种群与进化
The diversity and quality of natural systems have been a puzzle and inspiration for communities studying artificial life. It is now widely admitted that the adaptation mechanisms enabling these properties are largely influenced by the…
We present a stochastic epidemic model to study the effect of various preventive measures, such as uniform reduction of contacts and transmission, vaccination, isolation, screening and contact tracing, on a disease outbreak in a…
A binary phylogenetic network on a taxon set $X$ is a rooted acyclic digraph in which the degree of each nonleaf node is three and its leaves (i.e.degree-one nodes) are uniquely labeled with the taxa of $X$. It is tree-child if each nonleaf…
Modeling and analysis of the large scale Covid-19 pandemic data can yield inferences about it's dynamics and characteristics of disease propagation. These inferences can then be correlated with contextual factors like population density,…
A selfish learner seeks to maximize their own success, disregarding others. When success is measured as payoff in a game played against another learner, mutual selfishness typically fails to produce the optimal outcome for a pair of…
In order to accommodate the empirical fact that population structures are rarely simple, modern studies of evolutionary dynamics allow for complicated and highly-heterogeneous spatial structures. As a result, one of the most difficult…
Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Finding ways to overcome the temptation to exploit one another is still a challenge in behavioural sciences. In the framework of evolutionary game theory, punishing strategies are frequently used to promote cooperation in competitive…
Tracing potentially infected contacts of confirmed cases is important when fighting outbreaks of many infectious diseases. The COVID-19 pandemic has motivated researchers to examine how different contact tracing strategies compare in terms…
Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where…
To control African swine fever (ASF) efficiently, easily interpretable metrics of the outbreak dynamics are needed to plan and adapt the required measures. We found that the spread pattern of African Swine Fever cases in wild boar follows…
Many countries have experienced at least two waves of the COVID-19 pandemic. The second wave is far more dangerous as distinct strains appear more harmful to human health, but it stems from the complacency about the first wave. This paper…
We develop theoretical equivalences between stochastic and deterministic models for populations of individual cells stratified by age. Specifically, we develop a hierarchical system of equations describing the full dynamics of an…
Ecosystems around the world are at risk of critical transitions due to increasing anthropogenic pressures and climate change. Yet it is unclear where the risks are higher or where in the world ecosystems are more vulnerable. Here I measure…
Measuring gene expression simultaneously in both hosts and symbionts offers a powerful approach to explore the biology underlying species interactions. Such dual or simultaneous RNAseq approaches have primarily been used to gain insight…
We propose a model of the evolution of a matrix along a phylogenetic tree, in which transformations affect either entire rows or columns of the matrix. This represents the change of both lexical and phonological aspects of linguistic data,…
A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…
Since steep declines in a population's size also typically alter its composition, population bottlenecks are considered highly important for evolution. However, despite such significance, the mechanisms governing the impact of a given…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…