Related papers: Ancestral lines under recombination
Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years…
We have analyzed the relations between the mutational pressure, recombination and selection pressure in the bit-string model with sexual reproduction. For specific sets of these parameters we have found three phase transitions with one…
A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a pedigree by just observing sequence data…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
In mathematical population genetics, it is well known that one can represent the genealogy of a population by a tree, which indicates how the ancestral lines of individuals in the population coalesce as they are traced back in time. As the…
We introduce an evolutionary algorithm called recombinator-$k$-means for optimizing the highly non-convex kmeans problem. Its defining feature is that its crossover step involves all the members of the current generation, stochastically…
We consider weighted particle systems in which new generations are re-sampled from current particles with probabilities proportional to their weights. This covers a broad class of sequential Monte Carlo methods, widely used in applied…
The ancestral selection graph in population genetics was introduced by KroneNeuhauser (1997) as an analogue of the coalescent genealogy of a sample of genes from a neutrally evolving population. The number of particles in this graph,…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
This paper presents a new type of genetic algorithm for the set covering problem. It differs from previous evolutionary approaches first because it is an indirect algorithm, i.e. the actual solutions are found by an external decoder…
Understanding the time evolution of fragmented animal populations and their habitats, connected by migration, is a problem of both theoretical and practical interest. This paper presents a method for calculating the time evolution of the…
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 Moran model with recombination is considered, which describes the evolution of the genetic composition of a population under recombination and resampling. There are $n$ sites (or loci), a finite number of letters (or alleles) at every…
In this paper, we develop a set of genetic programming operators and an initialization population process based on concepts of functional programming rewriting for boosting inductive genetic programming. Such genetic operators are used…
We consider a neutral haploid population whose generations are not overlapping and whose size is large and constantly of $N$ individuals. Any generation is replaced by a new one and any individual has a single parent. We do not choose the…
An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
Infinite population models are important tools for studying population dynamics of evolutionary algorithms. They describe how the distributions of populations change between consecutive generations. In general, infinite population models…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…