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Über dieses Buch

This book is the first of its kind to explain the fundamentals of evolutionary genomics. The comprehensive coverage includes concise descriptions of a variety of genome organizations, a thorough discussion of the methods used, and a detailed review of genome sequence processing procedures. The opening chapters also provide the necessary basics for readers unfamiliar with evolutionary studies. Features: introduces the basics of molecular biology, DNA replication, mutation, phylogeny, neutral evolution, and natural selection; presents a brief evolutionary history of life from the primordial seas to the emergence of humans; describes the genomes of prokaryotes, eukaryotes, vertebrates, and humans; reviews methods for genome sequencing, phenotype data collection, homology searches and analysis, and phylogenetic tree and network building; discusses databases of genome sequences and related information, evolutionary distances, and population genomics; provides supplementary material at an associated website.



Basic Processes of Genome Evolution


1. Basic Metabolism Surrounding DNAs

Basic molecular processes of living beings with special reference to DNA are discussed in this chapter, including replication, transcription, and translation. Molecular natures of DNAs, RNAs, and proteins are described as well as their informational sides such as genetic codes and protein diversity.
Naruya Saitou

2. Mutation

Mutations, the fundamental sources of evolution, are described in detail. They include nucleotide substitutions, insertions/deletions of unique and repeat sequences, recombinations, gene conversions, gene duplications, and mutations affecting phenotypes. Mutation rate estimates and methods to estimate mutation rates are also discussed.
Naruya Saitou

3. Phylogeny

DNA replications generate phylogenies. Therefore, phylogenetic relationship of DNAs is fundamental for those of individuals, genes, and species. Their relationships and differences are discussed as well as the biologically important concepts such as gene genealogy, paralogy, orthology, and horizontal gene transfer. Basic concepts of trees and networks are then explained including mathematical definition, number of possible tree topologies, and description of trees and networks. Biological implications of trees and networks such as fission and fusion of species and populations and the relationship with taxonomy are also discussed.
Naruya Saitou

4. Neutral Evolution

Neutral evolution is the default process of the genome changes. This is because our world is finite and the randomness is important when we consider history of a finite world. The random nature of DNA propagation is discussed using branching process, coalescent process, Markov process, and diffusion process. Expected evolutionary patterns under neutrality are then discussed on fixation probability, rate of evolution, and amount of DNA variation kept in population. We then discuss various features of neutral evolution starting from evolutionary rates, synonymous and nonsynonymous substitutions, junk DNA, and pseudogenes.
Naruya Saitou

5. Natural Selection

Basic concept of natural selection is first discussed, and purifying (negative) selection is shown to be much more prevalent than positive selection. Natural selection on haploids and diploids is discussed under both large populations and small populations. Natural selection at the genomic level is then described, covering various topics such as gain and loss of genes and purifying selection at synonymous sites and at noncoding regions. Positive selection for ape and human genes and detection of positive selection through genome-wide searches are also discussed.
Naruya Saitou

Evolving Genomes


6. A Brief History of Life

The evolutionary history of organisms is summarized in this chapter, starting from the origin of life. Evolution of the genetic code is discussed with reference to tRNAs, and estimation of the phylogenetic relationship of metabolic pathways before the diversification of prokaryotes and eukaryotes is given. The history of eukaryotes follows with special reference to multicellular lineages, finally reaching us human beings.
Naruya Saitou

7. Prokaryote Genomes

The world of prokaryotes (Bacteria and Archaea) is much more diverse than eukaryotes. After glancing the diversity of prokaryotes and their genome sequencing efforts, the basic structure of prokaryote genomes is discussed using Escherichia coli as an example, followed by discussions on GC content heterogeneity, horizontal gene transfer, codon usage, and plasmids. Finally, we discuss prokaryotic metagenomes.
Naruya Saitou

8. Eukaryote Genomes

General overviews of eukaryote genomes are first discussed, including organelle genomes, introns, and junk DNAs. We then discuss the evolutionary features of eukaryote genomes, such as genome duplication, C-value paradox, and the relationship between genome size and mutation rates. Genomes of multicellular organisms, plants, fungi, and animals are then briefly discussed.
Naruya Saitou

9. Vertebrate Genomes

We first discuss the characteristics of vertebrate genome evolution in this chapter. Special attentions were given to two-round genome duplications and conserved noncoding sequences. We then move to brief description of vertebrate genomes for major phylogenetic lineages: teleost fish, amphibian, and amniotes. Mammals, in which many species genomes were already sequenced, were discussed in more details.
Naruya Saitou

10. Human Genome

The human genome can be considered as the representative of mammalian genomes. Basic characteristics of the human genome, such as the overall structure, protein coding genes, and RNA genes, are first discussed. Personal genome sequencing and genomic heterogeneity are described next. We then discuss genetic changes to produce humanness. At the end, ancient human genomes are briefly reviewed.
Naruya Saitou

Methods for Evolutionary Genomics


11. Genome Sequencing

The wet experimental steps are necessary for sequencing genomes. These steps are summarized in this chapter, starting from DNA sampling, followed by construction of genomic library and sequence determination. Computational tactics on determination of nucleotide sequences including base call, shotgun sequencing, minimum tiling array, haplotype sequence determination, and resequencing are also discussed.
Naruya Saitou

12. Omic Data Collection

Genome sequences are interacting with molecules inside and outside cells. With the same spirit as genomics to study all genetic informations, there are various categories on studying all transcripts, all proteins, all metabolites, and so on. We briefly discuss these omic worlds including ecome, coined in this book.
Naruya Saitou

13. Databases

Use of databases is essential for evolutionary genomics. Databases for genomes, nucleotide sequences, proteins, literatures, and other categories are discussed.
Naruya Saitou

14. Sequence Homology Handling

How to discover evolutionary homology of nucleotide and amino acid sequences and how to analyze these homologous sequences are discussed, including homology search, pairwise alignment, multiple alignment, and genome-wide sequence viewing.
Naruya Saitou

15. Evolutionary Distances

Estimation of various types of evolutionary distances from nucleotide and amino acid sequences is discussed. Many methods for estimation of nucleotide substitutions including one-parameter method, two-parameter method, and methods incorporating observed nucleotide frequencies were explained in detail. Methods for estimating synonymous and nonsynonymous substitutions and amino acid substitutions were also discussed.
Naruya Saitou

16. Tree and Network Building

Construction of phylogenetic trees from nucleotide or amino acid sequence data is one of the important areas of evolutionary genomics. We start from classification of tree-building methods, both by type of data and by type of tree search algorithm. Various distance matrix methods including UPGMA, minimum deviation methods, minimum evolution methods, transformed distance methods, and neighbor-joining method are explained. Among character-state methods, maximum parsimony methods, maximum likelihood methods, and Bayesian method are explained. These many phylogenetic tree-making methods were compared mainly based on computer simulation studies. Phylogenetic network constructions from distance matrix and from multiply aligned sequences are also discussed as well as phylogeny construction without multiple alignments.
Naruya Saitou

17. Population Genomics

Population genetics is a part of evolutionary studies. Now with genome sequences, population genomics emerged, starting from the analysis of multiple human mitochondrial DNA genome sequences. It was extended to nuclear DNA of human individuals, and genome-wide SNP data comparison is now flourishing, slowly followed by comparisons of personal genomes. This is also true in bacteria in which different strains of the same species are now determined and compared. As the genome sequencing cost is becoming drastically reduced, population genomics will definitely expand to many other organisms. We discuss both methods and examples of population genomics in this chapter.
Naruya Saitou


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