Related papers: The link between segregation and phylogenetic dive…
The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but…
We reconsider the deterministic haploid mutation-selection equation with two types. This is an ordinary differential equation that describes the type distribution (forward in time) in a population of infinite size. This paper establishes…
There is no much doubt that biotic interactions shape community assembly and ultimately the spatial co-variations between species. There is a hope that the signal of these biotic interactions can be observed and retrieved by investigating…
We propose a metric which can be used to compute the amount of heritable variation enabled by a given dynamical system. A distribution of selection pressures is used such that each pressure selects a particular fixed point via competitive…
Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
Complementarity among species with different traits is one of the basic processes affecting biodiversity, defined as the number of species in the ecosystem. We present here a soluble model ecosystem in which the species are characterized by…
We study a class of evolution models, where the breeding process involves an arbitrary exchangeable process, allowing for mutations to appear. The population size $n$ is fixed, hence after breeding, selection is applied. Individuals are…
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient…
Bedau has developed a general set of evolutionary statistics that quantify the adaptive component of evolutionary processes. On the basis of these measures, he has proposed a set of 4 classes of evolutionary system. All artificial life…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
For many taxa, the current high rates of extinction are likely to result in a significant loss of biodiversity. The evolutionary heritage of biodiversity is frequently quantified by a measure called phylogenetic diversity (PD). We predict…
We study the population genetics of two neutral alleles under reversible mutation in the \Lambda-processes, a population model that features a skewed offspring distribution. We describe the shape of the equilibrium allele frequency…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
The constant rate birth--death process is a popular null model for speciation and extinction. If one removes extinct and non-sampled lineages, this process induces `reconstructed trees' which describe the relationship between extant…
Species sampling processes have long served as the fundamental framework for modeling random discrete distributions and exchangeable sequences. However, data arising from distinct but related sources require a broader notion of…
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…
The loss of biodiversity due to the likely widespread extinction of species in the near future is a focus of current concern in conservation biology. One approach to measure the impact of this extinction is based on the predicted loss of…
This paper introduces link functions for transforming one probability distribution to another such that the Kullback-Leibler and R\'enyi divergences between the two distributions are symmetric. Two general classes of link models are…
The shape of allele-frequency clines maintained by migration-selection balance depends not only on the properties of migration and selection, but also on the dominance relations among alleles and on linkage to other loci under selection. We…