Related papers: Quantifying the effects of anagenetic and cladogen…
In a phylogenetic tree, we often don't have information about the time a speciation event (inner node) occured. Under a neutral model for speciation, I develop fast algorithms for calculating the probability that an inner node i is the k-th…
Evolutionary hypotheses to explain the greater numbers of species in the tropics than the temperate zone include greater age and area, higher temperature and metabolic rates, and greater ecological opportunity. These ideas make contrasting…
Collective cell migration plays a crucial role in numerous biological processes, including tumour growth, wound healing, and the immune response. Often, the migrating population consists of cells with various different phenotypes. This…
Mutations are typically classified by their effects on the nucleotide sequence and by their size. Here, we argue that if our main aim is to understand the effect of mutations on evolutionary outcomes (such as adaptation or speciation), we…
Due to the conventional distinction between ecological (rapid) and evolutionary (slow)timescales, ecological and population models to date have typically ignored the effects of evolution. Yet the potential for rapid evolutionary change has…
We introduce a model, based on the Evolutionary Game Theory, for studying the dynamics of group formation. The latter constitutes a relevant phenomenon observed in different animal species, whose individuals tend to cluster together forming…
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…
Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have…
Phenological timing -- i.e. the course of annually recurring development stages in nature -- is of particular interest since it can be understood as a proxy for the climate at a specific region; moreover changes in the so called…
We present a generalization of the Yule model for macroevolution in which, for the appearance of genera, we consider point processes with the order statistics property, while for the growth of species we use nonlinear time-fractional pure…
A simple way to model phenotypic evolution is to assume that after splitting, the trait values of the sister species diverge as independent Brownian motions. Relying only on a prior distribution for the underlying species tree (conditioned…
The observation that phenotypic variability is ubiquitous in isogenic populations has led to a multitude of experimental and theoretical studies seeking to probe the causes and consequences of this variability. Whether it be in the context…
We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…
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…
The biological theory of adaptive dynamics proposes a description of the long-term evolution of a structured asexual population. It is based on the assumptions of large population, rare mutations and small mutation steps, that lead to a…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
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…
Evolutionary dynamics can be studied in well-mixed or structured populations. Population structure typically arises from the heterogeneous distribution of individuals in physical space or on social networks. Here we introduce a new type of…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…