Related papers: Mathematical Framework for Phylogenetic Birth-And-…
Delay is an important and ubiquitous aspect of many biochemical processes. For example, delay plays a central role in the dynamics of genetic regulatory networks as it stems from the sequential assembly of first mRNA and then protein.…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic…
Our understanding of past evolutionary change is often based on reconstructions based on incomplete data, raising fundamental questions about the degree to which we can make reliable inferences about past evolutionary processes. This was…
Online genealogy datasets contain extensive information about millions of people and their past and present family connections. This vast amount of data can assist in identifying various patterns in human population. In this study, we…
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth scaling, as a characterization of…
What is aging? Mechanistic answers to this question remain elusive despite decades of research. Here, we propose a mathematical model of cellular aging based on a model gene interaction network. Our network model is made of only non-aging…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
Using a simple model with link removals as well as link additions, we show that an evolving network is scale free with a degree exponent in the range of (2, 4]. We then establish a relation between the network evolution and a set of…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
Covarion models of character evolution describe inhomogeneities in substitution processes through time. In phylogenetics, such models are used to describe changing functional constraints or selection regimes during the evolution of…
A stochastic genetic model for biological aging is introduced bridging the gap between the bit-string Penna model and the Pletcher-Neuhauser approach. The phenomenon of exponentially increasing mortality function at intermediate ages and…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…