|
Chapter 1 An Introduction to Human Evolutionary Genetics |
|
|
1 | (16) |
|
1.1 What is Human Evolutionary Genetics? |
|
|
1 | (1) |
|
1.2 Insights into Phenotypes and Diseases |
|
|
2 | (4) |
|
A shared evolutionary history underpins our understanding of biology |
|
|
2 | (2) |
|
Understanding evolutionary history is essential to understanding human biology today |
|
|
4 | (1) |
|
Understanding evolutionary history shapes our expectations about the future |
|
|
5 | (1) |
|
1.3 Complementary Records of the Human Past |
|
|
6 | (5) |
|
Understanding chronology allows comparison of evidence from different scientific approaches |
|
|
8 | (2) |
|
It is important to synthesize different records of the past |
|
|
10 | (1) |
|
None of the different records represents an unbiased picture of the past |
|
|
10 | (1) |
|
1.4 What Can We Know About the Past? |
|
|
11 | (1) |
|
1.5 The Ethics of Studying Human Populations |
|
|
12 | (5) |
|
|
|
14 | (1) |
|
|
|
14 | (3) |
|
Chapter 2 Organization and Inheritance of the Human Genome |
|
|
17 | (26) |
|
2.1 The Big Picture: An Overview of the Human Genome |
|
|
17 | (3) |
|
|
|
20 | (2) |
|
2.3 Genes, Transcription, and Translation |
|
|
22 | (4) |
|
Genes are made up of introns and exons, and include elements to initiate and regulate transcription |
|
|
22 | (2) |
|
The genetic code allows nucleotide sequences to be translated into amino acid sequences |
|
|
24 | (2) |
|
Gene expression is highly regulated in time and space |
|
|
26 | (1) |
|
|
|
26 | (2) |
|
Some DNA sequences in the genome are repeated in multiple copies |
|
|
27 | (1) |
|
2.5 Human Chromosomes and the Human Karyotype |
|
|
28 | (3) |
|
The human genome is divided into 46 chromosomes |
|
|
29 | (2) |
|
Size, centromere position, and staining methods allow chromosomes to be distinguished |
|
|
31 | (1) |
|
2.6 Mitosis, Meiosis, and the Inheritance of the Genome |
|
|
31 | (3) |
|
2.7 Recombination---The Great Reshuffler |
|
|
34 | (2) |
|
2.8 Nonrecombining Segments of the Genome |
|
|
36 | (7) |
|
The male-specific Y chromosome escapes crossing over for most of its length |
|
|
37 | (1) |
|
Maternally inherited mtDNA escapes from recombination |
|
|
37 | (3) |
|
|
|
40 | (1) |
|
|
|
41 | (1) |
|
|
|
41 | (2) |
|
Chapter 3 Human Genome Variation |
|
|
43 | (52) |
|
3.1 Genetic Variation and the Phenotype |
|
|
43 | (4) |
|
Some DNA sequence variation causes Mendelian genetic disease |
|
|
44 | (2) |
|
The relationship between genotype and phenotype is usually complex |
|
|
46 | (1) |
|
Mutations are diverse and have different rates and mechanisms |
|
|
46 | (1) |
|
3.2 Single Nucleotide Polymorphisms (SNPS) in the Nuclear Genome |
|
|
47 | (15) |
|
Base substitutions can occur through base misincorporation during DNA replication |
|
|
49 | (2) |
|
Base substitutions can be caused by chemical and physical mutagens |
|
|
51 | (1) |
|
Sophisticated DNA repair processes can fix much genome damage |
|
|
52 | (1) |
|
The rate of base substitution can be estimated indirectly or directly |
|
|
53 | (2) |
|
Because of their low mutation rate, SNPs usually show identity by descent |
|
|
55 | (1) |
|
The CpG dinucleotide is a hotspot for mutation |
|
|
55 | (2) |
|
Base substitutions and indels can affect the functions of genes |
|
|
57 | (1) |
|
Synonymous base substitutions |
|
|
57 | (1) |
|
Nonsynonymous base substitutions |
|
|
58 | (1) |
|
|
|
59 | (1) |
|
Base substitutions outside ORFs |
|
|
60 | (1) |
|
Whole-genome resequencing provides an unbiased picture of SNP diversity |
|
|
61 | (1) |
|
3.3 Sequence Variation in Mitochondrial DNA |
|
|
62 | (3) |
|
mtDNA has a high mutation rate |
|
|
62 | (2) |
|
The transmission of mtDNA mutations between generations is complex |
|
|
64 | (1) |
|
3.4 Variation in Tandemly Repeated DNA Sequences |
|
|
65 | (8) |
|
Microsatellites have short repeat units and repeat arrays, and mutate through replication slippage |
|
|
66 | (1) |
|
Microsatellite mutation rates and processes |
|
|
67 | (2) |
|
Minisatellites have longer repeat units and arrays, and mutate through recombination mechanisms |
|
|
69 | (1) |
|
Minisatellite diversity and mutation |
|
|
70 | (1) |
|
Telomeres contain specialized and functionally important repeat arrays |
|
|
71 | (1) |
|
Satellites are large, sometimes functionally important, repeat arrays |
|
|
72 | (1) |
|
3.5 Transposable Element Insertions |
|
|
73 | (2) |
|
3.6 Structural Variation in the Genome |
|
|
75 | (3) |
|
Some genomic disorders arise from recombination between segmental duplications |
|
|
76 | (1) |
|
Copy-number variation is widespread in the human genome |
|
|
77 | (1) |
|
Cytogenetic examination of chromosomes can reveal large-scale structural variants |
|
|
78 | (1) |
|
3.7 The Effects of Age and Sex on Mutation Rate |
|
|
78 | (3) |
|
3.8 The Effects of Recombination on Genome Variation |
|
|
81 | (14) |
|
Genomewide haplotype structure reveals past recombination behavior |
|
|
84 | (3) |
|
Recombination behavior can be revealed by direct studies in pedigrees and sperm DNA |
|
|
87 | (1) |
|
The process of gene conversion results in nonreciprocal exchange between DNA sequences |
|
|
88 | (2) |
|
|
|
90 | (1) |
|
|
|
91 | (1) |
|
|
|
92 | (3) |
|
Chapter 4 Finding and Assaying Genome Diversity |
|
|
95 | (38) |
|
|
|
96 | (2) |
|
4.2 The Polymerase Chain Reaction (PCR) |
|
|
98 | (2) |
|
4.3 Sanger Sequencing, the Human Reference Sequence, and SNP Discovery |
|
|
100 | (1) |
|
4.4 A Quantum Leap in Variation Studies: Next-Generation Sequencing |
|
|
101 | (7) |
|
Illumina sequencing is a widely used NGS method |
|
|
102 | (3) |
|
Sequencing can be targeted to regions of specific interest or the exome |
|
|
105 | (1) |
|
NGS data have to be processed and interpreted |
|
|
106 | (1) |
|
Third-generation methods use original, unamplified DNA |
|
|
107 | (1) |
|
4.5 SNP Typing: Low-, Medium-, and High-Throughput Methods for Assaying Variation |
|
|
108 | (4) |
|
PCR-RFLP typing is a simple low-throughput method |
|
|
108 | (1) |
|
Primer extension and detection by mass spectrometry is a medium-throughput method |
|
|
109 | (1) |
|
High throughput SNP chips simultaneously analyze more than 1 million SNPs |
|
|
110 | (1) |
|
Whole-genome SNP chips are based on a tag SNP design |
|
|
110 | (2) |
|
4.6 Databases of Sequence Variation |
|
|
112 | (1) |
|
4.7 Discovering and Assaying Variation at Microsatellites |
|
|
112 | (2) |
|
4.8 Discovering and Assaying Structural Variation on Different Scales |
|
|
114 | (5) |
|
Discovering and assaying variation at minisatellites |
|
|
114 | (1) |
|
Discovering and assaying variation at well-defined indels, including Alu/LINE polymorphisms |
|
|
115 | (1) |
|
Discovering and assaying structural polymorphisms and copy-number variants |
|
|
115 | (4) |
|
4.9 Phasing: From Genotypes to Haplotypes |
|
|
119 | (4) |
|
Haplotypes can be determined by physical separation |
|
|
120 | (1) |
|
Haplotypes can be determined by statistical methods |
|
|
120 | (2) |
|
Haplotypes can be determined by pedigree analysis |
|
|
122 | (1) |
|
4.10 Studying Genetic Variation in Ancient Samples |
|
|
123 | (10) |
|
DNA is degraded after death |
|
|
123 | (2) |
|
Contamination is a major problem |
|
|
125 | (2) |
|
Application of next-generation sequencing to aDNA analysis |
|
|
127 | (2) |
|
|
|
129 | (1) |
|
|
|
130 | (1) |
|
|
|
130 | (3) |
|
Chapter 5 Processes Shaping Diversity |
|
|
133 | (34) |
|
5.1 Basic Concepts in Population Genetics |
|
|
133 | (3) |
|
Why do we need evolutionary models? |
|
|
133 | (1) |
|
The Hardy--Weinberg equilibrium is a simple model in population genetics |
|
|
134 | (2) |
|
5.2 Generating Diversity by Mutation and Recombination |
|
|
136 | (5) |
|
Mutation changes allele frequencies |
|
|
137 | (1) |
|
Mutation can be modeled in different ways |
|
|
137 | (2) |
|
Meiotic recombination generates new combinations of alleles |
|
|
139 | (1) |
|
Linkage disequilibrium is a measure of recombination at the population level |
|
|
140 | (1) |
|
Recombination results in either crossing over or gene conversion, and is not uniform across the genome |
|
|
140 | (1) |
|
5.3 Eliminating Diversity by Genetic Drift |
|
|
141 | (8) |
|
The effective population size is a key concept in population genetics |
|
|
142 | (1) |
|
Different parts of the genome have different effective population sizes |
|
|
143 | (1) |
|
Genetic drift causes the fixation and elimination of new alleles |
|
|
143 | (1) |
|
Variation in census population size and reproductive success influence effective population size |
|
|
144 | (3) |
|
Population subdivision can influence effective population size |
|
|
147 | (1) |
|
Mate choice can influence effective population size |
|
|
148 | (1) |
|
Genetic drift influences the disease heritages of isolated populations |
|
|
149 | (1) |
|
5.4 The Effect of Selection on Diversity |
|
|
149 | (5) |
|
Mate choice can affect allele frequencies by sexual selection |
|
|
153 | (1) |
|
|
|
154 | (2) |
|
There are several models of migration |
|
|
154 | (1) |
|
There can be sex-specific differences in migration |
|
|
155 | (1) |
|
5.6 Interplay Among the Different Forces of Evolution |
|
|
156 | (4) |
|
There are important equilibria in population genetics |
|
|
157 | (1) |
|
|
|
157 | (1) |
|
Recombination--drift balance |
|
|
157 | (1) |
|
Mutation--selection balance |
|
|
158 | (1) |
|
Does selection or drift determine the future of an allele? |
|
|
159 | (1) |
|
5.7 The Neutral Theory of Molecular Evolution |
|
|
160 | (7) |
|
The molecular clock assumes a constant rate of mutation and can allow dating of speciation |
|
|
160 | (1) |
|
There are problems with the assumptions of the molecular clock |
|
|
161 | (2) |
|
|
|
163 | (1) |
|
|
|
164 | (1) |
|
|
|
164 | (3) |
|
Chapter 6 Making Inferences from Diversity |
|
|
167 | (58) |
|
6.1 What Data Can We Use? |
|
|
167 | (1) |
|
6.2 Summarizing Genetic Variation |
|
|
168 | (5) |
|
Heterozygosity is commonly used to measure genetic diversity |
|
|
168 | (1) |
|
Nucleotide diversity can be measured using the population mutation parameter theta (θ) |
|
|
169 | (3) |
|
The mismatch distribution can be used to represent genetic diversity |
|
|
172 | (1) |
|
6.3 Measuring Genetic Distance |
|
|
173 | (9) |
|
Genetic distances between populations can be measured using Fst or Nei's D statistics |
|
|
173 | (2) |
|
Distances between alleles can be calculated using models of mutation |
|
|
175 | (1) |
|
Genomewide data allow calculation of genetic distances between individuals |
|
|
176 | (1) |
|
Complex population structure can be analyzed statistically |
|
|
177 | (1) |
|
Population structure can be analyzed using genomic data |
|
|
178 | (1) |
|
Genetic distance and population structure can be represented using multivariate analyses |
|
|
179 | (3) |
|
|
|
182 | (8) |
|
Phylogenetic trees have their own distinctive terminology |
|
|
182 | (2) |
|
There are several different ways to reconstruct phylogenies |
|
|
184 | (1) |
|
Trees can be constructed from matrices of genetic distances |
|
|
184 | (1) |
|
Trees can be generated using character-based methods |
|
|
185 | (3) |
|
How confident can we be of a particular phylogenetic tree? |
|
|
188 | (1) |
|
Networks are methods for displaying multiple equivalent trees |
|
|
188 | (2) |
|
6.5 Coalescent Approaches to Reconstructing Population History |
|
|
190 | (4) |
|
The genealogy of a DNA sequence can be described mathematically |
|
|
191 | (1) |
|
Neutral mutations can be modeled on the gene genealogy using Poisson statistics |
|
|
192 | (1) |
|
Coalescent analysis can be a simulation tool for hypothesis testing |
|
|
193 | (1) |
|
Coalescent analysis uses ancestral graphs to model selection and recombination |
|
|
193 | (1) |
|
Coalescent models of large datasets are approximate |
|
|
194 | (1) |
|
6.6 Dating Evolutionary Events Using Genetic Data |
|
|
194 | (6) |
|
Dating population splits using FST and Nei's D statistics is possible, but requires a naive view of human evolution |
|
|
195 | (1) |
|
Evolutionary models can include the timing of evolutionary events as parameters |
|
|
195 | (1) |
|
Evolutionary models and effective population size |
|
|
196 | (1) |
|
An allele can be dated using diversity at linked loci |
|
|
197 | (1) |
|
|
|
198 | (1) |
|
Estimations of mutation rate can be derived from direct measurements in families or indirect comparisons of species |
|
|
198 | (1) |
|
An estimate of generation time is required to convert some genetic date estimates into years |
|
|
198 | (2) |
|
6.7 Has Selection Been Acting? |
|
|
200 | (16) |
|
Differences in gene sequences between species can be used to detect selection |
|
|
203 | (4) |
|
Comparing variation between species with variation within a species can detect selection |
|
|
207 | (1) |
|
Selection tests can be based on the analysis of allele frequencies at variant sites |
|
|
208 | (1) |
|
Comparing haplotype frequency and haplotype diversity can reveal positive selection |
|
|
209 | (1) |
|
Analysis of frequency differences between populations can indicate positive selection |
|
|
209 | (5) |
|
Other methods can be used to detect ongoing or very recent positive selection |
|
|
214 | (1) |
|
How can we combine information from different statistical tests? |
|
|
214 | (1) |
|
Tests for positive selection have severe limitations |
|
|
215 | (1) |
|
6.8 Analyzing Genetic Data in a Geographical Context |
|
|
216 | (9) |
|
Genetic data can be displayed on maps |
|
|
217 | (2) |
|
Genetic boundary analysis identifies the zones of greatest allele frequency change within a genetic landscape |
|
|
219 | (1) |
|
Spatial autocorrelation quantifies the relationship of allele frequency with geography |
|
|
219 | (1) |
|
Mantel testing is an alternative approach to examining a relationship between genetic distance and other distance measures |
|
|
220 | (1) |
|
|
|
220 | (1) |
|
|
|
221 | (1) |
|
|
|
222 | (3) |
|
|
|
225 | (32) |
|
Which nonhuman animals are the closest living relatives of humans? |
|
|
225 | (1) |
|
|
|
225 | (1) |
|
7.1 Evidence from Morphology |
|
|
226 | (6) |
|
Primates are an Order of mammals |
|
|
226 | (2) |
|
Hominoids share a number of phenotypic features with other anthropoids |
|
|
228 | (2) |
|
Ancestral relationships of hominoids are difficult to resolve on morphological evidence |
|
|
230 | (2) |
|
7.2 Evidence from Chromosomes |
|
|
232 | (4) |
|
Human and great ape karyotypes look similar, but not identical |
|
|
232 | (1) |
|
Molecular cytogenetic analyses support the picture from karyotype comparisons |
|
|
233 | (3) |
|
7.3 Evidence from Molecules |
|
|
236 | (6) |
|
Molecular data support a recent date of the ape--human divergence |
|
|
237 | (1) |
|
Genetic data have resolved the gorilla--chimpanzee--human trichotomy |
|
|
237 | (2) |
|
Sequence divergence is different among great apes across genetic loci |
|
|
239 | (2) |
|
Great apes differ by gains and losses of genetic material |
|
|
241 | (1) |
|
The DNA sequence divergence rates differ in hominoid lineages |
|
|
241 | (1) |
|
7.4 Genetic Diversity Among the Great Apes |
|
|
242 | (15) |
|
How many genera, species, and subspecies are there? |
|
|
247 | (1) |
|
Intraspecific diversity in great apes is greater than in humans |
|
|
247 | (3) |
|
Signatures of lineage-specific selection can be detected in ape genomes |
|
|
250 | (4) |
|
|
|
254 | (1) |
|
|
|
254 | (1) |
|
|
|
254 | (3) |
|
Chapter 8 What Genetic Changes Have Made Us Human? |
|
|
257 | (26) |
|
8.1 Morphological and Behavioral Changes En Route to Homo Sapiens |
|
|
258 | (7) |
|
Some human traits evolved early in hominin history |
|
|
260 | (3) |
|
|
|
263 | (2) |
|
Only a few phenotypes are unique to modern humans |
|
|
265 | (1) |
|
8.2 Genetic Uniqueness of Humans and Hominins |
|
|
265 | (8) |
|
The sequence and structural differences between humans and other great apes can be cataloged |
|
|
265 | (1) |
|
Humans have gained and lost a few genes compared with other great apes |
|
|
266 | (3) |
|
Humans differ in the sequence of genes compared with other great apes |
|
|
269 | (1) |
|
Humans differ from other apes in the expression levels of genes |
|
|
270 | (2) |
|
Genome sequencing has revealed a small number of fixed genetic differences between humans and both Neanderthals and Denisovans |
|
|
272 | (1) |
|
8.3 Genetic Basis of Phenotypic Differences Between Apes and Humans |
|
|
273 | (10) |
|
Mutations causing neoteny have contributed to the evolution of the human brain |
|
|
273 | (2) |
|
The genetic basis for laterality and language remains unclear |
|
|
275 | (3) |
|
|
|
278 | (1) |
|
|
|
278 | (1) |
|
|
|
279 | (1) |
|
|
|
279 | (4) |
|
Chapter 9 Origins of Modern Humans |
|
|
283 | (36) |
|
9.1 Evidence from Fossils and Morphology |
|
|
284 | (11) |
|
Some fossils that may represent early hominins from 4--7 MYA are known from Africa |
|
|
285 | (2) |
|
Fossils of australopithecines and their contemporaries are known from Africa |
|
|
287 | (3) |
|
The genus Homo arose in Africa |
|
|
290 | (4) |
|
The earliest anatomically modern human fossils are found in Africa |
|
|
294 | (1) |
|
The morphology of current populations suggests an origin in Africa |
|
|
295 | (1) |
|
9.2 Evidence from Archaeology and Linguistics |
|
|
295 | (5) |
|
Paleolithic archaeology has been studied extensively |
|
|
298 | (1) |
|
Evidence from linguistics suggests an origin of language in Africa |
|
|
299 | (1) |
|
9.3 Hypotheses to Explain the Origin of Modern Humans |
|
|
300 | (1) |
|
9.4 Evidence from the Genetics of Present-Day Populations |
|
|
301 | (6) |
|
Genetic diversity is highest in Africa |
|
|
301 | (3) |
|
Genetic phylogenies mostly root in Africa |
|
|
304 | (1) |
|
Mitochondrial DNA phylogeny |
|
|
304 | (1) |
|
|
|
305 | (1) |
|
|
|
305 | (1) |
|
Insights can be obtained from demographic models |
|
|
306 | (1) |
|
9.5 Evidence from Ancient DNA |
|
|
307 | (12) |
|
Ancient mtDNA sequences of Neanderthals and Denisovans are distinct from modern human variation |
|
|
308 | (1) |
|
A Neanderthal draft genome sequence has been generated |
|
|
309 | (1) |
|
A Denisovan genome sequence has been generated |
|
|
310 | (3) |
|
|
|
313 | (2) |
|
|
|
315 | (1) |
|
|
|
315 | (4) |
|
Chapter 10 The Distribution of Diversity |
|
|
319 | (22) |
|
10.1 Studying Human Diversity |
|
|
319 | (9) |
|
The history and ethics of studying diversity are complex |
|
|
319 | (1) |
|
Linnaeus' classification of human diversity |
|
|
320 | (1) |
|
Galton's "Comparative worth of different races" |
|
|
320 | (1) |
|
Modern attitudes to studying diversity |
|
|
320 | (3) |
|
|
|
323 | (1) |
|
A few large-scale studies of human genetic variation have made major contributions to human evolutionary genetics |
|
|
323 | (3) |
|
|
|
326 | (1) |
|
How many people should be analyzed? |
|
|
327 | (1) |
|
10.2 Apportionment of Human Diversity |
|
|
328 | (5) |
|
The apportionment of diversity shows that most variation is found within populations |
|
|
328 | (1) |
|
The apportionment of diversity can differ between segments of the genome |
|
|
329 | (1) |
|
Patterns of diversity generally change gradually from place to place |
|
|
330 | (1) |
|
The origin of an individual can be determined surprisingly precisely from their genotype |
|
|
331 | (1) |
|
The distribution of rare variants differs from that of common variants |
|
|
332 | (1) |
|
10.3 The Influence of Selection on the Apportionment of Diversity |
|
|
333 | (8) |
|
The distribution of levels of differentiation has been studied empirically |
|
|
334 | (1) |
|
Low differentiation can result from balancing selection |
|
|
334 | (1) |
|
High differentiation can result from directional selection |
|
|
335 | (1) |
|
Positive selection at EDAR |
|
|
336 | (2) |
|
|
|
338 | (1) |
|
|
|
339 | (1) |
|
|
|
339 | (2) |
|
Chapter 11 The Colonization of the Old World and Australia |
|
|
341 | (22) |
|
11.1 A Colder and More Variable Environment 15--100 KYA |
|
|
341 | (3) |
|
11.2 Fossil and Archaeological Evidence for Two Expansions of Anatomically Modern Humans Out of Africa in the Last ~130 KY |
|
|
344 | (9) |
|
Anatomically modern, behaviorally pre-modern humans expanded transiently into the Middle East ~90-120 KYA |
|
|
345 | (1) |
|
Modern human behavior first appeared in Africa after 100 KYA |
|
|
346 | (1) |
|
Fully modern humans expanded into the Old World and Australia ~50-70 KYA |
|
|
347 | (1) |
|
Modern human fossils in Asia, Australia, and Europe |
|
|
347 | (2) |
|
Initial colonization of Australia |
|
|
349 | (3) |
|
Upper Paleolithic transition in Europe and Asia |
|
|
352 | (1) |
|
11.3 A Single Major Migration Out of Africa 50--70 KYA |
|
|
353 | (4) |
|
Populations outside Africa carry a shared subset of African genetic diversity with minor Neanderthal admixture |
|
|
353 | (2) |
|
mtDNA and Y-chromosomal studies show the descent of all non-African lineages from a single ancestor for each who lived 55--75 KYA |
|
|
355 | (2) |
|
11.4 Early Population Divergence Between Australians and Eurasians |
|
|
357 | (6) |
|
|
|
360 | (1) |
|
|
|
361 | (1) |
|
|
|
361 | (2) |
|
Chapter 12 Agricultural Expansions |
|
|
363 | (46) |
|
12.1 Defining Agriculture |
|
|
363 | (2) |
|
12.2 The Where, When, and Why of Agriculture |
|
|
365 | (4) |
|
Where and when did agriculture develop? |
|
|
365 | (1) |
|
Why did agriculture develop? |
|
|
366 | (2) |
|
Which domesticates were chosen? |
|
|
368 | (1) |
|
12.3 Outcomes of Agriculture |
|
|
369 | (3) |
|
Agriculture had major impacts on demography and disease |
|
|
369 | (1) |
|
|
|
369 | (1) |
|
Malnutrition and infectious disease |
|
|
369 | (2) |
|
Agriculture led to major societal changes |
|
|
371 | (1) |
|
12.4 The Farming--Language Co-Dispersal Hypothesis |
|
|
372 | (2) |
|
Some language families have spread widely and rapidly |
|
|
372 | (1) |
|
Linguistic dating and construction of proto-languages have been used to test the hypothesis |
|
|
373 | (1) |
|
What are the genetic implications of language spreads? |
|
|
373 | (1) |
|
12.5 Out of the Near East into Europe |
|
|
374 | (14) |
|
Nongenetic evidence provides dates for the European Neolithic |
|
|
374 | (3) |
|
Different models of expansion give different expectations for genetic patterns |
|
|
377 | (1) |
|
Models are oversimplifications of reality |
|
|
378 | (1) |
|
Principal component analysis of classical genetic polymorphisms was influential |
|
|
379 | (1) |
|
Interpreting synthetic maps |
|
|
379 | (1) |
|
mtDNA evidence has been controversial, but ancient DNA data are transforming the field |
|
|
380 | (2) |
|
|
|
382 | (2) |
|
Y-chromosomal data show strong clines in Europe |
|
|
384 | (1) |
|
New developments for the Y chromosome |
|
|
384 | (2) |
|
Biparentally inherited nuclear DNA has not yet contributed much, but important ancient DNA data are now emerging |
|
|
386 | (1) |
|
|
|
387 | (1) |
|
What developments will shape debate in the future? |
|
|
388 | (1) |
|
12.6 Out of Tropical West Africa into Sub-Equatorial Africa |
|
|
388 | (6) |
|
There is broad agreement on the background to African agricultural expansion |
|
|
388 | (1) |
|
Rapid spread of farming economies |
|
|
389 | (1) |
|
Bantu languages spread far and rapidly |
|
|
390 | (2) |
|
Genetic evidence is broadly consistent, though ancient DNA data are lacking |
|
|
392 | (1) |
|
|
|
392 | (1) |
|
Evidence from mtDNA and the Y chromosome |
|
|
393 | (1) |
|
12.7 Genetic Analysis of Domesticated Animals and Plants |
|
|
394 | (15) |
|
Selective regimes had a massive impact on phenotypes and genetic diversity |
|
|
395 | (1) |
|
Key domestication changes in crops |
|
|
396 | (2) |
|
Effects on crop genetic diversity |
|
|
398 | (1) |
|
Phenotypic and genetic change in animals |
|
|
399 | (1) |
|
How have the origins of domesticated plants been identified? |
|
|
400 | (1) |
|
How have the origins of domesticated animals been identified? |
|
|
401 | (2) |
|
|
|
403 | (1) |
|
|
|
404 | (1) |
|
|
|
405 | (1) |
|
|
|
405 | (4) |
|
Chapter 13 Into New-Found Lands |
|
|
409 | (34) |
|
13.1 Settlement of the New Territories |
|
|
409 | (3) |
|
Sea levels have changed since the out-of-Africa migration |
|
|
409 | (2) |
|
What drives new settlement of uninhabited lands? |
|
|
411 | (1) |
|
13.2 Peopling of the Americas |
|
|
412 | (13) |
|
The changing environment has provided several opportunities for the peopling of the New World |
|
|
413 | (2) |
|
Fossil and archaeological evidence provide a range of dates for the settlement of the New World |
|
|
415 | (1) |
|
|
|
415 | (1) |
|
|
|
416 | (1) |
|
Clovis and the Paleoindians |
|
|
416 | (1) |
|
|
|
416 | (1) |
|
|
|
417 | (1) |
|
Did the first settlers go extinct? |
|
|
418 | (1) |
|
A three-migration hypothesis has been suggested on linguistic grounds |
|
|
419 | (1) |
|
Genetic evidence has been used to test the single- and the three-wave migration scenarios |
|
|
419 | (1) |
|
Mitochondrial DNA evidence |
|
|
420 | (2) |
|
Interpretation of the mtDNA data |
|
|
422 | (1) |
|
Evidence from the Y chromosome |
|
|
422 | (2) |
|
Evidence from the autosomes |
|
|
424 | (1) |
|
Conclusions from the genetic data |
|
|
425 | (1) |
|
13.3 Peopling of the Pacific |
|
|
425 | (18) |
|
Fossil and archaeological evidence suggest that Remote Oceania was settled more recently than Near Oceania |
|
|
427 | (1) |
|
Two groups of languages are spoken in Oceania |
|
|
428 | (2) |
|
Several models have been proposed to explain the spread of Austronesian speakers |
|
|
430 | (1) |
|
Austronesian dispersal models have been tested with genetic evidence |
|
|
431 | (1) |
|
|
|
431 | (1) |
|
|
|
432 | (1) |
|
|
|
433 | (3) |
|
|
|
436 | (1) |
|
|
|
437 | (1) |
|
Evidence from other species has been used to test the Austronesian dispersal models |
|
|
438 | (2) |
|
|
|
440 | (1) |
|
|
|
441 | (1) |
|
|
|
441 | (2) |
|
Chapter 14 What Happens When Populations Meet |
|
|
443 | (34) |
|
14.1 What is Genetic Admixture? |
|
|
443 | (4) |
|
Admixture has distinct effects on genetic diversity |
|
|
445 | (2) |
|
14.2 The Impact of Admixture |
|
|
447 | (3) |
|
Different sources of evidence can inform us about admixture |
|
|
447 | (1) |
|
Consequences of admixture for language |
|
|
447 | (1) |
|
Archaeological evidence for admixture |
|
|
448 | (1) |
|
The biological impact of admixture |
|
|
449 | (1) |
|
|
|
450 | (10) |
|
Methods based on allele frequency can be used to detect admixture |
|
|
450 | (3) |
|
Admixture proportions vary among individuals and populations |
|
|
453 | (1) |
|
Calculating individual admixture levels using multiple loci |
|
|
453 | (1) |
|
Calculating individual admixture levels using genomewide data |
|
|
454 | (2) |
|
Calculating admixture levels from estimated ancestry components |
|
|
456 | (1) |
|
Problems of measuring admixture |
|
|
457 | (1) |
|
Natural selection can affect the admixture proportions of individual genes |
|
|
458 | (2) |
|
14.4 Local Admixture and Linkage Disequilibrium |
|
|
460 | (4) |
|
How does admixture generate linkage disequilibrium? |
|
|
461 | (1) |
|
|
|
462 | (1) |
|
|
|
463 | (1) |
|
14.5 Sex-Biased Admixture |
|
|
464 | (3) |
|
What is sex-biased admixture? |
|
|
464 | (1) |
|
Detecting sex-biased admixture |
|
|
465 | (1) |
|
Sex-biased admixture resulting from directional mating |
|
|
465 | (2) |
|
The effect of admixture on our genealogical ancestry |
|
|
467 | (1) |
|
14.6 Transnational Isolates |
|
|
467 | (10) |
|
Roma and Jews are examples of widely spread transnational isolates |
|
|
468 | (1) |
|
|
|
468 | (1) |
|
|
|
469 | (2) |
|
|
|
471 | (1) |
|
|
|
472 | (1) |
|
|
|
473 | (4) |
|
Chapter 15 Understanding the Past, Present, and Future of Phenotypic Variation |
|
|
477 | (40) |
|
15.1 Normal and Pathogenic Variation in an Evolutionary Context |
|
|
477 | (1) |
|
15.2 Known Variation in Human Phenotypes |
|
|
478 | (7) |
|
What is known about human phenotypic variation? |
|
|
478 | (1) |
|
Morphology and temperature adaptation |
|
|
479 | (1) |
|
|
|
479 | (1) |
|
Tooth morphology and cranial proportions |
|
|
480 | (1) |
|
|
|
481 | (2) |
|
How do we uncover genotypes underlying phenotypes? |
|
|
483 | (2) |
|
What have we discovered about genotypes underlying phenotypes? |
|
|
485 | (1) |
|
15.3 Skin Pigmentation as an Adaptation to Ultraviolet Light |
|
|
485 | (10) |
|
Melanin is the most important pigment influencing skin color |
|
|
486 | (1) |
|
Variable ultraviolet light exposure is an adaptive explanation for skin color variation |
|
|
486 | (3) |
|
Several genes that affect human pigmentation are known |
|
|
489 | (3) |
|
Genetic variation in human pigmentation genes is consistent with natural selection |
|
|
492 | (1) |
|
Does sexual selection have a role in human phenotypic variation? |
|
|
493 | (2) |
|
15.4 Life at High Altitude and Adaptation to Hypoxia |
|
|
495 | (1) |
|
Natural selection has influenced the overproduction of red blood cells |
|
|
495 | (1) |
|
High-altitude populations differ in their adaptation to altitude |
|
|
496 | (1) |
|
15.5 Variation in the Sense of Taste |
|
|
496 | (4) |
|
Variation in tasting phenylthiocarbamide is mostly due to alleles of the TAS2R38 gene |
|
|
498 | (1) |
|
There is extensive diversity of bitter taste receptors in humans |
|
|
499 | (1) |
|
Sweet, umami, and sour tastes may show genetic polymorphism |
|
|
499 | (1) |
|
15.6 Adapting to a Changing Diet by Digesting Milk and Starch |
|
|
500 | (6) |
|
There are several adaptive hypotheses to explain lactase persistence |
|
|
501 | (1) |
|
Lactase persistence is caused by SNPs within an enhancer of the lactase gene |
|
|
502 | (2) |
|
Increased copy number of the amylase gene reflects an adaptation to a high-starch diet |
|
|
504 | (2) |
|
15.7 The Future of Human Evolution |
|
|
506 | (11) |
|
Have we stopped evolving? |
|
|
506 | (1) |
|
Natural selection acts on modern humans |
|
|
506 | (1) |
|
Can we predict the role of natural selection in the future? |
|
|
507 | (1) |
|
|
|
507 | (1) |
|
|
|
507 | (1) |
|
|
|
507 | (1) |
|
What will be the effects of future demographic changes? |
|
|
508 | (1) |
|
Increasing population size |
|
|
509 | (1) |
|
|
|
510 | (1) |
|
|
|
510 | (1) |
|
Differential generation time |
|
|
511 | (1) |
|
Will the mutation rate change? |
|
|
512 | (1) |
|
|
|
512 | (1) |
|
|
|
513 | (1) |
|
|
|
513 | (4) |
|
Chapter 16 Evolutionary Insights into Simple Genetic Diseases |
|
|
517 | (24) |
|
16.1 Genetic Disease and Mutation--Selection Balance |
|
|
520 | (3) |
|
Variation in the strength of purifying selection can affect incidence of genetic disease |
|
|
520 | (2) |
|
Variation in the deleterious mutation rate can affect incidence of genetic disease |
|
|
522 | (1) |
|
16.2 Genetic Drift, Founder Effects, and Consanguinity |
|
|
523 | (3) |
|
Jewish populations have a particular disease heritage |
|
|
524 | (1) |
|
Finns have a disease heritage very distinct from other Europeans |
|
|
525 | (1) |
|
Consanguinity can lead to increased rates of genetic disease |
|
|
526 | (1) |
|
16.3 Evolutionary Causes of Genomic Disorders |
|
|
526 | (3) |
|
Segmental duplications allow genomic rearrangements with disease consequences |
|
|
527 | (2) |
|
Duplications accumulated in ancestral primates |
|
|
529 | (1) |
|
16.4 Genetic Diseases and Selection by Malaria |
|
|
529 | (12) |
|
Sickle-cell anemia is frequent in certain populations due to balancing selection |
|
|
531 | (3) |
|
α-Thalassemias are frequent in certain populations due to balancing selection |
|
|
534 | (1) |
|
Glucose-6-phosphate dehydrogenase deficiency alleles are maintained at high frequency in malaria-endemic populations |
|
|
535 | (2) |
|
What can these examples tell us about natural selection? |
|
|
537 | (1) |
|
|
|
538 | (1) |
|
|
|
538 | (1) |
|
|
|
539 | (2) |
|
Chapter 17 Evolution and Complex Diseases |
|
|
541 | (30) |
|
17.1 Defining Complex Disease |
|
|
541 | (5) |
|
The genetic contribution to variation in disease risk varies between diseases |
|
|
544 | (1) |
|
Infectious diseases are complex diseases |
|
|
544 | (2) |
|
17.2 The Global Distribution of Complex Diseases |
|
|
546 | (3) |
|
Is diabetes a consequence of a post-agricultural change in diet? |
|
|
546 | (1) |
|
The drifty gene hypothesis |
|
|
547 | (1) |
|
Evidence from genomewide studies |
|
|
548 | (1) |
|
The thrifty phenotype hypothesis |
|
|
549 | (1) |
|
17.3 Identifying Alleles Involved in Complex Disease |
|
|
549 | (8) |
|
Genetic association studies are more powerful than linkage studies for detecting small genetic effects |
|
|
549 | (3) |
|
Candidate gene association studies have not generally been successful in identifying susceptibility alleles for complex disease |
|
|
552 | (1) |
|
Genomewide association studies can reliably identify susceptibility alleles to complex disease |
|
|
552 | (4) |
|
GWAS data have been used for evolutionary genetic analysis |
|
|
556 | (1) |
|
17.4 What Complex Disease Alleles Do We Expect to Find in the Population? |
|
|
557 | (6) |
|
Negative selection acts on disease susceptibility alleles |
|
|
557 | (3) |
|
Positive selection acts on disease resistance alleles |
|
|
560 | (1) |
|
|
|
560 | (1) |
|
Malaria and the Duffy antigen |
|
|
560 | (2) |
|
|
|
562 | (1) |
|
Unexpectedly, some disease susceptibility alleles with large effects are observed at high frequency |
|
|
562 | (1) |
|
Susceptibility to kidney disease, APOL1, and resistance to sleeping sickness |
|
|
562 | (1) |
|
Implications for other GWAS results |
|
|
563 | (1) |
|
17.5 Genetic Influence on Variable Response to Drugs |
|
|
563 | (8) |
|
Population differences in drug-response genes exist, but are not well understood |
|
|
564 | (3) |
|
|
|
567 | (1) |
|
|
|
568 | (1) |
|
|
|
569 | (2) |
|
Chapter 18 Identity and Identification |
|
|
571 | (37) |
|
18.1 Individual Identification |
|
|
572 | (8) |
|
The first DNA fingerprinting and profiling methods relied on minisatellites |
|
|
573 | (1) |
|
PCR-based microsatellite profiling superseded minisatellite analysis |
|
|
574 | (1) |
|
How do we interpret matching DNA profiles? |
|
|
574 | (2) |
|
Complications from related individuals, and DNA mixtures |
|
|
576 | (1) |
|
Large forensic identification databases are powerful tools in crime-fighting |
|
|
577 | (1) |
|
Controversial aspects of identification databases |
|
|
577 | (1) |
|
The Y chromosome and mtDNA are useful in specialized cases |
|
|
578 | (1) |
|
Y chromosomes in individual identification |
|
|
579 | (1) |
|
mtDNA in individual identification |
|
|
580 | (1) |
|
18.2 What DNA Can Tell Us About John or Jane Doe |
|
|
580 | (5) |
|
DNA-based sex testing is widely used and generally reliable |
|
|
580 | (1) |
|
|
|
581 | (1) |
|
Deletions of the AMELY locus in normal males |
|
|
582 | (1) |
|
Some other phenotypic characteristics are predictable from DNA |
|
|
582 | (1) |
|
Reliability of predicting population of origin depends on what DNA variants are analyzed |
|
|
583 | (1) |
|
Prediction from forensic microsatellite multiplexes |
|
|
583 | (1) |
|
Prediction from other systems |
|
|
584 | (1) |
|
The problem of admixed populations |
|
|
584 | (1) |
|
18.3 Deducing Family and Genealogical Relationships |
|
|
585 | (8) |
|
The probability of paternity can be estimated confidently |
|
|
586 | (2) |
|
Other aspects of kinship analysis |
|
|
588 | (1) |
|
The Y chromosome and mtDNA are useful in genealogical studies |
|
|
588 | (1) |
|
The Thomas Jefferson paternity case |
|
|
588 | (2) |
|
DNA-based identification of the Romanovs |
|
|
590 | (1) |
|
Y-chromosomal DNA has been used to trace modern diasporas |
|
|
591 | (1) |
|
Y-chromosomal haplotypes tend to correlate with patrilineal surnames |
|
|
592 | (1) |
|
18.4 The Personal Genomics Revolution |
|
|
593 | (15) |
|
The first personal genetic analysis involved the Y chromosome and mtDNA |
|
|
593 | (1) |
|
Personal genomewide SNP analysis is used for ancestry and health testing |
|
|
593 | (1) |
|
Personal genome sequencing provides the ultimate resolution |
|
|
593 | (3) |
|
Personal genomics offers both promise and problems |
|
|
596 | (1) |
|
|
|
597 | (1) |
|
|
|
597 | (1) |
|
|
|
598 | (3) |
|
|
|
601 | (1) |
|
|
|
601 | (1) |
|
|
|
602 | (1) |
|
|
|
602 | (1) |
|
What genes are encoded within the mitochondrial genome? |
|
|
602 | (1) |
|
What diseases are caused by mutations within mtDNA? |
|
|
602 | (1) |
|
How has the study of mtDNA diversity developed? |
|
|
602 | (1) |
|
How is information from the mtDNA variants in an individual combined? |
|
|
603 | (1) |
|
Why are all the deep-rooting clades called L? |
|
|
603 | (1) |
|
Why is mtDNA so useful for exploring the human past? |
|
|
603 | (2) |
|
What about possible selection pressures? |
|
|
605 | (1) |
|
|
|
605 | (1) |
|
|
|
605 | (1) |
|
What does the chromosome contain? |
|
|
605 | (1) |
|
How similar are Y chromosomes within and between species? |
|
|
606 | (1) |
|
What molecular polymorphisms are found on the Y chromosome? |
|
|
606 | (1) |
|
How should the polymorphic information from different variants be combined? |
|
|
606 | (2) |
|
What are the applications of studying Y-chromosomal diversity? |
|
|
608 | (1) |
|
Is there any evidence of selection on the Y chromosome? |
|
|
608 | (1) |
| References |
|
608 | (1) |
| Glossary |
|
609 | (32) |
| Index |
|
641 | |
