Related papers: Evolution models with base substitutions, insertio…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
A general population evolution model is considered. Any individual of the population is characterized by its score. Certain general conditions are assumed concerning the number of the individuals and their scores. Asymptotic theorems are…
Adaptive dynamics is a widely used framework for modeling long-term evolution of continuous phenotypes. It is based on invasion fitness functions, which determine selection gradients and the canonical equation of adaptive dynamics. Even…
We study in detail a recently proposed simple discrete model for evolution on smooth landscapes. An asymptotic solution of this model for long times is constructed. We find that the dynamics of the population are governed by correlation…
We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the…
We demonstrate with a thought experiment that fitness-based population dynamical approaches to evolution are not able to make quantitative, falsifiable predictions about the long-term behavior of evolutionary systems. A key characteristic…
Deep neural networks proved to be a very useful and powerful tool with many practical applications. They especially excel at learning from large data sets with labeled samples. However, in order to achieve good learning results, the network…
Applying the concepts and formalisms from Evolutionary Game Theory to the data regime, the fundamental paradigms of Evolutionary Data Theory are introduced. Interpreting data in matrix form as evolutionary entities, input data is mapped to…
Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution. However, these experiments deal with individual enzymes and explore a tiny part of the fitness…
Predicting evolution of expanding populations is critical to control biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system…
One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments which is crucial for evolvability. Recent work showed that when selective environments…
A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the…
We introduce a model of biological evolution where species evolve in response to biotic interactions and a fluctuating environmental stress. The species may either become extinct or mutate to acquire a new fitness value when the effective…
Any process in which competing solutions replicate with errors and numbers of their copies depend on their respective fitnesses is the evolutionary optimization process. As during carcinogenesis mutated genomes replicate according to their…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
An equation describing the evolution of phenotypic distribution is derived using methods developed in statistical physics. The equation is solved by using the singular perturbation method, and assuming that the number of bases in the…
The concept of fitness is central to evolution, but it quantifies only the expected number of offspring an individual will produce. The actual number of offspring is also subject to noise, arising from environmental or demographic…
We consider a population evolving under mutation and selection. The genotype of an individual is a word of length $\ell$ over a finite alphabet. Mutations occur during reproduction, independently on each locus; the fitness depends on the…