Main description:

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.

Contents:

Part I: Introduction: Bioinformatician's Primers

1. Introduction to Genome Biology and Diversity

Noor Youssef, Aidan Budd, and Joseph P. Bielawski

2. Probability, Statistics, and Computational Science

Niko Beerenwinkel and Juliane Siebourg

3. A Not-So-Long Introduction to Computational Molecular Evolution

Stephane Aris-Brosou and Nicolas Rodrigue

Part II: Genomic Alignment and Homology Inference

4. Whole-Genome Alignment

Colin Dewey

5. Inferring Orthology and Paralogy

Adrian M. Altenhoff, Natasha M. Glover, and Christophe Dessimoz

6. Transposable Elements and Their Identification

Wojciech Makalowski, Valer Gotea, Amit Pande, and Izabela Makalowska

Part III: Phylogenomics and Genome Evolution

7. Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model

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

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

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

9. The Methodology Behind Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution

Andrew K. Watson, Romain Lannes, Jananan S. Pathmanathan, Raphael Meheust, Slim Karkar, Philippe Colson, Eduardo Corel, Philippe Lopez, and Eric Bapteste

10. Bayesian Molecular Clock Dating Using Genome-Scale Datasets

Mario dos Reis and Ziheng Yang

11. Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species

Sylvain Glemin, Clementine M. Francois, and Nicolas Galtier

Part IV: Natural Selection and Innovation in Genomic Sequences

12. Selection Acting on Genomes

Carolin Kosiol and Maria Anisimova

13. Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship between Model and Data

Christopher T. Jones, Edward Susko, and Joseph P. Bielawski

14. Evolution of Viral Genomes: Interplay between Selection, Recombination, and Other Forces

Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, Brittany Rife Magalis, Michael Li, and Sergei L. Kosakovsky Pond

15. Evolution of Protein Domain Architectures

Sofia K. Forslund, Mateusz Kaduk, and Erik L.L. Sonnhammer

16. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

Lain Guio and Josefa Gonzalez

Part V: Population Genomics and Omics in Light of Disease and Evolution

17. Association Mapping and Disease: Evolutionary Perspectives

Soren Besenbacher, Thomas Mailund, Bjarni J. Vilhjalmsson, and Mikkel H. Schierup

18. Ancestral Population Genomics

Julien Y. Dutheil and Asger Hobolth

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

Caner Bagci, Sina Beier, Anna Gorska, and Daniel H. Huson

20. Multiple Data Analyses and Statistical Approaches for Analyzing Data from Metagenomic Studies and Clinical Trials

Suparna Mitra

21. Systems Genetics for Evolutionary Studies

Pjotr Prins, Geert Smant, Danny Arends, Megan K. Mulligan, Rob W. Williams, and Ritsert C. Jansen

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

Lars Feuerbach, Fabian Muller, Peter Ebert, Thomas Lengauer, Christoph Bock, Yassen Assenov

Part VI: Handling Genomic Data: Resources and Computation

23. Semantic Integration and Enrichment of Heterogeneous Biological Databases

Ana Claudia Sima, Kurt Stockinger, Tarcisio Mendes de Farias, and Manuel Gil

24. High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE

Guy Baele, Daniel L. Ayres, Andrew Rambaut, Marc A. Suchard, and Philippe Lemey

25. Scalable Workflows and Reproducible Data Analysis for Genomics

Francesco Strozzi, Roel Janssen, Ricardo Wurmus, Michael R. Crusoe, George Githinji, Paolo Di Tommaso, Dominique Belhachemi, Steffen Moeller, Geert Smant, Joep de Ligt, and Pjotr Prins

26. Sharing Programming Resources between Bio* Projects

Raoul J.P. Bonnal, Andrew Yates, Naohisa Goto, Laurent Gautier, Scooter Willis, Christopher Fields, Toshiaki Katayama, and Pjotr Prins