Weighted Minimum-Length Rearrangement Scenarios

We present the first known model of genome rearrangement with an arbitrary real-valued weight function on the rearrangements. It is based on the dominant model for the mathematical and algorithmic study of genome rearrangement, Double Cut and Join (DCJ). Our objective function is the sum or product of the weights of the DCJs in an evolutionary scenario, and the function can be minimized or maximized. If the likelihood of observing an independent DCJ was estimated based on biological conditions, for example, then this objective function could be the likelihood of observing the independent DCJs together in a scenario. We present an O(n^4)-time dynamic programming algorithm solving the Minimum Cost Parsimonious Scenario (MCPS) problem for co-tailed genomes with n genes (or syntenic blocks). Combining this with our previous work on MCPS yields a polynomial-time algorithm for general genomes. The key theoretical contribution is a novel link between the parsimonious DCJ (or 2-break) scenarios and quadrangulations of a regular polygon. To demonstrate that our algorithm is fast enough to treat biological data, we run it on syntenic blocks constructed for Human paired with Chimpanzee, Gibbon, Mouse, and Chicken. We argue that the Human and Gibbon pair is a particularly interesting model for the study of weighted genome rearrangements

Discovery of Unconventional Patterns for Sequence Analysis: Theory and Algorithms

The biology community is collecting a large amount of raw data, such as the genome sequences of organisms, microarray data, interaction data such as gene-protein interactions, protein-protein interactions, etc. This amount is rapidly increasing and the process of understanding the data is lagging behind the process of acquiring it. An inevitable first step towards making sense of the data is to study their regularities focusing on the non-random structures appearing surprisingly often in the input sequences: patterns. In this thesis we discuss three incarnations of the pattern discovery task, exploring three types of patterns that can model different regularities of the input dataset. While mask patterns have been designed to model short repeated biological sequences, showing a high conservation of their content at some specific positions, permutation patterns have been designed to detect repeated patterns whose parts maintain their physical adjacency but not their ordering in all the pattern occurrences. Transposons, instead, model mobile sequences in the input dataset, which can be discovered by comparing different copies of the same input string, detecting large insertions and deletions in their alignment

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

Systematics 2008 - Programme and Abstracts

The Göttingen conference „Systematics 2008“ is the first joint meeting of the Gesellschaft für Biologische Systematik (GfBS) and the German Botanical Society, section Biodiversity and Evolutionary Biology (DBG), being the 10th Annual Meeting of the GfBS and the 18th International Symposium „Biodiversity and Evolutionary Biology“ of the DBG. The conference programme covers biological systematics in the widest sense and provides ample opportunities for oral and poster presentations on new advances in plant, animal and microbial systematics. This volume brings together the abstracts of invited speaches from the plenary sessions on „Progress in Deep Phylogeny“, „Speciation and Phylogeography“, and „New Trends in Biological Systematics“ as well as those of submitted talks and poster sessions.The Göttingen conference „Systematics 2008“ is the first joint meeting of the Gesellschaft für Biologische Systematik (GfBS) and the German Botanical Society, section Biodiversity and Evolutionary Biology (DBG), being the 10th Annual Meeting of the GfBS and the 18th International Symposium „Biodiversity and Evolutionary Biology“ of the DBG. The conference programme covers biological systematics in the widest sense and provides ample opportunities for oral and poster presentations on new advances in plant, animal and microbial systematics. This volume brings together the abstracts of invited speaches from the plenary sessions on „Progress in Deep Phylogeny“, „Speciation and Phylogeography“, and „New Trends in Biological Systematics“ as well as those of submitted talks and poster sessions

Phylogeny and evolution of Monoplacophora and Mollusca

The Mollusca comprises eight classes which are highly diverse in their morphology as well as in molecular appearance. The class level relationships in molluscs were hotly debated during decades and are still under discussion as there is no overall support for one single concept. Morphological and recent phylogenomic studies support the hypothesis of Aculifera (Solenogastres, Caudofoveata and Polyplacophora) and summarize Bivalvia, Cephalopoda, Gastropoda, Monoplacophora and Scaphopoda as the Conchifera. Alternative concepts as Testaria (Bivalvia, Cephalopoda, Gastropoda, Monoplacophora, Scaphopoda and Polyplacophora) or Serialia (Monoplacophora + Polyplacophora) were suggested in the past based on morphological analyses (Testaria) or mainly molecular evidence (Serialia). In order to bring resolution to the class relationships and the early evolution within Mollusca we compiled several comprehensive taxon sets comprising different molecular datasets: combined nuclear and mitochondrial markers obtained via Sanger sequencing (“standard markers”), mitochondrial genomes (analyzing the phylogenetic information of the sequence data as well as comparing the gene arrangements) and phylogenomic data obtained via Next Generation Sequencing. We were able to generate novel data of several species of the elusive class Monoplacophora. Based on the set of standard markers, we found support for Serialia whereas the phylogenomic approach leads to Aculifera and Conchifera, providing first molecular evidence for Monoplacophora sister to Cephalopoda plus other conchiferans; a clade of Gastropoda and Scaphopoda is also supported. Both phylogenetic analyses were used for time estimations and resulted in congruent ages for the molluscan stem (Precambrian) and the diversification of Mollusca (584Mya). We were the first to present a complete mitochondrial genome of a monoplacophoran species ever. Analyzing the mitochondrial gene arrangements we were able to detect potential synapomorphies for Mollusca. Standard marker analyses on comprehensive taxon sets provided novel phylogenetic hypotheses on several molluscan subgroups, such as chitons and gastropods, in particular heterobranchs, challenging mitogenomic approaches and results in the latter. Overall, our studies addressed the phylogeny and evolution of Mollusca and subgroups with a variety of markers and methods and helped to pave the way from using multilocus markers and mitogenomics towards whole genomes

Programme and abstracts / Systematics 2008 : Göttingen 7-11 April 2008 / 10th Annual Meeting of the Gesellschaft für Biologische Systematik

The Göttingen conference Systematics 2008 is the first joint meeting of the Gesellschaft für Biologische Systematik (GfBS) and the German Botanical Society, section Biodiversity and Evolutionary Biology (DBG), being the 10th Annual Meeting of the GfBS and the 18th International Symposium Biodiversity and Evolutionary Biology of the DBG. The conference programme covers biological systematics in the widest sense and provides ample opportunities for oral and poster presentations on new advances in plant, animal and microbial systematics. This volume brings together the abstracts of invited speaches from the plenary sessions on Progress in Deep Phylogeny, Speciation and Phylogeography, and New Trends in Biological Systematics as well as those of submitted talks and poster sessions.The Göttingen conference Systematics 2008 is the first joint meeting of the Gesellschaft für Biologische Systematik (GfBp. and the German Botanical Society, section Biodiversity and Evolutionary Biology (DBG), being the 10th Annual Meeting of the GfBS and the 18th International Symposium Biodiversity and Evolutionary Biology of the DBG. The conference programme covers biological systematics in the widest sense and provides ample opportunities for oral and poster presentations on new advances in plant, animal and microbial systematics. This volume brings together the abstracts of invited speaches from the plenary sessions on Progress in Deep Phylogeny, Speciation and Phylogeography, and New Trends in Biological Systematics as well as those of submitted talks and poster sessions.Kongress: International Symposium Biodiversity and Evolutionary Biology ; 18 (Göttingen) : 2008.04.07-11 Annual meeting of the Gesellschaft für Biologische Systematik ; 10 (Göttingen) : 2008.04.07-11 Joint meeting of the Gesellschaft für Biologische Systematik and the German Botanical Society, Section Biodiversity and Evolutionary Biology ; 1 (Göttingen): 2008.04.07-1

Meiotic recombination and its implications for plant breeding

cum laude graduation (with distinction