the observables’ joint distribution. Our nonparametric estimator allows for deviation from conditional Gaussianity through non-zero, higher ordered, moments, like asymmetric, fat-tailed behavior, along with smooth, nonlinear, risk–return relationships. We use the parsimonious and relatively uninformative Bayesian Dirichlet process prior to overcoming the problem of having too many unknowns and not enough observations. Applying our Bayesian nonparametric model to more than a century’s worth of monthly US stock market returns and realized variances, we find strong, robust evidence of volatility feedback. Once volatility feedback is accounted for, we find an unambiguous positive, nonlinear, relationship between expected excess returns and expected log-realized variance. In addition to the conditional mean, volatility feedback impacts the entire joint distribution.

scholarly journals Experience rating with Poisson mixtures

2015 ◽  
Vol 9 (2) ◽  
pp. 304-321 ◽  
Author(s):  
Garfield O. Brown ◽  
Winston S. Buckley
Keyword(s):  
Life Insurance ◽  
Dirichlet Process ◽  
Posterior Probability ◽  
Mixture Distribution ◽  
Reversible Jump ◽  
Dirichlet Process Prior ◽  
Poisson Mixtures ◽  
Group Life ◽  
Insurance Portfolio ◽  
Poisson Mixture Model

AbstractWe propose a Poisson mixture model for count data to determine the number of groups in a Group Life insurance portfolio consisting of claim numbers or deaths. We take a non-parametric Bayesian approach to modelling this mixture distribution using a Dirichlet process prior and use reversible jump Markov chain Monte Carlo to estimate the number of components in the mixture. Unlike Haastrup, we show that the assumption of identical heterogeneity for all groups may not hold as 88% of the posterior probability is assigned to models with two or three components, and 11% to models with four or five components, whereas models with one component are never visited. Our major contribution is showing how to account for both model uncertainty and parameter estimation within a single framework.

Floral trait variation and links to climate in the mixed-mating annual Clarkia pulchella

Botany ◽  
2018 ◽  
Vol 96 (7) ◽  
pp. 425-435 ◽  
Author(s):  
Devin E. Gamble ◽  
Megan Bontrager ◽  
Amy L. Angert
Keyword(s):  
Mating System ◽  
Common Garden ◽  
Moisture Stress ◽  
Floral Traits ◽  
Mixed Mating ◽  
Floral Trait ◽  
Local Climate ◽  
Self Fertilization ◽  
Clarkia Pulchella ◽  
Watering Treatment

The benefits of self-fertilization can vary across environments, leading to selection for different reproductive strategies and influencing the evolution of floral traits. Although stressful conditions have been suggested to favour self-pollination, the role of climate as a driver of mating-system variation is generally not well understood. Here, we investigate the contributions of local climate to intraspecific differences in mating-system traits in Clarkia pulchella Pursh in a common-garden growth chamber experiment. We also tested for plastic responses to soil moisture with watering treatments. Herkogamy (anther–stigma spacing) correlated positively with dichogamy (timing of anther–stigma receptivity) and date of first flower, and northern populations had smaller petals and flowered earlier in response to experimental drought. Watering treatment alone had little effect on traits, and dichogamy unexpectedly decreased with annual precipitation. Populations also differed in phenological response to watering treatment, based on precipitation and winter temperature of their origin, indicating that populations from cool and dry sites have greater plasticity under different levels of moisture stress. While some variation in floral traits is attributable to climate, further investigation into variation in pollinator communities and the indirect effects of climate on mating system can improve our understanding of the evolution of plant mating.

A matrix-variate dirichlet process to model earthquake hypocentre temporal patterns

2020 ◽  
pp. 1471082X2093976
Author(s):  
Meredith A. Ray ◽  
Dale Bowman ◽  
Ryan Csontos ◽  
Roy B. Van Arsdale ◽  
Hongmei Zhang
Keyword(s):  
Dirichlet Process ◽  
Temporal Pattern ◽  
Temporal Trends ◽  
Temporal Patterns ◽  
The United States ◽  
Seismic Zone ◽  
Clustering Methods ◽  
Dirichlet Process Prior ◽  
And Performance ◽  
Over Time

Earthquakes are one of the deadliest natural disasters. Our study focuses on detecting temporal patterns of earthquakes occurring along intraplate faults in the New Madrid seismic zone (NMSZ) within the middle of the United States from 1996–2016. Based on the magnitude and location of each earthquake, we developed a Bayesian clustering method to group hypocentres such that each group shared the same temporal pattern of occurrence. We constructed a matrix-variate Dirichlet process prior to describe temporal trends in the space and to detect regions showing similar temporal patterns. Simulations were conducted to assess accuracy and performance of the proposed method and to compare to other commonly used clustering methods such as Kmean, Kmedian and partition-around-medoids. We applied the method to NMSZ data to identify clusters of temporal patterns, which represent areas of stress that are potentially migrating over time. This information can then be used to assist in the prediction of future earthquakes.

scholarly journals Modeling Unobserved Sources of Heterogeneity in Animal Abundance Using a Dirichlet Process Prior

Biometrics ◽  
2008 ◽  
Vol 64 (2) ◽  
pp. 635-644 ◽  
Author(s):  
Robert M. Dorazio ◽  
Bhramar Mukherjee ◽  
Li Zhang ◽  
Malay Ghosh ◽  
Howard L. Jelks ◽  
...  
Keyword(s):  
Dirichlet Process ◽  
Dirichlet Process Prior ◽  
Animal Abundance
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