Related papers: A paradigm shift, or a paradigm adjustment? The ev…
The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes drift and stabilizing selection and assumes that species evolve independently.…
Kuhn's framework of scientific progress (Kuhn, 1962) provides a useful framing of the paradigm shifts that have occurred in Artificial Intelligence over the last 60 years. The framework is also useful in understanding what is arguably a new…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
The Darwinian paradigm of biological evolution is based on the separability of the variation and selection processes. As a result, the population thinking had always been an integral part of the Darwinian approach. I propose an alternative…
Sexual selection is a fundamental aspect of evolution for all eukaryotic organisms with mating types. This paper suggests intersexual selection is best viewed as a mechanism to compensate for the unavoidable dynamics of coevolution between…
We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative Polymerase Chain Reaction (qPCR). It is tractable at the genetic, genomic, phenotypic…
It has recently been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter the other associated phenomena can be explained as evolution tuning the amount and…
Yule's 1925 paper introducing the branching model that bears his name was a landmark contribution to the biodiversity sciences. In his paper, Yule developed stochastic models to explain the observed distribution of species across genera and…
Thomas S. Kuhn interprets the development of the (natural) sciences as a specific dynamical process. Periods of piecemeal growth of knowledge based on widely accepted paradigms are interrupted by bursts of revolutionary changes which lead…
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…
We study the evolution of sexual and asexual populations in general fitness landscapes. We find deep relations between the mathematics of biological evolution and the formalism of quantum mechanics. We give the general structure of the…
Current phylogenetic comparative methods generally employ the Ornstein-Uhlenbeck(OU) process for modeling trait evolution. Being able of tracking the optimum of a trait within a group of related species, the OU process provides information…
Migration between different habitats is ubiquitous among biological populations. In this Letter, we study a simple quasispecies model for evolution in two different habitats, with different fitness landscapes, coupled through one-way…
We consider a model for Darwinian evolution in an asexual population with a large but non-constant populations size characterized by a natural birth rate, a logistic death rate modelling competition and a probability of mutation at each…
Our understanding of the evolutionary process has gone a long way since the publication, 150 years ago, of "On the origin of species" by Charles R. Darwin. The XXth Century witnessed great efforts to embrace replication, mutation, and…
This thesis concerns multivariate phylogenetic comparative methods. We investigate two aspects of them. The first is the bias caused by measurement error in regression studies of comparative data. We calculate the formula for the bias and…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
It has been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. This paper uses the well-known NKCS model to explore the effects of coevolution upon the behaviour of…
We introduce a new interacting particle system intended to model an example of ecological succession involving two species: the bracken and the european beech. The objective is to exhibit phase transitions by proving that there exist three…
Consider a mathematical model of evolutionary adaptation of fitness landscape and mutation matrix as a reaction to population changes. As a basis, we use an open quasispecies model, which is modified to include explicit death flow. We…