Introgression is an evolutionary process in which genes or other types of genetic material are introduced into a genome. It important that can, for example, play fundamental role speciation. Recently the concept overlaid species forest (OSF) was as discrete way to model introgression. Basically, OSF consists gene history form phylogenetic tree, collection lineage trees some interest, and map ov...

Molecular phylogenetics is a well-established field of research in biology wherein phylogenetic trees are analyzed to obtain insights into the evolutionary histories of organisms. Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by...

Abstract Many popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, problem is reduced to a graph where vertices and (undirected) edges given by pairs connected one operation (sometimes called move). Most classical nearest neighbour interchange, subtree prune regraft, bisection reconnection moves. T...

We study some properties of subtree-prune-and-regraft (SPR) operations on leaflabelled rooted binary trees in which internal vertices are totally ordered. Since biological events occur with certain time ordering, sometimes such totally-ordered trees must be used to avoid possible contradictions in representing evolutionary histories of biological sequences. Compared to the case of plain leaf-la...

Statistical phylogenetic inference methods use tree rearrangement operations to perform either hillclimbing local search or Markov chain Monte Carlo across tree topologies. The canonical class of such moves are the subtree-prune-regraft (SPR) moves that remove a subtree and reattach it somewhere else via the cut edge of the subtree. Phylogenetic trees and such moves naturally form the vertices ...

We use Dirichlet form methods to construct and analyze a reversible Markov process, the stationary distribution of which is the Brownian continuum random tree. This process is inspired by the subtree prune and re-graft (SPR)Markov chains that appear in phylogenetic analysis. A key technical ingredient in this work is the use of a novel Gromov– Hausdorff type distance to metrize the space whose ...

purposes: to report a case of primary graft failure (pgf) and systemic manifestations of herpes simplex virus (hsv) infection following transplantation of an hsv-contaminated donor cornea. patient and findings: a 28-year-old male with history of penetrating keratoplasty 12 days before, developed intraocular inflammation with marked anterior chamber reaction, graft edema and elevated intraocular...

Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under consideration, and the goal is to find the chara...

Horizontal gene transfer (HGT) plays a critical role in evolution across all domains of life with important biological and medical implications. I propose a simple class of stochastic models to examine HGT using multiple orthologous gene alignments. The models function in a hierarchical phylogenetic framework. The top level of the hierarchy is based on a random walk process in "tree space" that...