Related papers: Exact phylodynamic likelihood via structured Marko…
We construct a family of genealogy-valued Markov processes that are induced by a continuous-time Markov population process. We derive exact expressions for the likelihood of a given genealogy conditional on the history of the underlying…
We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes…
We introduce a filtration-based framework for studying when and why adding taxa improves phylodynamic inference, by constructing a natural ordering of observed tips and applying sequential Bayesian analysis to the resulting filtration. We…
We define the Sampled Moran Genealogy Process, a continuous-time Markov process on the space of genealogies with the demography of the classical Moran process, sampled through time. To do so, we begin by defining the Moran Genealogy Process…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
Spatial birth-and-death processes with a finite number of particles are obtained as unique solutions to certain stochastic equations. Conditions are given for existence and uniqueness of such solutions, as well as for continuous dependence…
Population structure can have a significant effect on evolution. For some systems with sufficient symmetry, analytic results can be derived within the mathematical framework of evolutionary graph theory which relate to the outcome of the…
We survey results on the description of stochastically evolving genealogies of populations and marked genealogies of multitype populations or spatial populations via tree-valued Markov processes on (marked) ultrametric measure spaces. In…
Representations of population models in terms of countable systems of particles are constructed, in which each particle has a `type', typically recording both spatial position and genetic type, and a level. For finite intensity models, the…
The parameters of many classes of birth-death processes cannot be inferred uniquely from phylogenetic trees: infinitely many parameter combinations yield the same distribution of phylogenetic trees. Here, we show that parameter…
The deterministic selection-recombination equation describes the evolution of the genetic type composition of a population under selection and recombination in a law of large numbers regime. So far, an explicit solution has seemed out of…
We study a density-dependent Markov jump process describing a population where each individual is characterized by a type, and reproduces at rates depending both on its type and on the population type distribution. We are interested in the…
Phylodynamics focuses on the problem of reconstructing past population size dynamics from current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology, but is particularly…
We define a multi-type coalescent point process of a general branching process with finitely many types. This multi-type coalescent fully describes the genealogy of the (quasi-stationary) standing population, providing types along ancestral…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an…
Inference for partially observed Markov process models has been a longstanding methodological challenge with many scientific and engineering applications. Iterated filtering algorithms maximize the likelihood function for partially observed…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…