MITOCHONDRIAL DNA AND HUMAN EVOLUTION

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Annu. Rev. Genomics Hum. Genet. 2005. 6:165–83 doi: 10.1146/annurev.genom.6.080604.162249 c 2005 by Annual Reviews. All rights reserved Copyright
First published online as a Review in Advance on May 2, 2005

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MITOCHONDRIAL DNA AND HUMAN EVOLUTION Brigitte Pakendorf and Mark Stoneking Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; email: [email protected], [email protected]

Key Words ancestry

polymorphism, mutation rate, recombination, maternal inheritance,

■ Abstract Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.

INTRODUCTION Human mitochondrial DNA (mtDNA) is a circular double-stranded molecule, 16,569 base pairs (bp) in length that codes for 13 subunits of the oxidative phosphorylation system, 2 ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs) (2) (Figure 1). It is present in hundreds to thousands of copies in each cell, not within the nucleus, but within the cell’s energy-generating organelles, the mitochondria. MtDNA consists predominantly of coding DNA, with the exception of a ∼1100-bp long fragment that has mainly regulatory functions and is therefore termed the control region. Since the first in-depth study of human mtDNA variation 25 years ago (22), it has become widely used for studies of human evolution, migration, and population histories (e.g., 24, 66, 68, 81, 93, 117, 157, 165, 170). This widespread use is due to unique features of mtDNA that make it particularly amenable to evolutionary studies. These features include a high copy number, maternal inheritance, lack of recombination, and a generally higher mutation rate than found in nuclear DNA. 1527-8204/05/0922-0165$20.00

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Figure 1 Schematic representation of the human mitochondrial DNA genome, with functional regions indicated as follows: two ribosomal RNA genes (12S and 16S), three genes for subunits of cytochrome oxidase (COI–COIII), seven genes for subunits of NADH dehydrogenase (N1-N6, N4L), two genes for subunits of F1ATPase (6 and 8), the cytochrome b gene, 22 transfer RNA genes (designated by the standard single letter code), two origins of replication (OH and OL ), and the control region (the major noncoding region).

PROPERTIES OF HUMAN MITOCHONDRIAL DNA High Copy Number MtDNA is present in high copy number in human cells. The average somatic cell has just two copies of any given nuclear gene or DNA segment, but hundreds to thousands of copies of mtDNA (123). This property, along with the extranuclear, cytoplasmic location of mtDNA, makes it easier to obtain mtDNA for analysis, and also makes mtDNA the molecule of choice for analyzing ancient DNA and for certain forensic DNA applications.

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However, this property also complicates the population genetics of mtDNA because there are several levels at which populations of mtDNA molecules can be defined—within a single mitochondrion, within a single cell, within a particular tissue, within an individual, and within a group of individuals (the traditional definition of a population). The multiple copies of the mtDNA genome within an individual need not all be identical; the existence of different mtDNA types within an individual is known as heteroplasmy. The observed frequency of heteroplasmy among humans depends on how it is measured. Initial estimates of little or no heteroplasmy relied on relatively insensitive methods; the current best estimate is that about 14% of the population has a second mtDNA type present at a frequency of at least 1% (167), and indeed it is quite likely that all of us harbor more than one mtDNA type among the trillions and trillions of mtDNA genomes in our bodies. Nevertheless, the overall homogeneity of mtDNA within individuals indicates that a substantial bottleneck in the number of mitochondria occurs early in oogenesis; studies of the segregation of mtDNA heteroplasmy across generations indicate that there are on the order of only 10 segregating units per individual (15, 21, 114).

Maternal Inheritance Although paternal inheritance of mtDNA occurs in mussels (184), and has been shown for inter- and intraspecific Drosophila, mouse, and bird hybrids (47, 70, 76, 83), for years the strictly maternal inheritance of human mtDNA was regarded as an unshakable dogma of the field (150, 153, 172). This uniparental mode of inheritance is one of the great advantages of mtDNA, as it enables researchers to trace related lineages back through time, highlighting the maternal ancestry of a population, without the confounding effects of biparental inheritance and recombination inherent in nuclear DNA. Recently, however, a report of a man with severe exercise intolerance whose muscular mtDNA was of predominantly paternal origin cast doubt on the validity of the assumption of strict maternal inheritance of mtDNA (134), and voices were raised calling for caution in making inferences about human populations and history based on the now-questionable assumption of strict maternal inheritance (20). Subsequent investigations of more patients with mitochondrial myopathies have yielded no further cases of paternal inheritance (39, 136, 160). It has been known for some years that sperm mitochondria are selectively destroyed in the oocyte (92, 139), and it has been shown that paternal mtDNA is marked for destruction in the oocyte by ubiquitination (155, 156). Therefore, it seems highly probable that the one case of paternal inheritance of mtDNA recorded in humans so far represents a breakdown in the normal recognition and elimination of the paternal mtDNA molecules, and that this remains an exceedingly rare phenomenon. Moreover, thousands of maternal-offspring comparisons have failed to yield any indication of paternal inheritance (45, 63, 67, and references therein). Therefore, at present maternal inheritance of mtDNA in humans can still be regarded as the rule (135).

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Lack of Recombination Another tenet of molecular anthropology that was shaken a few years ago is that mtDNA does not undergo recombination. This was regarded as an established fact (150, 153, 172) until 1999–2000, when four papers claimed evidence for recombination in human mtDNA (5, 6, 38, 49). Three of these studies were based on phylogenetic and statistical analyses of mtDNA sequences, with the authors arguing that the excess of homoplasmic sites observed in phylogenetic trees of mtDNA sequences (38), and the correlation of linkage disequilibrium with distance across the mtDNA genome (5, 6), provided evidence for recombination. The fourth study claimed to have direct evidence for recombination in Melanesia (49). However, it was subsequently shown that the phylogenetic/statistical studies used faulty data and/or questionable statistical methods, with reanalyses giving no significant results (3, 69, 82, 89, 95, 110), and the claim for direct observation of recombination in Melanesian mtDNAs was based on an alignment error and had to be retracted (50). Three subsequent studies of the correlation of linkage disequilibrium and distance in large data sets of complete mtDNA sequences (33, 66, 113) found no evidence for recombination, although again an excess of homoplasmic sites was detected (113)—this, however, is generally attributed to heterogeneous mutation rates in human mtDNA (37, 62, 151). Recently, however, a case of observed recombination in human mtDNA was reported in the only known human with both maternal and paternal mtDNA (78, 134). Here, recombination between the maternal and the paternal mtDNA occurred in approximately 0.7% of the total mtDNA in the patient’s muscle tissue. This finding underlines that recombination is possible because mitochondria possess a functional recombinase (161), although it is still unclear to what extent mitochondria within a cell are able to fuse and exchange contents (35, 86, 104). However, because leakage of paternal mtDNA is a very rare phenomenon, recombination is not the major issue that it is sometimes made out to be (48, 146)—in the absence of heteroplasmic DNA molecules, any recombination events would result in mtDNAs that do not differ from the original.

Mutation Rate The mutation rate of mtDNA is several orders of magnitude higher than that of nuclear genes, with an estimated rate of 0.017 × 10−6 substitutions per site per year for the whole genome excluding the control region (66). However, in the two hypervariable regions (HVR I and HVR II) of the noncoding control region, the rate is even higher—although exactly how high is a matter of controversy. Phylogenetic comparisons, based on either interspecific or intraspecific comparisons, yielded estimates of 0.075–0.165 × 10−6 substitutions/site/year (52, 152, 158, 174). However, direct observations of mtDNA mutations in families or deep-rooting pedigrees led to estimates ranging from 0.0–1.46 × 10−6 substitutions/site/year, with an overall average (based on more than 2600 transmissions) of 0.47 × 10−6 substitutions/site/year, which is significantly higher than phylogenetic

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estimates (63 and references therein). There is now a debate as to which rate reflects the “true” state of affairs, and which to use for studies of population history (56, 61, 63, 67, 90, 107, 111, 141). A clue to understanding the discrepancy between phylogenetic- and pedigreebased estimates of the mtDNA mutation rate comes from the observation that within the control region the mutation rate is very heterogeneous, with some “mutational hot spots” mutating four to five times as fast as the average site (37, 52, 56, 96, 171). Although some claim that recombination would be a better explanation for the observed recurrent mutations (38, 48), analyses of mutations in tumors, in pedigree studies, and at heteroplasmic sites have shown that such newly arising mutations occur preferentially at phylogenetically defined mutational hot spots (56, 151). Furthermore, DNA damage in ancient DNA occurs preferentially at phylogenetically defined mutational hot spots in the control region (44), suggesting that these mutational hot spots may be hypermutable because they are more prone to damage. The most likely explanation for the discrepancy between phylogenetically based and pedigree-based estimates of the mutation rate in human mtDNA is that fastevolving sites are preferentially detected in pedigree studies, whereas phylogenetic studies (which encompass a larger number of transmissions) pick up mutations at the slowly evolving sites as well (56, 67, 90, 107). However, Howell et al. (63) argue that the difference in mutation rates estimated from pedigree and phylogenetic studies does not have one causal factor, but instead is due to mutational hot spots, genetic drift, selection, and lack of detection of recurrent mutations in phylogenetic studies. In any event, because a significant number of the mutations observed in pedigree data have arisen recently and will probably not become fixed, the phylogenetic rate (which represents mutations that have reached an appreciable frequency in the population) may be preferable for studies of deep history, whereas it may be advisable to use the pedigree rate for studies of recent history (90, 107). Alternatively, studies of population history could incorporate models that allow for different classes of sites with different evolutionary rates (52, 56, 158). For example, Hasegawa et al. (52) showed that a model that includes rate variation in the mtDNA control region gave an estimate for the age of the human mtDNA ancestor that was half that obtained when a single mutational rate was assumed. Therefore, average estimates of the mutation rate for human mtDNA do not reflect the true state of affairs, and should be viewed as simplistic tools for phylogenetic studies.

HUMAN MITOCHONDRIAL DNA VARIATION What is Studied? Initial studies of human mtDNA variation were based on restriction fragment length polymorphisms (RFLPs) of either purified genomic DNA or purified mtDNA (e.g., 22, 24, 68). With the advent of the polymerase chain reaction (PCR) and methods

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of rapid sequencing of PCR products, RFLP analysis of mtDNA PCR products as well as sequence analysis of the first hypervariable segment (HVR I) of the control region took over, with a huge amount of data generated in the 1990s [a recent paper addressing the origins of the Saami analyzed 17,541 sequences from Eurasia alone (157)]. In recent years, with the development of high-throughput sequencing technology, it has become more and more common to sequence the whole mitochondrial genome, even for population studies (27, 40, 55, 65, 66, 77, 88, 159). Phylogenetic trees based on whole genome sequences do provide better resolution than trees based only on HVR1 sequences (64). However, it is not clear whether the additional effort involved in whole genome sequencing is truly worthwhile, as informative point mutations can be individually assayed by RFLP assays or, as recently shown, by multiplex SNaPshot assays (18). Furthermore, a potential future development is using sequencing microarrays for mtDNA; this was successfully tested for clinical purposes (91). Whole mtDNA genome sequence studies have yet to reveal any insights into human population history that were not already provided by RFLP and/or HVR1 sequence studies, although there are recent claims that HVR1 sequences alone do provide significantly lower estimates of the genetic distance between populations than do mtDNA coding sequences (176). It remains to be seen if the insights gained are worth the additional cost and effort of obtaining whole genome sequences versus RFLP and/or HVR1 sequences; a reasonable alternative might be to combine control region sequences with partial coding region sequences (77, 142).

How are the Data Analyzed? There are two basic approaches to using mtDNA in studies of human evolution: the lineage-based approach and the population-based approach. The lineage-based approach attempts to unravel the history of mtDNA lineages, called haplogroups, while the population-based approach attempts to study the prehistory of individual populations, of geographical regions, or of population migrations by using human population groups as the unit of study and applying population genetic methods to the data (42). The haplogroups studied in the lineage-based approach were initially defined by RFLP data (7, 131). Unfortunately, the detection, and therefore the naming, of new haplogroups and subhaplogroups has progressed in a rather haphazard manner, resulting in nonmonophyletic groupings receiving the same designation [e.g., macrohaplogroup L, cf. (88)], and branches of monophyletic groupings receiving different designations [e.g., the clade comprising branches N9, Y1b, and Y2 in figure 2 of Reference 159]. An organized attempt at a consistent nomenclature, as was accomplished for the Y-chromosome haplogroups (180), would be highly appreciated. Haplogroups represent related groups of sequences that are defined by shared mutations and which tend to show regional specificity. Thus, macrohaplogroup L with subgroups L1, L2, and L3 (all of which contain further subhaplogroups) is restricted to Africa (127, 175), whereas macrohaplogroups M and N originated in eastern Africa on a L3 background and dispersed into Eurasia and the New World (98, 115). Haplogroups H, I, J, N1b, T, U, V, and W

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are characteristic of people of European descent, and haplogroups A, B, C, and D are found in Asia and the New World, with haplogroups G, Y, and Z predominantly in Siberia (98, 133). Haplogroup X is found at low frequencies in North Africa and West Asia, in Europe and Central Asia, and in the New World; however, it is generally not found in Siberia or East Asia (119). Because haplogroups reflect shared ancestry of mtDNAs, they can be helpful for estimating admixture proportions in populations inhabiting known routes of migration (28, 162) or originating from diverse geographical regions (1, 112, 128). Furthermore, they were useful in establishing the bottleneck that occurred during the colonization of the New World (131, 148, 149, 165). A problem with the lineage-based approach of studying haplogroups is that it only elucidates the history of the haplogroups themselves, and does not provide direct insights into the history of the individual populations in which they are present. There has been an unfortunate tendency to equate the age of a haplogroup with the age of a population, and to assume that the spread of each individual haplogroup reflects a separate migration. The reality, of course, is that when a population migrates, it carries all of its haplogroups with it, not just one of them, and the ages of the haplogroups in the migrating population indicate when the point mutations defining the haplogroup occurred, not when the migration occurred (145). To study the prehistory of human populations, it is crucial to use statistical methods that examine population relationships, e.g., calculating genetic distance values and displaying population relationships in trees or multidimensional scaling (MDS) plots (Figure 2). Fortunately, more and more studies recognize the value of analyzing both haplogroup affiliations and population affinities using a population genetics approach (73, 122, 125, 157). Although HVR I sequence data alone do not have the resolving power to reveal all haplogroups, the high mutation rate of this segment ensures a sufficient number of polymorphic sites for population genetic analyses.

What Have We Learned? One important finding of mtDNA analyses is the corroboration of the “Recent African Origin” hypothesis of modern human origins, initially put forward on the basis of fossil evidence (19, 154). Studies of mtDNA variation in worldwide populations have repeatedly found further evidence for this hypothesis, with the most recent common ancestor of human mtDNA located in Africa about 100,000–200,000 years ago (24, 66, 88, 170). Moreover, direct analyses of mtDNA from fossils of Neandertals and their contemporaries, early modern humans from Europe, indicate no contribution of Neandertal mtDNA to modern humans (25, 79–81, 106, 130, 137). Another insight gained from studies of mtDNA is a better understanding of the migrations that shaped human populations, such as the peopling of the New World (75, 131, 142, 148, 149, 165), the colonization of the Pacific (87, 94, 100, 118), the initial migration to New Guinea and Australia (65, 116, 117, 168), and the settlement of Europe (120, 121, 144, 163). However, mtDNA is only one locus, and

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only reflects the maternal history of a population; the history of a single locus may not accurately reflect the history of a population because of chance (drift) effects or because of selection acting on that locus. It has therefore become abundantly clear that studies of mtDNA variation need to be complemented with data on the male-specific Y-chromosome, and ideally with autosomal data as well (9, 14, 29, 102, 138, 157, 179). The use of mtDNA alone in studies of human evolution will probably decrease in the future, which indicates that studies of human variation are maturing beyond the single locus approach. However, the field has recently been confronted with several serious issues that need careful consideration. First, there is the increasing realization that nuclear inserts of mtDNA (numts) are more common than formerly thought (16, 53, 97, 103, 166). Analyses of the human genome sequence have revealed between 250 and more than 600 such inserts of differing length, with the largest fragment encompassing nearly the whole mitochondrial genome (16, 97, 166). Because mitochondrial inserts in the nuclear genome evolve at the nuclear rate, which is lower than that of mtDNA, known numts may have their uses as “molecular fossils” (97, 183). However, a problem with numts is that they may not be detectable with standard methods (17, 103), and there are examples of numts that were mistakenly thought to represent authentic mtDNA sequences, leading to erroneous phylogenetic or medical conclusions precisely because of their slower rate of evolution (30, 31, 57, 103, 173). A second problem is the lack of quality control in published data. Reports of incorrect mtDNA sequences being published and submitted to databases are increasing in number (4, 11, 41, 124, 182), and even forensic databases have been accused of containing erroneous data (12, 181). However, not all purported errors are truly errors (10, 13, 23a), and the phylogenetic and forensic conclusions are rarely severely affected (e.g., 23a, 54, 143). Nevertheless, it is highly desirable that the data used in population genetic and evolutionary studies are of the highest quality, and statistical methods that aid in the detection of sequencing artefacts (e.g., 11) can be useful and should be used routinely. However, statistical analyses alone cannot uncover all errors, and are by no means a substitute for good laboratory practice. Unfortunately, we notice to our dismay a trend for more and more laboratories to sequence only one strand of the PCR product (e.g., 164), which in our experience does not ensure adequate detection of sequencing artefacts. A third serious issue is the increasing evidence that mtDNA may not be selectively neutral, as previously assumed (34, 51, 98, 99, 101, 126, 178). The rate of nonsynonymous mutations at several mitochondrial genes is higher than that of synonymous mutations within humans, but not between humans and chimps (51, 101, 178). This could be due to most mutations being slightly deleterious, so that they would contribute to polymorphism within populations, but would not become fixed and so would not contribute to differences between species (51, 101). However, the apparent excess of polymorphism within species could actually reflect an underestimate of the true divergence between species, due to the inability to detect recurrent mutations (43), which have occurred since the divergence of chimpanzees and humans (74).

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It has also been suggested that the geographical variation seen in mtDNA haplogroups may reflect selection acting on specific lineages as humans spread from Africa to different climatic conditions (98, 126). In particular, it has been claimed that haplogroups A, C, and D, which are characteristic of Siberians and Native Americans, have been strongly influenced by selection to uncouple the heat production and ATP production aspects of mitochondrial oxidative phosphorylation in order to produce more heat in colder climates (126). However, these provocative claims rest largely on statistical analyses of the distribution of nonsynonymous versus synonymous mutations in a phylogenetic tree of complete mtDNA sequences from the various haplogroups; detailed biochemical analyses are required to determine if there indeed has been a functional change in oxidative phosphorylation in individuals with these haplogroups. Because the A, C, and D haplogroups also occur in tropical environments in the Americas, where they have presumably been for at least 10,000 years (132), a further test of this hypothesis would be to see if these haplogroups have undergone further mutations in the Americas to more tightly couple heat and ATP generation. Moreover, Elson et al. (34) see no such evidence for climate-induced geographically varied selection in a data set of 560 coding region sequences. They do see evidence for mainly negative selection acting on the 13 protein-coding genes of mtDNA, with the exception of ATP6, which shows signs of balancing or positive selection in Europeans and Asians [in agreement with the findings of Mishmar et al. (98)]. There also is evidence of regional violations of clock-like evolution of mtDNA in Africa (60, 164). The overall consensus is that mainly purifying selection has been acting on human mtDNA; because the unit of inheritance is the whole genome, which does not undergo recombination, the noncoding control region is subject to the same selective forces as the coding DNA. This means that care must be taken when using mtDNA data to date phylogenetic events, as the underlying assumption of neutral clock-like evolution may not hold. However, the basic results of mtDNA studies, such as a recent initial migration out of Africa and subsequent world-wide dispersal of modern humans, are not affected by non-neutral evolution, and, furthermore, are supported by a wide array of other loci (26, 36).

What is mtDNA Still Good For? Even though mtDNA will probably be used less and less as the sole marker for elucidating human evolution and population history, it is still important for a wide range of questions. First of all, it is useful for unraveling socio-cultural effects that might have influenced human evolution, such as polygyny (32, 71, 129, 177), the effects of matrilocality versus patrilocality (105, 176), or the social stratification induced by the caste system (8, 179). Furthermore, because of the high copy number of mtDNA versus the diploid autosomes and haploid Y-chromosome, mtDNA is crucial in studies of ancient DNA and in some applications of forensics. Depending on the age of the fossil sample, often only mtDNA will still be present, and therefore this is the only insight one can get into the genetic affinities of ancient populations (72, 148,

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149, 169). However, a major problem with ancient DNA studies is contamination with modern DNA, an issue that is unfortunately not yet widely recognized (58, 108). This is particularly a problem when ancient samples of modern humans are analyzed, because the contaminating mtDNA will not differ greatly from the authentic mtDNA. Therefore, caution should be exercised when evaluating studies of ancient DNA in modern humans. This holds especially true for very old fossils, such as Neandertals or ancient modern humans. Nevertheless, it was possible to amplify and sequence mtDNA in a number of these (25, 79–81, 106, 130, 137). And in forensic applications, using mtDNA enables identification of otherwise unidentifiable victims, if maternal relatives are alive for comparison (46, 147). This is becoming increasingly relevant for victims of war or terror (59, 84, 85). Problems and issues in the use of mtDNA in forensic analyses were recently reviewed in this journal (23). Finally, mtDNA is increasingly used in so-called personalized genetic histories (140). This is the use of genetic testing to investigate individual genealogies, including tracing the origins of immigrant/slave ancestors. Currently, of 11 companies offering such testing, 7 use mtDNA in addition to Y-chromosomal markers, and 2 companies offer only mtDNA analyses (140). Unfortunately, this use of mtDNA is fraught with difficulties that the average customer may not be aware of. For example, many people request such testing with the expectation that they will learn a very specific place of origin, such as which village they come from. The reality is that current mtDNA databases are not sufficiently detailed to allow such a high degree of geographic resolution, and even if they were, mtDNA types in general do not show sufficient geographic specificity to allow one to pinpoint such a specific origin. Furthermore, many customers inevitably confuse the place of origin of their maternal lineage with the place of origin of all of their biological ancestry, with potentially profound effects on how they view themselves and their identity. It must be kept in mind that mtDNA comprises only 0.0006% of the total human genome; as informative as mtDNA analyses have been and will continue to be for understanding human population history and evolution, when it comes to questions about personal genetic ancestry (as well as questions about human population history and evolution), it would be desirable to have some information on the remaining 99.9994% of the genome. The Annual Review of Genomics and Human Genetics is online at http://genom.annualreviews.org LITERATURE CITED 1. Alves-Silva J, da Silva Santos M, Guimaraes PE, Ferreira AC, Bandelt HJ, et al. 2000. The ancestry of Brazilian mtDNA lineages. Am. J. Hum. Genet. 67:444–61 2. Anderson S, Bankier AT, Barrell BG, de

Bruijn MHL, Coulson AR, et al. 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457–65 3. Arctander P. 1999. Mitochondrial recombination? Science 284:2090–91

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mtDNA AND HUMAN EVOLUTION 4. Arnason E. 2003. Genetic heterogeneity of Icelanders. Ann. Hum. Genet. 67:5– 16 5. Awadalla P, Eyre-Walker A, Maynard Smith J. 1999. Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 286:2524–25 6. Awadalla P, Eyre-Walker A, Smith JM. 2000. Science 288:1931a 7. Ballinger SW, Schurr TG, Torroni A, Gan YY, Hodge JA, et al. 1992. Southeast Asian mitochondrial DNA analysis reveals genetic continuity of ancient mongoloid migrations. Genetics 130:139–52 8. Bamshad MJ, Watkins WS, Dixon ME, Jorde LB, Rao BB, et al. 1998. Female gene flow stratifies Hindu castes. Nature 395:651–52 9. Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB. 2003. Human population genetic structure and inference of group membership. Am. J. Hum. Genet. 72:578–89 10. Bandelt HJ. 2004. Etruscan artifacts. Am. J. Hum. Genet. 75:919–20 11. Bandelt HJ, Quintana-Murci L, Salas A, Macaulay V. 2002. The fingerprint of phantom mutations in mitochondrial DNA data. Am. J. Hum. Genet. 71:1150– 60 12. Bandelt HJ, Salas A, Bravi C. 2004. Problems in FBI mtDNA database. Science 305:1402–4 13. Barbujani G, Vernesi C, Caramelli D, Castri L, Lalueza-Fox C, Bertorelle G. 2004. Etruscan artifacts: much ado about nothing. Am. J. Hum. Genet. 75:923–27 14. Basu A, Mukherjee N, Roy S, Sengupta S, Banerjee S, et al. 2003. Ethnic India: a genomic view, with special reference to peopling and structure. Genome Res. 13:2277–90 15. Bendall KE, Macaulay VA, Baker JR, Sykes BC. 1996. Heteroplasmic point mutations in the human mtDNA control region. Am. J. Hum. Genet. 59:1276–87 16. Bensasson D, Feldman MW, Petrov DA. 2003. Rates of DNA duplication and mi-

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25.

175

tochondrial DNA insertion in the human genome. J. Mol. Evol. 57:343–54 Bensasson D, Zhang D, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol. Evol. 16:314–21 Brandstatter A, Parsons TJ, Parson W. 2003. Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups. Int. J. Legal Med. 117:291–98 Br¨auer G. 1984. A craniological approach to the origin of anatomically modern Homo sapiens in Africa and implications for the appearance of modern Europeans. In The Origins of Modern Humans: A World Survey of theFossil Evidence, ed. CB Stringer, P Mellars, pp. 327–410. New York: Alan R. Liss Bromham L, Eyre-Walker A, Smith NH, Maynard Smith J. 2003. Mitochondrial Steve: paternal inheritance of mitochondria in humans. Trends E col. Evol. 18:2– 4 Brown DT, Samuels DC, Michael EM, Turnbull DM, Chinnery PF. 2001. Random genetic drift determines the level of mutant mtDNA in human primary oocytes. Am. J. Hum. Genet. 68:533–36 Brown WM. 1980. Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis. Proc. Natl. Acad. Sci. USA 77:3605–9 Budowle B, Allard MW, Wilson MR, Chakraborty R. 2003. Forensics and mitochondrial DNA: applications, debates, and foundations. Annu. Rev. Genomics Hum. Genet. 4:119–41 Budowle B, Polanskey D. 2005. FBI mtDNA Database: a cogent perspective. Science 307:845–46 Cann RL, Stoneking M, Wilson AC. 1987. Mitochondrial DNA and human evolution. Nature 325:31–36 Caramelli D, Lalueza-Fox C, Vernesi C, Lari M, Casoli A, et al. 2003. Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically

20 Aug 2005 11:13

176

26.

Annu. Rev. Genom. Human Genet. 2005.6:165-183. Downloaded from www.annualreviews.org by Universidad de Granada on 05/03/12. For personal use only.

27.

28.

29.

30.

31.

32.

33.

34.

35.

AR

AR252-GG06-08.tex

PAKENDORF




XMLPublishSM (2004/02/24)

P1: KUV

STONEKING

modern Europeans. Proc. Natl. Acad. Sci. USA 100:6593–97 Cavalli-Sforza LL, Feldman MW. 2003. The application of molecular genetic approaches to the study of human evolution. Nat. Genet. 33(Suppl.):266–75 Coble MD, Just RS, O’Callaghan JE, Letmanyi IH, Peterson CT, et al. 2004. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int. J. Legal Med. 118:137–46 Comas D, Calafell F, Mateu E, PerezLezaun A, Bosch E, et al. 1998. Trading genes along the silk road: mtDNA sequences and the origin of central Asian populations. Am. J. Hum. Genet. 63: 1824–38 Cordaux R, Weiss G, Saha N, Stoneking M. 2004. The northeast Indian passageway: a barrier or corridor for human migrations? Mol. Biol. Evol. 21:1525–33 Davis RE, Miller S, Herrnstadt C, Ghosh SS, Fahy E, et al. 1997. Mutations in mitochondrial cytochrome c oxidase genes segregate with late-onset Alzheimer disease. Proc. Natl. Acad. Sci. USA 94:4526– 31 Davis RE, Miller S, Herrnstadt C, Ghosh SS, Fahy E, et al. 1998. Retraction, Genetics. Proc. Natl. Acad. Sci. USA 95:12069 Dupanloup I, Pereira L, Bertorelle G, Calafell F, Prata MJ, et al. 2003. A recent shift from polygyny to monogamy in humans is suggested by the analysis of worldwide Y-chromosome diversity. J. Mol. Evol. 57:85–97 Elson JL, Andrews RM, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 2001. Analysis of European mtDNAs for recombination. Am. J. Hum. Genet. 68:145–53 Elson JL, Turnbull DM, Howell N. 2004. Comparative genomics and the evolution of human mitochondrial DNA: assessing the effects of selection. Am. J. Hum. Genet. 74:229–38 Enriquez JA, Cabezas-Herrera J, Bayona-

36.

37.

38.

39.

40.

41. 42.

43.

44.

45.

46.

Bafaluy MP, Attardi G. 2000. Very rare complementation between mitochondria carrying different mitochondrial DNA mutations points to intrinsic genetic autonomy of the organelles in cultured human cells. J. Biol. Chem. 275:11207–15 Excoffier L. 2002. Human demographic history: refining the recent African origin model. Curr. Opin. Genet. Dev. 12:675– 82 Excoffier L, Yang Z. 1999. Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees. Mol. Biol. Evol. 16:1357– 68 Eyre-Walker A, Smith NH, Smith JM. 1999. How clonal are human mitochondria? Proc. R. Soc. London B Biol. Sci. 266:477–83 Filosto M, Mancuso M, Vives-Bauza C, Vila MR, Shanske S, et al. 2003. Lack of paternal inheritance of muscle mitochondrial DNA in sporadic mitochondrial myopathies. Ann. Neurol. 54:524–26 Finnila S, Lehtonen MS, Majamaa K. 2001. Phylogenetic network for European mtDNA. Am. J. Hum. Genet. 68:1475–84 Forster P. 2003. To err is human. Ann. Hum. Genet. 67:2–4 Forster P, Torroni A, Renfrew C, R¨ohl A. 2001. Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution. Mol. Biol. Evol. 18:1864–81 Gerber AS, Loggins R, Kumar S, Dowling TE. 2001. Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes? Annu. Rev. Genet. 35:539–66 Gilbert MT, Willerslev E, Hansen AJ, Barnes I, Rudbeck L, et al. 2003. Distribution patterns of postmortem damage in human mitochondrial DNA. Am. J. Hum. Genet. 72:32–47 Giles RE, Blanc H, Cann HM, Wallace DC. 1980. Maternal inheritance of human mitochondrial DNA. Proc. Natl. Acad. Sci. USA 77:6715–19 Gill P, Ivanov PL, Kimpton C, Piercy R,

20 Aug 2005 11:13

AR

AR252-GG06-08.tex

XMLPublishSM (2004/02/24)

P1: KUV

mtDNA AND HUMAN EVOLUTION

47.

Annu. Rev. Genom. Human Genet. 2005.6:165-183. Downloaded from www.annualreviews.org by Universidad de Granada on 05/03/12. For personal use only.

48.

49.

50.

51.

52.

53.

54.

55.

Benson N, et al. 1994. Identification of the remains of the Romanov family by DNA analysis. Nat. Genet. 6:130–35 Gyllensten U, Wharton D, Josefsson A, Wilson AC. 1991. Paternal inheritance of mitochondrial DNA in mice. Nature 352: 255–57 Hagelberg E. 2003. Recombination or mutation rate heterogeneity? Implications for Mitochondrial Eve. Trends Genet. 19: 84–90 Hagelberg E, Goldman N, Lio P, Whelan S, Schiefenh¨ovel W, et al. 1999. Evidence for mitochondrial DNA recombination in a human population of island Melanesia. Proc. R. Soc. London B Biol. Sci. 266:485–92 Hagelberg E, Goldman N, Lio P, Whelan S, Schiefenh¨ovel W, et al. 2000. Evidence for mitochondrial DNA recombination in a human population of island Melanesia: correction. Proc. R. Soc. London B Biol. Sci. 267:1595–96 Hasegawa M, Cao Y, Yang Z. 1998. Preponderance of slightly deleterious polymorphism in mitochondrial DNA: Nonsynonymous/synonymous rate ratio is much higher within species than between species. Mol. Biol. Evol. 15:1499–505 Hasegawa M, Di Rienzo A, Kocher TD, Wilson AC. 1993. Toward a more accurate time scale for the human mitochondrial DNA tree. J. Mol. Evol. 37:347–54 Hazkani-Covo E, Sorek R, Graur D. 2003. Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications. J. Mol. Evol. 56:169–74 Helgason A, Stefansson K. 2003. Erroneous claims about the impact of mitochondrial DNA sequence database errors. Am. J. Hum. Genet. 73:974–75 Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, et al. 2002. Reducedmedian-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian,

56.

57.

58.

59.

60.

61.

62.

63.

64.

177

and European haplogroups. Am. J. Hum. Genet. 70:1152–71 Heyer E, Zietkiewicz E, Rochowski A, Yotova V, Puymirat J, Labuda D. 2001. Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees. Am. J. Hum. Genet. 69:1113– 26 Hirano M, Shtilbans A, Mayeux R, Davidson MM, DiMauro S, et al. 1997. Apparent mtDNA heteroplasmy in Alzheimer’s disease patients and in normals due to PCR amplification of nucleus-embedded mtDNA pseudogenes. Proc. Natl. Acad. Sci. USA 94:14894–99 Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S. 2001. Ancient DNA. Nat. Rev. Genet. 2:353–59 Holland MM, Fisher DL, Mitchell LG, Rodriquez WC, Canik JJ, et al. 1993. Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the Vietnam War. J. Forensic Sci. 38:542–53 Howell N, Elson JL, Turnbull DM, Herrnstadt C. 2004. African haplogroup L mtDNA sequences show violations of clock-like evolution. Mol. Biol. Evol. 21: 1843–54 Howell N, Mackey DA. 1997. Reply to Macauley et al. Am. J. Hum. Genet. 61: 986–90 Howell N, Smejkal CB. 2000. Persistent heteroplasmy of a mutation in the human mtDNA control region: hypermutation as an apparent consequence of simple-repeat expansion/contraction. Am. J. Hum. Genet. 66:1589–98 Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, Herrnstadt C. 2003. The pedigree rate of sequence divergence in the human mitochondrial genome: There is a difference between phylogenetic and pedigree rates. Am. J. Hum. Genet. 72:659–70 Ingman M, Gyllensten U. 2001. Analysis of the complete human mtDNA genome:

20 Aug 2005 11:13

178

65.

Annu. Rev. Genom. Human Genet. 2005.6:165-183. Downloaded from www.annualreviews.org by Universidad de Granada on 05/03/12. For personal use only.

66.

67.

68.

69.

70.

71.

72.

73.

74.

AR

AR252-GG06-08.tex

PAKENDORF




XMLPublishSM (2004/02/24)

P1: KUV

STONEKING

methodology and inferences for human evolution. J. Hered. 92:454–61 Ingman M, Gyllensten U. 2003. Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Res. 13: 1600–6 Ingman M, Kaessmann H, P¨aa¨ bo S, Gyllensten U. 2000. Mitochondrial genome variation and the origin of modern humans. Nature 408:708–13 Jazin E, Soodyall H, Jalonen P, Lindholm E, Stoneking M, Gyllensten U. 1998. Mitochondrial mutation rate revisited: hot spots and polymorphism. Nat. Genet. 18:109–10 Johnson MJ, Wallace DC, Ferris SD, Rattazzi MC, Cavalli-Sforza LL. 1983. Radiation of human mitochondria DNA types analyzed by restriction endonuclease cleavage patterns. J. Mol. Evol. 19: 255–71 Jorde LB, Bamshad M. 2000. Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a Kaneda H, Hayashi J, Takahama S, Taya C, Lindahl KF, Yonekawa H. 1995. Elimination of paternal mitochondrial DNA in intraspecific crosses during early mouse embryogenesis. Proc. Natl. Acad. Sci. USA 92:4542–46 Kayser M, Brauer S, Weiss G, Schiefenhovel W, Underhill P, et al. 2003. Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea. Am. J. Hum. Genet. 72:281–302 Keyser-Tracqui C, Crubezy E, Ludes B. 2003. Nuclear and mitochondrial DNA analysis of a 2,000-year-old necropolis in the Egyin Gol Valley of Mongolia. Am. J. Hum. Genet. 73:247–60 Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, et al. 2004. Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am. J. Hum. Genet. 75:752–70 Kocher TD, Wilson AC. 1991. Sequence

75.

76.

77.

78.

79.

80.

81.

82.

83.

84.

evolution of mitochondrial DNA in humans and chimpanzees: control region and a protein-coding region. In Evolution of Life: Fossils, Molecules, and Culture, ed. S Osawa, T Honjo, pp. 391–413. Tokyo: Springer-Verlag Kolman CJ, Sambuugiin N, Bermingham E. 1996. Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders. Genetics 142:1321–34 Kondo R, Satta Y, Matsuura ET, Ishiwa H, Takahata N, Chigusa SI. 1990. Incomplete maternal transmission of mitochondrial DNA in Drosophila. Genetics 126:657– 63 Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, Zhang YP. 2003. Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences. Am. J. Hum. Genet. 73:671–76 Kraytsberg Y, Schwartz M, Brown TA, Ebralidse K, Kunz WS, et al. 2004. Recombination of human mitochondrial DNA. Science 304:981 Krings M, Capelli C, Tschentscher F, Geisert H, Meyer S, et al. 2000. A view of Neandertal genetic diversity. Nat. Genet. 26:144–46 Krings M, Geisert H, Schmitz RW, Krainitzki H, P¨aa¨ bo S. 1999. DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc. Natl. Acad. Sci. USA 96: 5581–85 Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, P¨aa¨ bo S. 1997. Neandertal DNA sequences and the origin of modern humans. Cell 90:19–30 Kumar S, Hedrick P, Dowling T, Stoneking M. 2000. Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a Kvist L, Martens J, Nazarenko AA, Orell M. 2003. Paternal leakage of mitochondrial DNA in the great tit (Parus major). Mol. Biol. Evol. 20:243–47 Ladika S. 2001. DNA forensics. Laying

20 Aug 2005 11:13

AR

AR252-GG06-08.tex

XMLPublishSM (2004/02/24)

P1: KUV

mtDNA AND HUMAN EVOLUTION

85.

Annu. Rev. Genom. Human Genet. 2005.6:165-183. Downloaded from www.annualreviews.org by Universidad de Granada on 05/03/12. For personal use only.

86.

87.

88.

89.

90.

91.

92.

93.

94.

ghosts to rest in Bosnia. Science 293: 1422–23 Lawler A. 2001. Terrorism. Massive DNA identification effort gets under way. Science 294:278–79 Legros F, Lombes A, Frachon P, Rojo M. 2002. Mitochondrial fusion in human cells is efficient, requires the inner membrane potential, and is mediated by mitofusins. Mol. Biol. Cell 13:4343–54 Lum JK, Cann RL. 2000. mtDNA lineage analyses: origins and migrations of Micronesians and Polynesians. Am. J. Phys. Anthropol. 113:151–68 Maca-Meyer N, Gonzalez AM, Larruga JM, Flores C, Cabrera VM. 2001. Major genomic mitochondrial lineages delineate early human expansions. BMC Genet. 2:13 Macaulay V, Richards M, Sykes B. 1999. Mitochondrial DNA recombination-no need to panic. Proc. R. Soc. London B Biol. Sci. 266:2037–39 Macaulay VA, Richards MB, Forster P, Bendall KE, Watson E, et al. 1997. mtDNA mutation rates—no need to panic. Am. J. Hum. Genet. 61:983–86 Maitra A, Cohen Y, Gillespie SE, Mambo E, Fukushima N, et al. 2004. The Human MitoChip: a high-throughput sequencing microarray for mitochondrial mutation detection. Genome Res. 14:812–19 Manfredi G, Thyagarajan D, Papadopoulou LC, Pallotti F, Schon EA. 1997. The fate of human sperm-derived mtDNA in somatic cells. Am. J. Hum. Genet. 61:953–60 Melton T, Clifford S, Martinson J, Batzer M, Stoneking M. 1998. Genetic evidence for the proto-Austronesian homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes. Am. J. Hum. Genet. 63:1807–23 Melton T, Peterson R, Redd AJ, Saha N, Sofro AS, et al. 1995. Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. Am. J. Hum. Genet. 57:403–14

179

95. Merriwether DA, Kaestle FA. 1999. Mitochondrial recombination? (continued). Science 285:837 96. Meyer S, Weiss G, von Haeseler A. 1999. Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152: 1103–10 97. Mishmar D, Ruiz-Pesini E, Brandon M, Wallace DC. 2004. Mitochondrial DNAlike sequences in the nucleus (NUMTs): insights into our African origins and the mechanism of foreign DNA integration. Hum. Mutat. 23:125–33 98. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, et al. 2003. Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. USA 100:171–76 99. Moilanen JS, Finnila S, Majamaa K. 2003. Lineage-specific selection in human mtDNA: lack of polymorphisms in a segment of MTND5 gene in haplogroup J. Mol. Biol. Evol. 20:2132–42 100. Murray-McIntosh RP, Scrimshaw BJ, Hatfield PJ, Penny D. 1998. Testing migration patterns and estimating founding population size in Polynesia by using human mtDNA sequences. Proc. Natl. Acad. Sci. USA 95:9047–52 101. Nachman MW, Brown WM, Stoneking M, Aquadro CF. 1996. Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics 142:953–63 102. Nasidze I, Ling EY, Quinque D, Dupanloup I, Cordaux R, et al. 2004. Mitochondrial DNA and Y-chromosome variation in the caucasus. Ann. Hum. Genet. 68: 205–21 103. Olson LE, Yoder AD. 2002. Using secondary structure to identify ribosomal numts: cautionary examples from the human genome. Mol. Biol. Evol. 19:93–100 104. Ono T, Isobe K, Nakada K, Hayashi JI. 2001. Human cells are protected from mitochondrial dysfunction by complementation of DNA products in fused mitochondria. Nat. Genet. 28:272–75

20 Aug 2005 11:13

Annu. Rev. Genom. Human Genet. 2005.6:165-183. Downloaded from www.annualreviews.org by Universidad de Granada on 05/03/12. For personal use only.

180

AR

AR252-GG06-08.tex

PAKENDORF




XMLPublishSM (2004/02/24)

P1: KUV

STONEKING

105. Oota H, Settheetham-Ishida W, Tiwawech D, Ishida T, Stoneking M. 2001. Human mtDNA and Y-chromosome variation is correlated with matrilocal versus patrilocal residence. Nat. Genet. 29:20– 21 106. Ovchinnikov IV, Gotherstrom A, Romanova GP, Kharitonov VM, Liden K, Goodwin W. 2000. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404:490–93 107. P¨aa¨ bo S. 1996. Mutational hot spots in the mitochondrial microcosmos. Am. J. Hum. Genet. 59:493–96 108. P¨aa¨ bo S, Poinar H, Serre D, JaenickeDespres V, Hebler J, et al. 2004. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38:645–79 109. Pakendorf B, Wiebe V, Tarskaia LA, Spitsyn VA, Soodyall H, et al. 2003. Mitochondrial DNA evidence for admixed origins of central Siberian populations. Am. J. Phys. Anthropol. 120:211–24 110. Parsons TJ, Irwin JA. 2000. Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a 111. Parsons TJ, Muniec DS, Sullivan K, Woodyatt N, Alliston-Greiner R, et al. 1997. A high observed substitution rate in the human mitochondrial DNA control region. Nat. Genet. 15:363–68 112. Pereira L, Macaulay V, Torroni A, Scozzari R, Prata MJ, Amorim A. 2001. Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade. Ann. Hum. Genet. 65:439–58 113. Piganeau G, Eyre-Walker A. 2004. A reanalysis of the indirect evidence for recombination in human mitochondrial DNA. Heredity 92:282–88 114. Poulton J, Marchington DR. 2002. Segregation of mitochondrial DNA (mtDNA) in human oocytes and in animal models of mtDNA disease: clinical implications. Reproduction 123:751–55 115. Quintana-Murci L, Semino O, Bandelt HJ, Passarino G, McElreavey K,

116.

117.

118.

119.

120.

121.

122.

123.

124.

125.

Santachiara-Benerecetti AS. 1999. Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nat. Genet. 23:437–41 Redd AJ, Roberts-Thomson J, Karafet T, Bamshad M, Jorde LB, et al. 2002. Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome. Curr. Biol. 12:673–77 Redd AJ, Stoneking M. 1999. Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations. Am. J. Hum. Genet. 65:808–28 Redd AJ, Takezaki N, Sherry ST, McGarvey ST, Sofro AS, Stoneking M. 1995. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific. Mol. Biol. Evol. 12:604– 15 Reidla M, Kivisild T, Metspalu E, Kaldma K, Tambets K, et al. 2003. Origin and diffusion of mtDNA haplogroup X. Am. J. Hum. Genet. 73:1178–90 Richards M, Corte-Real H, Forster P, Macaulay V, Wilkinson-Herbots H, et al. 1996. Paleolithic and neolithic lineages in the European mitochondrial gene pool. Am. J. Hum. Genet. 59:185–203 Richards M, Macaulay V, Hickey E, Vega E, Sykes B, et al. 2000. Tracing European founder lineages in the Near Eastern mtDNA pool. Am. J. Hum. Genet. 67: 1251–76 Richards M, Macaulay V, Torroni A, Bandelt HJ. 2002. In search of geographical patterns in European mitochondrial DNA. Am. J. Hum. Genet. 71:1168–74 Robin ED, Wong R. 1988. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J. Cell. Physiol. 136:507–13 R¨ohl A, Brinkmann B, Forster L, Forster P. 2001. An annotated mtDNA database. Int. J. Legal Med. 115:29–39 Rosa A, Brehm A, Kivisild T, Metspalu E, Villems R. 2004. MtDNA profile of West Africa Guineans: towards a better

20 Aug 2005 11:13

AR

AR252-GG06-08.tex

XMLPublishSM (2004/02/24)

P1: KUV

mtDNA AND HUMAN EVOLUTION

126.

Annu. Rev. Genom. Human Genet. 2005.6:165-183. Downloaded from www.annualreviews.org by Universidad de Granada on 05/03/12. For personal use only.

127.

128.

129.

130.

131.

132.

133.

134.

understanding of the Senegambia region. Ann. Hum. Genet. 68:340–52 Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC. 2004. Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 303:223–26 Salas A, Richards M, De la Fe T, Lareu MV, Sobrino B, et al. 2002. The making of the African mtDNA landscape. Am. J. Hum. Genet. 71:1082–111 Salas A, Richards M, Lareu MV, Scozzari R, Coppa A, et al. 2004. The African diaspora: mitochondrial DNA and the Atlantic slave trade. Am. J. Hum. Genet. 74:454– 65 Salem AH, Badr FM, Gaballah MF, P¨aa¨ bo S. 1996. The genetics of traditional living: Y-chromosomal and mitochondrial lineages in the Sinai Peninsula. Am. J. Hum. Genet. 59:741–43 Schmitz RW, Serre D, Bonani G, Feine S, Hillgruber F, et al. 2002. The Neandertal type site revisited: interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. Proc. Natl. Acad. Sci. USA 99:13342–47 Schurr TG, Ballinger SW, Gan YY, Hodge JA, Merriwether DA, et al. 1990. Amerindian mitochondrial DNAs have rare Asian mutations at high frequencies, suggesting they derived from four primary maternal lineages. Am. J. Hum. Genet. 46: 613–23 Schurr TG, Sherry ST. 2004. Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: evolutionary and demographic evidence. Am. J. Hum. Biol. 16:420–39 Schurr TG, Sukernik RI, Starikovskaya YB, Wallace DC. 1999. Mitochondrial DNA variation in Koryaks and Itel’men: population replacement in the Okhotsk Sea-Bering Sea region during the Neolithic. Am. J. Phys. Anthropol. 108:1–39 Schwartz M, Vissing J. 2002. Paternal inheritance of mitochondrial DNA. N. Engl. J. Med. 347:576–80

181

135. Schwartz M, Vissing J. 2003. New patterns of inheritance in mitochondrial disease. Biochem. Biophys. Res. Commun. 310:247–51 136. Schwartz M, Vissing J. 2004. No evidence for paternal inheritance of mtDNA in patients with sporadic mtDNA mutations. J. Neurol. Sci. 218:99–101 137. Serre D, Langaney A, Chech M, TeschlerNicola M, Paunovic M, et al. 2004. No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol. 2:E57 138. Shen P, Lavi T, Kivisild T, Chou V, Sengun D, et al. 2004. Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation. Hum. Mutat. 24:248– 60 139. Shitara H, Hayashi JI, Takahama S, Kaneda H, Yonekawa H. 1998. Maternal inheritance of mouse mtDNA in interspecific hybrids: segregation of the leaked paternal mtDNA followed by the prevention of subsequent paternal leakage. Genetics 148:851–57 140. Shriver MD, Kittles RA. 2004. Genetic ancestry and the search for personalized genetic histories. Nat. Rev. Genet. 5:611– 18 141. Sigurdardottir S, Helgason A, Gulcher JR, Stefansson K, Donnelly P. 2000. The mutation rate in the human mtDNA control region. Am. J. Hum. Genet. 66:1599–609 142. Silva WA Jr, Bonatto SL, Holanda AJ, Ribeiro-Dos-Santos AK, Paixao BM, et al. 2002. Mitochondrial genome diversity of Native Americans supports a single early entry of founder populations into America. Am. J. Hum. Genet. 71:187–92 143. Silva WAJ, Bonatto SL, Holanda AJ, Ribeiro-dos-Santos AK, Paixao BM, et al. 2003. Correction: mitochondrial DNA variation in Amerindians. Am. J. Hum. Genet. 72:1346–48 144. Simoni L, Calafell F, Pettener D, Bertranpetit J, Barbujani G. 2000. Geographic

20 Aug 2005 11:13

182

145.

Annu. Rev. Genom. Human Genet. 2005.6:165-183. Downloaded from www.annualreviews.org by Universidad de Granada on 05/03/12. For personal use only.

146.

147.

148.

149.

150. 151.

152.

153.

154.

155.

156.

AR

AR252-GG06-08.tex

PAKENDORF




XMLPublishSM (2004/02/24)

P1: KUV

STONEKING

patterns of mtDNA diversity in Europe. Am. J. Hum. Genet. 66:262–78 Simoni L, Calafell F, Pettener D, Bertranpetit J, Barbujani G. 2000. Reconstruction of prehistory on the basis of genetic data. Am. J. Hum. Genet. 66:1177–79 Slate J, Gemmell N. 2004. Eve ‘n’ Steve: recombination of human mitochondrial DNA. Trends Ecol. Evol. 19:561–63 Stone AC, Starrs JE, Stoneking M. 2001. Mitochondrial DNA analysis of the presumptive remains of Jesse James. J. Forensic Sci. 46:173–76 Stone AC, Stoneking M. 1993. Ancient DNA from a pre-Columbian Amerindian population. Am. J. Phys. Anthropol. 92: 463–71 Stone AC, Stoneking M. 1998. mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World. Am. J. Hum. Genet. 62:1153– 70 Stoneking M. 1993. DNA and recent human evolution. Evol. Anthropol. 2:60–73 Stoneking M. 2000. Hypervariable sites in the mtDNA control region are mutational hotspots. Am. J. Hum. Genet. 67:1029–32 Stoneking M, Sherry ST, Redd AJ, Vigilant L. 1992. New approaches to dating suggest a recent age for the human mtDNA ancestor. Philos. Trans. R. Soc. London B Biol. Sci. 337:167–75 Stoneking M, Soodyall H. 1996. Human evolution and the mitochondrial genome. Curr. Opin. Genet. Dev. 6:731–36 Stringer CB, Andrews P. 1988. Genetic and fossil evidence for the origin of modern humans. Science 239:1263–68 Sutovsky P, Moreno RD, Ramalho-Santos J, Dominko T, Simerly C, Schatten G. 1999. Ubiquitin tag for sperm mitochondria. Nature 402:371–72 Sutovsky P, Moreno RD, Ramalho-Santos J, Dominko T, Simerly C, Schatten G. 2000. Ubiquitinated sperm mitochondria, selective proteolysis, and the regulation of mitochondrial inheritance in mammalian embryos. Biol. Reprod. 63:582–90

157. Tambets K, Rootsi S, Kivisild T, Help H, Serk P, et al. 2004. The western and eastern roots of the Saami–the story of genetic “outliers” told by mitochondrial DNA and Y chromosomes. Am. J. Hum. Genet. 74:661–82 158. Tamura K, Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512–26 159. Tanaka M, Cabrera VM, Gonzalez AM, Larruga JM, Takeyasu T, et al. 2004. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res. 14:1832–50 160. Taylor RW, McDonnell MT, Blakely EL, Chinnery PF, Taylor GA, et al. 2003. Genotypes from patients indicate no paternal mitochondrial DNA contribution. Ann. Neurol. 54:521–24 161. Thyagarajan B, Padua RA, Campbell C. 1996. Mammalian mitochondria possess homologous DNA recombination activity. J. Biol. Chem. 271:27536–43 162. Tolk HV, Barac L, Pericic M, Klaric IM, Janicijevic B, et al. 2001. The evidence of mtDNA haplogroup F in a European population and its ethnohistoric implications. Eur. J. Hum. Genet 9:717–23 163. Torroni A, Bandelt HJ, D’Urbano L, Lahermo P, Moral P, et al. 1998. mtDNA analysis reveals a major late Paleolithic population expansion from southwestern to northeastern Europe. Am. J. Hum. Genet. 62:1137–52 164. Torroni A, Rengo C, Guida V, Cruciani F, Sellitto D, et al. 2001. Do the four clades of the mtDNA haplogroup L2 evolve at different rates? Am. J. Hum. Genet. 69: 1348–56 165. Torroni A, Schurr TG, Cabell MF, Brown MD, Neel JV, et al. 1993. Asian affinities and continental radiation of the four founding Native American mtDNAs. Am. J. Hum. Genet. 53:563–90 166. Tourmen Y, Baris O, Dessen P, Jacques C, Malthiery Y, Reynier P. 2002. Structure

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167.

168.

169.

170.

171.

172.

173.

174.

175.

and chromosomal distribution of human mitochondrial pseudogenes. Genomics 80:71–77 Tully LA, Parsons TJ, Steighner RJ, Holland MM, Marino MA, Prenger VL. 2000. A sensitive denaturing gradient-gel electrophoresis assay reveals a high frequency of heteroplasmy in hypervariable region 1 of the human mtDNA control region. Am. J. Hum. Genet. 67:432–43 van Holst Pellekaan S, Frommer M, Sved J, Boettcher B. 1998. Mitochondrial control region sequence variation in aboriginal Australians. Am. J. Hum. Genet. 62: 435–49 Vernesi C, Caramelli D, Dupanloup I, Bertorelle G, Lari M, et al. 2004. The Etruscans: a population-genetic study. Am. J. Hum. Genet. 74:694–704 Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC. 1991. African populations and the evolution of human mitochondrial DNA. Science 253:1503– 7 Wakeley J. 1993. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37:613–23 Wallace DC, Brown MD, Lott MT. 1999. Mitochondrial DNA variation in human evolution and disease. Gene 238:211–30 Wallace DC, Stugard C, Murdock D, Schurr T, Brown MD. 1997. Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations. Proc. Natl. Acad. Sci. USA 94:14900–5 Ward RH, Frazier BL, Dew-Jager K, P¨aa¨ bo S. 1991. Extensive mitochondrial diversity within a single Amerindian tribe. Proc. Natl. Acad. Sci. USA 88:8720– 24 Watson E, Forster P, Richards M, Bandelt HJ. 1997. Mitochondrial footprints of hu-

176.

177.

178.

179.

180.

181.

182.

183.

184.

183

man expansions in Africa. Am. J. Hum. Genet. 61:691–704 Wilder JA, Kingan SB, Mobasher Z, Pilkington MM, Hammer MF. 2004. Global patterns of human mitochondrial DNA and Y-chromosome structure are not influenced by higher migration rates of females versus males. Nat. Genet. 36:1122–25 Wilder JA, Mobasher Z, Hammer MF. 2004. Genetic evidence for unequal effective population sizes of human females and males. Mol. Biol. Evol. 21:2047–57 Wise CA, Sraml M, Easteal S. 1998. Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees. Genetics 148:409–21 Wooding S, Ostler C, Prasad BV, Watkins WS, Sung S, et al. 2004. Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Ychromosomal data. Hum. Genet. 115: 221–29 Y− Chromosome− Consortium. 2002. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12:339–48 Yao YG, Bravi CM, Bandelt HJ. 2004. A call for mtDNA data quality control in forensic science. Forensic Sci. Int. 141:1– 6 Yao YG, Macauley V, Kivisild T, Zhang YP, Bandelt HJ. 2003. To trust or not to trust an idiosyncratic mitochondrial data set. Am. J. Hum. Genet. 72:1341–46 Zischler H, Geisert H, von Haeseler A, P¨aa¨ bo S. 1995. A nuclear ‘fossil’ of the mitochondrial D-loop and the origin of modern humans. Nature 378:489–92 Zouros E, Freeman KR, Ball AO, Pogson GH. 1992. Direct evidence for extensive paternal mitochondrial DNA inheritance in the marine mussel Mytilus. Nature 359:412–14

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Figure 2 Comparison of the lineage-based and population-based approaches in studies of population history. (a) Median-joining (MJ) network of HVR1 sequences from six Eurasian populations, with fast-evolving sites downweighted and singletons excluded. Yellow, Kazakh; green, Kirghiz; gray, Yakut; black, Tuvans; red, Evens; blue, Evenks. Data from Reference 109 and references therein. The mutated nucleotide positions are indicated on the branches. The MJ network thus indicates how the mtDNA lineages have evolved, but it is difficult to visualize how the populations are related. (b) Multidimensional scaling (MDS) plot based on genetic (Fst) distances of the same data. The population relationships are clearly visualized in the MDS plot, but there is no indication as to how the mtDNA sequences are related.

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Annu. Rev. Genom. Human Genet. 2005.6:165-183. Downloaded from www.annualreviews.org by Universidad de Granada on 05/03/12. For personal use only.

CONTENTS A PERSONAL SIXTY-YEAR TOUR OF GENETICS AND MEDICINE, Alfred G. Knudson COMPLEX GENETICS OF GLAUCOMA SUSCEPTIBILITY, Richard T. Libby, Douglas B. Gould, Michael G. Anderson, and Simon W.M. John NOONAN SYNDROME AND RELATED DISORDERS: GENETICS AND PATHOGENESIS, Marco Tartaglia and Bruce D. Gelb

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SILENCING OF THE MAMMALIAN X CHROMOSOME, Jennifer C. Chow, Ziny Yen, Sonia M. Ziesche, and Carolyn J. Brown

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THE GENETICS OF PSORIASIS AND AUTOIMMUNITY, Anne M. Bowcock EVOLUTION OF THE ATP-BINDING CASSETTE (ABC) TRANSPORTER SUPERFAMILY IN VERTEBRATES, Michael Dean and Tarmo Annilo TRADE-OFFS IN DETECTING EVOLUTIONARILY CONSTRAINED SEQUENCE BY COMPARATIVE GENOMICS, Eric A. Stone, Gregory M. Cooper, and Arend Sidow MITOCHONDRIAL DNA AND HUMAN EVOLUTION, Brigitte Pakendorf and Mark Stoneking THE GENETIC BASIS FOR CARDIAC REMODELING, Ferhaan Ahmad, J.G. Seidman, and Christine E. Seidman

1 15

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HUMAN TASTE GENETICS, Dennis Drayna

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MODIFIER GENETICS: CYSTIC FIBROSIS, Garry R. Cutting ADVANCES IN CHEMICAL GENETICS, Inese Smukste and Brent R. Stockwell THE PATTERNS OF NATURAL VARIATION IN HUMAN GENES, Dana C. Crawford, Dayna T. Akey, and Deborah A. Nickerson A SCIENCE OF THE INDIVIDUAL: IMPLICATIONS FOR A MEDICAL SCHOOL CURRICULUM, Barton Childs, Charles Wiener, and David Valle COMPARATIVE GENOMIC HYBRIDIZATION, Daniel Pinkel and Donna G. Albertson SULFATASES AND HUMAN DISEASE, Graciana Diez-Roux and Andrea Ballabio

237 261 287 313 331 355 v

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DISEASE GENE DISCOVERY THROUGH INTEGRATIVE GENOMICS, Cosmas Giallourakis, Charlotte Henson, Michael Reich, Xiaohui Xie, and Vamsi K. Mootha

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BIG CAT GENOMICS, Stephen J. O’Brien and Warren E. Johnson

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INDEXES Subject Index Cumulative Index of Contributing Authors, Volumes 1–6 Cumulative Index of Chapter Titles, Volumes 1–6

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ERRATA An online log of corrections to Annual Review of Genomics and Human Genetics chapters may be found at http://genom.annualreviews.org/