Human Evolutionary Genetics 2nd Edition by Mark Jobling, Edward Hollox, Matthew Hurles, Toomas Kivisild, Chris Tyler Smith ISBN 0815341482 9780815341482

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ISBN 10: 0815341482 
ISBN 13: 9780815341482
Author: Mark Jobling, Edward Hollox, Matthew Hurles, Toomas Kivisild, Chris Tyler-Smith

Human Evolutionary Genetics 2nd Table of contents:

Chapter 1: An Introduction to Human Evolutionary Genetics
1.1 What is human evolutionary genetics?
1.2 Insights into phenotypes and diseases
A shared evolutionary history underpins our understanding of biology
Understanding evolutionary history is essential to understanding human biology today
Understanding evolutionary history shapes our expectations about the future
1.3 Complementary records of the human past
Understanding chronology allows comparison of evidence from different scientific approaches
It is important to synthesize different records of the past
None of the different records represents an unbiased picture of the past
1.4 What can we know about the past?
1.5 The ethics of studying human populations
Summary
References
Section 1: How do we study genome diversity?
Chapter 2: Organization and inheritance of the human genome
2.1 The Big Picture: An Overview of the human genome
2.2 Structure of DNA
2.3 Genes, Transcription, and Translation
Genes are made up of introns and exons, and include elements to initiate and regulate transcription
The genetic code allows nucleotide sequences to be translated into amino acid sequences
Gene expression is highly regulated in time and space
2.4 Noncoding DNA
Some DNA sequences in the genome are repeated in multiple copies
2.5 Human chromosomes and the human karyotype
The human genome is divided into 46 chromosomes
Size, centromere position, and staining methods allow chromosomes to be distinguished
2.6 Mitosis, meiosis, and the inheritance of the genome
2.7 Recombination—the great reshuffler
2.8 Nonrecombining segments of the genome
The male-specific Y chromosome escapes crossing over for most of its length
Maternally inherited mtDNA escapes from recombination
Summary
Questions
References
Chapter 3: Human genome variation
3.1 Genetic Variation and the Phenotype
Some DNA sequence variation causes Mendelian genetic disease
The relationship between genotype and phenotype is usually complex
Mutations are diverse and have different rates and mechanisms
3.2 Single Nucleotide Polymorphisms (Snps) in the Nuclear Genome
Base substitutions can occur through base misincorporation during DNA replication
Base substitutions can be caused by chemical and physical mutagens
Sophisticated DNA repair processes can fix much genome damage
The rate of base substitution can be estimated indirectly or directly
Because of their low mutation rate, SNPs usually show identity by descent
The CpG dinucleotide is a hotspot for mutation
Base substitutions and indels can affect the functions of genes
Synonymous base substitutions
Nonsynonymous base substitutions
Indels within genes
Base substitutions outside ORFs
Whole-genome resequencing provides an unbiased picture of SNP diversity
3.3 Sequence Variation in Mitochondrial DNA
mtDNA has a high mutation rate
The transmission of mtDNA mutations between generations is complex
3.4 Variation in Tandemly Repeated DNA Sequences
Microsatellites have short repeat units and repeat arrays, and mutate through replication slippage
Microsatellite mutation rates and processes
Minisatellites have longer repeat units and arrays, and mutate through recombination mechanisms
Minisatellite diversity and mutation
Telomeres contain specialized and functionally important repeat arrays
Satellites are large, sometimes functionally important, repeat arrays
3.5 Transposable Element Insertions
3.6 Structural Variation in the Genome
Some genomic disorders arise from recombination between segmental duplications
Copy-number variation is widespread in the human genome
Cytogenetic examination of chromosomes can reveal large-scale structural variants
3.7 The Effects of Age and sex on Mutation Rate
3.8 The effects of Recombination on Genome Variation
Genomewide haplotype structure reveals past recombination behavior
Recombination behavior can be revealed by direct studies in pedigrees and sperm DNA
The process of gene conversion results in nonreciprocal exchange between DNA sequences
Summary
Questions
References
Chapter 4: Finding and assaying genome diversity
4.1 First, Find Your DNA
4.2 The polymerase chain reaction (PCR)
4.3 Sanger sequencing, the human reference sequence, and snp discovery
4.4 A Quantum Leap in variation studies: next-generation sequencing
Illumina sequencing is a widely used NGS method
Sequencing can be targeted to regions of specific interest or the exome
NGS data have to be processed and interpreted
Third-generation methods use original, unamplifiedDNA
4.5 SNP typing: low-, medium-, and high-throughput methods for assaying variation
PCR-RFLP typing is a simple low-throughput method
Primer extension and detection by mass spectrometry is a medium-throughput method
High throughput SNP chips simultaneously analyze more than 1 million SNPs
Whole-genome SNP chips are based on a tag SNP design
4.6 Databases of sequence variation
4.7 Discovering and assaying variation at microsatellites
4.8 Discovering And Assaying structural variation on different scales
Discovering and assaying variation at minisatellites
Discovering and assaying variation at well-defined indels, including Alu/LINE polymorphisms
Discovering and assaying structural polymorphisms and copy-number variants
4.9 Phasing: from genotypes to haplotypes
Haplotypes can be determined by physical separation
Haplotypes can be determined by statistical methods
4.10 Studying genetic variation in ancient samples
DNA is degraded after death
Contamination is a major problem
Application of next-generation sequencing to aDNA analysis
Summary
Questions
References
Section 2: How do we interpret genetic variation?
Chapter 5: Processes shaping diversity
5.1 Basic concepts in population genetics
Why do we need evolutionary models?
The Hardy–Weinberg equilibrium is a simple model in population genetics
5.2 Generating diversity by mutation and recombination
Mutation changes allele frequencies
Mutation can be modeled in different ways
Meiotic recombination generates new combinations of alleles
Linkage disequilibrium is a measure of recombination at the population level
Recombination results in either crossing over or gene conversion, and is not uniform across the genome
5.3 Eliminating diversity by genetic drift
The effective population size is a key concept in population genetics
Different parts of the genome have different effective population sizes
Genetic drift causes the fixation and elimination of new alleles
Variation in census population size and reproductive success influence effective population size
Population subdivision can influence effective population size
Mate choice can influence effective population size
Genetic drift influences the disease heritages of isolated populations
5.4 The effect of selection on diversity
Mate choice can affect allele frequencies by sexual selection
5.5 Migration
There are several models of migration
There can be sex-specific differences in migration
5.6 Interplay among the different forces of evolution
There are important equilibria in population genetics
Mutation–drift balance
Recombination–drift balance
Mutation–selection balance
Does selection or drift determine the future of an allele?
5.7 The neutral theory of molecular evolution
The molecular clock assumes a constant rate of mutation and can allow dating of speciation
There are problems with the assumptions of the molecular clock
Summary
Questions
References
Chapter 6: Making inferences from diversity
6.1 What data can we use?
6.2 Summarizing genetic variation
Heterozygosity is commonly used to measure genetic diversity
Nucleotide diversity can be measured using the population mutation parameter theta (θ)
The mismatch distribution can be used to represent genetic diversity
6.3 Measuring genetic distance
Genetic distances between populations can be measured using FST or Nei’s D statistics
Distances between alleles can be calculated using models of mutation
Genomewide data allow calculation of genetic distances between individuals
Complex population structure can be analyzed statistically
Population structure can be analyzed using genomic data
Genetic distance and population structure can be represented using multivariate analyses
6.4 Phylogenetics
Phylogenetic trees have their own distinctive terminology
There are several different ways to reconstruct phylogenies
Trees can be constructed from matrices of genetic distances
Trees can be generated using character-based methods
How confident can we be of a particular phylogenetic tree?
Networks are methods for displaying multiple equivalent trees
6.5 Coalescent approaches to reconstructing population history
The genealogy of a DNA sequence can be described mathematically
Neutral mutations can be modeled on the gene genealogy using Poisson statistics
Coalescent analysis can be a simulation tool for hypothesis testing
Coalescent analysis uses ancestral graphs to model selection and recombination
Coalescent models of large datasets are approximate
6.6 Dating evolutionary events using genetic data
Dating population splits using FST and Nei’s D statistics is possible, but requires a naive view of human evolution
Evolutionary models can include the timing of evolutionary events as parameters
Evolutionary models and effective population size
An allele can be dated using diversity at linked loci
Interpreting TMRCA
Estimations of mutation rate can be derived from direct measurements in families or indirect comparisons of species
An estimate of generation time is required to convert some genetic date estimates into years
6.7 Has selection been acting?
Differences in gene sequences between species can be used to detect selection
Comparing variation between species with variation within a species can detect selection
Selection tests can be based on the analysis of allele frequencies at variant sites
Comparing haplotype frequency and haplotype diversity can reveal positive selection
Analysis of frequency differences between populations can indicate positive selection
Other methods can be used to detect ongoing or very recent positive selection
How can we combine information from different statistical tests?
Tests for positive selection have severe limitations
6.8 Analyzing genetic data in a geographical context
Genetic data can be displayed on maps
Genetic boundary analysis identifies the zones of greatest allele frequency change within a genetic landscape
Spatial autocorrelation quantifies the relationship of allele frequency with geography
Mantel testing is an alternative approach to examining a relationship between genetic distance and other distance measures
Summary
Questions
References
Section 3: Where and when did humans originate?
Chapter 7: Humans as apes
Which nonhuman animals are the closest living relatives of humans?
Are humans typical apes?
7.1 Evidence from morphology
Primates are an Order of mammals
Hominoids share a number of phenotypic features with other anthropoids
Ancestral relationships of hominoids are difficult to resolve on morphological evidence
7.2 Evidence from chromosomes
Human and great ape karyotypes look similar, but not identical
Molecular cytogenetic analyses support the picture from karyotype comparisons
7.3 Evidence from molecules
Molecular data support a recent date of the ape–human divergence
Genetic data have resolved the gorilla–chimpanzee–human trichotomy
Sequence divergence is different among great apes across genetic loci
Great apes differ by gains and losses of genetic material
The DNA sequence divergence rates differ in hominoid lineages
7.4 Genetic diversity among the great apes
How many genera, species, and subspecies are there?
Intraspecific diversity in great apes is greater than in humans
Signatures of lineage-specific selection can be detected in ape genomes
Summary
Questions
References
Chapter 8: What Genetic Changes Have Made us Human?
8.1 Morphological and behavioral changes en route to homo sapiens
some human traits evolved early in hominin history
The human mind is unique
Only a few phenotypes are unique to modern humans
8.2 Genetic uniqueness of humans and hominins
The sequence and structural differences between humans and other great apes can be cataloged
Humans have gained and lost a few genes compared with other great apes
Humans differ in the sequence of genes compared with other great apes
Humans differ from other apes in the expression levels of genes
Genome sequencing has revealed a small number of fixed genetic differences between humans and both Neanderthals and Denisovans
8.3 Genetic basis of phenotypic differences between apes and humans
Mutations causing neoteny have contributed to the evolution of the human brain
The genetic basis for laterality and language remains unclear
What next?
Summary
Questions
References
Chapter 9: Origins of Modern Humans
9.1 Evidence from fossils and morphology
Some fossils that may represent early hominins from 4–7 MYA are known from Africa
Fossils of australopithecines and their contemporaries are known from Africa
The genus Homo arose in Africa
The earliest anatomically modern human fossils are found in Africa
The morphology of current populations suggests an origin in Africa
9.2 Evidence from archaeology and linguistics
Paleolithic archaeology has been studied extensively
Evidence from linguistics suggests an origin of language in Africa
9.3 Hypotheses to explain the origin of modern humans
9.4 Evidence from the genetics of present-day populations
Genetic diversity is highest in Africa
Genetic phylogenies mostly root in Africa
Mitochondrial DNA phylogeny
Y-chromosomal phylogeny
Other phylogenies
Insights can be obtained from demographic models
9.5 Evidence from ancient dna
Ancient mtDNA sequences of Neanderthals and Denisovans are distinct from modern human variation
A Neanderthal draft genome sequence has been generated
A Denisovan genome sequence has been generated
Summary
Questions
References
Section 4: How did humans colonize the world?
Chapter 10: The Distribution of Diversity
10.1 Studying human diversity
The history and ethics of studying diversity are complex
Linnaeus’ classification of human diversity
Galton’s “Comparative worth of different races”
Modern attitudes to studying diversity
Who should be studied?
A few large-scale studies of human genetic variation have made major contributions to human evolutionary genetics
What is a population?
How many people should be analyzed?
10.2 Apportionment of human diversity
The apportionment of diversity shows that most variation is found within populations
The apportionment of diversity can differ between segments of the genome
Patterns of diversity generally change gradually from place to place
The origin of an individual can be determined surprisingly precisely from their genotype
The distribution of rare variants differs from that of common variants
10.3 The influence of selection on the apportionment of diversity
The distribution of levels of differentiation has been studied empirically
Low differentiation can result from balancing selection
High differentiation can result from directional selection
Positive selection at EDAR
Summary
Questions
References
Chapter 11: The colonization of the old world and australia
11.1 A Colder and more variable environment 15–100 Kya
100–70 Kya
Glacial maximum,70–55 Kya
55–25 Kya
Last glacial maximum (LGM),23–14 Kya
Holocene, 12 KYA to present
11.2 Fossil and archaeological evidence for two expansions of anatomically modern humans out of africa in the last ∼130 KY
Anatomically modern, behaviorally pre-modern humans expanded transiently into the Middle East ∼90–120 KYA
Modern human behavior first appeared in Africa after 100 KYA
Fully modern humans expanded into the Old World and Australia ∼50–70 KYA
Modern human fossils in Asia, Australia, and Europe
Initial colonization of Australia
Upper Paleolithic transition in Europe and Asia
11.3 A single major migration out of africa 50–70 KYA
Populations outside Africa carry a shared subset of African genetic diversity with minor Neanderthal admixture
mtDNA and Y-chromosomal studies show the descent of all non-African lineages from a single ancestor for each who lived 55–75 KYA
11.4 Early population divergence between australians and eurasians
Summary
Questions
References
Chapter 12: Agricultural expansions
12.1 Defining agriculture
12.2 The where, when, and why of agriculture
Where and when did agriculture develop?
Why did agriculture develop?
Which domesticates were chosen?
12.3 Outcomes of agriculture
Agriculture had major impacts on demography and disease
Rapid demographic growth
Malnutrition and infectious disease
Agriculture led to major societal changes
12.4 The farming–language co-dispersal hypothesis
Some language families have spread widely and rapidly
Linguistic dating and construction of proto-languages have been used to test the hypothesis
What are the genetic implications of language spreads?
12.5 Out of the near east into europe
Nongenetic evidence provides dates for the European Neolithic
Different models of expansion give different expectations for genetic patterns
Models are oversimplifications of reality
Principal component analysis of classical genetic polymorphisms was influential
Interpreting synthetic maps
mtDNA evidence has been controversial, but ancient DNA data are transforming the field
Data from ancient mtDNA
Y-chromosomal data show strong clines in Europe
New developments for the Y chromosome
Biparentally inherited nuclear DNA has not yet contributed much, but important ancient DNA data are now emerging
Ancient DNA data
What developments will shape debate in the future?
12.6 Out of tropical west africa into sub-equatorial africa
There is broad agreement on the background to African agricultural expansion
Rapid spread of farming economies
Bantu languages spread far and rapidly
Genetic evidence is broadly consistent, though ancient DNA data are lacking
Genomewide evidence
Evidence from mtDNA and the Y chromosome
12.7 Genetic analysis of domesticated animals and plants
Selective regimes had a massive impact on phenotypes and genetic diversity
Key domestication changes in crops
Effects on crop genetic diversity
Phenotypic and genetic change in animals
How have the origins of domesticated plants been identified?
How have the origins of domesticated animals been identified?
Cattle domestication
Summary
Questions
References
Chapter 13: Into New-Found Lands
13.1 Settlement of the new territories
Sea levels have changed since the out-of-Africa migration
What drives new settlement of uninhabited lands?
13.2 Peopling of the americas
The changing environment has provided several opportunities for the peopling of the New World
Fossil and archaeological evidence provide a range of dates for the settlement of the New World
Fossils
Archaeological remains
Clovis and the Paleoindians
Pre-Clovis sites
Unresolved issues
Did the first settlers go extinct?
A three-migration hypothesis has been suggested on linguistic grounds
Genetic evidence has been used to test the single- and the three-wave migration scenarios
Mitochondrial DNA evidence
Interpretation of the mtDNA data
Evidence from the Y chromosome
Evidence from the autosomes
Conclusions from the genetic data
13.3 Peopling of the pacific
Fossil and archaeological evidence suggest that Remote Oceania was settled more recently than Near Oceania
Two groups of languages are spoken in Oceania
Several models have been proposed to explain the spread of Austronesian speakers
Austronesian dispersal models have been tested with genetic evidence
Classical polymorphisms
Globin gene mutations
Mitochondrial DNA
The Y chromosome
Autosomal evidence
Evidence from other species has been used to test the Austronesian dispersal models
Summary
Questions
References
Chapter 14: What Happens when Populations Meet
14.1 What is genetic admixture?
Admixture has distinct effects on genetic diversity
14.2 The impact of admixture
Dierent sources of evidence can inform us about admixture
Consequences of admixture for language
Archaeological evidence for admixture
The biological impact of admixture
14.3 Detecting admixture
Methods based on allele frequency can be used to detect admixture
Admixture proportions vary among individuals and populations
Calculating individual admixture levels using multiple loci
Calculating individual admixture levels using genomewide data
Calculating admixture levels from estimated ancestry components
Problems of measuring admixture
Natural selection can affect the admixture proportions of individual genes
14.4 Local admixture and linkage disequilibrium
How does admixture generate linkage disequilibrium?
Admixture mapping
Admixture dating
14.5 Sex-Biased admixture
What is sex-biased admixture?
Detecting sex-biased admixture
Sex-biased admixture resulting from directional mating
The effect of admixture on our genealogical ancestry
14.6 Transnational isolates
Roma and Jews are examples of widely spread transnational isolates
European Roma
The Jews
Summary
Questions
References
Section 5: How is an evolutionary perspective useful?
Chapter 15: Understanding the past, present, and future of phenotypic variation
15.1 Normal and pathogenic variation in an evolutionary context
15.2 Known variation in human phenotypes
What is known about human phenotypic variation?
Morphology and temperature adaptation
Facial features
Tooth morphology and cranial proportions
Behavioral differences
How do we uncover genotypes underlying phenotypes?
What have we discovered about genotypes underlying phenotypes?
15.3 Skin pigmentation as an adaptation to ultraviolet light
Melanin is the most important pigment influencing skin color
Variable ultraviolet light exposure is an adaptive explanation for skin color variation
Short-term UVR exposure causes sunburn
Long-term UVR exposure causes cancers
UVR causes nutrient photodegradation in the skin
Several genes that affect human pigmentation are known
Genetic variation in human pigmentation genes is consistent with natural selection
Does sexual selection have a role in human phenotypic variation?
15.4 Life at high altitude and adaptation to hypoxia
Natural selection has influenced the overproduction of red blood cells
High-altitude populations differ in their adaptation to altitude
15.5 Variation in the sense of taste
Variation in tasting phenylthiocarbamide is mostly due to alleles of the TAS2R38 gene
There is extensive diversity of bitter taste receptors in humans
Sweet, umami, and sour tastes may show genetic polymorphism
15.6 Adapting to a changing diet by digesting milk and starch
There are several adaptive hypotheses to explain lactase persistence
Lactase persistence is caused by SNPs within an enhancer of the lactase gene
Increased copy number of the amylase gene reflects an adaptation to a high-starch diet
15.7 The future of human evolution
Have we stopped evolving?
Natural selection acts on modern humans
Can we predict the role of natural selection in the future?
Climate change
Dietary change
Infectious disease
What will be the effects of future demographic changes?
Increasing population size
Increased mobility
differential fertility
differential generation time
Will the mutation rate change?
Summary
Questions
References
Chapter 16: Evolutionary Insights into Simple Genetic Diseases
16.1 Genetic disease and mutation–selection balance
Variation in the strength of purifying selection can affect incidence of genetic disease
Variation in the deleterious mutation rate can affect incidence of genetic disease
16.2 Genetic drift, founder effects, and consanguinity
Jewish populations have a particular disease heritage
Finns have a disease heritage very distinct from other Europeans
Consanguinity can lead to increased rates of genetic disease
16.3 Evolutionary causes of genomic disorders
Segmental duplications allow genomic rearrangements with disease consequences
Duplications accumulated in ancestral primates
16.4 Genetic diseases and selection by malaria
Sickle-cell anemia is frequent in certain populations due to balancing selection
α-Thalassemias are frequent in certain populations due to balancing selection
Glucose-6-phosphate dehydrogenase deficiency alleles are maintained at high frequency in malaria-endemic populations
What can these examples tell us about natural selection?
Summary
Questions
References
Chapter 17: Evolution and Complex Diseases
17.1 Defining complex disease
The genetic contribution to variation in disease risk varies between diseases
Infectious diseases are complex diseases
17.2 The global distribution of complex diseases
Is diabetes a consequence of a post-agricultural change in diet?
The drifty gene hypothesis
Evidence from genomewide studies
The thrifty phenotype hypothesis
17.3 Identifying alleles involved in complex disease
Genetic association studies are more powerful than linkage studies for detecting small genetic effects
Candidate gene association studies have not generally been successful in identifying susceptibility alleles for complex disease
Genomewide association studies can reliably identify susceptibility alleles to complex disease
GWAS data have been used for evolutionary genetic analysis
17.4 What complex disease alleles do we expect to find in the population?
Negative selection acts on disease susceptibility alleles
Positive selection acts on disease resistance alleles
Severe sepsis and CASP12
Malaria and the Duffy antigen
HIV-1 and CCR5Δ32
Unexpectedly, some disease susceptibility alleles with large effects are observed at high frequency
Susceptibility to kidney disease, APOL1, and resistance to sleeping sickness
Implications for other GWAS results
17.5 Genetic influence on variable response to drugs
Population differences in drug-response genes exist, but are not well understood
Summary
Questions
References
Chapter 18: Identity and identification
18.1 Individual Identification
The first DNA fingerprinting and profiling methods relied on mini satellites
PCR-based microsatellite profiling superseded minisatellite analysis
How do we interpret matching DNA profiles?
Complications from related individuals, and DNA mixtures
Large forensic identification databases are powerful tools in crime-fighting
Controversial aspects of identification databases
The Y chromosome and mtDNA are useful in specialized cases
Y chromosomes in individual identification
mtDNA in individual identification
18.2 What dna can tell us about john or jane doe
DNA-based sex testing is widely used and generally reliable
Sex reversal
Deletions of the AMELY locus in normal males
Some other phenotypic characteristics are predictable from DNA
Reliability of predicting population of origin depends on what DNA variants are analyzed
Prediction from forensic microsatellite multiplexes
Prediction from other systems
The problem of admixed populations
18.3 Deducing family and genealogical relationships
The probability of paternity can be estimated confidently
Other aspects of kinship analysis
The Y chromosome and mtDNA are useful in genealogical studies
The Thomas Jefferson paternity case
DNA-based identification of the Romanovs
Y-chromosomal DNA has been used to trace modern diasporas
Y-chromosomal haplotypes tend to correlate with patrilineal surnames
18.4 The personal genomics revolution
The first personal genetic analysis involved the Y chromosome and mtDNA
Personal genomewide SNP analysis is used for ancestry and health testing
Personal genome sequencing provides the ultimate resolution
Personal genomics offers both promise and problems

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