Related papers: Adaptive preferential sampling in phylodynamics
Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population…
The Ancestral Selection Graph (ASG) is an important genealogical process which extends the well-known Kingman coalescent to incorporate natural selection. We show that the number of lineages of the ASG with and without mutation is…
In the study of natural and artificial complex systems, responses that are not completely determined by the considered decision variables are commonly modelled probabilistically, resulting in response distributions varying across decision…
We consider a stochastic individual-based population model with competition, trait-structure affecting reproduction and survival, and changing environment. The changes of traits are described by jump processes, and the dynamics can be…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…
Multitype branching processes with immigration in one type are used to model the dynamics of stage-structured plant populations. Parametric inference is first carried out when count data of all types are observed. Statistical…
Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species.…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
Severe acute respiratory disease SARS-CoV-2 has had a found impact on public health systems and healthcare emergency response especially with respect to making decisions on the most effective measures to be taken at any given time. As…
We show that each member of a broad class of Markovian population models induces a unique stochastic process on the space of genealogies. We construct this genealogy process and derive exact expressions for the likelihood of an observed…
We consider the problem of inference for the states and parameters of a continuous-time multitype branching process from partially observed time series data. Exact inference for this class of models, typically using sequential Monte Carlo,…
We study coalescent processes conditional on the population pedigree under the exchangeable diploid bi-parental population model of \citet{BirknerEtAl2018}. While classical coalescent models average over all reproductive histories, thereby…
An innovative sampling strategy is proposed, which applies to large-scale population-based surveys targeting a rare trait that is unevenly spread over a geographical area of interest. Our proposal is characterised by the ability to tailor…
In population genetic studies, the allele frequency spectrum (AFS) efficiently summarizes genome-wide polymorphism data and shapes a variety of allele frequency-based summary statistics. While existing theory typically features equilibrium…
Consider a haploid population which has evolved through an exchangeable reproduction dynamics, and in which all individuals alive at time $t$ have a most recent common ancestor (MRCA) who lived at time $A_t$, say. As time goes on, not only…
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 introduce a broad class of spatial models to describe how spatially heterogeneous populations live, die, and reproduce. Individuals are represented by points of a point measure, whose birth and death rates can depend both on spatial…
Consider a graph where the sites are distributed in space according to a Poisson point process on $\mathbb R^n$. We study a population evolving on this network, with individuals jumping between sites with a rate which decreases…
We present a nonparametric framework to model a short sequence of probability distributions that vary both due to underlying effects of sequential progression and confounding noise. To distinguish between these two types of variation and…
We establish convergence to the Kingman coalescent for the genealogy of a geographically - or otherwise - structured version of the Wright-Fisher population model with fast migration. The new feature is that migration probabilities may…