相关论文: The link between segregation and phylogenetic dive…

We present a model for evolving population which maintains genetic polymorphism. By introducing random mutation in the model population at a constant rate, we observe that the population does not become extinct but survives, keeping…

Scientific studies in many areas of biology routinely employ evolutionary analyses based on the probabilistic inference of phylogenetic trees from molecular sequence data. Evolutionary processes that act at the molecular level are highly…

In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…

In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…

The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rates (speciation rate $\lambda(t)$ and extinction rate…

In this article, we introduce a random (directed) graph model for the simultaneous forwards and backwards description of a rather broad class of Cannings models with a seed bank mechanism. This provides a simple tool to establish a sampling…

The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have…

Using a tensorial approach, we show how to construct a one-one correspondence between pattern probabilities and edge parameters for any group-based model. This is a generalisation of the "Hadamard conjugation" and is equivalent to standard…

Predicting adaptive evolutionary trajectories is a primary goal of evolutionary biology. One can differentiate between forward and backward predictability, where forward predictability measures the likelihood of the same adaptive trajectory…

Our world is ambiguous and this is reflected in the data we use to train our algorithms. This is particularly true when we try to model natural processes where collected data is affected by noisy measurements and differences in measurement…

The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…

We suggest a natural approach that leads to a modification of classical quasispecies models and incorporates the possibility of population extinction in addition to growth. The resulting modified models are called open. Their essential…

Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…

Biogeographical regions (geographically distinct assemblages of species and communities) constitute a cornerstone for ecology, biogeography, evolution and conservation biology. Species turnover measures are often used to quantify…

We construct a pathwise formulation of a growing population of cells, based on two different samplings of lineages within the population, namely the forward and backward samplings. We show that a general symmetry relation, called…

We propose a neural hybrid model consisting of a linear model defined on a set of features computed by a deep, invertible transformation (i.e. a normalizing flow). An attractive property of our model is that both p(features), the density of…

We define a general class of models representing natural selection between two alleles. The population size and spatial structure are arbitrary, but fixed. Genetics can be haploid, diploid, or otherwise; reproduction can be asexual or…

The impact of environmental fluctuation on species diversity is studied with a model of the evolutionary ecology of microorganisms. We show that environmental fluctuation induces evolutionary branching and assures the consequential…

In subdivided populations, migration acts together with selection and genetic drift and determines their evolution. Building up on a recently proposed method, which hinges on the emergence of a time scale separation between local and global…