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Mitochondrial Genome Sequences and Their Phylogeographic Interpretation

  1. Vincent Macaulay1,
  2. Martin B Richards2

Published Online: 19 SEP 2013

DOI: 10.1002/9780470015902.20843.pub2



How to Cite

Macaulay, V. and Richards, M. B. 2013. Mitochondrial Genome Sequences and Their Phylogeographic Interpretation. eLS. .

Author Information

  1. 1

    University of Glasgow, Glasgow, UK

  2. 2

    University of Huddersfield, Huddersfield, UK

Publication History

  1. Published Online: 19 SEP 2013


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.


  • phylogeography;
  • phylogeny;
  • mtDNA;
  • archaeogenetics;
  • genealogy;
  • founder analysis