Related papers: Galactic Phylogenetics
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…
Metals -- heavy elements synthesized during various phases of stellar evolution or during supernova explosions -- play a fundamental role in shaping galaxy evolution. In fact, their relative abundances, spatial distribution, and scaling…
We explore the motivation behind large stellar surveys in Galactic astronomy, in particular, surveys that measure the photometric, phase space and abundance properties of thousands or millions of stars. These observations are essential to…
A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…
Due to the inherently nonlinear nature of gravity cosmological N-body simulations have become an invaluable tool when the growth of structure is being studied and modelled closer to the present epoch. Large simulations with high dynamical…
We develop a toy-model for the chemical evolution of the intracluster medium, polluted by the galactic winds from elliptical galaxies. The model follows the "galaxy formation history" of cluster galaxies, constrained by the observed…
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…
Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive…
Increasingly good statistical data on the galaxy population at high and low redshift enable the development of new phenomenological approaches to galaxy evolution based on application of the simplest continuity equations. This has given new…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Surveys of the local and distant Universe are the means to test and improve our models of galaxy formation. Substantial successes in the models are evident, while there is also considerable recent progress in identifying what remains to be…
This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units…
Species' interactions are shaped by their traits. Thus, we expect traits -- in particular, trait (dis)similarity -- to play a central role in determining whether a particular set of species coexists. Traits are, in turn, the outcome of an…
Stellar Populations are the fossil record of Galactic evolution. Interpretation of this record in the Local Group allows one to determine reliably the dominant physics controlling the evolution of those galaxies which are typical of the…