Evolutionary Genomics, Softcover reprint of the original 1st ed. 2012 Statistical and Computational Methods, Volume 2 Methods in Molecular Biology Series, Vol. 856

Together with early theoretical work in population genetics, the debate on sources of genetic makeup initiated by proponents of the neutral theory made a solid contribution to the spectacular growth in statistical methodologies for molecular evolution. Evolutionary Genomics: Statistical and Computational Methods is intended to bring together the more recent developments in the statistical methodology and the challenges that followed as a result of rapidly improving sequencing technologies.  Presented by top scientists from a variety of disciplines, the collection includes a wide spectrum of articles encompassing theoretical works and hands-on tutorials, as well as many reviews with key biological insight.  Volume 2 begins with phylogenomics and continues with in-depth coverage of natural selection, recombination, and genomic innovation. The remaining chapters treat topics of more recent interest, including population genomics, -omics studies, and computational issues related to the handling of large-scale genomic data.  Written in the highly successful Methods in Molecular Biology? series format, this work provides the kind of advice on methodology and implementation that is crucial for getting ahead in genomic data analyses.

Part I: Phylogenomics

1. Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Non-Coalescent Genes

            Christian Anderson, Liang Liu, Dennis Pearl, and Scott V. Edwards

2. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord

            Gergely J Szöllősi and Vincent Daubin

3. Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life

            Pere Puigbò, Yuri I. Wolf, and Eugene V. Koonin

4. Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns

            Eric Bapteste, Frederic Bouchard, and Richard M. Burian

Part II: Natural Selection, Recombination, and Innovation in Genomic Sequences

5. Selection on the Protein Coding Genome

            Carolin Kosiol and Maria Anisimova

6. Methods to Detect Selection on Non-Coding DNA

            Ying Zhen and Peter Andolfatto

7. The Origin and Evolution of New Genes

            Margarida Cardoso-Moreira and Manyuan Long

8. Evolution of Protein Domain Architectures

            Kristoffer Forslund and Erik L.L. Sonnhammer

9. Estimating Recombination Rates from Genetic Variation in Humans

            Adam Auton and Gil McVean

10. Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces

            Sergei L. Kosakovsky Pond, Ben Murrell, and Art F.Y. Poon

Part III: Population Genomics

11. Association Mapping and Disease: Evolutionary Perspectives

            Søren Besenbacher, Thomas Mailund, and Mikkel H. Schierup

12. Ancestral Population Genomics

            Julien Y. Dutheil and Asger Hobolth

13. Non-Redundant Representation of Ancestral Recombinations Graphs

            Laxmi Parida

Part IV: The "-omics"

14. Using Genomic Tools to Study Regulatory Evolution

            Yoav Gilad

15. Characterization and Evolutionary Analysis of Protein-Protein Interaction Networks

            Gabriel Musso, Andrew Emili, and Zhaolei Zhang

16. Statistical Methods in Metabolomics

            Alexander Korman, Amy Oh, Alexander Raskind, and David Banks

17. Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN

            Daniel H. Huson and Suparna Mitra

18. Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases

            Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Müller, Christoph Bock, and Thomas Lengauer

19. Genetical Genomics for Evolutionary Studies

            Pjotr Prins, Geert Smant, and Ritsert C. Jansen

Part V: Handling Genomic Data: Resources and Computation

20. Genomics Data Resources: Frameworks and Standards

            Mark D. Wilkinson

21. Sharing Programming Resources Between Bio* Projects through Remote Procedure Call and Native Call Stack Strategies

            Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields, and Toshiaki Katayama

22. Scalable Computing for Evolutionary Genomics

            Pjotr Prins, Dominique Belhachemi, Steffen Möller, and Geert Smant

Serves as an ideal reference for young and experienced researchers alike

Features practical, step-by-step guidance to methodologies being used in the field

Includes key implementation advice from the experts