Related papers: Selection and Coalescence in a Finite State Model
Kingman derived the Ewens sampling formula for random partitions from the genealogy model defined by a Poisson process of mutations along lines of descent governed by a simple coalescent process. M\"ohle described the recursion which…
Few problems in statistics are as perplexing as variable selection in the presence of very many redundant covariates. The variable selection problem is most familiar in parametric environments such as the linear model or additive variants…
We consider a family of models describing the evolution under selection of a population whose dynamics can be related to the propagation of noisy traveling waves. For one particular model, that we shall call the exponential model, the…
We propose Partition Tree, a novel tree-based framework for conditional density estimation over general outcome spaces that supports both continuous and categorical variables within a unified formulation. Our approach models conditional…
In mathematical population genetics, it is well known that one can represent the genealogy of a population by a tree, which indicates how the ancestral lines of individuals in the population coalesce as they are traced back in time. As the…
Kingman derived the Ewens sampling formula for random partitions describing the genetic variation in a neutral mutation model defined by a Poisson process of mutations along lines of descent governed by a simple coalescent process, and…
This paper introduces the Partition Tree Weighting technique, an efficient meta-algorithm for piecewise stationary sources. The technique works by performing Bayesian model averaging over a large class of possible partitions of the data…
Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…
Understanding why we age is a long-lived open problem in evolutionary biology. Aging is prejudicial to the individual and evolutionary forces should prevent it, but many species show signs of senescence as individuals age. Here, I will…
The constant rate birth--death process is a popular null model for speciation and extinction. If one removes extinct and non-sampled lineages, this process induces `reconstructed trees' which describe the relationship between extant…
Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, suggesting a possible role in…
The recent realization that entire communities fuse and separate (community coalescence) has led to a reappraisal of the forces determining species diversity and dynamics, especially in microbial communities where coalescence is likely…
Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
The investigation of correlations in Monte Carlo power iteration has been long dominated by the question of generational correlations and their effects on the estimation of statistical uncertainties. More recently, there has been a growing…
Sweepstakes reproduction refers to a highly skewed individual recruitment success without involving natural selection and may apply to individuals in broadcast spawning populations characterised by Type III survivorship. We consider an…
Random forests have long been considered as powerful model ensembles in machine learning. By training multiple decision trees, whose diversity is fostered through data and feature subsampling, the resulting random forest can lead to more…
An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
We consider a fitness-structured population model with competition and migration between nearest neighbors. Under a combination of large population and rare migration limits we are particularly interested in the asymptotic behavior of the…