Harvesting the fruit of the human mtDNA tree.

Human mitochondrial DNA (mtDNA) studies have entered a new phase since the blossoming of complete genome analyses. Sequencing complete mtDNAs is more expensive and more labour intensive than restriction analysis or simply sequencing the control region of the molecule. But the efforts are paying off, as the phylogenetic resolution of the mtDNA tree has been greatly improved, and, in turn, phylogeographic interpretations can be given correspondingly greater precision in terms of the timing and direction of human dispersals. Therefore, despite mtDNA being only a fraction of our total genome, the deciphering of its evolution is profoundly changing our perception about how modern humans spread across our planet. Here we illustrate the phylogeographic approach with two case studies: the initial dispersal out of Africa, and the colonization of Europe.

[1]  H. Bandelt,et al.  mtDNA analysis reveals a major late Paleolithic population expansion from southwestern to northeastern Europe. , 1998, American journal of human genetics.

[2]  N. Maca-Meyer,et al.  Major genomic mitochondrial lineages delineate early human expansions , 2001, BMC Genetics.

[3]  Hans-Jürgen Bandelt,et al.  The emerging limbs and twigs of the East Asian mtDNA tree. , 2002, Molecular biology and evolution.

[4]  A. Torroni,et al.  mtDNA and the origin of Caucasians: identification of ancient Caucasian-specific haplogroups, one of which is prone to a recurrent somatic duplication in the D-loop region. , 1994, American journal of human genetics.

[5]  J. Jouzel,et al.  Evidence for general instability of past climate from a 250-kyr ice-core record , 1993, Nature.

[6]  A Coppa,et al.  A signal, from human mtDNA, of postglacial recolonization in Europe. , 2001, American journal of human genetics.

[7]  Hartmut Schulz,et al.  Correlation between Arabian Sea and Greenland climate oscillations of the past 110,000 years , 1998, Nature.

[8]  H. Bandelt,et al.  Saami and Berbers--an unexpected mitochondrial DNA link. , 2005, American journal of human genetics.

[9]  P. Rudan,et al.  Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. , 2004, Molecular biology and evolution.

[10]  D. Gurwitz,et al.  The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. , 2006, American journal of human genetics.

[11]  Alfredo Coppa,et al.  The Role of Selection in the Evolution of Human Mitochondrial Genomes , 2006, Genetics.

[12]  A. Torroni,et al.  Classification of European mtDNAs from an analysis of three European populations. , 1996, Genetics.

[13]  W. Brown Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Massimo Zeviani,et al.  Haplogroup effects and recombination of mitochondrial DNA: novel clues from the analysis of Leber hereditary optic neuropathy pedigrees. , 2006, American journal of human genetics.

[15]  L L Cavalli-Sforza,et al.  The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations , 2001, Annals of human genetics.

[16]  D. Mackey,et al.  Sequence analysis of the mitochondrial genomes from Dutch pedigrees with Leber hereditary optic neuropathy. , 2003, American journal of human genetics.

[17]  L L Cavalli-Sforza,et al.  The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. , 2000, Nature Reviews Genetics.

[18]  A. Di Rienzo,et al.  Tracing European founder lineages in the Near Eastern mtDNA pool. , 2000, American journal of human genetics.

[19]  Hans-Jürgen Bandelt,et al.  Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences. , 2003, American journal of human genetics.

[20]  A. Redd,et al.  A nomenclature system for the tree of human Y-chromosomal binary haplogroups. , 2002, Genome research.

[21]  Alice A. Lin,et al.  The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. , 2000 .

[22]  Lounès Chikhi,et al.  Estimating the impact of prehistoric admixture on the genome of Europeans. , 2004, Molecular biology and evolution.

[23]  D. Behar,et al.  High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium. , 2005, Genome research.

[24]  M. Zeviani,et al.  The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. , 2004, American journal of human genetics.

[25]  C. Renfrew,et al.  Archaeogenetics : DNA and the population prehistory of Europe , 2000 .

[26]  Clive Gamble,et al.  The Archaeological and Genetic Foundations of the European Population during the Late Glacial: Implications for ‘Agricultural Thinking’ , 2005, Cambridge Archaeological Journal.

[27]  D. F. Roberts,et al.  The History and Geography of Human Genes , 1996 .

[28]  M. Hofreiter,et al.  Assessing ancient DNA studies. , 2005, Trends in ecology & evolution.

[29]  H. Bandelt,et al.  Human Mitochondrial DNA and the Evolution of Homo sapiens , 2006 .

[30]  S. Pääbo,et al.  Mitochondrial genome variation and the origin of modern humans , 2000, Nature.

[31]  H. Bandelt,et al.  Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa , 1999, Nature Genetics.

[32]  J V Neel,et al.  Asian affinities and continental radiation of the four founding Native American mtDNAs. , 1993, American journal of human genetics.

[33]  M. Hurles,et al.  MtDNA Markers for Celtic and Germanic Language Areas in the British Isles Chapter 8 MtDNA Markers for Celtic and Germanic Language Areas in the British Isles , 2004 .

[34]  Q. Kong,et al.  Low "penetrance" of phylogenetic knowledge in mitochondrial disease studies. , 2005, Biochemical and biophysical research communications.

[35]  Li Jin,et al.  Y chromosome sequence variation and the history of human populations , 2000, Nature Genetics.

[36]  G. Koki,et al.  Expanding Southwest Pacific mitochondrial haplogroups , 2005 .

[37]  H. Bandelt,et al.  In search of geographical patterns in European mitochondrial DNA. , 2002, American journal of human genetics.

[38]  Q. Kong,et al.  The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. , 2006, Molecular biology and evolution.

[39]  T. Parsons,et al.  Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians , 2004, International Journal of Legal Medicine.

[40]  H. Bandelt Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity , 2005, European Journal of Human Genetics.

[41]  A. Torroni,et al.  The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs. , 1999, American journal of human genetics.

[42]  Anne Cambon-Thomsen,et al.  Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe. , 2004, American journal of human genetics.

[43]  K. Ohno,et al.  Distinct clustering of point mutations in mitochondrial DNA among patients with mitochondrial encephalomyopathies and with Parkinson's disease. , 1991, Biochemical and biophysical research communications.

[44]  M. Stoneking,et al.  Mitochondrial DNA and human evolution , 1987, Nature.

[45]  K. Ohno,et al.  Patients with idiopathic cardiomyopathy belong to the same mitochondrial DNA gene family of Parkinson's disease and mitochondrial encephalomyopathy. , 1991, Biochemical and biophysical research communications.

[46]  G. Chaubey,et al.  Reconstructing the Origin of Andaman Islanders , 2005, Science.

[47]  L. Moore,et al.  Mitochondrial DNA analysis in Tibet: implications for the origin of the Tibetan population and its adaptation to high altitude. , 1994, American journal of physical anthropology.

[48]  C. Renfrew,et al.  Examining the Farming/Language Dispersal Hypothesis , 2003 .

[49]  Jonathan Scott Friedlaender,et al.  Expanding Southwest Pacific mitochondrial haplogroups P and Q. , 2005, Molecular biology and evolution.

[50]  Martin Jones Traces of Ancestry: Studies in honour of Colin Renfrew , 2004 .

[51]  H. Bandelt,et al.  Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes , 2005, Science.

[52]  Colin Renfrew,et al.  ARCHAEOLOGY, GENETICS AND LINGUISTIC DIVERSITY* , 1992 .

[53]  M. Hayakawa,et al.  Genotype and phenotype of severe mitochondrial cardiomyopathy: a recipient of heart transplantation and the genetic control. , 1995, Biochemical and biophysical research communications.

[54]  M. Lehtonen,et al.  Phylogenetic network for European mtDNA. , 2001, American journal of human genetics.

[55]  Shuichi Matsumura,et al.  Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites , 1975, Science.

[56]  B. Sykes,et al.  Phylogeography of mitochondrial DNA in western Europe , 1998, Annals of human genetics.

[57]  H. Bandelt,et al.  Paleolithic and neolithic lineages in the European mitochondrial gene pool. , 1996, American journal of human genetics.

[58]  R. Villems,et al.  Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. , 2004, American journal of human genetics.

[59]  Hans-Jürgen Bandelt,et al.  Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. , 2004, American journal of human genetics.

[60]  H. Bandelt,et al.  Mitochondrial footprints of human expansions in Africa. , 1997, American journal of human genetics.

[61]  Hidetoshi Shimodaira,et al.  Mitochondrial genome variation in eastern Asia and the peopling of Japan. , 2004, Genome research.

[62]  D. Turnbull,et al.  Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA , 1999, Nature Genetics.

[63]  J. Avise Phylogeography: The History and Formation of Species , 2000 .