Full likelihood inference from the site frequency spectrum based on the optimal tree resolution.

We develop a novel importance sampler to compute the full likelihood function of a demographic or structural scenario given the site frequency spectrum (SFS) at a locus free of intra-locus recombination. This sampler, instead of representing the hidden genealogy of a sample of individuals by a labelled binary tree, uses the minimal level of information about such a tree that is needed for the likelihood of the SFS and thus takes advantage of the huge reduction in the size of the state space that needs to be integrated. We assume that the population may have demographically changed and may be non-panmictically structured, as reflected by the branch lengths and the topology of the genealogical tree of the sample, respectively.

A nonlinear dynamical system approach for the yielding behaviour of a viscoplastic material.

A nonlinear dynamical system model that approximates a microscopic Gibbs field model for the yielding of a viscoplastic material subjected to varying external stresses recently reported in R. Sainudiin, M. Moyers-Gonzalez and T.

The transmission process: A combinatorial stochastic process for the evolution of transmission trees over networks.

We derive a combinatorial stochastic process for the evolution of the transmission tree over the infected vertices of a host contact network in a susceptible-infected (SI) model of an epidemic. Models of transmission trees are crucial to understanding the evolution of pathogen populations. We provide an explicit description of the transmission process on the product state space of (rooted planar ranked labelled) binary transmission trees and labelled host contact networks with SI-tags as a discrete-state continuous-time Markov chain.

A Beta-splitting model for evolutionary trees.

In this article, we construct a generalization of the Blum-François Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric shares of diversification rates (or diversification 'potential') between two sister species in an evolutionarily interpretable manner, as well as the addition of extinction to the model in a natural way. We describe the incremental evolutionary construction of a tree with n leaves by splitting or freezing extant lineages through the generating, organizing and deleting processes.

A microscopic Gibbs field model for the macroscopic yielding behaviour of a viscoplastic fluid.

We present a Gibbs random field model for the microscopic interactions in a viscoplastic fluid. The model has only two parameters which are sufficient to describe the internal energy of the material in the absence of external stress and a third parameter for a constant externally applied stress. The energy function is derived from the Gibbs potential in terms of the external stress and internal energy.

Finding the best resolution for the Kingman-Tajima coalescent: theory and applications.

Many summary statistics currently used in population genetics and in phylogenetics depend only on a rather coarse resolution of the underlying tree (the number of extant lineages, for example). Hence, for computational purposes, working directly on these resolutions appears to be much more efficient. However, this approach seems to have been overlooked in the past.

Terrorist attacks escalate in frequency and fatalities preceding highly lethal attacks.

Highly lethal terrorist attacks, which we define as those killing 21 or more people, account for 50% of the total number of people killed in all terrorist attacks combined, yet comprise only 3.5% of terrorist attacks. Given the disproportionate influence of these incidents, uncovering systematic patterns in attacks that precede and anticipate these highly lethal attacks may be of value for understanding attacks that exact a heavy toll on life.

Human-assisted spread of a maladaptive behavior in a critically endangered bird.

Conservation management often focuses on counteracting the adverse effects of human activities on threatened populations. However, conservation measures may unintentionally relax selection by allowing the 'survival of the not-so-fit', increasing the risk of fixation of maladaptive traits. Here, we report such a case in the critically-endangered Chatham Island black robin (Petroica traversi) which, in 1980, was reduced to a single breeding pair.

Experiments with the site frequency spectrum.

Evaluating the likelihood function of parameters in highly-structured population genetic models from extant deoxyribonucleic acid (DNA) sequences is computationally prohibitive. In such cases, one may approximately infer the parameters from summary statistics of the data such as the site-frequency-spectrum (SFS) or its linear combinations. Such methods are known as approximate likelihood or Bayesian computations.

Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces.

Background: In phylogenetic inference one is interested in obtaining samples from the posterior distribution over the tree space on the basis of some observed DNA sequence data. One of the simplest sampling methods is the rejection sampler due to von Neumann. Here we introduce an auto-validating version of the rejection sampler, via interval analysis, to rigorously draw samples from posterior distributions over small phylogenetic tree spaces.

Relative Contribution of Seed-Transmitted Inoculum to Foliar Populations of Phaeosphaeria nodorum.

ABSTRACT A marked-isolate, release-recapture experiment was conducted to assess the relative contributions of seed-transmitted (released isolates) versus all other inocula to foliar and grain populations of Phaeosphaeria nodorum in winter wheat rotated with nonsusceptible crops in New York and Georgia, United States. Seed infected with two distinct groups of marked isolates of P. nodorum containing rare alleles (identified by amplified fragment length polymorphisms [AFLPs]) and balanced for mating type were planted in experimental field plots in two locations in each state.

Simple models of genomic variation in human SNP density.

Background: Descriptive hierarchical Poisson models and population-genetic coalescent mixture models are used to describe the observed variation in single-nucleotide polymorphism (SNP) density from samples of size two across the human genome.

Results: Using empirical estimates of recombination rate across the human genome and the observed SNP density distribution, we produce a maximum likelihood estimate of the genomic heterogeneity in the scaled mutation rate theta. Such models produce significantly better fits to the observed SNP density distribution than those that ignore the empirically observed recombinational heterogeneities.

Identification of physicochemical selective pressure on protein encoding nucleotide sequences.

Background: Statistical methods for identifying positively selected sites in protein coding regions are one of the most commonly used tools in evolutionary bioinformatics. However, they have been limited by not taking the physiochemical properties of amino acids into account.

Results: We develop a new codon-based likelihood model for detecting site-specific selection pressures acting on specific physicochemical properties.

Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system.

Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties under selection. This is accomplished by first partitioning the codons on the basis of some property of the encoded amino acids.

Microsatellite mutation models: insights from a comparison of humans and chimpanzees.

Using genomic data from homologous microsatellite loci of pure AC repeats in humans and chimpanzees, several models of microsatellite evolution are tested and compared using likelihood-ratio tests and the Akaike information criterion. A proportional-rate, linear-biased, one-phase model emerges as the best model. A focal length toward which the mutational and/or substitutional process is linearly biased is a crucial feature of microsatellite evolution.