Tangled Trees: The Challenge of Inferring Species Trees from Coalescent and Non-Coalescent Genes -- Modeling Gene Family Evolution and Reconciling Phylogenetic Discord -- Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life -- Philosophy and Evolution: Minding the Gap Between Evolutionary Patterns and Tree-Like Patterns -- Selection on the Protein Coding Genome -- Methods to Detect Selection on Non-Coding DNA -- The Origin and Evolution of New Genes -- Evolution of Protein Domain Architectures -- Estimating Recombination Rates from Genetic Variation in Humans -- Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces -- Association Mapping and Disease: Evolutionary Perspectives -- Ancestral Population Genomics -- Non-Redundant Representation of Ancestral Recombinations Graphs -- Using Genomic Tools to Study Regulatory Evolution -- Characterization and Evolutionary Analysis of Protein-Protein Interaction Networks -- Statistical Methods in Metabolomics -- Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN -- Analyzing Epigenome Data in Context of Genome Evolution and Human Diseases -- Genetical Genomics for Evolutionary Studies -- Genomics Data Resources: Frameworks and Standards -- Sharing Programming Resources Between Bio* Projects through Remote Procedure Call and Native Call Stack Strategies -- Scalable Computing for Evolutionary Genomics.

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.   Comprehensive and cutting-edge, Evolutionary Genomics: Statistical and Computational Methods is a treasure chest of state-of the-art methods to study genomic and omics data, certain to inspire both young and experienced readers to join the interdisciplinary field of evolutionary genomics.