Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

Molecular Phylogenetics and Evolution

Volumn 49, Issue 3, 2008, Pages 832-842

  Eckert, Andrew J ^a   Carstens, Bryan C ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

COAL; Estimating species phylogenies; Gene flow; Incomplete lineage sorting; Minimizing deep coalescence; Rhododendron

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER SIMULATION; DNA SEQUENCE; GENE FLOW; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; MONTE CARLO METHOD; PHYLOGENY; POPULATION GENETICS; RHODODENDRON; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC SPECIATION; GENETICS, POPULATION; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; MONTE CARLO METHOD; PHYLOGENY; RHODODENDRON; SEQUENCE ANALYSIS, DNA;

AVES; CONIFEROPHYTA; RHODODENDRON;

EID: 56549103832     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.09.008     Document Type: Article

References (57)

1. Anisimova M., and Gascuel O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 55 (2006) 539-552
2. Avise J.C. Phylogeography: The History and Formation of Species (2000), Harvard University Press, Cambridge, MA
3. Beerli P., and Felsenstein J. Maximum likelihood estimation of migration rates and population numbers of two populations using a coalescent approach. Genetics 152 (1999) 763-773
4. Beerli P., and Felsenstein J. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Nat. Acad. Sci. USA 98 (2001) 4563-4568
5. Brumfield R.T., Liu L., Lum D.E., and Edwards S.V. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae: Manacus) from multilocus sequence data. Syst. Biol. 57 (2008) 719-731
6. Carling M.D., and Brumfield R.T. Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings. Genetics 178 (2008) 363-377
7. Carstens B.C., and Knowles L.L. Estimating phylogeny from gene tree probabilities in Melanoplus grasshoppers despite incomplete lineage sorting. Syst. Biol. 56 (2007) 400-411
8. Cox P.A., and Cox K.N.E. The Encyclopedia of Rhododendron Species (1997), Glendoick Publishing, Perth, Scotland
9. Cummings M.P. Transmission patterns of eukaryotic transposable elements: arguments for and against horizontal transfer. Trends Ecol. Evol. 9 (1994) 141-145
10. Degnan J.H., and Salter L.A. Gene tree distributions under the coalescent process. Evolution 59 (2005) 24-37
11. Degnan J.H., and Rosenberg N.A. Discordance of species trees with their most likely gene trees. PLoS Genet. 3 (2006) e68
12. Edwards S.V., Liu L., and Pearl D.K. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 104 (2007) 5936-5941
13. Excoffier L., Novembre J., and Schneider S. SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J. Hered. 91 (2000) 506-509
14. Felsenstein J. Confidence limits on phylogenies. An approach using the bootstrap. Evolution 39 (1985) 783-789
15. Felsenstein J. Inferring Phylogenies (2004), Sinauer Associates, Sunderland, MA
16. Fitch W.M. Distinguishing homologous from analogous proteins. Syst. Zool. 19 (1970) 99-113
17. Goetsch L., Eckert A.J., and Hall B.D. The molecular systematics of Rhododendron (Ericaceae): a phylogeny based upon RPB2 gene sequences. Syst. Bot. 30 (2005) 616-626
18. Hickerson M.J., Stahl E., and Takebayashi N. MsBayes: a flexible pipeline for comparative phylogeographic inference using approximate Bayesian computation (ABC). BMC Bioinformatics 8 (2007) e268
19. Hey J. Recent advances in assessing gene flow between diverging populations and species. Curr. Opin. Genet. Dev. 16 (2006) 592-596
20. Hey J., and Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. Persimilis. Genetics 167 (2004) 747-760
21. Hey J., and Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104 (2007) 2785-2790
22. Hudson R.R. Testing the constant-rate neutral allele model with protein sequence data. Evolution 37 (1983) 203-217
23. Hudson R.R. Gene genealogies and the coalescent process. In: Futuyma D.J., and Antonovics J. (Eds). Oxford Survey Evolutionary Biology (1990), Oxford University Press, New York 1-44
24. Hudson R.R. Gene trees, species trees and the segregation of ancestral alleles. Genetics 131 (1992) 509-512
25. Kingman J.F.C. The coalescent. Stochastic Process. Appl. 13 (1982) 235-248
26. Knowles L.L., and Carstens B.C. Estimating a geographically explicit model of population divergence for statistical phylogeography. Evolution 61 (2007) 477-493
27. Knowles L.L., and Maddison W.P. Statistical phylogeography. Mol. Ecol. 11 (2002) 2623-2635
28. Kron K.A., Judd W.S., Stevens P.F., Crayn D.M., Anderberg A.A., Gadek P.A., Quinn C.J., and Luteyn J.L. Phylogenetic classification of Ericaceae: molecular and morphological evidence. Bot. Rev. 68 (2002) 335-423
29. Kubatko L.S., and Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56 (2007) 17-24
30. Kuhner M.K. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22 (2006) 768-770
31. Kuhner M.K., Yamato J., and Felsenstein J. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149 (1998) 429-434
32. Liu, L., Pearl, D. K. 2006. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Technical report #53. Ohio State University.
33. Liu L., and Pearl D.K. Species trees from gene trees: reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Bio. 56 (2007) 504-514
34. Maddison W.P. Gene trees in species trees. Syst. Biol. 46 (1997) 523-536
35. Maddison W.P., and Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55 (2006) 21-30
36. Maddison, W.P., Maddison, D.R., 2004. MESQUITE: a modular system for evolutionary analysis. Version 1.01. Available from: .
37. Minin V., Abdo Z., Joyce P., and Sullivan J. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol. 52 (2003) 674-683
38. Nielsen R. Molecular signatures of natural selection. Ann. Rev. Genet. 39 (2005) 197-218
39. Milne R.I. Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a tertiary relict distribution. Mol. Phylogenet. Evol. 33 (2004) 389-401
40. Nielsen R., and Wakeley J.W. Distinguishing Migration from Isolation: an MCMC approach. Genetics 158 (2001) 885-896
41. Page R.D.M., and Charleston M. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7 (1997) 231-240
42. Pamilo P., and Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 5 (1988) 568-583
43. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
44. Ree R.H., and Smith S.A. Maximum-likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Syst. Biol. 57 (2008) 4-414
45. Rosenberg N.A. The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61 (2002) 225-247
46. Rosenberg N.A. The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57 (2003) 1465-1477
47. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
48. Slatkin M., and Maddison W.P. A cladistic measure of gene flow inferred from phylogenies of alleles. Genetics 123 (1989) 603-613
49. Slowinski J.B., and Page R.D.M. How should species phylogenies be inferred from sequence data?. Syst. Biol. 48 (1999) 814-825
50. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (and other methods). Version 4 (2002), Sinauer Associates, Sunderland, Massachusetts
51. Syring J., Farrell K., Businsky R., Cronn R., and Liston A. Widespread genealogical nonmonophyly in species of the Pinus subgenus Strobus. Syst. Biol. 56 (2007) 163-181
52. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics 105 (1983) 437-460
53. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
54. Takahata N., and Nei M. Gene genealogy and variance of interpopulation nucleotide differences. Genetics 110 (1985) 325-344
55. Takahata N. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122 (1989) 957-966
56. Wall J.D. Estimating ancestral population size and divergence times. Genetics 163 (2003) 395-404
57. Yang Z. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162 (2002) 1811-1823