Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

Journal of Theoretical Biology

Volumn 374, Issue , 2015, Pages 35-47

  Chifman, Julia ^a   Kubatko, Laura ^b  

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Algebraic statistics; Identifiability; Phylogenetics

Indexed keywords

BIOGEOGRAPHY; DNA; EVOLUTIONARY BIOLOGY; IDENTIFICATION METHOD; NUMERICAL MODEL; PHYLOGENETICS; TOPOLOGY; TREE;

ARTICLE; DNA SEQUENCE; EVOLUTIONARY HOMOLOGY; FUZZY SYSTEM; GENE DUPLICATION; GENE LOSS; GENETIC CONSERVATION; HORIZONTAL GENE TRANSFER; MATHEMATICS; MEMBRANE STRUCTURE; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENTIATION; TAXONOMY; ALGORITHM; BIOLOGICAL MODEL; MARKOV CHAIN; MOLECULAR EVOLUTION; MUTATION; TIME FACTOR;

DNA;

ALGORITHMS; DNA; EVOLUTION, MOLECULAR; GENETIC SPECIATION; MARKOV CHAINS; MODELS, BIOLOGICAL; MUTATION; PHYLOGENY; PROBABILITY; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

EID: 84926469966     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2015.03.006     Document Type: Article

References (38)

1. Allman E.S., Rhodes J.A. The identifiability of tree topology for phylogenetic models, including covarion and mixture models. J. Comput. Biol. 2006, 13(5):1101-1113.
2. Allman E.S., Rhodes J.A. Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites. Math. Biosci. 2008, 211:18-33.
3. Allman E.S., Rhodes J.A. The identifiability of covarion models in phylogenetics. IEEE/ACM Trans. Comput. Biol. Bioinform. 2009, 6:76-88.
4. Allman E.S., Ané C., Rhodes J.A. Identifiability of a Markovian model of molecular evolution with gamma-distributed rates. Adv. Appl. Probab. 2008, 40:228-249.
5. Allman E.S., Petrovic S., Rhodes J.A., Sullivant S. Identifiability of 2-tree mixtures for group-based models. IEEE/ACM Trans. Comput. Biol. Bioinform. 2011, 8(3):710-722.
6. 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, 62:833-862.
7. Allman E.S., Degnan J.H., Rhodes J.A. Determining species tree topologies from clade probabilities under the coalescent. J. Theor. Biol. 2011, 289:96-106. 10.1016/j.jtbi.2011.08.006.
8. Bryant D., Bouckaert R., Felsenstein J., Rosenberg N., Roy Choudhury A. Inferring species trees directly from biallelic genetic markers. bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 2012, 29(8):1917-1932.
9. Cavender J.A. Mechanized derivation of linear invariants. Mol. Biol. Evol. 1989, 6(3):301-316.
10. Chifman J., Kubatko L. Quartet inference from SNP data under the coalescent model. Bioinformatics 2014, 30(23):3317-3324. 10.1093/bioinformatics/btu53.
11. Eriksson N. Tree construction using singular value decomposition. Algebraic Statistics for Computational Biology 2005, 347-358. Cambridge University Press, New York, (Chapter 19). L. Pachter, B. Sturmfels (Eds.).
12. Felsenstein J. Evolutionary trees from DNA sequences. a maximum likelihood approach. J. Mol. Evol. 1981, 17(6):368-376.
13. Fu Y. Linear invariants under Jukes[U+05F3] and Cantor[U+05F3]s one-parameter model. J. Theor. Biol. 1995, 173(4):339-352.
14. Fu Y., Li W. Construction of linear invariants in phylogenetic inference. Math. Biosci. 1992, 109(2):201-228.
15. Gunning R., Rossi H. Analytic Functions of Several Complex Variables 2009, AMS Chelsea Publishing, URL: 〈http://books.google.com/books?id=L0zJmamx5AAC〉.
16. Hasegawa M., Kishino H., Yano T. Dating of human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 1985, 22(2):160-174.
17. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27(3):570-580.
18. Jukes T., Cantor C.R. Evolution of protein molecules. Mammalian Protein Metabolism 1969, 21-123. Academic Press, New York. H.N. Munro (Ed.).
19. Kimura M. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16:111-120.
20. Kingman J.F.C. On the genealogy of large populations. J. Appl. Probab. 1982, 19A:27-43.
21. Kingman J.F.C. The coalescent. Stoch. Process. Appl. 1982, 13:235-248.
22. Kubatko L.S., Carstens B.C., Knolwes L.L. STEM. species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25(7):971-973.
23. Lake J.A. A rate independent technique for analysis of nucleic acid sequences. evolutionary parsimony. Mol. Biol. Evol. 1987, 4(2):167-191.
24. Lewis P.O. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 2001, 50(6):913-925. 10.1080/106351501753462876.
25. Liu L., Edwards S.V. Phylogenetic analysis in the anomaly zone. Syst. Biol. 2009, 58(4):452-460.
26. Liu L., Pearl D. Species trees from gene trees. reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 2007, 56:504-514.
27. Liu L., Yu L., Edwards S. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10(302).
28. Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
29. Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5(5):568-583.
30. Rannala B., Yang Z. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 2003, 164:1645-1656.
31. Snir S., Rao S. Quartet MaxCut. a fast algorithm for amalgamating quartet trees. Mol. Phylogenet. Evol. 2012, 62:1-8.
32. Strimmer K., von Haeseler A. Quartet puzzling. a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 1996, 13:964-969.
33. Strimmer K., Goldman N., von Haeseler A. Bayesian probabilities and quartet puzzling. Mol. Biol. Evol. 1997, 14:210-213.
34. Tamura K., Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 1993, 10(3):512-526.
35. Tavaré S. Line-of-descent and genealogical processes and their applications in population genetics models. Theor. Popul. Biol. 1984, 26:119-164.
36. Tavare, S., 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Lectures on Mathematics in the Life Sciences (American Mathematical Society), vol. 17. pp. 57-86.
37. Yang Z. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 1993, 10:1396-1401.
38. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites. approximate methods. J. Mol. Evol. 1994, 39(3):306-314. 10.1007/BF00160154.