Mitochondrial Genome Sequences and Their Phylogeographic Interpretation

Vincent Macaulay, University of Glasgow, Glasgow, UK
Martin Richards, University of Leeds, Leeds, UK

Published online: May 2008

DOI: 10.1002/9780470015902.a0020843

The strong phylogenetic signal provided by complete mitochondrial deoxyribonucleic acid (mtDNA) sequences within species is being exploited to reconstruct the maternal genealogy and anchor it in space and time. This is the starting point for interpretations of the processes in population history that led to those patterns, as illustrated here for humans.

Keywords: genealogy; founder; phylogeography; phylogeny; mtDNA

Figure 1. The effect of a single migration event on the genealogy, motivating the idea of founder analysis. (a) All individuals in the settled region trace back to three individuals who migrated from the source region. The source genealogy is deep (left); the settled gene genealogy (right) consists of a small number of clusters of closely individuals that trace back to the three pioneers. (b) The reflection of this signal in the DNA sequences. Green circles are DNA sequences recovered from the settled region, red circles from the source region and the links in the network indicate the mutations that relate the sequences. (Small black filled circles are inferred sequences not actually observed.) The common ancestor is shown with a star. Founder analysis seeks to identify those sequences (marked by crosses) that migrated, and use the mutations that have accumulated on top of these ‘founder types’ to derive a lower bound on the time of the migration event. By identifying founder sequences explicitly, mutations that arose before the migration event (somewhere in the dashed part of the tree, upper right) will not be included in the time estimation.
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 References
    book Ammerman AJ and Cavalli-Sforza LL (1984) The Neolithic Transition and the Genetics of Populations in Europe. Princeton, NJ: Princeton University Press.
    Bandelt H-J, Herrnstadt C, Yao Y-G et al. (2003) Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats. Annals of Human Genetics 67: 512–524.
    Hill C, Soares P, Mormina M et al. (2007) A mitochondrial stratigraphy for Island Southeast Asia. American Journal of Human Genetics 80: 29–43.
    Hudjashov G, Kivisild T, Underhill PA et al. (2007) Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proceedings of the National Academy of Sciences of the USA 104: 8726–8730.
    Kivisild T, Reidla M, Metspalu E et al. (2004) Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the Gate of Tears. American Journal of Human Genetics 75: 752–770.
    Kong Q-P, Bandelt H-J, Sun C et al. (2006) Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations. Human Molecular Genetics 15: 2076–2086.
    Macaulay V, Hill C, Achilli A et al. (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308: 1034–1036.
    Olivieri A, Achilli A, Pala M et al. (2006) The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 314: 1767–1770.
    Richards M, Macaulay V, Hickey E et al. (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. American Journal of Human Genetics 67: 1251–1276.
    Richards M, Rengo C, Cruciani F et al. (2003) Extensive female-mediated gene flow from sub-Saharan Africa into Near Eastern Arab populations. American Journal of Human Genetics 72: 1058–1064.
    Salas A, Richards M, De La Fe T et al. (2002) The making of the African mtDNA landscape. American Journal of Human Genetics 71: 1082–1111.
    Sun C, Kong Q-P, Palanichamy MG et al. (2006) The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. Molecular Biology and Evolution 23: 683–690.
    Vigilant L, Stoneking M, Harpending H, Hawkes K and Wilson AC (1991) African populations and the evolution of human mitochondrial DNA. Science 253: 1503–1507.
 Further Reading
    book Avise JC (2000) Phylogeography: The History and Formation of Species. Cambridge, MA: Harvard University Press.
    book Bandelt H-J, Macaulay V and Richards M (eds) (2006) Human Mitochondrial DNA and the Evolution of Homo sapiens. Berlin: Springer.
    book Oppenheimer S (2003) Out of Eden: The Peopling of the World. London: Constable.
    book Renfrew C and Boyle K (eds) (2000) Archaeogenetics: DNA and the Population Prehistory of Europe. Cambridge: McDonald Institute for Archaeological Research.
    Richards M (2003) The Neolithic invasion of Europe. Annual Review of Anthropology 32: 135–162.
    Richards M and Macaulay V (2001) The mitochondrial gene tree comes of age. American Journal of Human Genetics 68: 1315–1320.
    Templeton AR (2005) Haplotype trees and modern human origins. Yearbook of Physical Anthropology 48: 33–59.
    book Templeton AR (2006) Population Genetics and Microevolutionary Theory. Hoboken, NJ: Wiley.
    Torroni A, Achilli A, Macaulay V, Richards M and Bandelt H-J (2006) Harvesting the fruit of the human mtDNA tree. Trends in Genetics 22: 339–345.

Related Sub-Topics:

Reconstruction of Phylogeny | Molecular Evolution | Human Evolution | Population Structure and Genetics
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Article Title: Mitochondrial Genome Sequences and Their Phylogeographic Interpretation
 
How to Cite close
Macaulay, Vincent, and Richards, Martin(May 2008) Mitochondrial Genome Sequences and Their Phylogeographic Interpretation. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020843]