Related papers: Mitochondrial Dna Replacement Versus Nuclear Dna P…

We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…

Major discrepancies have been noted for some time between fossil ages and molecular divergence dates for a variety of taxa. Recently, systematic trends within avian clades have been uncovered. The trends show that the disparity is much…

Technical signs of progress during the last decades has led to a situation in which the accumulation of genome sequence data is increasingly fast and cheap. The huge amount of molecular data available nowadays can help addressing new and…

This paper shows that differentiating the lifetimes of two phenotypes independently from their fertility can lead to a qualitative change in the equilibrium of a population: since survival and reproduction are distinct functional aspects of…

Genetic drift is stochastic fluctuations of alleles frequencies in a population due to sampling effects. We consider a model of drift in an equilibrium population, with high mutation rates: few functional mutations per generation. Such…

Collecting genomics data across multiple heterogeneous populations (e.g., across different cancer types) has the potential to improve our understanding of disease. Despite sequencing advances, though, resources often remain a constraint…

Motivated by the wide range of known self-replicating systems, some far from genetics, we study a system composed by individuals having an internal dynamics with many possible states that are partially stable, with varying mutation rates.…

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…

A new method for determining whether or not a mitrochondrial DNA (mtDNA) sequence belongs to a vertebrate is described and tested. This method only needs the mtDNA sequence of the organism in question, and unlike alignment based methods, it…

Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…

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…

Consider a supercritical birth and death process where the children acquire mutations. We study the mutation rates along the ancestral lineages in a sample of size $n$ from the population at time $T$. The mutation rate is time-inhomogenous…

Non-African populations have experienced major bottlenecks in the time since their split from West Africans, which has led to the hypothesis that natural selection to remove weakly deleterious mutations may have been less effective in…

A crucial test any proposed evolutionary scenario must pass is can the birth rate of the sources we see be sustained by the proposed progenitor population? In this review, I investigate the methods used to determine the birth rates of…

Asynchronous replication of the genome has been associated with different rates of point mutation and copy number variation (CNV) in human populations. Here, we explored if the bias in the generation of CNV that is associated to DNA…

The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…

Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…

This paper proposes an original theory of aging of multicellular organisms. The cells of multicellular organisms, in contrast to unicellular organisms, are burdened with a two- part genome: housekeeping and specialized (multicellular),…

We consider the Moran model of population genetics with two types, mutation, and selection, and investigate the line of descent of a randomly-sampled individual from a contemporary population. We trace this ancestral line back into the…

In this paper, we review recent results of ours concerning branching processes with general lifetimes and neutral mutations, under the infinitely many alleles model, where mutations can occur either at birth of individuals or at a constant…