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Register a new userIdentifiability of a Markovian model of molecular evolution with Gamma-distributed rates
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Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips of the tree. Rate heterogeneity is present in most real data sets and is accounted for by the use of flexible mixture models where each site is allowed its own rate. Very little has been rigorously established concerning the identifiability of the models currently in common use in data analysis, although non-identifiability was proven for a semi-parametric model and an incorrect proof of identifiability was published for a general parametric model (GTR+Gamma+I). Here we prove that one of the most widely used models (GTR+Gamma) is identifiable for generic parameters, and for all parameter choices in the case of 4-state (DNA) models. This is the first proof of identifiability of a phylogenetic model with a continuous distribution of rates.
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Many areas of agriculture rely on honey bees to provide pollination services and any decline in honey bee numbers can impact on global food security. In order to understand the dynamics of honey bee colonies we present a discrete time marked renewal process model for the size of a colony. We demonstrate that under mild conditions this attains a stationary distribution that depends on the distribution of the numbers of eggs per batch, the probability an egg hatches and the distributions of the times between batches and bee lifetime. This allows an analytic examination of the effect of changing these quantities. We then extend this model to cyclic annual effects where for example the numbers of eggs per batch and {the probability an egg hatches} may vary over the year.
Gaussian process regression (GPR) model is a popular nonparametric regression model. In GPR, features of the regression function such as varying degrees of smoothness and periodicities are modeled through combining various covarinace kernels, which are supposed to model certain effects. The covariance kernels have unknown parameters which are estimated by the EM-algorithm or Markov Chain Monte Carlo. The estimated parameters are keys to the inference of the features of the regression functions, but identifiability of these parameters has not been investigated. In this paper, we prove identifiability of covariance kernel parameters in two radial basis mixed kernel GPR and radial basis and periodic mixed kernel GPR. We also provide some examples about non-identifiable cases in such mixed kernel GPRs.
Much is now known about the consistency of Bayesian updating on infinite-dimensional parameter spaces with independent or Markovian data. Necessary conditions for consistency include the prior putting enough weight on the correct neighborhoods of the data-generating distribution; various sufficient conditions further restrict the prior in ways analogous to capacity control in frequentist nonparametrics. The asymptotics of Bayesian updating with mis-specified models or priors, or non-Markovian data, are far less well explored. Here I establish sufficient conditions for posterior convergence when all hypotheses are wrong, and the data have complex dependencies. The main dynamical assumption is the asymptotic equipartition (Shannon-McMillan-Breiman) property of information theory. This, along with Egorovs Theorem on uniform convergence, lets me build a sieve-like structure for the prior. The main statistical assumption, also a form of capacity control, concerns the compatibility of the prior and the data-generating process, controlling the fluctuations in the log-likelihood when averaged over the sieve-like sets. In addition to posterior convergence, I derive a kind of large deviations principle for the posterior measure, extending in some cases to rates of convergence, and discuss the advantages of predicting using a combination of models known to be wrong. An appendix sketches connections between these results and the replicator dynamics of evolutionary theory.
The bifactor model and its extensions are multidimensional latent variable models, under which each item measures up to one subdimension on top of the primary dimension(s). Despite their wide applications to educational and psychological assessments, this type of multidimensional latent variable models may suffer from non-identifiability, which can further lead to inconsistent parameter estimation and invalid inference. The current work provides a relatively complete characterization of identifiability for the linear and dichotomous bifactor models and the linear extended bifactor model with correlated subdimensions. In addition, similar results for the two-tier models are also developed. Illustrative examples are provided on checking model identifiability through inspecting the factor loading structure. Simulation studies are reported that examine estimation consistency when the identifiability conditions are/are not satisfied.
Background and Aims: Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype x environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional-structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods: The GreenLab model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings of the species-specific parameters of the model. The QTL Cartographer software was used to study QTL detection of simulated plant traits. A genetic algorithm was implemented to define the ideotype for yield maximization based on the model parameters and the associated allelic combination. Key Results and Conclusions: By keeping the environmental factors constant and using a virtual population with a large number of individuals generated by a Mendelian genetic model, results for an ideal case could be simulated. Virtual QTL detection was compared in the case of phenotypic traits - such as cob weight - and when traits were model parameters, and was found to be more accurate in the latter case. The practical interest of this approach is illustrated by calculating the parameters (and the corresponding genotype) associated with yield optimization of a GreenLab maize model. The paper discusses the potentials of GreenLab to represent environment x genotype interactions, in particular through its main state variable, the ratio of biomass supply over demand.
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