Related papers: Predicting evolution from the shape of genealogica…
Seasonal variation in environmental variables, and in rates of contact among individuals, are fundamental drivers of infectious disease dynamics. Unlike most periodically-forced physical systems, for which the precise pattern of forcing is…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
A central challenge in every field of biology is to use existing measurements to predict the outcomes of future experiments. In this work, we consider the wealth of antibody inhibition data against variants of the influenza virus. Due to…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…
Commonly recognized evolutionarily relevant effects of sexual reproduction include increased diversity, accelerated adaptation, and constrained accumulation of deleterious mutations, along with a secondary effect of species genotype…
Tree shape statistics quantify some aspect of the shape of a phylogenetic tree. They are commonly used to compare reconstructed trees to evolutionary models and to find evidence of tree reconstruction bias. Historically, to find a useful…
Groups - social communities are important components of entire societies, analysed by means of the social network concept. Their immanent feature is continuous evolution over time. If we know how groups in the social network has evolved we…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
Analyses and visualizations by the ISSCOR method of influenza virus hemagglutinin genes of different A-subtypes revealed some rather striking temporal relationships between groups of individual gene subsets. Based on these findings we…
The Influenza virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Hemagglutinin (HA) gene of the virus can be a target for antiviral drug development…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
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…
In evolution theory the concept of a fitness landscape has played an important role, evolution itself being portrayed as a hill-climbing process on a rugged landscape. In this article it is shown that in general, in the presence of other…
The paper discusses a connection between asymmetric reproduction -- that is reproduction in a parent-child relationship where the parent does not mutate during reproduction --, the fact that all non-viral lifeforms bear genes of their…
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…
Consider a continuous-time binary branching process conditioned to have population size n at some time t, and with a chance p for recording each extinct individual in the process. Within the family tree of this process, we consider the…
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…
For a family of models of evolving population under selection, which can be described by noisy traveling wave equations, the coalescence times along the genealogical tree scale like $\log^\alpha N$, where $N$ is the size of the population,…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
A model describing the dynamics related to the spreading of non-lethal infectious diseases in a fixed-size population is proposed. The model consists of a non-linear delay-differential equation describing the time evolution of the increment…