Rooting gene trees without outgroups: EP rooting

Genome Biology and Evolution

Volumn 4, Issue 8, 2012, Pages 709-719

  Sinsheimer, Janet S ^a,b   Little, Roderick J A ^c   Lake, James A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF MICHIGAN SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Bayesian statistics; Evolutionary parsimony; Gene sequences; Linear invariants; Metazoa; Rooting; Trees

Indexed keywords

ACOELOMORPHA; ANIMALIA; ARTHROPODA; DEUTEROSTOMIA; ECDYSOZOA; METAZOA; NEMATODA; PLATYHELMINTHES; XENOTURBELLA;

EID: 84866430606     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs047     Document Type: Article

References (41)

1. Aguinaldo AMA, et al. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387:489-493.
2. Allman ES, Rhodes JA. 2003. Phylogenetic invariants for the general Markov model of sequence mutation. Math Biosci. 186:113-144.
3. Barry D, Hartigan JA. 1987a. Asynchronous distance between homologous DNA sequences. Biometrics 43:261-276.
4. Barry D, Hartigan JA. 1987b. Statistical analysis of Hominoid molecular evolution. Stat Sci. 2:191-210.
5. Brown WM, Prager EM, Wang A, Wilson AC. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol. 18: 225-239.
6. Burnham KP, Anderson DR. 1998. Model selection and inferences: a practical information theoretic approach. New York: Springer-Verlag.
7. Cavender J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301-316.
8. Cavender J, Felsenstein J. 1987. Invariants of phylogenies in a simple case with discrete states. J Classif. 4:57-71.
9. Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. 2008. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci U S A. 105: 20356-20361.
10. Dayhoff MO, Hunt LT, McLaughlin PJ, Jones DD. 1972. Gene duplications in evolution. In: Dayhoff MO, editor. Atlas of protein sequence and structure. Washington (DC): National Biomedical Research Foundation, p. 17-30.
11. Evans SN, Zhou X. 1998. Constructing and counting phylogenetic invariants. J Comput Biol. 5:713-724.
12. Ferretti V, Lang BF, Sankoff D. 1994. Skewed base compositions, asymmetric transition matrices, and phylogenetic invariants. J Comput Biol. 1:77-92.
13. Halanych KM, et al. 1995. Evidence from 18s ribosomal DNA that the lophophorates are protostome animals. Science 267: 1641-1643.
14. HendyMD, Penny D. 1996. Complete families of linear invariants for some stochastic models of sequence evolution, with and without the molecular clock assumption. J Comput Biol. 3:19-31.
15. Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167-181.
16. Lake JA. 1987b. Determining evolutionary distances from highly diverged nucleic acid sequences - operator metrics. J Mol Evol. 24:59-73.
17. Lake JA. 1990. Origin of the Metazoa. Proc Natl Acad Sci U S A. 87: 763-766.
18. Lake JA. 1997. Phylogenetic inference: how much evolutionary history is knowable. Mol Biol Evol. 14:213-219.
19. Lake JA. 2009. Evidence for an early prokaryotic endosymbiosis. Nature 460:967-971.
20. Lake JA, RiveraMC. 2004. Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol Biol Evol. 21:681-690.
21. Lake JA, Skophammer RG, Herbold CW, Servin JA. 2009. Genome beginnings: rooting the tree of life. Phil Trans R Soc B. 364: 2177-2187.
22. Madsen O, et al. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-614.
23. Mood AM, Graybill FA, Boes DC. 1974. Introduction to the theory of statistics. New York: McGraw-Hill.
24. Murphy WJ, et al. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618.
25. Murphy WJ, et al. 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2355.
26. Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60-76.
27. Philippe H, et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255-260.
28. Ragan MA, McInerney JO, Lake JA. 2009. The network of life: genome beginnings and evolution. Phil Trans R Soc B. 364: 2169-2175.
29. Rao CR. 1973. Linear statistic inference and its applications. New York: Wiley.
30. Reich D, Green RE, Kircher M. 2011. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-1060.
31. Rivera MC, Lake JA. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:74-76.
32. Scally M, et al. 2001. Molecular evidence for the major clades of placental mammals. J Mamm Evol. 8:239-277.
33. Simonson AB, et al. 2005. Decoding the genomic tree of life. Proc Natl Acad Sci U S A. 102:6608-6613.
34. Sinsheimer JS. 1994. Extensions to evolutionary parsimony [dissertation]. [Los Angeles (CA)]: UCLA.
35. Sinsheimer JS, Lake JA, Little RJA. 1996. Bayesian hypothesis testing of four-taxon topologies using molecular sequence data. Biometrics 52: 193-210.
36. Steel MA, Fu YX. 1995. Classifying and counting linear phylogenetic invariants for the Jukes-Cantor model. J Comput Biol. 2:39-47.
37. Steel MA, Hendy MD, Penny D. 1998. Reconstructing probabilities from nucleotide pattern probabilities: a survey and some new results. Discr App Math. 88:367-396.
38. Steel MA, Szekely L, Erdos PL, Waddell PJ. 1993. A complete family of phylogenetic invariants for any number of taxa under Kimura's 3ST model. New Zeal J Botany. 31:289-296.
39. Waddell PJ, Okada N, Hasegawa M. 1999. Towards resolving the interordinal relationships of placental mammals. Syst Biol. 48:1-5.
40. Waddell PJ, Penny D, Moore T. 1997. Extending Hadamard conjugations to model sequence evolution with variable rates across sites.Mol Phylo Evol. 8:33-50.
41. Yap VB, Speed T. 2005. Rooting a phylogenetic tree with nonreversible substitution models. BMC Evol Biol. 5:2.