Explorative Graph Visualization

Netzwerkstrukturen (Graphen) sind heutzutage weit verbreitet. Ihre Untersuchung dient dazu, ein besseres Verständnis ihrer Struktur und der durch sie modellierten realen Aspekte zu gewinnen. Die Exploration solcher Netzwerke wird zumeist mit Visualisierungstechniken unterstützt. Ziel dieser Arbeit ist es, einen Überblick über die Probleme dieser Visualisierungen zu geben und konkrete Lösungsansätze aufzuzeigen. Dabei werden neue Visualisierungstechniken eingeführt, um den Nutzen der geführten Diskussion für die explorative Graphvisualisierung am konkreten Beispiel zu belegen.Network structures (graphs) have become a natural part of everyday life and their analysis helps to gain an understanding of their inherent structure and the real-world aspects thereby expressed. The exploration of graphs is largely supported and driven by visual means. The aim of this thesis is to give a comprehensive view on the problems associated with these visual means and to detail concrete solution approaches for them. Concrete visualization techniques are introduced to underline the value of this comprehensive discussion for supporting explorative graph visualization

LIPIcs, Volume 244, ESA 2022, Complete Volume

LIPIcs, Volume 244, ESA 2022, Complete Volum

Vertebrate phylogenomics and gene family evolution

This thesis is about 2 topics; the evolution of gene families by the birth-death process of gene duplication and gene loss, and phylogenetic inference. It is a central theme that these two processes are intimately associated - the phylogenies of gene families (of any gene) are shaped by the processes of gene duplication and gene loss, as much as by the processes of speciation and extinction occurring among the species the gene is evolving in. This has two results. Firstly, that we need to know, or assume, something about the processes of gene duplication and loss to correctly understand the pattern of speciation, or cladogenesis, in a group of organisms. Secondly, that we need to know, or assume, something about this pattern if we are to fully appreciate the effect of gene duplication and loss on a gene family phylogeny.The main part of this thesis investigates the use of reconciled tree methods in unravelling species phylogeny and the evolution of gene families. Part of this investigation involves placing reconciled tree methods (and the use of these methods to infer species phylogeny, known as gene tree parsimony), in the context of some related methods: supertree methods and "simultaneous analysis" of combined data. Two empirical studies complete this part of the thesis - one attempting to infer the higher-level phylogeny of vertebrates using gene tree parsimony, and another focusing on a lower taxonomic level, on primate phylogeny. This chapter attempts an integrated study of gene duplication and species phylogeny, which uses information about gene duplication to help date evolutionary events.Despite the close relationship between gene duplication and speciation on phylogenies, it is possible to study gene duplication independently. If we restrict ourselves to genes sampled from a single genome, gene family trees represent gene duplications and gene losses occurring during the history of a single species, so the complication of speciation and extinction is eliminated. By realising that the processes of gene duplication and loss in these trees are analogous to the processes of speciation and extinction in species phylogenies, we can harness a toolkit of methods developed for more traditional phylogenies to study these molecular processes. Two such methods are models of cladistic tree shape and birth-death models, which allow the first estimates of the rate of gene loss

Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward