Related papers: Historical contingency and entrenchment in protein…
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…
A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we show that the two most commonly used methods to disentangle the…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a…
Biases in molecular evolution can significantly influence evolutionary trajectories. They have been described in a variety of contexts such as development and mutation, but not for acquiring new functions (i.e. emergence). Here, we…
The theory of life history evolution provides a powerful framework to understand the evolutionary dynamics of pathogens in both epidemic and endemic situations. This framework, however, relies on the assumption that pathogen populations are…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
Biological evolution depends on the passing down to subsequent generations of genetic information encoding beneficial traits, and on the removal of unfit individuals by a selection mechanism. However, selection acts on phenotypes, and is…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci and the genome-wide patterns of polymorphism show signatures consistent with…
A probability model is presented for the dynamics of mutation-selection balance in a haploid infinite-population infinite-sites setting sufficiently general to cover mutation-driven changes in full age-specific demographic schedules. The…
Selection, mutation and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically…
Epochal dynamics, in which long periods of stasis in an evolving population are punctuated by a sudden burst of change, is a common behavior in both natural and artificial evolutionary processes. We analyze the population dynamics for a…
We consider an infinitely large population under stabilising selection and mutation in which the allelic effects determining a polygenic trait vary between loci. We obtain analytical expressions for the stationary genetic variance as a…
We investigate through numerical simulations the effect of selection on two summary statistics for nucleotide variation in a sample of two genes from a population of N asexually reproducing haploid individuals. One is the mean time since…
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…
A mutator is an allele that increases the mutation rate throughout the genome by disrupting some aspect of DNA replication or repair. Mutators that increase the mutation rate by the order of 100 fold have been observed to spontaneously…
The length distribution of proteins measured in amino acids follows the CoHSI (Conservation of Hartley-Shannon Information) probability distribution. In previous papers we have verified various predictions of this using the Uniprot database…
We study the evolutionary dynamics of an asexual population of nonmutators and mutators on a class of epistatic fitness landscapes. We consider the situation in which all mutations are deleterious and mutators are produced from nonmutators…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…