Related papers: Universal constraints on selection strength in lin…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary…
Standard evolutionary theories of aging and mortality, implicitly based on assumptions of spatial averaging, hold that natural selection cannot favor shorter lifespan without direct compensating benefit to individual reproductive success.…
We propose a mathematical framework for natural selection in finite populations. Traditionally, many of the selection-based processes used to describe cultural and genetic evolution (such as imitation and birth-death models) have been…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of…
Geographic ranges of communities of species evolve in response to environmental, ecological, and evolutionary forces. Understanding the effects of these forces on species' range dynamics is a major goal of spatial ecology. Previous…
We consider a stochastic evolutionary model for a phenotype developing amongst n related species with unknown phylogeny. The unknown tree is modelled by a Yule process conditioned on n contemporary nodes. The trait value is assumed to…
We extend classical results on simple varieties of trees (asymptotic enumeration, average behavior of tree parameters) to trees counted by their number of leaves. Motivated by genome comparison of related species, we then apply these…
There is little doubt in scientific circles that--counting from the origin of life towards today--evolution has led to an increase in the amount of information stored within the genomes of the biosphere. This trend of increasing information…
This article is a presentation of specific recent results describing scaling limits of individual-based models. Thanks to them, we wish to relate the time-scales typical of demographic dynamics and natural selection to the parameters of the…
Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a…
Statistical analysis of alignments of large numbers of protein sequences has revealed "sectors" of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein,…
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations:…
In evolutionary algorithms, the fitness of a population increases with time by mutating and recombining individuals and by a biased selection of more fit individuals. The right selection pressure is critical in ensuring sufficient…
We construct a pathwise formulation of a growing population of cells, based on two different samplings of lineages within the population, namely the forward and backward samplings. We show that a general symmetry relation, called…
Hubbell's neutral theory of biodiversity has successfully explained the observed composition of many ecological communities but it relies on strict demographic equivalence among species and provides no room for evolutionary processes like…
We show how concepts from statistical physics, such as order parameter, thermodynamic limit, and quantum phase transition, translate into biological concepts in mutation-selection models for sequence evolution and can be used there. The…