Handbook of Human Molecular Evolution, 2 Volume Set

by Cooper, David N.; Kehrer-Sawatzki, Hildegard

• ISBN13: 9780470517468
• ISBN10: 0470517468
• Edition: 1st
• Format: Hardcover
• Copyright: 2008-10-13
• Publisher: Wiley

Summary

"This splendid compendium... will be the standard reference work for years to come: a handbook to browse, to consult, to look things up in, and to read with pleasure, wonder and post-Darwinian exhilaration." Richard Dawkins"This is a marvellous book... It should be in every university library - preferably in several copies - and every reader of this journal should add it to their next grant application. It really is that good... I have already found this book to be invaluable... For many years to come, these two volumes will be the starting point for anyone wishing to find out about virtually any subject relating to human genetics... Any scientist working on humans or other animals will find many things in these pages that will stimulate, inform and inspire. The authors, editors and publishers are to be congratulated for their work... order a copy now!" HUMAN GENETICS"The publishers and editors deserve to be congratulated for publishing this major book which coincides with the 200 th anniversary of the birth of Charles Darwin. The book is well-timed, with biologists, theologians and sociologists engaged in intense debate on the Darwinian Theory on the origin of species, evolution and natural selection... There is little doubt that this marvellous publication should be in the library of universities and academic institutions dealing with basic and applied biology research and education... It will not be surprising if the individual academic or researcher decides to invest in this resource and enrich their personal collection of leading books in genetics and genomics." GENOMIC MEDICINEA Unique Collection of High-Quality Articles - Derived from the Acclaimed Encyclopedia of Life SciencesThe revolution in human molecular genetics which has taken place over the last three decades has yielded a wealth of information not only on the structure and function of our genes, but also on gene expression, mutation and polymorphic variation. Over the last five years, the focus has moved from genes to genomes. Even though the annotation of our ~30,000 genes is still in progress, genome-wide studies have already yielded abundant evidence for the signatures of past selection and adaptive evolution within human gene sequences. Further, the completion of the sequencing of the 3 billion base-pair human genome, coupled with the increasing availability of other vertebrate genome sequences, has ushered in a new era of comparative genomics. We are now able to identify many of the molecular events (from the chromosomal level down to the single base-pair) that have occurred during vertebrate, mammalian, primate and hominid evolution. Indeed, the detailed comparison of the human and chimpanzee genomes has begun to reveal some of the genetic changes that have been involved in the development of human lineage-specific traits. We are thus acquiring the ability to ask searching questions about our origins, about the demographic processes associated with the global radiation of humankind, as well as some of the unique adaptations that make us human.Evolutionary biology has become so broad that its impact may be felt across the spectrum of the biological sciences. The aim of the Handbook of Human Molecular Evolution is relatively straightforward: to bring together under the same cover the many and varied strands of our knowledge of human/primate/vertebrate molecular evolution. Hence, the 282 chapters that comprise this essential reference work have been thematically arranged into twelve sections, covering the whole scope of research into human molecular evolution:General Concepts in Evolutionary Genetics Mutation, Adaptation and Natural Selection Evolutionary and Population Genetics Human Evolution Human Genome Evolution Evolu

Author Biography

David N. Cooper has been Professor of Human Molecular Genetics at Cardiff University since 1996. His research interests focus largely on molecular mechanisms of mutagenesis and genotype-phenotype relationships in a variety of different inherited disorders, population genetics, gene expression, cancer genetics, growth hormone genetics, and molecular evolution. He has written or co-authored Human Gene Mutation (1993), The Molecular Genetics of Haemostasis and Its Inherited Disorders (1994), Venous Thrombosis: From Genes to Clinical Medicine (1997), Human Gene Evolution (1999) and The Molecular Genetics of Lung Cancer (2005). He has also co-edited The Functional Analysis of the Human Genome (1995), Gene Therapy (1996), Neurofibromatosis Type 1: From Genotype to Phenotype (1998) and Fascioscapulohumeral Muscular Dystrophy: Clinical Medicine and Molecular Cell Biology (2004). He acted as Editor-in-Chief of the Nature Encyclopedia of the Human Genome (2003) and is currently Editor of the Genetics & Disease section of the Wiley Encyclopedia of Life Sciences. He has been European Editor of the journal Human Genetics since 1997 and Curator of the Human Gene Mutation Database (www.hgmd.org) since 1996.

Hildegard Kehrer Sawatzki is a Senior Research Fellow in the Institute of Human Genetics, University of Ulm, Germany where she has been a group leader since 2000. She has published extensively in the field of molecular medicine and molecular evolution. Alongside her long-term work on the tumour predisposition syndrome, type 1 neurofibromatosis, she has developed a keen interest in the comparative analysis of the human, chimpanzee and macaque genomes in order to identify inter-species genetic differences, particularly those which are human-specific. She has characterized, at the molecular level, the microscopically-visible chromosomal differences between human and chimpanzee known as pericentric inversions. In addition, she has performed detailed genomic comparisons which have contributed to the identification of the hundreds of small submicroscopic inversions, insertions, deletions and copy number differences that are largely responsible for the genetic divergence of the primates. In 2007, she received the Merckle Research Prize for her work on evolutionary and disease-associated chromosomal breakpoints.
David Cooper and Hildegard Kehrer-Sawatzki are the ELS section editors for Genetics & Disease and Evolution & Diversity of Life, respectively.

Table of Contents

General Concepts in Evolutionary Genetics

Views of Evolution

Evolution: Selectionist View

Evolution: Neutralist View

The Neo-selectionist Theory of Genome Evolution

Fitness and Selection

Genetic Drift in Human Populations

Heterozygosity

Effective Population Size

Population Differentiation: Measures

Evolutionary Distance

Gene Trees and Species Trees

Homologous, Orthologous and Paralogous Genes

Evolution: Convergent and Parallel Evolution

Mutation, Adaptation and Natural Selection

Genetic Variation: Polymorphisms and Mutations

Polymorphisms: Origins and Maintenance

Molecular Evolution: Introduction

Molecular Evolution: Overview

Molecular Evolution: Genetics of Adaptation

Neutral Theory of Molecular Evolution

Molecular Evolution: Nearly Neutral Theory

Molecular Evolution: Rates

Molecular Evolution: Patterns and Rates

Nucleotide Substitution: Rate of

Synonymous and Nonsynonymous Rates

Mutational Change in Evolution

Mutations and New Variation: Overview

Single-base Mutation

Mutation Rate

Mutation Rates: Evolution

Spectrum of Mutations in the Human Genome Inferred by Single Nucleotide Polymorphisms

Mutational Biases

Mutations: Dating

Diffusion Theory

Molecular Clocks in Mammals

Purifying Selection: Action on Silent Sites

Selection against Amino Acid Replacements in Human Proteins

Identifying Regions of the Human Genome that Exhibit Evidence for Positive Selection

Positive Selection on Genes in Humans as Compared to Chimpanzees

Selection Operating on Protein-coding Genes in the Human Genome

Selective and Structural Constraints

Substitution Matrices

Fixation Probabilities and Times

Genetic Code: Evolution

Codon Usage in Molecular Evolution

Linkage Disequilibrium

Recombination and Human Genetic Diversity

Comparison of Rates and Patterns of Meiotic Recombination between Human and Chimpanzees

Rapid Evolution of Genes on the Human X-chromosome

Evolutionary and Population Genetics

Gene Flow, Haplotype Patterns and Modern Human Origins

HapMap Project

Migration

Nonrandom Mating

Human Population Stratification and its Assessment by Microarray Genotyping

Sequence Alignment

Sequence Similarity

Phylogenetics

Phylogenetic Footprinting

Molecular Phylogeny Reconstruction

Evolutionary Distance: Estimation

Coalescent Theory

Stationary Allele Frequency Distributions

Developmental Evolution

Morphological Diversity: Evolution

Male-driven Evolution

Coevolution: Molecular

Concerted Evolution

Sociobiology, Evolutionary Psychology and Genetics

Are Humans Still Evolving?

Human Evolution

Hominids: Molecular Phylogenetics

Human Evolution: Overview

Molecular Clocks: Determining the Age of the Human-Chimpanzee Divergence

On the Number of Ancestral Human Species

Human Evolution: Early Radiations

Human Evolution: Radiations in the Last 300000 Years

Modern Humans: Origin and Evolution

Modern Human Origins: The `Out of Africa' Debate

Origin of Modern Humans: Interpreting the Molecular Evidence

Human Populations: Evolution

Human Populations: Origins and Evolution

Humans: Demographic History

DNA Markers and Human Evolution

Reconstructing Human History Using Autosomal, Y-Chromosomal and Mitochondrial Markers

Population History and Linkage Disequilibrium

Human Population Genetics: Drift and Migration

Human Genetics and Languages

Surnames and Genetics

Population History of Europe: Genetics

Genetic Diversity in Africa

Genetic Diversity in the German Population

Genetics and the History of the Basque People

Genetics and the Origins of the British Population

Genetics and the Origins of the Chinese

Genetics and the Origins of the Finns

Genetics and the Origins of the Irish

Genetics and the Origins of the Polynesians

Origins of the Australian and New Guinean Aborigines

Origins of the Austro-Asiatic Populations

Peopling of India: Insights from Genetics

Population Genetics of the Ashkenazim

Roma (Gypsies): Genetic Studies

The Peopling of the Americas as Revealed by Molecular Genetic Studies

Primates and the Origin of Culture

Human Genome Evolution

Evolution of Genome Organization

Genome Organization of Vertebrates

Evolutionary History of the Human Genome

Sequencing the Human Genome: Novel Insights into its Structure and Function

Single Nucleotide Polymorphism (SNP)

Human Genetic Diversity

Human and Chimpanzee Nucleotide Diversity

Divergence between the Human and Chimpanzee Genomes and its Impact on Protein and Transcriptome Evolution

Indels in the Evolution of the Human and Chimpanzee Genomes

Inferring the Process of Human-Chimpanzee Speciation

Human Genome Diversity Project (HGDP)

Blocks of Limited Haplotype Diversity

Gene Conversion during Primate Evolution

Biased Gene Conversion and its Impact on Human Genome Evolution

Repetitive DNA: Evolution

Simple Sequence Repeats in the Human Genome: Evolution

Evolution of Microsatellite DNA

Evolution of Alpha Satellite DNA

Comparative Genetics of Trinucleotide Repeats in the Human and Ape Genomes

Endogenous Retroviral Sequences; their Evolutionary Contribution to the Human Genome

Human Endogenous Retroviruses; Evolutionary Dynamics, Chromosomal Location and Host Benefit

Evolutionary History and Impact of Human DNA Transposons

Evolution of Human Retrosequences: Alu

Long Interspersed Nuclear Elements (LINEs): Evolution

Bacterial DNA in the Human Genome

Chromosome-specific Repeats (Low-copy Repeats)

Telomere

Telomeric and Subtelomeric Repeat Sequences

Subtelomeres: Evolution in the Human Genome

The Evolution of Centromeric DNA Sequences

Segmental Duplications and Their Role in the Evolution of the Human Genome

Copy Number Variation in the Human Genome

Gene Duplication: Evolution

Gene Families: Formation and Evolution

Gene Families: Multigene Families and Superfamilies

Gene Clustering in Eukaryotes

Clustering of Highly Expressed Genes in the Human Genome

Gene Distribution in Human Chromosomes

Evolution of Gene Deserts in the Human Genome

The Impact of Gene Duplication on Human Genome Evolution

Genetic Redundancy

DNA Methylation: Evolution

Evolution of Imprinting: Imprinted Gene Function in Human Disease

Imprinting: Evolution

Epigenetic Variation in Humans

Dosage Compensation Mechanisms: Evolution

Evolution of X-chromosome Inactivation

Ultraconserved DNA Sequence Elements in the Human Genome

The Biological Significance of Conserved Non-Generic DNA

Evolutionarily Conserved Noncoding DNA

Human-specific Accelerated Evolution of Noncoding Sequences

Rapidly Evolving Regions of the Human Genome

GC-Rich Isochores in the Interphase Nucleus

Evolution of Human Gene Structure and Function

Gene Structure: Evolution

Gene Evolution and Human Adaptation

The Evolution of Introns in Human Genes

Intron Evolution in Duplicated Human Genes

Intron Loss and Gain

Introns: Movements

Introns: Phase Compatibility

Evolutionarily Conserved Intronic Splicing Regulatory Elements in the Human Genome

Evolutionary Conservation of Splice Sites

Alternative Splicing: Evolution

Alternative Splicing in the Human Genome and its Evolutionary Consequences

Dual-coding Regions in Alternatively Spliced Human Genes

Birth and Evolution of Human Exons

Exons and Protein Modules

Insertion and Deletion of Exons During Human Gene Evolution

Exons: Shuffling

Pseudoexons

Domain Duplication and Gene Elongation

The Contribution of Frameshift Translation to the Generation of Novel Human Proteins

Transposable Element-driven Duplications during Hominoid Genome Evolution

The Contribution of Transposable Elements to Human Proteins

Evolutionary Emergence of Genes Through Retrotransposition

Multigene Families: Evolution

Paralogous Genes and Chromosomal Regions

Bi-directional Gene Pairs in the Human Genome

Gene Fusion

Protein Families: Evolution

Fibroblast Growth Factors: Evolution

Globin Genes: Evolution

Hox Genes and Body Plan: Evolution

Pax Genes: Evolution and Function

Low-density Lipoprotein Receptor (LDLR) Family: Genetics and Evolution

Major Histocompatibility Complex (MHC) Genes: Evolution

Major Histocompatibility Complex (MHC) Genes: Polymorphism

Vertebrate Immune System: Evolution

Evolution of the Human Immune System

Complement System: Evolution

Somatic Hypermutation of Antigen Receptor Genes: Evolution

Neuropeptides and their Receptors: Evolution

Nuclear Receptor Genes: Evolution

Olfactory Receptor Genes: Evolution

Visual Pigment Genes: Evolution

Bitter Taste Sensitivity in Humans and Chimpanzees

Evolution of Skin Pigmentation Differences in Humans

Population Genetics of Lactase Persistence and Lactose Intolerance

Defensins: Evolution

Cystic Fibrosis Transmembrane Conductance Regulator Sequences: Comparative Analysis

ATP-binding Cassette (ABC) Transporter Supergene Family: Genetics and Evolution

Proteases: Evolution

Serpins: Evolution

Adaptive Evolution of Primate Sperm Proteins

Drug Metabolism: Evolution

rRNA Genes: Evolution

MicroRNA Evolution in the Human Genome

Pseudogene Evolution in the Human Genome

Human Lineage-specific Gene Inactivation

Pseudogenes: Age

Pseudogenes: Patterns of Mutation

Processed Pseudogenes and Their Functional Resurrection in the Human and Mouse Genomes

Evolution of Gene Expression

Transcriptional Regulation: Evolution

Promoters: Evolution

Evolution of Human Gene Expression Control

Positive Selection and the Evolution of Prodynorphin

Human Transcriptome Evolution

Evolution of Gene Expression in Human and Chimpanzee Brains

Human and Chimpanzee Transcriptomes: Comparative Evolution

Human and Macaque Transcriptiomes: A comparison

Transcription Factor-binding Sites: Recent Evolution in the Human Lineage

Alternative Polyadenylation in the Human Genome: Evolution

Mitochondrial Genome Evolution

Mitochondrial Genome: Evolution

Mitochondrial Non-Mendelian Inheritance: Evolutionary Origin and Consequences

Mitochondrial Genome Sequences and Their Phylogeographic Interpretation

Mitochondrial Origins of Human Nuclear Genes and DNA Sequences

Chromosomal Evolution

Chromosomes in Mammals: Diversity and Evolution

Chromosome Numbers in Mammals

Chromosome Rearrangement Patterns in Mammalian Evolution

Hotspots of Mammalian Chromosome Evolution

Chromosomal Rearrangements in Primates

Chromosomal Rearrangements in the Human and Chimpanzee Lineages

Human Chromosome Evolution

Polyploid Origin of the Human Genome

Chromatin Structure and Human Genome Evolution

Mammalian Sex Chromosome Evolution

Evolution of the Mammalian X Chromosome

Y Chromosome Evolution

X and Y Chromosomes: Homologous Regions

Evolution of Common Fragile Sites

Comparative Genomics

Comparative Cytogenetics

Comparative Cytogenetics Technologies

Reconstruction of Ancestral Genomes

Comparative Human Genomics

Orthologues, Paralogues and Xenologues in Human and Other Genomes

Comparing the Human and Sea Urchin Genomes

Comparing the Human and Fish Genomes

Comparing the Human and Medaka Genomes

Fugu: The Pufferfish Model Genome

The Mouse Genome as a Rodent Model in Evolutionary Studies

The Rat Genome as a Rodent Model in Evolutionary Studies

Comparing the Human and Canine Genomes

Primate Phylogenetics

The Sequencing of the Rhesus Macaque Genome and its Comparison with the Genome Sequences of Human and Chimpanzee

The Chimpanzee Genome Project

Comparing the Human and Chimpanzee Genomes

Nucleotide Sequence Divergence between Humans and Chimpanzees

Human-specific Changes of Genome Structure

Evolution and Disease Susceptibility

Evolutionary Thinking in the Medical Sciences

Pathological Missense Mutations Provide New Insights into the Evolution of Trypsinogen Genes

Balancing Selection in Human Evolution

Selective Constraints on Human Disease Mutations and Polymorphisms

Genetic of Large Populations and Association Studies

Genetic Disease in the Ashkenazim: Role of a Founder Effect

Single Nucleotide Polymorphisms in Human Disease and Evolution: Phylogenies and Genealogies

Structural Diversity of the Human Genome and Disease Susceptibility

María Gutiérrez-Arcelus

Segmental Duplications and Genetic Disease

Genetics of Susceptibility to Human Infectious Diseases

The Genetics of Malarial Resistance and Susceptibility

The Evolution of Fatness and Susceptibility to Obesity

Thrifty Genotype Hyphothesis and Complex Genetic Disease

An Evolutionary Framework for Common Disease

On Sequence Variants that Influence the Risk of Common Diseases

An Evolutionary Genetic Framework for Heritable Disorders

Analysis of Ancient DNA

Ancient DNA: Recovery and Analysis

Ancient DNA: Phylogenetic Applications

Neanderthal Mitochondrial DNA

Reconstructing Ancient DNA Sequences in Silico

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