Related papers: Galactic Phylogenetics
Galactic bulges are central to understanding galaxy formation and evolution. Here we report on recent studies using micro-lensing events to obtain spectra of high resolution and moderately high signal-to-noise ratios of dwarf stars in the…
The formation and evolution of galaxies is one of the great outstanding problems of astrophysics. Within the broad context of hierachical structure formation, we have only a crude picture of how galaxies like our own came into existence. A…
Polyploidization is an evolutionary process by which a species acquires multiple copies of its complete set of chromosomes. The reticulate nature of the signal left behind by it means that phylogenetic networks offer themselves as a…
One-zone Galactic Chemical Evolution (GCE) models have provided useful insights on a great wealth of average abundance patterns in many environments, especially for the Milky Way and its satellites. However, the scatter of such abundance…
Open clusters are the only example of single-age, single initial chemical composition populations in the Galaxy, and they play an important role in the study of the formation and evolution of the Galactic disk. In addition, they have been…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
Understanding the origin and long-term evolution of the Solar System is a fundamental goal of planetary science and astrophysics. This chapter describes our current understanding of the key processes that shaped our planetary system,…
The formalism of the simple model of galactic chemical evolution (GCE) and its main ingredients (stellar properties, initial mass function, star formation rate and gas flows) are presented in this tutorial. It is stressed that GCE is not…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
Identifying and understanding the large-scale biodiversity patterns in time and space is vital for conservation and addressing fundamental ecological and evolutionary questions. Network-based methods have proven useful for simplifying and…