Determining species tree topologies from clade probabilities under the coalescent

Journal of Theoretical Biology

Volumn 289, Issue 1, 2011, Pages 96-106

  Allman, Elizabeth S ^a   Degnan, James H ^b   Rhodes, John A ^a  

^a UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Coalescent; Consensus; Identifiability; Phylogenetics; Statistical consistency

Indexed keywords

ALGORITHM; CLADISTICS; COALESCENCE; EVOLUTIONARY BIOLOGY; GENETIC ANALYSIS; PHYLOGENETICS; PROBABILITY; STATISTICAL ANALYSIS; TOPOLOGY; TREE;

ARTICLE; CLADISTICS; GENE LOCATION; LINEAR SYSTEM; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROBABILITY; SPECIES DISTRIBUTION; SPECIES TREE TOPOLOGY; STATISTICAL ANALYSIS; STATISTICAL MODEL; THEORETICAL STUDY;

ALGORITHMS; ANIMALS; BIOLOGICAL EVOLUTION; GENETIC SPECIATION; MODELS, GENETIC; PHYLOGENY;

EID: 80052517011     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.08.006     Document Type: Article

References (22)

1. Allman E.S., Degnan J.H., Rhodes J.A. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent. J. Math. Biol. 2011, 62(6):833-862.
2. Ané C., Larget B., Baum D.A., Smith S.D., Rokas A. Bayesian estimation of concordance factors. Mol. Biol. Evol. 2007, 24:412-426.
3. Bryant D. A classification of consensus methods for phylogenies. BioConsensus. DIMACS. AMS 2003, 163-183. M. Janowitz, F.J. Lapointe, F.R. McMorris, B. Mirkin, F.S. Roberts (Eds.).
4. Cranston K.A., Hurwitz B., Ware D., Stein L., Wing R.A. Species trees from highly incongruent gene trees in rice. Syst. Biol. 2009, 58:489-500.
5. Degnan J.H., DeGiorgio M., Bryant D., Rosenberg N.A. Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. 2009, 58:35-54.
6. Degnan J.H., Rosenberg N.A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 2009, 24:332-340.
7. Degnan J.H., Salter L.A. Gene tree distributions under the coalescent process. Evolution 2005, 59:24-37.
8. Ebersberger I., Galgoczy P., Taudien S., Taenzer S. Mapping human genetic ancestry. Mol. Biol. Evol. 2007, 24:2266-2277.
9. Edwards S.V. Is a new and general theory of systematics emerging?. Evolution 2009, 63:1-19.
10. Eldon B., Wakeley J. Coalescent processes when the distribution of offspring number among individuals is highly skewed. Genetics 2006, 172:2621-2633.
11. Ewing G.B., Ebersberger I., Schmidt H.A., von Haeseler A. Rooted triple consensus and anomalous gene trees. BMC Evol. Biol. 2008, 8:118.
12. Greuel, G.-M., Pfister, G., Schönemann, H., 2009. Singular 3.1.0-A Computer Algebra System for Polynomial Computations. Technical Report, Centre for Computer Algebra, University of Kaiserslautern http://www.singular.uni-kl.de.
13. Estimating Species Trees: Practical and Theoretical Aspects. 2010, Wiley-Blackwell, Hoboken, NJ. L.L. Knowles, L.S. Kubatko (Eds.).
14. Larget B.R., Kotha S.K., Dewey C.N., Ané C. BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 2010, 26:2910-2911.
15. Liu L., Yu L., Edwards S.V. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10:302.
16. Nei M. Molecular Evolutionary Genetics 1987, Columbia University Press, NY.
17. Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5:568-583.
18. Pitman J. Coalescents with multiple collisions. Ann. Prob. 1999, 27:1870-1902.
19. Rannala B., Yang Z. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 2003, 164:1645-1656.
20. Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
21. Rosenberg N.A. The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 2002, 61:225-247.
22. Semple C., Steel M. Phylogenetics 2003, Oxford University Press, Oxford, UK.