Molecular Biology and Evolution, Vol 13, 933-942, Copyright © 1996 by Society for Molecular Biology and Evolution
R Zardoya and A Meyer
A large number of studies in evolutionary biology utilize phylogenetic
information obtained from mitochondrial DNA. Researchers place trust in
this molecule and expect it generally to be a reliable marker for
addressing questions ranging from population genetics to phylogenies among
distantly related lineages. Yet, regardless of the phylogenetic method and
weighting treatment, individual mitochondrial genes might potentially
produce misleading evolutionary inferences and hence might not constitute
an adequate representation neither of the entire mitochondrial genome nor
of the evolutionary history of the organisms from which they are derived.
We investigated the performance of all mitochondrial protein-coding genes
to recover two expected phylogenies of tetrapods and mammals. According to
these tests, mitochondrial protein-coding genes can be roughly classified
into three groups of good (ND4, ND5, ND2, cytb, and COI), medium (COII,
COIII, ND1, and ND6), and poor (ATPase 6, ND3, ATPase 8, and ND4L)
phylogenetic performers in recovering these expected trees among
phylogenetically distant relatives. How general our findings are is
unclear. Simple length differences and rate differences between these genes
cannot account for their different phylogenetic performance. The
phylogenetic performance of these mitochondrial genes might depend on
various factors that play a role in determining the probability of
discovering the correct phylogeny such as the density of lineage creation
events in time, the phylogenetic "depth" of the question, lineage-specific
rate heterogeneity, and the completeness of taxa representation.
ORIGINAL ARTICLE
Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates
Department of Ecology and Evolution, State University of New York at Stony Brook 11794-5245, USA. rzardoya@life.bio.sunysb.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. San Mauro, D. J. Gower, T. Massingham, M. Wilkinson, R. Zardoya, and J. A. Cotton Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear rag1 Syst Biol, August 18, 2009; (2009) syp043v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Aguileta, S. Marthey, H. Chiapello, M.-H. Lebrun, F. Rodolphe, E. Fournier, A. Gendrault-Jacquemard, and T. Giraud Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies Syst Biol, August 1, 2008; 57(4): 613 - 627. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Barber and S. L Boyce Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae Proc R Soc B, August 22, 2006; 273(1597): 2053 - 2061. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. E. Broughton and P. C. Reneau Spatial Covariation of Mutation and Nonsynonymous Substitution Rates in Vertebrate Mitochondrial Genomes Mol. Biol. Evol., August 1, 2006; 23(8): 1516 - 1524. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. L. Mueller Evolutionary Rates, Divergence Dates, and the Performance of Mitochondrial Genes in Bayesian Phylogenetic Analysis Syst Biol, April 1, 2006; 55(2): 289 - 300. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Ren, H. Tanaka, and Z. Yang An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction Syst Biol, October 1, 2005; 54(5): 808 - 818. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. J. Baker, L. J. Huynen, O. Haddrath, C. D. Millar, and D. M. Lambert Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas of New Zealand PNAS, June 7, 2005; 102(23): 8257 - 8262. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Zhang, H. Zhou, Y.-Q. Chen, Y.-F. Liu, and L.-H. Qu Mitogenomic Perspectives on the Origin and Phylogeny of Living Amphibians Syst Biol, June 1, 2005; 54(3): 391 - 400. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Brinkmann, B. Venkatesh, S. Brenner, and A. Meyer Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates PNAS, April 6, 2004; 101(14): 4900 - 4905. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. G. Inoue, M. Miya, K. Tsukamoto, and M. Nishida Evolution of the Deep-Sea Gulper Eel Mitochondrial Genomes: Large-Scale Gene Rearrangements Originated Within the Eels Mol. Biol. Evol., November 1, 2003; 20(11): 1917 - 1924. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Yang, J. Wang, J. Kijas, B. Liu, H. Han, M. Yu, H. Yang, S. Zhao, and K. Li Genetic Diversity Present Within the Near-Complete mtDNA Genome of 17 Breeds of Indigenous Chinese Pigs J. Hered., September 1, 2003; 94(5): 381 - 385. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Grande, J. Templado, J. Lucas Cervera, and R. Zardoya The Complete Mitochondrial Genome of the Nudibranch Roboastra europaea (Mollusca: Gastropoda) Supports the Monophyly of Opisthobranchs Mol. Biol. Evol., October 1, 2002; 19(10): 1672 - 1685. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Miya, A. Kawaguchi, and M. Nishida Mitogenomic Exploration of Higher Teleostean Phylogenies: A Case Study for Moderate-Scale Evolutionary Genomics with 38 Newly Determined Complete Mitochondrial DNA Sequences Mol. Biol. Evol., November 1, 2001; 18(11): 1993 - 2009. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Zardoya and A. Meyer On the origin of and phylogenetic relationships among living amphibians PNAS, May 30, 2001; (2001) 111455498. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. S. Springer, R. W. DeBry, C. Douady, H. M. Amrine, O. Madsen, W. W. de Jong, and M. J. Stanhope Mitochondrial Versus Nuclear Gene Sequences in Deep-Level Mammalian Phylogeny Reconstruction Mol. Biol. Evol., February 1, 2001; 18(2): 132 - 143. [Abstract] [Full Text]
|
|
|
|
|
|
J. Schmitz, M. Ohme, and H. Zischler The Complete Mitochondrial Genome of Tupaia belangeri and the Phylogenetic Affiliation of Scandentia to Other Eutherian Orders Mol. Biol. Evol., September 1, 2000; 17(9): 1334 - 1343. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Zardoya and A. Meyer Mitochondrial Evidence on the Phylogenetic Position of Caecilians (Amphibia: Gymnophiona) Genetics, June 1, 2000; 155(2): 765 - 775. [Abstract] [Full Text]
|
|
|
|
|
|
P. S. Corneli and R. H. Ward Mitochondrial Genes and Mammalian Phylogenies: Increasing the Reliability of Branch Length Estimation Mol. Biol. Evol., February 1, 2000; 17(2): 224 - 234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Zardoya and A. Meyer On the origin of and phylogenetic relationships among living amphibians PNAS, June 19, 2001; 98(13): 7380 - 7383. [Abstract] [Full Text] [PDF]
|
|