相关论文: The coalescent and its descendants
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
We study the effect of biological confounders on the model selection problem between Kingman coalescents with population growth, and Xi-coalescents involving simultaneous multiple mergers. We use a low dimensional, computationally tractable…
Consider a population evolving from year to year through three seasons: spring, summer and winter. Every spring starts with $N$ dormant individuals waking up independently of each other according to a given distribution. Once an individual…
We consider a model of a population of fixed size $N$ undergoing selection. Each individual acquires beneficial mutations at rate $\mu_N$, and each beneficial mutation increases the individual's fitness by $s_N$. Each individual dies at…
We introduce an individual-based model for structured populations undergoing demographic bottlenecks, i.e. drastic reductions in population size that last many generations and can have arbitrary shapes. We first show that the…
Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no…
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…
Most species are structured and influenced by processes that either increased or reduced gene flow between populations. However, most population genetic inference methods ignore population structure and reconstruct a history characterized…
Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past…
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…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
Take a continuous-time Galton-Watson tree. If the system survives until a large time $T$, then choose $k$ particles uniformly from those alive. What does the ancestral tree drawn out by these $k$ particles look like? Some special cases are…
Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…
Evolution occurs in populations of reproducing individuals. The structure of a biological population affects which traits evolve. Understanding evolutionary game dynamics in structured populations is difficult. Precise results have been…
Consider an arbitrary large population at the present time, originated at an unspecified arbitrary large time in the past, where individuals in the same generation reproduce independently, forward in time, with the same offspring…
Consider a population of fixed size that evolves over time. At each time, the genealogical structure of the population can be described by a coalescent tree whose branches are traced back to the most recent common ancestor of the…
The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…
Inference with population genetic data usually treats the population pedigree as a nuisance parameter, the unobserved product of a past history of random mating. However, the history of genetic relationships in a given population is a…
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…
Kingman's coalescent is a random tree that arises from classical population genetic models such as the Moran model. The individuals alive in these models correspond to the leaves in the tree and the following two laws of large numbers…