Mitochondrial Genome Sequences and Their Phylogeographic Interpretation

Abstract

The strong phylogenetic signal provided by 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. Mitochondrial phylogeography began by revolutionising our view of modern human origins, with the demonstration that modern humans dispersed from Africa approximately 60 000 years ago. Now benefitting from the high genealogical and chronological resolution afforded by whole‐mtDNA sequences, and despite the advent of genome‐wide analyses, mtDNA continues to illuminate prehistoric settlement and dispersal history. It has often led to challenges to received wisdom, such as the stress on pre‐Neolithic dispersals at the end of the Ice Age in many parts of the world, and the database of contemporary variation is currently being augmented by rapidly increasing information from ancient DNA.

Key Concepts:

  • Mitochondrial DNA is now routinely analysed at the level of whole‐mtDNA genome sequences.

  • The human mtDNA gene tree is an estimate of the maternal genealogy and preserves a record of the dispersal history of our species, in the distribution of its branching points in space and time, or ‘phylogeography’.

  • A time scale is provided by an independently calibrated mutation rate, the ‘molecular clock’, which is now available for whole‐mtDNA sequences and allows for the effects of purifying selection.

  • Although phylogeographic inference can be criticised for lacking a formal hypothesis testing framework, proposed alternatives based on simulation are currently insufficient to tackle the nuances of real human dispersal histories.

  • Variation in mtDNA has led to a number of revolutionary models in human evolutionary history, beginning with the African origin of modern humans.

  • More recent suggestions have included a single southern‐coastal dispersal route out of Africa and the importance to the shaping of extant human diversity of hunter–gatherer dispersals and expansions at the end of the last Ice Age.

  • An increasing volume of data from ancient DNA holds great promise not only for testing interpretations of contemporary variation but also for identifying both ancient processes that left no trace in the modern gene pool and more recent dispersals that studying extant cannot resolve.

  • Genome‐wide analyses now allow both testing of hypotheses arising from mtDNA studies and access to many previously unanswerable questions, but mtDNA nevertheless retains a vital role due to its relative genealogical and chronological precision.

Keywords: phylogeography; phylogeny; mtDNA; archaeogenetics; genealogy; founder analysis

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 related 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 solid black 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 at the time estimation.

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Further Reading

Avise JC (2000) Phylogeography: The History and Formation of Species. Cambridge, MA: Harvard University Press.

Bandelt H‐J, Macaulay V and Richards M (eds) (2006) Human Mitochondrial DNA and the Evolution of Homo sapiens. Berlin: Springer.

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Jobling M, Hollox E, Kivisild T, Tyler‐Smith C, Hurles M (2013) Human Evolutionary Genetics: Origins, Peoples and Disease. 2nd edn. Oxford: Garland Science.

Oppenheimer S (2003) Out of Eden: The Peopling of the World. London: Constable.

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.

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.

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Macaulay, Vincent, and Richards, Martin B(Sep 2013) Mitochondrial Genome Sequences and Their Phylogeographic Interpretation. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.20843.pub2]