Human Mitochondrial DNA And the Evolution of Homo Sapiens

by Bandelt, Hans-jurgen; Macaulay, Vincent; Richards, Martin

• ISBN13: 9783540317883
• ISBN10: 3540317880
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-07-06
• Publisher: Springer Verlag

Summary

Mitochondrial DNA is one of the most explored genetic systems because of what it can tell us about the human past. This volume takes a unique perspective, presenting the disparate strands that must be tied together to exploit this system. From molecular biology to anthropology, statistics to ancient DNA, this first volume of three presents the global picture of human mitochondrial DNA variation. It takes a critical look at the field, flagging the problems, as well as the successes, and always placing the mitochondrial phylogeny centre stage.

Table of Contents

Part I Prerequisites and Caveats
Mitochondrial DNA in Homo Sapiens
P.F. CHINNERY	3	(14)
1 Introduction	3	(1)
2 Mitochondria—Structure and Function	3	(2)
3 Mitochondrial Biogenesis	5	(1)
4 Human mtDNA	6	(2)
5 mtDNA Transcription, Translation, and Replication	8	(1)
6 Pathogenic Mutations of mtDNA, Heteroplasmy, and the Threshold Effect	9	(1)
7 The Role of Homoplasmic mtDNA Mutations in Human Disease	10	(1)
8 Conclusions	11	(1)
References	12	(5)
The Transmission and Segregation of Mitochondrial DNA in Homo Sapiens
P.F. CHINNERY	17	(14)
1 Introduction	17	(1)
2 mtDNA Mutations and Human Disease	17	(1)
3 Mechanisms That Can Change the Level of Heteroplasmy	18	(1)
4 The Inheritance of mtDNA	19	(5)
4.1 Maternal Inheritance	19	(1)
4.2 The Mitochondrial Genetic Bottleneck	20	(4)
5 Segregation During Early Development	24	(1)
6 Conclusions and Future Perspectives	25	(1)
References	26	(5)
Numts Revisited
C M. BRAVI, W. PARSON, H.-J. BANDELT	31	(16)
1 Introduction	31	(2)
2 Numts in Humans	33	(1)
3 A Numt from an Egyptian Mummy	34	(2)
4 A Numt from the Sperm's Head?	36	(1)
5 A Bouquet of Numts?	36	(4)
6 Adverse Laboratory Conditions	40	(1)
7 Conclusion	41	(1)
References	42	(5)
Estimation of Mutation Rates and Coalescence Times: Some Caveats
H.-J. BANDELT, Q.-P. KONG, M. RICHARDS, V. MACAULAY	47	(44)
1 Introduction	47	(2)
2 Prerequisite: a Global mtDNA Tree	49	(6)
3 Transition/Transversion Rate Ratio	55	(4)
4 Spectrum of Relative Mutational Rates Along the Molecule	59	(4)
5 Pitfalls with Estimation of Positional Rate Variability	63	(10)
6 Calibration of the Mutational Clock	73	(7)
7 Pitfalls with Age Estimations	80	(4)
8 Conclusion	84	(1)
References	85	(6)
Postmortem Damage of Mitochondrial DNA
M.T.P. GILBERT	91	(26)
1 Introduction	91	(1)
2 Ancient DNA	91	(1)
3 DNA Damage in Ancient Samples	92	(10)
3.1 DNA Degradation Immediately Following Cell Death	92	(1)
3.2 Long-term DNA Degradation	93	(4)
3.3 Damage-Driven DNA Miscoding Lesion	97	(5)
4 Insights from Miscoding Lesions into in Vivo mtDNA Mutation	102	(7)
4.1 Muational Hotspots and: mtDNA Recombination	102	(1)
4.2 Effects of mtDNA Secondary and Tertiary Structure	103	(1)
4.3 Hotspots for Postmortem mtDNA Damage	103	(5)
4.4 Sequence Motifs with Limited DNA Damage	108	(1)
5 Implications of Postmortem Damage Hotspots on Sequence Authenticity	109	(1)
6 Conclusion	110	(1)
References	111	(6)
Lab-Specific Mutation Processes
H.-J. BANDELT, T. KIVISILD, J. PARIK R. VILLEMS, C. BRAVI, Y.-G. YAO, A. BRANDSTÄTTER, W. PARSON	117	(32)
1 Introduction	117	(1)
2 The Sequencing Process and Data Handling	118	(1)
3 Sources of Error	119	(4)
4 Pitfalls of mtDNA Sequencing	123	(8)
5 'Ancient' DNA	131	(3)
6 Conclusion	134	(6)
References	140	(9)
Part II Evolution of Human mtDNA
The World mtDNA Phylogeny
T. KIVISILD, M. METSPALU, H.-J. BANDELT, M. RICHARDS, R. VILLEMS	149	(32)
1 Haplotypes and Trees	147	(6)
2 Haplogroup Structure and Definition	153	(4)
3 Phylogeographic Inferences	157	(6)
4 African mtDNA Variation and Haplogroup Structure	163	(4)
5 mtDNA Variation Outside Africa	167	(3)
6 The Role of Selection on mtDNA Variability	170	(2)
References	172	(9)
The Pioneer Settlement of Modern Humans in Asia
M. METSPALU, T. KIVISILD, H.-J. BANDELT, M. RICHARDS, R. VILLEMS	181	(20)
1 Introduction	181	(1)
2 Palaeoclimatological Context	182	(1)
3 Archaeological and Palaeontological Evidence of the Peopling of Asia by AMH	183	(2)
4 How to Infer 'Pioneer Settlement' from Extant mtDNA Variation?	185	(1)
5 The Peopling of Asia as Seen Through the Lens of mtDNA Diversity	186	(4)
6 A Route Through Northern Asia?	190	(4)
7 Conclusion	194	(1)
References	194	(7)
Ancient DNA and the Neanderthals
W. GOODWIN, I. OVCHINNIKOV	201	(1)
1 Introduction	201	(1)
2 Origins of the Neanderthals	202	(1)
3 DNA Analysis of Neanderthal Specimens	203	(2)
4 The Limitations of Ancient DNA Analysis	205	(2)
5 DNA Degradation	207	(1)
6 The Extraction and Analysis of Neanderthal DNA: Assessing the Preservation	207	(1)
7 Environmental Factors	208	(1)
8 Molecular Preservation	209	(1)
9 Isolation of Neanderthal DNA	210	(1)
10 DNA Extraction	210	(1)
11 Amplification and Sequence Analysis of Neanderthal DNA	211	(2)
12 Ancient DNA Artefacts	213	(1)
13 Authentication	214	(1)
14 Evaluation of Neanderthal DNA	215	(1)
15 Phylogenetic Analysis	216	(2)
16 Admixture between Modern Humans and Neanderthals	218	(2)
17 Neanderthal Diversity	220	(1)
18 The Age of Divergence	220	(1)
19 Conclusions	221	(1)
References	222	(3)
A Model for the Dispersal of Modern Humans out of Africa
M. RICHARDS, H.-J. BANDELT, T. KIVISILD, S. OPPENHEIMER	225	(42)
1 Introduction: Setting the Agenda	225	(1)
2 Genetics and the Traditional Debate over Human Origins	226	(7)
2.1 The Debate Continues	228	(4)
2.2 Moving on	232	(1)
3 How Many Dispersals of Modern Humans from Africa?	233	(8)
3.1 The mtDNA Evidence and Multiple Dispersals	234	(4)
3.2 Y-Chromosome Founders	238	(3)
4 Which Way out of Africa?	241	(14)
4.1 mtDNA and the Indian Staging Post	243	(2)
4.2 A Far Eastern Ancestry?	245	(2)
4.3 Opening up the West	247	(1)
4.4 Y-Chromosome Passage to India and Be Ton A	248	(4)
4.5 In Context	252	(3)
References	255	(12)
Subject Index	267