Skip Navigation


MBE Advance Access originally published online on June 9, 2004
Molecular Biology and Evolution 2004 21(10):1843-1854; doi:10.1093/molbev/msh184
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow Supplementary Material
Right arrow All Versions of this Article:
21/10/1843    most recent
msh184v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (18)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Howell, N.
Right arrow Articles by Herrnstadt, C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Howell, N.
Right arrow Articles by Herrnstadt, C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Molecular Biology and Evolution vol. 21 no. 10 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

African Haplogroup L mtDNA Sequences Show Violations of Clock-like Evolution

Neil Howell*,{dagger}, Joanna L. Elson{ddagger}, D. M. Turnbull{ddagger} and Corinna Herrnstadt*

* MitoKor Inc., San Diego, California; {dagger} Department of Radiation Oncology, The University of Texas Medical Branch, Galveston; and {ddagger} Mitochondrial Research Group, School of Neurology, Neurobiology, and Psychiatry, The Medical School, The University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom

E-mail: howelln{at}mitokor.com

A set of 96 complete mtDNA sequences that belong to the three major African haplogroups (L1, L2, and L3) was analyzed to determine if mtDNA has evolved as a molecular clock. Likelihood ratio tests (LRTs) were carried out with each of the haplogroups and with combined haplogroup sequence sets. Evolution has not been clock-like, neither for the coding region nor for the control region, in combined sets of African haplogroup L mtDNA sequences. In tests of individual haplogroups, L2 mtDNAs showed violations of a molecular clock under all conditions and in both the control and coding regions. In contrast, haplogroup L1 and L3 sequences, both for the coding and control regions, show clock-like evolution. In clock tests of individual L2 subclades, the L2a sequences showed a marked violation of clock-like evolution within the coding region. In addition, the L2a and L2c branch lengths of both the coding and control regions were shorter relative to those of the L2b and L2d sequences, a result that indicates lower levels of sequence divergence. Reduced median network analyses of the L2a sequences indicated the occurrence of marked homoplasy at multiple sites in the control region. After exclusion of the L2a and L2c sequences, African mtDNA coding region evolution has not significantly departed from a molecular clock, despite the results of neutrality tests that indicate the mitochondrial coding region has evolved under nonneutral conditions. In contrast, control region evolution is clock-like only at the haplogroup level, and it thus appears to have evolved essentially independently from the coding region. The results of the clock tests, the network analyses, and the branch length comparisons all caution against the use of simple mtDNA clocks.

Key Words: mitochondrial DNA • molecular evolution • phylogenetic analysis • molecular clock • human evolution


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
B. M. Henn, C. R. Gignoux, M. W. Feldman, and J. L. Mountain
Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates
Mol. Biol. Evol., January 1, 2009; 26(1): 217 - 230.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. Howell, J. L. Elson, C. Howell, and D. M. Turnbull
Relative Rates of Evolution in the Coding and Control Regions of African mtDNAs
Mol. Biol. Evol., October 1, 2007; 24(10): 2213 - 2221.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. W. Carter
Mitochondrial diversity within modern human populations
Nucleic Acids Res., May 25, 2007; 35(9): 3039 - 3045.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
L. Pereira, J. Goncalves, R. Franco-Duarte, J. Silva, T. Rocha, C. Arnold, M. Richards, and V. Macaulay
No Evidence for an mtDNA Role in Sperm Motility: Data from Complete Sequencing of Asthenozoospermic Males
Mol. Biol. Evol., March 1, 2007; 24(3): 868 - 874.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Rosset
Efficient inference on known phylogenetic trees using Poisson regression
Bioinformatics, January 15, 2007; 23(2): e142 - e147.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. Fraumene, E. M. S. Belle, L. Castri, S. Sanna, G. Mancosu, M. Cosso, F. Marras, G. Barbujani, M. Pirastu, and A. Angius
High Resolution Analysis and Phylogenetic Network Construction Using Complete mtDNA Sequences in Sardinian Genetic Isolates
Mol. Biol. Evol., November 1, 2006; 23(11): 2101 - 2111.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. Sun, Q.-P. Kong, M. g. Palanichamy, S. Agrawal, H.-J. Bandelt, Y.-G. Yao, F. Khan, C.-L. Zhu, T. K. Chaudhuri, and Y.-P. Zhang
The Dazzling Array of Basal Branches in the mtDNA Macrohaplogroup M from India as Inferred from Complete Genomes
Mol. Biol. Evol., March 1, 2006; 23(3): 683 - 690.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. Santos, R. Montiel, B. Sierra, C. Bettencourt, E. Fernandez, L. Alvarez, M. Lima, A. Abade, and M. P. Aluja
Understanding Differences Between Phylogenetic and Pedigree-Derived mtDNA Mutation Rate: A Model Using Families from the Azores Islands (Portugal)
Mol. Biol. Evol., June 1, 2005; 22(6): 1490 - 1505.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.