Molecular Biology and Evolution, Vol 12, 814-822, Copyright © 1995 by Society for Molecular Biology and Evolution
MP Cummings, SP Otto and J Wakeley
We inferred phylogenetic trees from individual genes and random samples of
nucleotides from the mitochondrial genomes of 10 vertebrates and compared
the results to those obtained by analyzing the whole genomes. Individual
genes are poor samples in that they infrequently lead to the whole-genome
tree. A large number of nucleotide sites is needed to exactly determine the
whole-genome tree. A relatively small number of sites, however, often
results in a tree close to the whole-genome tree. We found that blocks of
contiguous sites were less likely to lead to the whole-genome tree than
samples composed of sites drawn individually from throughout the genome.
Samples of contiguous sites are not representative of the entire genome, a
condition that violates a basic assumption of the bootstrap method as it is
applied in phylogenetic studies.
ORIGINAL ARTICLE
Sampling properties of DNA sequence data in phylogenetic analysis
Department of Integrative Biology, University of California at Berkeley, USA.
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]
|
|
|
|
 |
|
 K. Vijayan, W.-J. Zhang, and C.-H. Tsou Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences Am. J. Botany, July 1, 2009; 96(7): 1348 - 1360. [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]
|
|
|
|
|
|
J. Gatesy, R. DeSalle, and N. Wahlberg How Many Genes Should a Systematist Sample? Conflicting Insights from a Phylogenomic Matrix Characterized by Replicated Incongruence Syst Biol, April 1, 2007; 56(2): 355 - 363. [Full Text] [PDF]
|
|
|
|
 |
|
 L. Vitorino, I. M. Chelo, F. Bacellar, and L. Ze-Ze Rickettsiae phylogeny: a multigenic approach Microbiology, January 1, 2007; 153(1): 160 - 168. [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]
|
|
|
|
|
|
V. Dvornyk Subfamilies of cpmA, a gene involved in circadian output, have different evolutionary histories in cyanobacteria Microbiology, January 1, 2006; 152(1): 75 - 84. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Rubinoff and B. S. Holland Between Two Extremes: Mitochondrial DNA is neither the Panacea nor the Nemesis of Phylogenetic and Taxonomic Inference Syst Biol, December 1, 2005; 54(6): 952 - 961. [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]
|
|
|
|
 |
|
 S. V Edwards, W Bryan Jennings, and A. M Shedlock Phylogenetics of modern birds in the era of genomics Proc R Soc B, May 22, 2005; 272(1567): 979 - 992. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Rokas and S. B. Carroll More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy Mol. Biol. Evol., May 1, 2005; 22(5): 1337 - 1344. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Adekambi and M. Drancourt Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2095 - 2105. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. H. Jordal and G. M. Hewitt The Origin and Radiation of Macaronesian Beetles Breeding in Euphorbia: The Relative Importance of Multiple Data Partitions and Population Sampling Syst Biol, October 1, 2004; 53(5): 711 - 734. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Nishiyama, P. G. Wolf, M. Kugita, R. B. Sinclair, M. Sugita, C. Sugiura, T. Wakasugi, K. Yamada, K. Yoshinaga, K. Yamaguchi, et al. Chloroplast Phylogeny Indicates that Bryophytes Are Monophyletic Mol. Biol. Evol., October 1, 2004; 21(10): 1813 - 1819. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. P. Simmons, K. M. Pickett, and M. Miya How Meaningful Are Bayesian Support Values? Mol. Biol. Evol., January 1, 2004; 21(1): 188 - 199. [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]
|
|
|
|
|
|
G. Gutierrez, D. Sanchez, and A. Marin A Reanalysis of the Ancient Mitochondrial DNA Sequences Recovered from Neandertal Bones Mol. Biol. Evol., August 1, 2002; 19(8): 1359 - 1366. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. C. Cronn, R. L. Small, T. Haselkorn, and J. F. Wendel Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes Am. J. Botany, April 1, 2002; 89(4): 707 - 725. [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]
|
|
|
|
|
|
D. T. J. Littlewood, P. D. Olson, M. J. Telford, E. A. Herniou, and M. Riutort Elongation Factor 1-Alpha Sequences Alone Do Not Assist in Resolving the Position of the Acoela Within the Metazoa Mol. Biol. Evol., March 1, 2001; 18(3): 437 - 442. [Full Text]
|
|
|
|
|
|
R. G. Olmstead, C. W. dePamphilis, A. D. Wolfe, N. D. Young, W. J. Elisons, and P. A. Reeves Disintegration of the Scrophulariaceae Am. J. Botany, February 1, 2001; 88(2): 348 - 361. [Abstract] [Full Text]
|
|
|
|
|
|
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]
|
|
|
|
|
|
D. D. Pollock, J. A. Eisen, N. A. Doggett, and M. P. Cummings A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity Mol. Biol. Evol., December 1, 2000; 17(12): 1776 - 1788. [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]
|
|
|
|
|
|
D. M. Hillis SINEs of the perfect character PNAS, August 31, 1999; 96(18): 9979 - 9981. [Full Text] [PDF]
|
|
|
|
|
|
R. Nielsen and Z. Yang Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene Genetics, March 1, 1998; 148(3): 929 - 936. [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]
|
|