CHAPTER 3 The Origin of New Genes 27
ClllIallzhllFan, J. J. Emerson, and Many"an Long
Introduction 27
Recent Discoveries of New Genes 27
Mechanisms to Generate New Genes 30
Evolutionary Forces for New Gene Retention 32
The Location and Movement of New Genes 33
Inferring the Functionality of New Genes 33
General Methods to Detect New Genes 35
Early filldings 35
Comparative molecular cytogenetic allalyses 35
Computatiollal genomic analysis 35
Comparative Genomic Hybridization to Detect New Genes 36
Challellges ill using array-based CGH ill new gene studies 39
Outlooks and Perspectives 42
CHAPTER 4 Lateral Gene Transfer 45
w. Ford Doolittle, Camilla L. Nesbg, Eric Bapteste, and Olga Zhaxybayeva
Introduction 45
Defining terms 45
A Very Brief History of Lateral Genomics 46
Mechanisms of Lateral Gene Transfer 46
Transduction 47
Conjugation 48
Transformation 50
Detecting LGT 51
Compositional methods 51
Unusual phyletic similarity patterns 51
Phylogenetic incongruence 52
PatcilY (anomalous) gene distribution among phyla and species 52
Strain-specific genes (patchy distribution within species) 53
Physical methods
57
Ever-Present Alternatives 58
Quantifying LGT 61
GenOllle-centric approaclles 61
Gene-centric methods 61
An LGT-Resistant Core 63
The complexity hypothesis 64
The tiny universal core 65
Do core genes have a common history? 66
LGT and Microevolution 67
HR and the biological species concept (jor bacteria) 67
Paralogs and xenologs 68
Adaptive LGT 69
Neutral LGT 69
LGT and Macroevolution 70
Eukaryotes, the Other Iceberg 72
LGT from inside: endosymbiotic gem transfer 72
LGT from outside: prokaryotes to eukaryotes 76
Eukaryotes to eukanjotes 77
Eukaryotes to prokaryotes 78
Reuniting Process and Pattern 78
CHAPTER 5 Evolution of Genomic Expression 81
Bemardo Lei/lOS,Christian R. Landry, PierreFontanillas, SlIsan C. p, Reml,
Rob KlIlathinal, KyleM. Brown, and Daniel L. Hartl
Introduction 81
The Complex Regulation of Genomic Expression 81
Classical Transcriptional Regulation in
Cis and TrailS 83
Promoters, enhallcers, repressors, transcription factors, and regulatory proteins 83
Epigenetic Regulation and Chromatin Modifications 86
DNA methylation 87
Histone modifications 88
Chromosome territories and nue/ear architecture 89
Post-Transcriptional Regulation 91
Measuring Attributes of Genomic Expression with Experimental
and Computational Tools 93
Experimental approaches 93
Coplputational approaches 99
The Evolution of Genomic Expression: What Do We Know? 103
Genomic expression and morphological evolution 104
Molecular evolution of regulatory sequences 105
Stabilizing selectiOlJ,positive selection, and neutrality
of gene expression levels 107
GelJomic attributes and rates of gelJe expression evolution 109
Inheritance of gene expression levels: Regulatory variation in
cis and trans 111
GelJotype-by-environment interactions, sex-biased genes, and epistasis 115
