Related papers: Methods for calculating coexistence mechanisms: Be…
Species experience both internal feedbacks with endogenous factors such as trait evolution and external feedbacks with exogenous factors such as weather. These feedbacks can play an important role in determining whether populations persist…
Coevolution is expected to follow two alternative dynamics, often called trench warfare and arms races in plant-pathogen systems. Trench warfare situations are stable cycles of allele frequencies at the coevolving loci of both host and…
The possible coexistence of one host, one aggressive parasite and one non-lethal parasite is simulated using the Penna model of biological ageing. If the aggressive parasites survive the difficult initial times where they have to adjust…
My analysis uses methods developed for data mining microarray experiments, adapted for ageing research. Methods bridge knowledge of statistical mechanics with data mining methods developed in statistical mathematics. Analyses can reveal how…
In the classical Lotka-Volterra population models, the interacting species affect each other's growth rate. We propose an alternative model, in which the species affect each other through the limitation coefficients, rather then through the…
Ancestral inference for branching processes in random environments involves determining the ancestor distribution parameters using the population sizes of descendant generations. In this paper, we introduce a new methodology for ancestral…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
In nonlinear voter models the transitions between two states depend in a nonlinear manner on the frequencies of these states in the neighborhood. We investigate the role of these nonlinearities on the global outcome of the dynamics for a…
We propose a model of multispecies populations surviving on distributed resources. System dynamics are investigated under changes in abiotic factors such as the climate, as parameterized through environmental temperature. In particular, we…
We employ Monte Carlo simulations to numerically study the temporal evolution and transient oscillations of the population densities, the associated frequency power spectra, and the spatial correlation functions in the (quasi-)steady state…
Estimation of molecular evolutionary divergence times requires models of rate change. These vary with regard to the assumption of what quantity is penalized. The possibilities considered are the rate of evolution, the log of the rate of…
The n-person Prisoner's Dilemma is a widely used model for populations where individuals interact in groups. The evolutionary stability of populations has been analysed in the literature for the case where mutations in the population may be…
Quantifying interaction strength between species is of interest in food web studies for understanding population dynamics. Theory has run ahead of experiment in solving equations describing ecological systems (the Lotka-Volterra equations,…
Species introductions to new habitats can cause a decline in the population size of competing native species and consequently also in their genetic diversity. We are interested in why these adverse effects are weak in some cases whereas in…
Species interactions through cross-feeding via leakage and uptake of chemicals are important in microbial communities, and play an essential role in the coexistence of diverse species. Here, we study a simple dynamical model of a microbial…
In this article, we review the different models and methods to understand and estimate correlated evolution within the same genome, individual or species. We describe correlated evolution among traits, among genetic components and finally…
A spatial co-location pattern represents a subset of spatial features whose instances are prevalently located together in a geographic space. Although many algorithms of mining spatial co-location pattern have been proposed, there are still…
Resource competition theory predicts coexistence and exclusion patterns based on species R*s, the minimum resource values required for a species to persist. A central assumption of the theory is that all species have equal access to…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
Analyses of urban scaling laws assume that observations in different cities are independent of the existence of nearby cities. Here we introduce generative models and data-analysis methods that overcome this limitation by modelling…