Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 11 April 1997:
Vol. 276. no. 5310, pp. 227 - 232
DOI: 10.1126/science.276.5310.227
Prev | Table of Contents | Next

Articles

Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context

John P. Huelsenbeck, * Bruce Rannala

The use of molecular phylogenies to examine evolutionary questions has become commonplace with the automation of DNA sequencing and the availability of efficient computer programs to perform phylogenetic analyses. The application of computer simulation and likelihood ratio tests to evolutionary hypotheses represents a recent methodological development in this field. Likelihood ratio tests have enabled biologists to address many questions in evolutionary biology that have been difficult to resolve in the past, such as whether host-parasite systems are cospeciating and whether models of DNA substitution adequately explain observed sequences.

The authors are in the Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.
*   To whom correspondence should be addressed. E-mail: johnh{at}mws4.biol.berkeley.edu

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Genome size in Hieracium subgenus Hieracium (Asteraceae) is strongly correlated with major phylogenetic groups.
J. Chrtek Jr, J. Zahradnicek, K. Krak, and J. Fehrer (2009)
Ann. Bot. 104, 161-178
   Abstract »    Full Text »    PDF »
Does horizontal transmission invalidate cultural phylogenies?.
S. J. Greenhill, T. E. Currie, and R. D. Gray (2009)
Proc R Soc B 276, 2299-2306
   Abstract »    Full Text »    PDF »
Phylogeographic patterns and demographic history of Schiedea globosa (Caryophyllaceae) on the Hawaiian Islands.
L. E. Wallace, S. G. Weller, W. L. Wagner, A. K. Sakai, and M. Nepokroeff (2009)
Am. J. Botany 96, 958-967
   Abstract »    Full Text »    PDF »
Species Delineation and Evolutionary History of the Globally Distributed Spotted Eagle Ray (Aetobatus narinari).
V. P. Richards, M. Henning, W. Witzell, and M. S. Shivji (2009)
J. Hered. 100, 273-283
   Abstract »    Full Text »    PDF »
Gene Duplications and Losses within the Cyclooxygenase Family of Teleosts and Other Chordates.
J. C. Havird, M. M. Miyamoto, K. P. Choe, and D. H. Evans (2008)
Mol. Biol. Evol. 25, 2349-2359
   Abstract »    Full Text »    PDF »
An ancient tripartite symbiosis of plants, ants and scale insects.
S. Ueda, S.-P. Quek, T. Itioka, K. Inamori, Y. Sato, K. Murase, and T. Itino (2008)
Proc R Soc B 275, 2319-2326
   Abstract »    Full Text »    PDF »
PhyloWidget: web-based visualizations for the tree of life.
G. E. Jordan and W. H. Piel (2008)
Bioinformatics 24, 1641-1642
   Abstract »    Full Text »    PDF »
Codivergence in Heteromyid Rodents (Rodentia: Heteromyidae) and Their Sucking Lice of the Genus Fahrenholzia (Phthiraptera: Anoplura).
J. E. Light and M. S. Hafner (2008)
Syst Biol 57, 449-465
   Abstract »    Full Text »    PDF »
Once a Batesian mimic, not always a Batesian mimic: mimic reverts back to ancestral phenotype when the model is absent.
K. L Prudic and J. C Oliver (2008)
Proc R Soc B 275, 1125-1132
   Abstract »    Full Text »    PDF »
DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae).
T.L Whitworth, R.D Dawson, H Magalon, and E Baudry (2007)
Proc R Soc B 274, 1731-1739
   Abstract »    Full Text »    PDF »
The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.
A. J Roger and L. A Hug (2006)
Phil Trans R Soc B 361, 1039-1054
   Abstract »    Full Text »    PDF »
Post-Miocene expansion, colonization, and host switching drove speciation among extant nematodes of the archaic genus Trichinella.
D. S. Zarlenga, B. M. Rosenthal, G. La Rosa, E. Pozio, and E. P. Hoberg (2006)
PNAS 103, 7354-7359
   Abstract »    Full Text »    PDF »
Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation.
L. Mateiu and B. Rannala (2006)
Syst Biol 55, 259-269
   Abstract »    Full Text »    PDF »
Evolution of Transcription Regulatory Genes Is Linked to Niche Specialization in the Bacterial Pathogen Streptococcus pyogenes.
D. E. Bessen, A. Manoharan, F. Luo, J. E. Wertz, and D. A. Robinson (2005)
J. Bacteriol. 187, 4163-4172
   Abstract »    Full Text »    PDF »
The {beta}-amylase genes of grasses and a phylogenetic analysis of the Triticeae (Poaceae).
R. J. Mason-Gamer (2005)
Am. J. Botany 92, 1045-1058
   Abstract »    Full Text »    PDF »
Aspergillus lentulus sp. nov., a New Sibling Species of A. fumigatus.
S. A. Balajee, J. L. Gribskov, E. Hanley, D. Nickle, and K. A. Marr (2005)
Eukaryot. Cell 4, 625-632
   Abstract »    Full Text »    PDF »
Evolutionary Dynamics of Insertion Sequences in Helicobacter pylori.
A. Kalia, A. K. Mukhopadhyay, G. Dailide, Y. Ito, T. Azuma, B. C. Y. Wong, and D. E. Berg (2004)
J. Bacteriol. 186, 7508-7520
   Abstract »    Full Text »    PDF »
Phylogenetic relationships of Malvatheca (Bombacoideae and Malvoideae; Malvaceae sensu lato) as inferred from plastid DNA sequences.
D. A. Baum, S. DeWitt Smith, A. Yen, W. S. Alverson, R. Nyffeler, B. A. Whitlock, and R. L. Oldham (2004)
Am. J. Botany 91, 1863-1871
   Abstract »    Full Text »    PDF »
African Haplogroup L mtDNA Sequences Show Violations of Clock-like Evolution.
N. Howell, J. L. Elson, D. M. Turnbull, and C. Herrnstadt (2004)
Mol. Biol. Evol. 21, 1843-1854
   Abstract »    Full Text »    PDF »
Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect on Functional Inference.
N. M. Krishnan, H. Seligmann, C.-B. Stewart, A. P. J. de Koning, and D. D. Pollock (2004)
Mol. Biol. Evol. 21, 1871-1883
   Abstract »    Full Text »    PDF »
"Candidatus Endobugula glebosa," a Specific Bacterial Symbiont of the Marine Bryozoan Bugula simplex.
G. E. Lim and M. G. Haygood (2004)
Appl. Envir. Microbiol. 70, 4921-4929
   Abstract »    Full Text »    PDF »
Phylogeny and Divergence-Date Estimates of Rapid Radiations in Muroid Rodents Based on Multiple Nuclear Genes.
S. J. Steppan, R. M. Adkins, and J. Anderson (2004)
Syst Biol 53, 533-553
   Abstract »    Full Text »    PDF »
Selection Pressure-Driven Evolution of the Epstein-Barr Virus-Encoded Oncogene LMP1 in Virus Isolates from Southeast Asia.
J. M. Burrows, L. Bromham, M. Woolfit, G. Piganeau, J. Tellam, G. Connolly, N. Webb, L. Poulsen, L. Cooper, S. R. Burrows, et al. (2004)
J. Virol. 78, 7131-7137
   Abstract »    Full Text »    PDF »
Modeling Compositional Heterogeneity.
P. G. Foster (2004)
Syst Biol 53, 485-495
   Abstract »    Full Text »    PDF »
Bayesian Phylogenetic Model Selection Using Reversible Jump Markov Chain Monte Carlo.
J. P. Huelsenbeck, B. Larget, and M. E. Alfaro (2004)
Mol. Biol. Evol. 21, 1123-1133
   Abstract »    Full Text »    PDF »
Molecular evidence links cryptic diversification in polar planktonic protists to Quaternary climate dynamics.
K. F. Darling, M. Kucera, C. J. Pudsey, and C. M. Wade (2004)
PNAS 101, 7657-7662
   Abstract »    Full Text »    PDF »
Phylogeny of Agrodiaetus Hubner 1822 (Lepidoptera: Lycaenidae) Inferred from mtDNA Sequences of COI and COII and Nuclear Sequences of EF1-{alpha}: Karyotype Diversification and Species Radiation.
N. P. Kandul, V. A. Lukhtanov, A. V. Dantchenko, J. W. S. Coleman, C. H. Sekercioglu, D. Haig, and N. E. Pierce (2004)
Syst Biol 53, 278-298
   Abstract »    Full Text »    PDF »
Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1 env Evolution During Chronic Infection.
D. Shriner, R. Shankarappa, M. A. Jensen, D. C. Nickle, J. E. Mittler, J. B. Margolick, and J. I. Mullins (2004)
Genetics 166, 1155-1164
   Abstract »    Full Text »    PDF »
Phylogenetic Estimation of Context-Dependent Substitution Rates by Maximum Likelihood.
A. Siepel and D. Haussler (2004)
Mol. Biol. Evol. 21, 468-488
   Abstract »    Full Text »    PDF »
Molecular evidence for bicontinental hybridogenous genomic constitution in Lepidium sensu stricto (Brassicaceae) species from Australia and New Zealand.
K. Mummenhoff, P. Linder, N. Friesen, J. L. Bowman, J.-Y. Lee, and A. Franzke (2004)
Am. J. Botany 91, 254-261
   Abstract »    Full Text »    PDF »
WHEN CLOCKS (AND COMMUNITIES) COLLIDE: ESTIMATING DIVERGENCE TIME FROM MOLECULES AND THE FOSSIL RECORD.
(2004)
Journal of Paleontology 78, 1-6
MOLECULAR CLOCK DIVERGENCE ESTIMATES AND THE FOSSIL RECORD OF CETARTIODACTYLA.
(2004)
Journal of Paleontology 78, 39-44
Natural Selection and Evolution of Streptococcal Virulence Genes Involved in Tissue-Specific Adaptations.
A. Kalia and D. E. Bessen (2004)
J. Bacteriol. 186, 110-121
   Abstract »    Full Text »    PDF »
Structure and Function of CC-Chemokine Receptor 5 Homologues Derived from Representative Primate Species and Subspecies of the Taxonomic Suborders Prosimii and Anthropoidea.
K. J. Kunstman, B. Puffer, B. T. Korber, C. Kuiken, U. R. Smith, J. Kunstman, J. Stanton, M. Agy, R. Shibata, A. D. Yoder, et al. (2003)
J. Virol. 77, 12310-12318
   Abstract »    Full Text »    PDF »
Increased Rates of Sequence Evolution in Endosymbiotic Bacteria and Fungi with Small Effective Population Sizes.
M. Woolfit and L. Bromham (2003)
Mol. Biol. Evol. 20, 1545-1555
   Abstract »    Full Text »    PDF »
Circulation of Endemic Type 2 Vaccine-Derived Poliovirus in Egypt from 1983 to 1993.
C.-F. Yang, T. Naguib, S.-J. Yang, E. Nasr, J. Jorba, N. Ahmed, R. Campagnoli, H. van der Avoort, H. Shimizu, T. Yoneyama, et al. (2003)
J. Virol. 77, 8366-8377
   Abstract »    Full Text »    PDF »
Ancestral Gene Reconstruction and Synthesis of Ancient Rhodopsins in the Laboratory.
B. S. W. Chang (2003)
Integr. Comp. Biol. 43, 500-507
   Abstract »    Full Text »    PDF »
Using Evolutionary Rates to Investigate Protein Functional Divergence and Conservation: A Case Study of the Carbonic Anhydrases.
B. Knudsen, M. M. Miyamoto, P. J. Laipis, and D. N. Silverman (2003)
Genetics 164, 1261-1269
   Abstract »    Full Text »    PDF »
Dinucleotide Repeats in the Drosophila and Human Genomes Have Complex, Length-Dependent Mutation Processes.
P. Calabrese and R. Durrett (2003)
Mol. Biol. Evol. 20, 715-725
   Abstract »    Full Text »    PDF »
Evolutionary, Structural and Biochemical Evidence for a New Interaction Site of the Leptin Obesity Protein.
E. A. Gaucher, M. M. Miyamoto, and S. A. Benner (2003)
Genetics 163, 1549-1553
   Abstract »    Full Text »    PDF »
Why Do Paralogs Persist? Molecular Evolution of CYCLOIDEA and Related Floral Symmetry Genes in Antirrhineae (Veronicaceae).
L. C. Hileman and D. A. Baum (2003)
Mol. Biol. Evol. 20, 591-600
   Abstract »    Full Text »    PDF »
Estimation of the Age of Extant Ephedra Using Chloroplast rbcL Sequence Data.
J. Huang and R. A. Price (2003)
Mol. Biol. Evol. 20, 435-440
   Abstract »    Full Text »    PDF »
A Novel Use of Equilibrium Frequencies in Models of Sequence Evolution.
N. Goldman and S. Whelan (2002)
Mol. Biol. Evol. 19, 1821-1831
   Abstract »    Full Text »    PDF »
Immune-Mediated Positive Selection Drives Human Immunodeficiency Virus Type 1 Molecular Variation and Predicts Disease Duration.
H. A. Ross and A. G. Rodrigo (2002)
J. Virol. 76, 11715-11720
   Abstract »    Full Text »    PDF »
The phylogenetic utility of nucleotide sequences of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae).
E. Bortiri, S.-H. Oh, F.-Y. Gao, and D. Potter (2002)
Am. J. Botany 89, 1697-1708
   Abstract »    Full Text »    PDF »
Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting.
F. Delsuc, M. Scally, O. Madsen, M. J. Stanhope, W. W. de Jong, F. M. Catzeflis, M. S. Springer, and E. J. P. Douzery (2002)
Mol. Biol. Evol. 19, 1656-1671
   Abstract »    Full Text »    PDF »
Power Analysis of Tests for Loss of Selective Constraint in Cave Crayfish and Nonphotosynthetic Plant Lineages.
J. Leebens-Mack and C. dePamphilis (2002)
Mol. Biol. Evol. 19, 1292-1302
   Abstract »    Full Text »    PDF »
A Reanalysis of the Ancient Mitochondrial DNA Sequences Recovered from Neandertal Bones.
G. Gutierrez, D. Sanchez, and A. Marin (2002)
Mol. Biol. Evol. 19, 1359-1366
   Abstract »    Full Text »    PDF »
Accuracy and Power of Bayes Prediction of Amino Acid Sites Under Positive Selection.
M. Anisimova, J. P. Bielawski, and Z. Yang (2002)
Mol. Biol. Evol. 19, 950-958
   Abstract »    Full Text »    PDF »
Influence of Recombination and Niche Separation on the Population Genetic Structure of the Pathogen Streptococcus pyogenes.
A. Kalia, B. G. Spratt, M. C. Enright, and D. E. Bessen (2002)
Infect. Immun. 70, 1971-1983
   Abstract »    Full Text »    PDF »
A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins.
B. Knudsen and M. M. Miyamoto (2001)
PNAS 98, 14512-14517
   Abstract »    Full Text »    PDF »
Multiple origins of sequestrate fungi related to Cortinarius (Cortinariaceae).
U. Peintner, N. L. Bougher, M. A. Castellano, J.-M. Moncalvo, M. M. Moser, J. M. Trappe, and R. Vilgalys (2001)
Am. J. Botany 88, 2168-2179
   Abstract »    Full Text »    PDF »
Directional Gene Movement from Human-Pathogenic to Commensal-Like Streptococci.
A. Kalia, M. C. Enright, B. G. Spratt, and D. E. Bessen (2001)
Infect. Immun. 69, 4858-4869
   Abstract »    Full Text »    PDF »
Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data.
M. J. Sanderson and J. A. Doyle (2001)
Am. J. Botany 88, 1499-1516
   Full Text »
Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology.
A. van Belkum, M. Struelens, A. de Visser, H. Verbrugh, and M. Tibayrenc (2001)
Clin. Microbiol. Rev. 14, 547-560
   Abstract »    Full Text »    PDF »
Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach.
N. Takebayashi and P. L. Morrell (2001)
Am. J. Botany 88, 1143-1150
   Abstract »    Full Text »    PDF »
Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models.
M. A. Suchard, R. E. Weiss, and J. S. Sinsheimer (2001)
Mol. Biol. Evol. 18, 1001-1013
   Abstract »    Full Text »
The TprK Protein of Treponema pallidum Is Periplasmic and Is Not a Target of Opsonic Antibody or Protective Immunity.
K. R.O. Hazlett, T. J. Sellati, T. T. Nguyen, D. L. Cox, M. L. Clawson, M. J. Caimano, and J. D. Radolf (2001)
J. Exp. Med. 193, 1015-1026
   Abstract »    Full Text »    PDF »
Special Feature: A novel microbial habitat in the mid-ocean ridge subseafloor.
M. Summit and J. A. Baross (2001)
PNAS 98, 2158-2163
   Abstract »    Full Text »    PDF »
Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors.
E. A. Gaucher, M. M. Miyamoto, and S. A. Benner (2001)
PNAS 98, 548-552
   Abstract »    Full Text »    PDF »
Genetic Distinctiveness of Endangered Dwarf Blue Sheep (Pseudois nayaur schaeferi): Evidence From Mitochondrial Control Region and Y-Linked ZFY Intron Sequences.
J. Feng, C. Lajia, D. J. Taylor, and M. S. Webster (2001)
J. Hered. 92, 9-15
   Abstract »    Full Text »    PDF »
Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E.
J. P. Anderson, A. G. Rodrigo, G. H. Learn, A. Madan, C. Delahunty, M. Coon, M. Girard, S. Osmanov, L. Hood, and J. I. Mullins (2000)
J. Virol. 74, 10752-10765
   Abstract »    Full Text »
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 »
Heteroduplex mobility assay-guided sequence discovery: Elucidation of the small subunit (18S) rDNA sequences of Pfiesteria piscicida and related dinoflagellates from complex algal culture and environmental sample DNA pools.
D. W. Oldach, C. F. Delwiche, K. S. Jakobsen, T. Tengs, E. G. Brown, J. W. Kempton, E. F. Schaefer, H. A. Bowers, H. B. Glasgow Jr., J. M. Burkholder, et al. (2000)
PNAS 97, 4303-4308
   Abstract »    Full Text »    PDF »
Evolutionary Rate and Genetic Drift of Hepatitis C Virus Are Not Correlated with the Host Immune Response: Studies of Infected Donor-Recipient Clusters.
J.-P. Allain, Y. Dong, A.-M. Vandamme, V. Moulton, and M. Salemi (2000)
J. Virol. 74, 2541-2549
   Abstract »    Full Text »
Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B.
S. Mathews, R. C. Tsai, and E. A. Kellogg (2000)
Am. J. Botany 87, 96-107
   Abstract »    Full Text »
Conserved structural features and sequence patterns in the GroES fold family.
B. Taneja and S. C. Mande (1999)
Protein Eng. Des. Sel. 12, 815-818
   Abstract »    Full Text »    PDF »
Molecular phylogenetics of Fouquieriaceae: evidence from nuclear rDNA ITS studies.
L. M. Schultheis and B. G. Baldwin (1999)
Am. J. Botany 86, 578-589
   Abstract »    Full Text »    PDF »
Evolution of the RECQ Family of Helicases: A Drosophila Homolog, Dmblm, Is Similar to the Human Bloom Syndrome Gene.
K. Kusano, M. E. Berres, and W. R. Engels (1999)
Genetics 151, 1027-1039
   Abstract »    Full Text »
Models of Molecular Evolution and Phylogeny.
P. Liò and N. Goldman (1998)
Genome Res. 8, 1233-1244
   Abstract »    Full Text »
Age and rate of diversification of the Hawaiian silversword alliance (Compositae).
B. G. Baldwin and M. J. Sanderson (1998)
PNAS 95, 9402-9406
   Abstract »    Full Text »    PDF »
The role of robustness and changeability on the origin and evolution of genetic codes.
T. Maeshiro and M. Kimura (1998)
PNAS 95, 5088-5093
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)