Related papers: Phylogenetic invariants for stationary base compos…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…
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…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
Our understanding of evolution is shaped strongly by how we conceive of its fundamental causes. In the original Modern Synthesis, evolution was defined as a process of shifting the frequencies of available alleles at many loci affecting a…
We consider evolution algebras and their related substructures: evolution ideals and evolution subalgebras. After exposing some of the concepts related to them in the literature, we explore the order structures that arise in the sets of…
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 process of pattern formation for a multi-species model anchored on a time varying network is studied. A non homogeneous perturbation superposed to an homogeneous stable fixed point can amplify, as follows a novel mechanism of…
Multiple systems play an important role in the evolution of star clusters. First we discuss several formation mechanisms which depend on the presence of binaries, either primordial or of dynamical origin. Hierarchical configurations are…
Cells generally change their internal state to adapt to an environmental change, and accordingly evolve in response to the new conditions. This process involves phenotypic changes that occur over several different time scales, ranging from…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…
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…
We formulate the notion of continuous evolution algebra in terms of differentiable matrix-valued functions, to then study those such algebras arising as solutions of ODE problems. Given their dependence on natural bases, matrix Lie groups…
Rapid developments in genetics and biology have led to phylogenetic methods becoming an important direction in the study of cancer and viral evolution. Although our understanding of gene biology and biochemistry has increased and is…
There is a classical geometric construction which uses a binary quadratic form to define an involution on the space of binary d-ics. We give a complete characterization of a general class of such involutions which are definable using…
A derangement is a permutation with no fixed point, and a nonderangement is a permutation with at least one fixed point. There is a one-term recurrence for the number of derangements of $n$ elements, and we describe a bijective proof of…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Rate variation among the sites of a molecular sequence is commonly found in applications of phylogenetic inference. Several approaches exist to account for this feature but they do not usually enable the investigator to pinpoint the sites…