Related papers: A Quantitative Test of Population Genetics Using S…

Many imaging techniques for biological systems -- like fixation of cells coupled with fluorescence microscopy -- provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics…

Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…

This survey focuses on the most important aspects of the mathematical theory of population genetic models of selection and migration between discrete niches. Such models are most appropriate if the dispersal distance is short compared to…

We study a one-dimensional spatial population model where the population sizes at each site are chosen according to a translation invariant and ergodic distribution and are uniformly bounded away from 0 and infinity. We suppose that the…

We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…

We model an enclosed system of bacteria, whose motility-induced phase separation is coupled to slow population dynamics. Without noise, the system shows both static phase separation and a limit cycle, in which a rising global population…

Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years…

Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…

Bacteria are prolific at colonizing diverse surfaces under a widerange of environmental conditions, and exhibit fascinating examples of self-organization across scales. Though it has recently attracted considerable interest, the role of…

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…

Mechanical interactions among cells in a growing microbial colony can significantly influence the colony's spatial genetic structure and, thus, evolutionary outcomes such as the fates of rare mutations. Here, we computationally investigate…

We present a proof-of-concept of a model comparison approach for analyzing spatio-temporal observations of interacting populations. Our model variants are a collection of structurally similar Bayesian networks. Their distinct Noisy-Or…

The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in…

The advent of high-throughput sequencing technologies has made data from DNA material readily available, leading to a surge of microbiome-related research establishing links between markers of microbiome health and specific outcomes.…

Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…

Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…

In this paper we develop and test algorithmic techniques to estimate genotypes fitnesses by analysis of observed daily frequency data monitoring the long-term evolution of bacterial populations. In particular, we develop a non-linear least…

Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…

We introduce and study a stochastic model for the dynamics of colonial species, which reproduce through fission or fragmentation. The fission rate depends on the relative sizes of colonies in the population, and the growth rate of colonies…

We review and extend results for mutation, selection, genetic drift, and migration in a one-dimensional continuous population. The population is described by a continuous limit of the stepping stone model, which leads to the stochastic…