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.
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
John P. Huelsenbeck,1*Fredrik Ronquist,2Rasmus Nielsen,3Jonathan P. Bollback1
As a discipline, phylogenetics is becoming transformed by a
flood of molecular data. These data allow broad questions to beasked
about the history of life, but also present difficult statisticaland
computational problems. Bayesian inference of phylogeny bringsa new
perspective to a number of outstanding issues in evolutionarybiology,
including the analysis of large phylogenetic trees andcomplex
evolutionary models and the detection of the footprintof natural
selection in DNA sequences.
1 Department of Biology, University of
Rochester, Rochester, NY 14627, USA.
2 Department of
Systematic Zoology, Evolutionary Biology Centre, Uppsala University,
Norbyv. 18D, SE-752 36 Uppsala, Sweden.
3 Department
of Biometrics, Cornell University, Ithaca, NY 14853-1643, USA.
*
To whom correspondence should be addressed. E-mail:
johnh{at}brahms.biology.rochester.edu
The editors suggest the following Related Resources on Science sites:
In Science Magazine
NEWS OF THE WEEK
Elizabeth Pennisi (14 December 2001) Science294 (5550), 2266b.
[DOI: 10.1126/science.294.5550.2266b] |Summary »|Full Text »|PDF »
BOOKS
Axel Meyer (14 December 2001) Science294 (5550), 2297.
[DOI: 10.1126/science.1067581] |Summary »|Full Text »|PDF »
REPORTS
William J. Murphy, Eduardo Eizirik, Stephen J. O'Brien, Ole Madsen, Mark Scally, Christophe J. Douady, Emma Teeling, Oliver A. Ryder, Michael J. Stanhope, Wilfried W. de Jong, and Mark S. Springer (14 December 2001) Science294 (5550), 2348.
[DOI: 10.1126/science.1067179] |Abstract »|Full Text »|PDF »|Supplemental Data »
REPORTS
Kenneth G. Karol, Richard M. McCourt, Matthew T. Cimino, and Charles F. Delwiche (14 December 2001) Science294 (5550), 2351.
[DOI: 10.1126/science.1065156] |Abstract »|Full Text »|PDF »|Supplemental Data »
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Substitution of the Gene for Chloroplast RPS16 Was Assisted by Generation of a Dual Targeting Signal.
M. Ueda, T. Nishikawa, M. Fujimoto, H. Takanashi, S.-i. Arimura, N. Tsutsumi, and K.-i. Kadowaki (2008)
Mol. Biol. Evol.
25, 1566-1575
|Abstract »|Full Text »|PDF »
From the Cover: Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos).
C. E. Valdiosera, J. L. Garcia-Garitagoitia, N. Garcia, I. Doadrio, M. G. Thomas, C. Hanni, J.-L. Arsuaga, I. Barnes, M. Hofreiter, L. Orlando, et al. (2008)
PNAS
105, 5123-5128
|Abstract »|Full Text »|PDF »
Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs.
J. E. Horvath, D. W. Weisrock, S. L. Embry, I. Fiorentino, J. P. Balhoff, P. Kappeler, G. A. Wray, H. F. Willard, and A. D. Yoder (2008)
Genome Res.
18, 489-499
|Abstract »|Full Text »|PDF »
ITS Evolution in Platanus (Platanaceae): Homoeologues, Pseudogenes and Ancient Hybridization.
A monograph of the entomopathogenic genera Hypocrella, Moelleriella, and Samuelsia gen. nov. (Ascomycota, Hypocreales, Clavicipitaceae), and their aschersonia-like anamorphs in the Neotropics.
Alignment-independent bilinear multivariate modelling (AIBIMM) for global analyses of 16S rRNA gene phylogeny..
K. Rudi, M. Zimonja, and T. Naes (2006)
Int J Syst Evol Microbiol
56, 1565-1575
|Abstract »|Full Text »|PDF »
Molecular systematics of the subaerial green algal order Trentepohliales: an assessment based on morphological and molecular data..
J. M. Lopez-Bautista, F. Rindi, and M. D. Guiry (2006)
Int J Syst Evol Microbiol
56, 1709-1715
|Abstract »|Full Text »|PDF »
Comparing Phylogenetic Codivergence between Polyomaviruses and Their Hosts..
M. Perez-Losada, R. G. Christensen, D. A. McClellan, B. J. Adams, R. P. Viscidi, J. C. Demma, and K. A. Crandall (2006)
J. Virol.
80, 5663-5669
|Abstract »|Full Text »|PDF »
Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences.
F. Ababneh, L. S. Jermiin, C. Ma, and J. Robinson (2006)
Bioinformatics
22, 1225-1231
|Abstract »|Full Text »|PDF »
Phylogeny of Rhaponticum (Asteraceae, Cardueae-Centaureinae) and Related Genera Inferred from Nuclear and Chloroplast DNA Sequence Data: Taxonomic and Biogeographic Implications.
O. HIDALGO, N. GARCIA-JACAS, T. GARNATJE, and A. SUSANNA (2006)
Ann. Bot.
97, 705-714
|Abstract »|Full Text »|PDF »
Comment on "Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees".
F. Ronquist, B. Larget, J. P. Huelsenbeck, J. B. Kadane, D. Simon, and P. van der Mark (2006)
Science
312, 367a
|Abstract »|Full Text »|PDF »
Molecular evolution of dengue 2 virus in Puerto Rico: positive selection in the viral envelope accompanies clade reintroduction..
S. N. Bennett, E. C. Holmes, M. Chirivella, D. M. Rodriguez, M. Beltran, V. Vorndam, D. J. Gubler, and W. O. McMillan (2006)
J. Gen. Virol.
87, 885-893
|Abstract »|Full Text »|PDF »
A Bayesian Approach for Discriminating Among Alternative Inheritance Hypotheses in Plant Polyploids: The Allotetraploid Origin of Genus Borderea (Dioscoreaceae).
P. Catalan, J. G. Segarra-Moragues, M. Palop-Esteban, C. Moreno, and F. Gonzalez-Candelas (2006)
Genetics
172, 1939-1953
|Abstract »|Full Text »|PDF »
Divergence in the Plasminogen-binding Group A Streptococcal M Protein Family: FUNCTIONAL CONSERVATION OF BINDING SITE AND POTENTIAL ROLE FOR IMMUNE SELECTION OF VARIANTS.
M. Sanderson-Smith, M. Batzloff, K. S. Sriprakash, M. Dowton, M. Ranson, and M. J. Walker (2006)
J. Biol. Chem.
281, 3217-3226
|Abstract »|Full Text »|PDF »
A Hotspot of Gene Order Rearrangement by Tandem Duplication and Random Loss in the Vertebrate Mitochondrial Genome.
D. San Mauro, D. J. Gower, R. Zardoya, and M. Wilkinson (2006)
Mol. Biol. Evol.
23, 227-234
|Abstract »|Full Text »|PDF »
Regiocrella, a new entomopathogenic genus with a pycnidial anamorph and its phylogenetic placement in the Clavicipitaceae..
P. Chaverri, J. F. Bischoff, H. C. Evans, and K. T. Hodge (2005)
Mycologia
97, 1225-1237
|Abstract »|Full Text »|PDF »
Characterization of a Novel vpu-Harboring Simian Immunodeficiency Virus from a Dent's Mona Monkey (Cercopithecus mona denti).
M.-C. Dazza, M. Ekwalanga, M. Nende, K. B. Shamamba, P. Bitshi, D. Paraskevis, and S. Saragosti (2005)
J. Virol.
79, 8560-8571
|Abstract »|Full Text »|PDF »
Evaluation of the monophyly of Fomitopsis using parsimony and MCMC methods.
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.
D. Paraskevis, K. Deforche, P. Lemey, G. Magiorkinis, A. Hatzakis, and A.-M. Vandamme (2005)
Bioinformatics
21, 1274-1275
|Abstract »|Full Text »|PDF »
A Bayesian Analysis of Metazoan Mitochondrial Genome Arrangements.
B. Larget, D. L. Simon, J. B. Kadane, and D. Sweet (2005)
Mol. Biol. Evol.
22, 486-495
|Abstract »|Full Text »|PDF »
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.
Phylogenetic relationships in subfamily Tillandsioideae (Bromeliaceae) based on DNA sequence data from seven plastid regions.
M. H. J. Barfuss, R. Samuel, W. Till, and T. F. Stuessy (2005)
Am. J. Botany
92, 337-351
|Abstract »|Full Text »|PDF »
A Comprehensive Analysis of Mammalian Mitochondrial Genome Base Composition and Improved Phylogenetic Methods.
A. Gibson, V. Gowri-Shankar, P. G. Higgs, and M. Rattray (2005)
Mol. Biol. Evol.
22, 251-264
|Abstract »|Full Text »|PDF »
A Globin Gene of Ancient Evolutionary Origin in Lower Vertebrates: Evidence for Two Distinct Globin Families in Animals.
A. Roesner, C. Fuchs, T. Hankeln, and T. Burmester (2005)
Mol. Biol. Evol.
22, 12-20
|Abstract »|Full Text »|PDF »
Evolution of Human Immunodeficiency Virus Type 1 Coreceptor Usage during Antiretroviral Therapy: a Bayesian Approach.
C. M. R. Kitchen, S. Philpott, H. Burger, B. Weiser, K. Anastos, and M. A. Suchard (2004)
J. Virol.
78, 11296-11302
|Abstract »|Full Text »|PDF »
Discovery of Rare and Highly Toxic Microcystins from Lichen-Associated Cyanobacterium Nostoc sp. Strain IO-102-I.
I. Oksanen, J. Jokela, D. P. Fewer, M. Wahlsten, J. Rikkinen, and K. Sivonen (2004)
Appl. Envir. Microbiol.
70, 5756-5763
|Abstract »|Full Text »|PDF »
Metabolically Active Eukaryotic Communities in Extremely Acidic Mine Drainage.
B. J. Baker, M. A. Lutz, S. C. Dawson, P. L. Bond, and J. F. Banfield (2004)
Appl. Envir. Microbiol.
70, 6264-6271
|Abstract »|Full Text »|PDF »
Relationships and host range of human, canine, simian and porcine isolates of simian virus 5 (parainfluenza virus 5).
N. Chatziandreou, N. Stock, D. Young, J. Andrejeva, K. Hagmaier, D. J. McGeoch, and R. E. Randall (2004)
J. Gen. Virol.
85, 3007-3016
|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 »
Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior.
I. Mayrose, D. Graur, N. Ben-Tal, and T. Pupko (2004)
Mol. Biol. Evol.
21, 1781-1791
|Abstract »|Full Text »|PDF »
Systematics of Ipomoea subgenus Quamoclit (Convolvulaceae) based on ITS sequence data and a Bayesian phylogenetic analysis.
R. E. Miller, J. A. McDonald, and P. S. Manos (2004)
Am. J. Botany
91, 1208-1218
|Abstract »|Full Text »|PDF »
Genome Phylogenetic Analysis Based on Extended Gene Contents.
Paralogy and Orthology in the Malvaceae rpb2 Gene Family: Investigation of Gene Duplication in Hibiscus.
B. E. Pfeil, C. L. Brubaker, L. A. Craven, and M. D. Crisp (2004)
Mol. Biol. Evol.
21, 1428-1437
|Abstract »|Full Text »|PDF »
Repeat-type distribution in trnL intron does not correspond with species phylogeny: comparison of the genetic markers 16S rRNA and trnL intron in heterocystous cyanobacteria.
I. Oksanen, K. Lohtander, K. Sivonen, and J. Rikkinen (2004)
Int J Syst Evol Microbiol
54, 765-772
|Abstract »|Full Text »|PDF »
Molecular Evolution and Mosaicism of Leptospiral Outer Membrane Proteins Involves Horizontal DNA Transfer.
D. A. Haake, M. A. Suchard, M. M. Kelley, M. Dundoo, D. P. Alt, and R. L. Zuerner (2004)
J. Bacteriol.
186, 2818-2828
|Abstract »|Full Text »|PDF »
The Mitochondrial Genome of the House Centipede Scutigera and the Monophyly Versus Paraphyly of Myriapods.
E. Negrisolo, A. Minelli, and G. Valle (2004)
Mol. Biol. Evol.
21, 770-780
|Abstract »|Full Text »|PDF »
Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism.
K. A. Borkovich, L. A. Alex, O. Yarden, M. Freitag, G. E. Turner, N. D. Read, S. Seiler, D. Bell-Pedersen, J. Paietta, N. Plesofsky, et al. (2004)
Microbiol. Mol. Biol. Rev.
68, 1-108
|Abstract »|Full Text »|PDF »
Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences.
Comparative Genomic Analysis of Hyperthermophilic Archaeal Fuselloviridae Viruses.
B. Wiedenheft, K. Stedman, F. Roberto, D. Willits, A.-K. Gleske, L. Zoeller, J. Snyder, T. Douglas, and M. Young (2004)
J. Virol.
78, 1954-1961
|Abstract »|Full Text »|PDF »
Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods.
A. Reyes, C. Gissi, F. Catzeflis, E. Nevo, G. Pesole, and C. Saccone (2004)
Mol. Biol. Evol.
21, 397-403
|Abstract »|Full Text »|PDF »
Domain Shuffling Has Been the Main Mechanism Forming New Hominoid Killer Cell Ig-Like Receptors.
R. Rajalingam, P. Parham, and L. Abi-Rached (2004)
J. Immunol.
172, 356-369
|Abstract »|Full Text »|PDF »
How Meaningful Are Bayesian Support Values?.
M. P. Simmons, K. M. Pickett, and M. Miya (2004)
Mol. Biol. Evol.
21, 188-199
|Abstract »|Full Text »|PDF »
H.-S. Yoon, M. H. Lee, J. Xiong, and J. W. Golden (2003)
J. Bacteriol.
185, 6995-7000
|Abstract »|Full Text »|PDF »
Analysis of the Evolutionary Relationships of HIV-1 and SIVcpz Sequences Using Bayesian Inference: Implications for the Origin of HIV-1.
D. Paraskevis, P. Lemey, M. Salemi, M. Suchard, Y. Van de Peer, and A.-M. Vandamme (2003)
Mol. Biol. Evol.
20, 1986-1996
|Abstract »|Full Text »|PDF »
Conserved Subgroups and Developmental Regulation in the Monocot rop Gene Family.
T. M. Christensen, Z. Vejlupkova, Y. K. Sharma, K. M. Arthur, J. W. Spatafora, C. A. Albright, R. B. Meeley, J. P. Duvick, R. S. Quatrano, and J. E. Fowler (2003)
Plant Physiology
133, 1791-1808
|Abstract »|Full Text »
Seasonal Dynamics of Previously Unknown Fungal Lineages in Tundra Soils.
C. W. Schadt, A. P. Martin, D. A. Lipson, and S. K. Schmidt (2003)
Science
301, 1359-1361
|Abstract »|Full Text »|PDF »
Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family.
The Role of Phylogenetics in Comparative Genetics.
D. E. Soltis and P. S. Soltis (2003)
Plant Physiology
132, 1790-1800
|Full Text »|PDF »
The Application of a Molecular Clock Based on Molecular Sequences and the Fossil Record to Explain Biogeographic Distributions Within the Alexandrium tamarense "Species Complex" (Dinophyceae).
U. John, R. A. Fensome, and L. K. Medlin (2003)
Mol. Biol. Evol.
20, 1015-1027
|Abstract »|Full Text »|PDF »
Sympatric speciation through intraspecific social parasitism.
An Argonaute-Like Protein Is Required for Meiotic Silencing.
D. W. Lee, R. J. Pratt, M. McLaughlin, and R. Aramayo (2003)
Genetics
164, 821-828
|Abstract »|Full Text »|PDF »
Phylogenetic evaluation of Xylothamia, Gundlachia, and related genera (Asteraceae, Astereae) based on ETS and ITS nrDNA sequence data.
L. E. Urbatsch, R. P. Roberts, and V. Karaman (2003)
Am. J. Botany
90, 634-649
|Abstract »|Full Text »|PDF »
Gunnerales are sister to other core eudicots: implications for the evolution of pentamery.
D. E. Soltis, A. E. Senters, M. J. Zanis, S. Kim, J. D. Thompson, P. S. Soltis, L. P. Ronse De Craene, P. K. Endress, and J. S. Farris (2003)
Am. J. Botany
90, 461-470
|Abstract »|Full Text »|PDF »
The Phylogenetic Extent of Metabolic Enzymes and Pathways.
J. M. Peregrin-Alvarez, S. Tsoka, and C. A. Ouzounis (2003)
Genome Res.
13, 422-427
|Abstract »|Full Text »|PDF »
Identification of Residues in Glutathione Transferase Capable of Driving Functional Diversification in Evolution. A NOVEL APPROACH TO PROTEIN REDESIGN.
Y. Ivarsson, A. J. Mackey, M. Edalat, W. R. Pearson, and B. Mannervik (2003)
J. Biol. Chem.
278, 8733-8738
|Abstract »|Full Text »|PDF »
Understanding missense mutations in the BRCA1 gene: An evolutionary approach.
M. A. Fleming, J. D. Potter, C. J. Ramirez, G. K. Ostrander, and E. A. Ostrander (2003)
PNAS
100, 1151-1156
|Abstract »|Full Text »|PDF »
Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability.
C. J. Douady, F. Delsuc, Y. Boucher, W. F. Doolittle, and E. J. P. Douzery (2003)
Mol. Biol. Evol.
20, 248-254
|Abstract »|Full Text »|PDF »
Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence.
M. E. Alfaro, S. Zoller, and F. Lutzoni (2003)
Mol. Biol. Evol.
20, 255-266
|Abstract »|Full Text »|PDF »
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics.
From the Cover: The single, ancient origin of chromist plastids.
H. S. Yoon, J. D. Hackett, G. Pinto, and D. Bhattacharya (2002)
PNAS
99, 15507-15512
|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 »
A single origin of the peridinin- and fucoxanthin-containing plastids in dinoflagellates through tertiary endosymbiosis.
H. S. Yoon, J. D. Hackett, and D. Bhattacharya (2002)
PNAS
99, 11724-11729
|Abstract »|Full Text »|PDF »
Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution.
H. Jow, C. Hudelot, M. Rattray, and P. G. Higgs (2002)
Mol. Biol. Evol.
19, 1591-1601
|Abstract »|Full Text »|PDF »
A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians.
I. Ruiz-Trillo, J. Paps, M. Loukota, C. Ribera, U. Jondelius, J. Baguna, and M. Riutort (2002)
PNAS
99, 11246-11251
|Abstract »|Full Text »|PDF »
The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation.