A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora

Evolution

Volumn 57, Issue 12, 2003, Pages 2703-2720

  Dettman, Jeremy R ^a   Jacobson, David J ^a   Taylor, John W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Biological species; Genealogical concordance; Hybridization; Lineage sorting; Phylogenetic species; Species concepts; Species recognition

Indexed keywords

FUNGUS; GENEALOGY; PHYLOGENETICS; REPRODUCTION; SPECIES CONCEPT;

EUKARYOTA; FUNGI; NEUROSPORA; NEUROSPORA CRASSA; NEUROSPORA INTERMEDIA;

EID: 0344863884     PISSN: 00143820     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.0014-3820.2003.tb01514.x     Document Type: Article

References (67)

1. Aanen, D. K., T. W. Kuyper, T. H. M. Mes, and R. F. Hoekstra. 2000. The evolution of reproductive isolation in the ectomycorrhizal Hebeloma crustuliniforme aggregate (Basidiomycetes) in northwestern Europe: a phylogenetic approach. Evolution 54: 1192-1206.
2. Alfaro, M. E., S. Zoller, and F. Lutzoni. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20:255-266.
3. Avise, J. C., and R. M. Ball. 1990. Principles of genealogical concordance in species concepts and biological taxonomy. Pp. 45-67 in D. Futuyma and J. Antonovics, eds. Oxford surveys in evolutionary biology. Oxford Univ. Press, Oxford, U.K.
4. Avise, J. C., and K. Wollenberg. 1997. Phylogenetics and the origin of species. Proc. Natl. Acad. Sci. USA 94:7748-7755.
5. Baum, D. A., and K. L. Shaw. 1995. Genealogical perspectives on the species problem. Pp. 289-303 in P. C. Hoch and A. G. Stephenson, eds. Experimental and molecular approaches to plant biosystematics. Missouri Botanical Garden, St. Louis, MO.
6. Bean, L. E., W. H. Dvorachek, E. L. Braun, A. Errett, G. S. Saenz, M. D. Giles, M. Werner-Washburne, M. A. Nelson, and D. O. Natvig. 2001. Analysis of the pdx-1 (snz-1/sno-1) region of the Neurospora crassa genome: correlation of pyridoxine-requiring phenotypes with mutations in two structural genes. Genetics 157: 1067-1075.
7. Bremer, K. 1990. Combinable component consensus. Cladistics 6: 369-378.
8. Carbone, I., J. B. Anderson, and L. M. Kohn. 1999. Patterns of descent in clonal lineages and their multilocus fingerprints are resolved with combined gene genealogies. Evolution 53:11-21.
9. Cruse, M., R. Telerant, T. Gallagher, T. Lee, and J. W. Taylor. 2002. Cryptic species in Stachybotrys chartarum. Mycologia 94: 814-822.
10. Cunningham, C. 1997. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol. 14:733-740.
11. Darlu, P., and G. Lecointre. 2002. When does the incongruence length difference test fail? Mol. Biol. Evol. 19:432-437.
12. Davis, R. H. 2000. Neurospora: contributions of a model organism. Oxford Univ. Press, New York.
13. Davis, R. H., and D. D. Perkins. 2002. Neurospora: a model of model microbes. Nat. Rev. Genet. 3:7-13.
14. de Queiroz, K. 1998. The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. Pp. 57-75 in D. J. Howard and S. H. Berlocher, eds. Endless forms: species and speciation. Oxford Univ. Press, Oxford, U.K.
15. Dettman, J. R., F. M. Harbinski, and J. W. Taylor. 2001. Ascospore morphology is a poor predictor of the phylogenetic relationships of Neurospora and Gelasinospora. Fungal Genet. Biol. 34:49-61.
16. Dettman, J. R., D. J. Jacobson, E. Turner, A. Pringle, and J. W. Taylor. 2003. Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryote. Evolution 57:2721-2741.
17. Donoghue, M. J. 1985. A critique of the biological species concept and recommendations for a phylogenetic alternative. Bryologist 88:172-181.
18. Farris, J. S., M. Kallersjo, A. G. Kluge, and C. Bult. 1995. Testing significance of incongruence. Cladistics 10:315-319.
19. Galagan, J., and 76 others. 2003. The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-868.
20. Geiser, D. M., J. I. Pitt, and J. W. Taylor. 1998. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc. Natl. Acad. Sci. USA 95:388-393.
21. Gleason, J. M., E. C. Griffith, and J. R. Powell. 1998. A molecular phylogeny of the Drosophila willistoni group: Conflicts between species concepts? Evolution 52:1093-1103.
22. Hare, M. P., and J. C. Avise. 1998. Population structure in the American oyster as inferred by nuclear gene genealogies. Mol. Biol. Evol. 15:119-128.
23. Hare, M. P., F. Cipriano, and S. R. Palumbi. 2002. Genetic evidence on the demography of speciation in allopatric dolphin species. Evolution 56:804-816.
24. Hillis, D. M., and J. J. Bull. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
25. Hilton, H., and J. Hey. 1997. A multilocus view of speciation in the Drosophila virilis species group reveals complex histories and taxonomic conflicts. Genet. Res. 70:185-194.
26. Hudson, R. R., and J. A. Coyne. 2002. Mathematical consequences of the genealogical species concept. Evolution 56:1557-1565.
27. Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
28. Jacobson, D. J., A. J. Powell, J. R. Dettman, G. S. Saenz, M. M. Barton, M. D. Hiltz, W. H. Dvorachek, N. L. Glass, J. W. Taylor, and D. O. Natvig. 2004. Neurospora in temperate forests of western North America. Mycologia 96:66-74.
29. Kasuga, T., J. W. Taylor, and T. J. White. 1999. Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulation Darling. J. Clin. Microbiol. 37:653-663.
30. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
31. Kliman, R. M., P. Andolfatto, J. A. Coyne, F. Depaulis, M. Kreitman, A. J. Berry, J. McCarter, J. Wakeley, and J. Hey. 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156:1913-1931.
32. Koufopanou, V., A. Burt, and J. W. Taylor. 1997. Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc. Natl. Acad. Sci. USA 94: 5478-5482.
33. Kroken, S., and J. W. Taylor. 2001. A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93:38-53.
34. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
35. Larget, B., and D. L. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
36. Mayden, R. L. 1997. A hierarchy of species concepts: the denouement in the saga of the species problem. Pp. 381-424 in M. F. Claridge, H. A. Dawah, and M. R. Wilson, eds. Species: the units of biodiversity. Chapman and Hall, London.
37. Natvig, D. O., and G. May. 1996. Fungal evolution and speciation. J. Genet. 75:441-452.
38. Natvig, D. O., D. A. Jackson, and J. W. Taylor. 1987. Random-fragment hybridization analysis of evolution in the genus Neurospora: the status of four-spored strains. Evolution 41: 1003-1021.
39. O'Donnell, K., H. C. Kistler, B. K. Tacke, and H. H. Casper. 2000a. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. Proc. Natl. Acad. Sci. USA 97:7905-7910.
40. O'Donnell, K., H. I. Nirenberg, T. Aoki, and E. Cigelnik. 2000b. A multigene phylogeny of the Gibberella fujikuroi species complex: detection of additional phylogenetically distinct species. Mycoscience 41:61-78.
41. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
42. Perkins, D. D., and B. C. Turner. 1988. Neurospora from natural populations: toward the population biology of a haploid eukaryote. Exp. Mycol. 12:91-131.
43. Perkins, D. D., B. C. Turner, and E. G. Barry. 1976. Strains of Neurospora collected from nature. Evolution 30:281-313.
44. Piercey-Normore, M. D., K. N. Egger, and J. A. Berube. 1998. Molecular phylogeny and evolutionary divergence of North American biological species of Armillaria. Mol. Phylogenet. Evol. 10:49-66.
45. Pöggeler, S. 1999. Phylogenetic relationships between mating-type sequences from homothallic and heterothallic ascomycetes. Curr. Genet. 36:222-231.
46. Posada, D., and K. A. Crandall. 1998. ModelTest: testing the model of DNA substitution. Bioinformatics 14:817-818.
47. Randall, T. A., and R. L. Metzenberg. 1995. Species-specific and mating type-specific DNA regions adjacent to mating type idiomorphs in the genus Neurospora. Genetics 141:119-136.
48. Rannala, B., and Z. Yang. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
49. Rosenberg, N. A. 2002. The probability of topological concordance of gene trees and species trees. Theor. Popul. Biol. 61:225-247.
50. _. 2003. The shapes of neutral gene genealogies in two species: probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57:1465-1477.
51. Schulte, U., I. Becker, H. W. Mewes, and G. Mannhaupt. 2002. Large scale analysis of sequences from Neurospora crassa. J. Biotech. 94:3-13.
52. Shew, H. W. 1978. New mutants and wild-type standard reference strains of Neurospora intermedia. Neurospora Newsl. 25:25.
53. Simpson, G. G. 1951. The species concept. Evolution 5:285-298.
54. Skupski, M. P., D. A. Jackson, and D. O. Natvig. 1997. Phylogenetic analysis of heterothallic Neurospora species. Fungal Genet. Biol. 21:153-162.
55. Swofford, D. L. 2001. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer, Sunderland, MA.
56. Tajima, F. 1983. Evolutionary relationships of DNA sequences in finite populations. Genetics 105:437-460.
57. Takahata, N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122:957-966.
58. Taylor, J. W., and D. O. Natvig. 1989. Mitochondrial DNA and evolution of heterothallic and pseudohomothallic Neurospora species. Mycol. Res. 93:257-272.
59. Taylor, J. W., D. J. Jacobson, S. Kroken, T. Kasuga, D. M. Geiser, D. S. Hibbett, and M. C. Fisher. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol. 31:21-32.
60. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
61. Turner, B. C. 1987. Two ecotypes of Neurospora intermedia. My-cologia 79:425-432.
62. Turner, B. C., D. D. Perkins, and A. Fairfield. 2001. Neurospora from natural populations: a global study. Fungal Genet. Biol. 32:67-92.
63. Tuveson, R. W., and J. F. Peterson. 1972. Virus-like particles in certain slow-growing strains of N. crassa. Virology 47:527-531.
64. Vogel, H. J. 1964. Distribution of lysine pathways among fungi: evolutionary implications. Am. Nat. 98:435-466.
65. Wilcox, T. P., D. J. Zwickl, T. A. Heath, and D. M. Hullis. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25:361-371.
66. Wiley, E. O. 1978. The evolutionary species concept reconsidered. Syst. Zool. 27:17-26.
67. Xu, J. P., R. Vilgalys, and T. G. Mitchell. 2000. Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungus Cryptococcus neoformans. Mol. Ecol. 9:1471-1481.