Related Content
Search Google Scholar for:
|
|
Science 29 April 1994: Vol. 264. no. 5159, pp. 671 - 677 DOI: 10.1126/science.8171318
|
|
Articles
Science, Vol 264, Issue 5159, 671-677
Copyright © 1994 by American Association for the Advancement of Science
Application and accuracy of molecular phylogenies
DM Hillis,
JP Huelsenbeck,
and
CW Cunningham
Department of Zoology, University of Texas, Austin 78712.
Molecular investigations of evolutionary history are being used to study subjects as diverse as the epidemiology of acquired immune deficiency syndrome and the origin of life. These studies depend on accurate estimates of phylogeny. The performance of methods of phylogenetic analysis can be assessed by numerical simulation studies and by the experimental evolution of organisms in controlled laboratory situations. Both kinds of assessment indicate that existing methods are effective at estimating phylogenies over a wide range of evolutionary conditions, especially if information about substitution bias is used to provide differential weightings for character transformations.
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
- Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index.
- P. Hraber, C. Kuiken, M. Waugh, S. Geer, W. J. Bruno, and T. Leitner (2008)
J. Gen. Virol.
89, 2098-2107
| Abstract »
| Full Text »
| PDF »
- More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States.
- G. Li, M. Steel, and L. Zhang (2008)
Syst Biol
57, 647-653
| Full Text »
| PDF »
- The role of molecular genetics in sculpting the future of integrative biogeography.
- B. R. Riddle, M. N. Dawson, E. A. Hadly, D. J. Hafner, M. J. Hickerson, S. J. Mantooth, and A. D. Yoder (2008)
Progress in Physical Geography
32, 173-202
| Abstract »
| PDF »
- Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes.
- M. D. Rasmussen and M. Kellis (2007)
Genome Res.
17, 1932-1942
| Abstract »
| Full Text »
| PDF »
- Reconstruction and Function of Ancestral Center-of-Tree Human Immunodeficiency Virus Type 1 Proteins.
- M. Rolland, M. A. Jensen, D. C. Nickle, J. Yan, G. H. Learn, L. Heath, D. Weiner, and J. I. Mullins (2007)
J. Virol.
81, 8507-8514
| Abstract »
| Full Text »
| PDF »
- Estimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers.
- B. C. Carstens and L. L. Knowles (2007)
Syst Biol
56, 400-411
| Abstract »
| Full Text »
| PDF »
- Assessment of phylogenomic and orthology approaches for phylogenetic inference.
- B. E. Dutilh, V. van Noort, R. T. J. M. van der Heijden, T. Boekhout, B. Snel, and M. A. Huynen (2007)
Bioinformatics
23, 815-824
| Abstract »
| Full Text »
| PDF »
- A statistical phylogeography of influenza A H5N1.
- R. G. Wallace, H. HoDac, R. H. Lathrop, and W. M. Fitch (2007)
PNAS
104, 4473-4478
| Abstract »
| Full Text »
| PDF »
- Mitochondrial Genomes and Avian Phylogeny: Complex Characters and Resolvability without Explosive Radiations.
- G. C. Gibb, O. Kardailsky, R. T. Kimball, E. L. Braun, and D. Penny (2007)
Mol. Biol. Evol.
24, 269-280
| Abstract »
| Full Text »
| PDF »
- Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling.
- S. M. Hedtke, T. M. Townsend, and D. M. Hillis (2006)
Syst Biol
55, 522-529
| Full Text »
| PDF »
- Resolving Deep Phylogenetic Relationships in Salamanders: Analyses of Mitochondrial and Nuclear Genomic Data.
- D. W. Weisrock, L. J. Harmon, and A. Larson (2005)
Syst Biol
54, 758-777
| Abstract »
| Full Text »
| PDF »
- On Probability and Systematics: Possibility, Probability, and Phylogenetic Inference.
- M. H. Haber (2005)
Syst Biol
54, 831-841
| Full Text »
| PDF »
- Counterexample to a Claim About the Reconstruction of Ancestral Character States.
- B. Lucena and D. Haussler (2005)
Syst Biol
54, 693-695
| Full Text »
| PDF »
- Towards Building the Tree of Life: A Simulation Study for All Angiosperm Genera.
- N. Salamin, T. R. Hodkinson, and V. Savolainen (2005)
Syst Biol
54, 183-196
| Abstract »
| Full Text »
| PDF »
- Comparison of the Accuracies of Several Phylogenetic Methods Using Protein and DNA Sequences.
- B. G. Hall (2005)
Mol. Biol. Evol.
22, 792-802
| Abstract »
| Full Text »
| PDF »
- A Statistical Characterization of Consistent Patterns of Human Immunodeficiency Virus Evolution Within Infected Patients.
- S. Williamson, S. M. Perry, C. D. Bustamante, M. E. Orive, M. N. Stearns, and J. K. Kelly (2005)
Mol. Biol. Evol.
22, 456-468
| Abstract »
| Full Text »
| PDF »
- Morphology's Role in Phylogeny Reconstruction: Perspectives from Paleontology.
- N. D. Smith and A. H. Turner (2005)
Syst Biol
54, 166-173
| Full Text »
| PDF »
- Reconstructing large regions of an ancestral mammalian genome in silico.
- M. Blanchette, E. D. Green, W. Miller, and D. Haussler (2004)
Genome Res.
14, 2412-2423
| Abstract »
| Full Text »
| PDF »
- Tracing the Decay of the Historical Signal in Biological Sequence Data.
- S. Y.W. Ho and L. S. Jermiin (2004)
Syst Biol
53, 623-637
| Abstract »
| Full Text »
| PDF »
- Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss.
- K. Kiontke, N. P. Gavin, Y. Raynes, C. Roehrig, F. Piano, and D. H. A. Fitch (2004)
PNAS
101, 9003-9008
| Abstract »
| Full Text »
| PDF »
- Accepting Partnership by Submission? Morphological Phylogenetics in a Molecular Millennium.
- R. A. Jenner (2004)
Syst Biol
53, 333-359
| Full Text »
| PDF »
- Genetic relationships among avian isolates classified as Pasteurella haemolytica, 'Actinobacillus salpingitidis' or Pasteurella anatis with proposal of Gallibacterium anatis gen. nov., comb. nov. and description of additional genomospecies within Gallibacterium gen. nov..
- H. Christensen, M. Bisgaard, A. M. Bojesen, R. Mutters, and J. E. Olsen (2003)
Int J Syst Evol Microbiol
53, 275-287
| Abstract »
| Full Text »
| PDF »
- Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes.
- R. C. Cronn, R. L. Small, T. Haselkorn, and J. F. Wendel (2002)
Am. J. Botany
89, 707-725
| Abstract »
| Full Text »
| PDF »
- Evolutionary History of Cucumber Mosaic Virus Deduced by Phylogenetic Analyses.
- M. J. Roossinck (2002)
J. Virol.
76, 3382-3387
| Abstract »
| Full Text »
| PDF »
- A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data.
- S. L. Baldauf, A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle (2000)
Science
290, 972-977
| Abstract »
| Full Text »
- STRATIGRAPHY IN PHYLOGENY RECONSTRUCTION.
- (2000)
Journal of Paleontology
74, 763-766
- Timing the Ancestor of the HIV-1 Pandemic Strains.
- B. Korber, M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinsky, and T. Bhattacharya (2000)
Science
288, 1789-1796
| Abstract »
| Full Text »
| PDF »
- Typing of Candida glabrata in Clinical Isolates by Comparative Sequence Analysis of the Cytochrome c Oxidase Subunit 2 Gene Distinguishes Two Clusters of Strains Associated with Geographical Sequence Polymorphisms.
- G. F. O. Sanson and M. R. S. Briones (2000)
J. Clin. Microbiol.
38, 227-235
| Abstract »
| Full Text »
- Morphological analysis of the mammalian postcranium: A developmental perspective.
- C. O. Lovejoy, M. J. Cohn, and T. D. White (1999)
PNAS
96, 13247-13252
| Abstract »
| Full Text »
| PDF »
- Evolution of Envelope Sequences of Human Immunodeficiency Virus Type 1 in Cellular Reservoirs in the Setting of Potent Antiviral Therapy.
- H. F. Gunthard, S. D. W. Frost, A. J. Leigh-Brown, C. C. Ignacio, K. Kee, A. S. Perelson, C. A. Spina, D. V. Havlir, M. Hezareh, D. J. Looney, et al. (1999)
J. Virol.
73, 9404-9412
| Abstract »
| Full Text »
| PDF »
- Developments in Fungal Taxonomy.
- J. Guarro, J. Gene, and A. M. Stchigel (1999)
Clin. Microbiol. Rev.
12, 454-500
| Abstract »
| Full Text »
| PDF »
- Mitochondrial sequences show diverse evolutionary histories of African hominoids.
- P. Gagneux, C. Wills, U. Gerloff, D. Tautz, P. A. Morin, C. Boesch, B. Fruth, G. Hohmann, O. A. Ryder, and D. S. Woodruff (1999)
PNAS
96, 5077-5082
| Abstract »
| Full Text »
| PDF »
- Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes.
- A. R. Mushegian, J. R. Garey, J. Martin, and L. X. Liu (1998)
Genome Res.
8, 590-598
| Abstract »
| Full Text »
- Genetic Analysis of the Diversity and Origin of Hantaviruses in Peromyscus leucopus Mice in North America.
- S. P. Morzunov, J. E. Rowe, T. G. Ksiazek, C. J. Peters, S. C. St. Jeor, and S. T. Nichol (1998)
J. Virol.
72, 57-64
| Abstract »
| Full Text »
| PDF »
- A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis.
- A. J. Roger, C. G. Clark, and W. F. Doolittle (1996)
PNAS
93, 14618-14622
| Abstract »
| Full Text »
| PDF »
- The Emerging Genetic Diversity of HIV: The Importance of Global Surveillance for Diagnostics, Research, and Prevention.
- D. J. Hu, T. J. Dondero, M. A. Rayfield, J. R. George, G. Schochetman, H. W. Jaffe, C.-C. Luo, M. L. Kalish, B. G. Weniger, C.-P. Pau, et al. (1996)
JAMA
275, 210-216
| Abstract »
| PDF »
- DNA ``Fossils'' and Phylogenetic Analysis.
- A. V. Furano and K. Usdin (1995)
J. Biol. Chem.
270, 25301-25304
| Full Text »
| PDF »
- Response.
- D. M. Hillis and J. P. Huelsenbeck (1995)
Science
267, 255-256
| PDF »
- Evolutionary History of the Symbiosis Between Fungus-Growing Ants and Their Fungi.
- I. H. Chapela, S. A. Rehner, T. R. Schultz, and U. G. Mueller (1994)
Science
266, 1691-1694
| Abstract »
| PDF »
- The Complete Sequence of the Zebrafish (Danio rerio) Mitochondrial Genome and Evolutionary Patterns in Vertebrate Mitochondrial DNA.
- R. E. Broughton, J. E. Milam, and B. A. Roe (2001)
Genome Res.
11, 1958-1967
| Abstract »
| Full Text »
| PDF »
|
|