Related papers: Ancestral lines under recombination
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Ancestral inference for branching processes in random environments involves determining the ancestor distribution parameters using the population sizes of descendant generations. In this paper, we introduce a new methodology for ancestral…
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
The progression of a cell population where each individual is characterized by the value of an internal variable varying with time (e.g. size, weight, and protein concentration) is typically modeled by a Population Balance Equation, a first…
Population dynamics and in particular microbial population dynamics, though they are complex but also intrinsically discrete and random, are conventionally represented as deterministic differential equations systems. We propose to revisit…
We present a model for evolving population which maintains genetic polymorphism. By introducing random mutation in the model population at a constant rate, we observe that the population does not become extinct but survives, keeping…
We consider an exponentially growing population of cells undergoing mutations and ask about the effect of reproductive fluctuations (genetic drift) on its long-term evolution. We combine first step analysis with the stochastic dynamics of a…
Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
We calculate the probability distribution of repetitions of ancestors in a genealogical tree for simple neutral models of a closed population with sexual reproduction and non-overlapping generations. Each ancestor at generation g in the…
Genetic programming (GP) is an evolutionary computation technique to solve problems in an automated, domain-independent way. Rather than identifying the optimum of a function as in more traditional evolutionary optimization, the aim of GP…
We study a continuous-time dynamical system that models the evolving distribution of genotypes in an infinite population where genomes may have infinitely many or even a continuum of loci, mutations accumulate along lineages without…
We derive the asymptotic behaviour of the genealogy of a logistic branching process in the setting where the equilibrium population size is large. In three regimes on the tail of the offspring distribution we recover the Kingman,…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
In a (two-type) Wright-Fisher diffusion with directional selection and two-way mutation, let $x$ denote today's frequency of the beneficial type, and given $x$, let $h(x)$ be the probability that, among all individuals of today's…
Spatial models where growth is limited to the edge of the expansions have been instrumental to understand the population dynamics and the clone size distribution in growing cellular populations, such as microbial colonies and avascular…