Related papers: A mathematical model for gene evolution after whol…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…
This paper presents the study of a DNA replication model grounded in the biochemical kinetics of DNA polymerases, which copy each DNA strand into a complementary strand, except for rare point-like mutations caused by nucleotide substitution…
White dwarf (WD) stars evolve simply and predictably, making them reliable age indicators. However, self-consistent validation of the methods for determining WD total ages has yet to be widely performed. This work uses 1565 wide ( > 100 au)…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
This paper is concerned with an extended Galton-Watson process so as to allow individuals to live and reproduce for more than one unit time. We assume that each individual can live $k$ seasons (time-units) with probability $h_k$, and…
This contribution is concerned with mathematical models for the dynamics of the genetic composition of populations evolving under recombination. Recombination is the genetic mechanism by which two parent individuals create the mixed type of…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…
This paper develops a two gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by $ \sigma_{via} $, yields a…
Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly…
In recent years there has been increased interest in understanding the interplay between deep generative models (DGMs) and the manifold hypothesis. Research in this area focuses on understanding the reasons why commonly-used DGMs succeed or…
Gene-sharing networks provide a powerful framework to study the evolution of viruses and mobile genetic elements. These bipartite networks, which link genes to the genomes that contain them, exhibit characteristic degree distributions: a…
The dynamics of wild-type (wt) RNA viruses and their defective viral genomes (DVGs) have been extensively studied both experimentally and theoretically. This research has paid special attention to the interference effects of DVGs on wt…
As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
The total-evidence approach to divergence-time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
We present a proof-of-concept study, based on numerical-relativity simulations, of how gravitational waves (GWs) from neutron star merger remnants can probe the nature of matter at extreme densities. Phase transitions and extra degrees of…
White dwarfs (WDs) are powerful tools to study the evolutionary history of stars and binaries in the Galaxy. But do we understand their multiplicity from a theoretical point of view? This can be tested by a comparison with the sample of WDs…
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model.…