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mtDNA in phylogeny

Friday 14 November 2003

Human mitochondrial DNA (mtDNA) is a nonrecombining genome that codes for 13 subunits of the mitochondrial oxidative phosphorylation system, 2 rRNAs and 22 tRNAs.

mtDNA and phylogeny

- Mutations have accumulated sequentially in mtDNA lineages that have diverged tens of thousands of years ago. The genes in mtDNA are subject to different functional constraints and are therefore expected to evolve at different rates, but the rank order of these rates should be the same in all lineages of a phylogeny.

- The advent of complete mitochondrial DNA (mtDNA) sequence data has ushered in a new phase of human evolutionary studies. Even quite limited volumes of complete mtDNA sequence data can now be used to identify the critical polymorphisms that define sub-clades within an mtDNA haplogroup, providing a springboard for large-scale high-resolution screening of human mtDNAs.

- Because mitochondria are transmitted along only female lineages and mtDNA is genetically haploid, the effective size of a population of mtDNAs is a quarter of that of the corresponding autosomes. The mutation rate of the mitochondrial genome is about ten times higher than that of nuclear DNA, which provides an abundance of polymorphic sites, but creates difficulties in reconstructing genealogies owing to repeated and reverse mutations. Like the non-recombining part of the Y chromosome (NRY), there is no evidence for recombination in mtDNA although low-frequency rearrangements of somatic mtDNA have been observed in heart muscle.


- Single deletions of mitochondrial DNA (mtDNA) are associated with three major clinical conditions:

  • Kearns-Sayre syndrome, a multisystem disorder
  • Pearson syndrome, a disorder of the hematopoietic system
  • progressive external ophthalmoplegia, primarily affecting the ocular muscles.

- mitochondrial DNA (mtDNA) depletion syndrome is a quantitative defect of mtDNA resulting from dysfunction of one of several nuclear-encoded factors responsible for maintenance of mitochondrial deoxyribonucleoside triphosphate (dNTP) pools or replication of mtDNA.

  • Markedly decreased succinyl-CoA synthetase activity due to a deleterious mutation in SUCLA2, the gene encoding the beta subunit of the ADP-forming succinyl-CoA synthetase ligase (15877282).


-  Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ. Harvesting the fruit of the human mtDNA tree. Trends Genet. 2006 Jun;22(6):339-45. PMID: 16678300

- Chen XJ, Butow RA. The organization and inheritance of the mitochondrial genome. Nat Rev Genet. 2005 Nov;6(11):815-25. PMID: 16304597

- Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis KK, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knjiff P, Feldman MW, Cavalli-Sforza LL, Oefner PJ. The role of selection in the evolution of human mitochondrial genomes. Genetics. 2005 Sep 19 PMID: 16172508