Phylogeny of lichen- and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets

Systematic Biology

Volumn 46, Issue 3, 1997, Pages 373-397

  Lutzoni, François M ^a,b  

^a DUKE UNIVERSITY   (United States)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Basidiomycetes; Data set combinability; Data set homogeneity; Fungi; Lichen symbiosis; Model system; Molecular phylogenies: Mutualism; Nuclear ribosomal DNA; Omphalina; Phylogenetic signal

Indexed keywords

ARRHENIA; BASIDIOMYCOTA; FUNGI; GERRONEMA; OMPHALINA;

FUNGAL DNA;

AGARICALES; ARTICLE; CLASSIFICATION; GENETICS; LICHENS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY; SYMBIOSIS;

AGARICALES; BASE SEQUENCE; DNA, FUNGAL; LICHENS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE HOMOLOGY, NUCLEIC ACID; SYMBIOSIS;

EID: 0031223089     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.2307/2413688     Document Type: Article

References (84)

1. AHMADJIAN, V., AND S. PARACER. 1986. Symbiosis: An introduction to biological associations. Univ. Press New England, Hanover, New Hampshire.
2. ALROY, J. 1994. Four permutation tests for the presence of phylogenetic structure. Syst. Biol. 43:430-437.
3. ARCHIE, J. W. 1989 A randomization test for phylogenetic information in systematic data. Syst. Zool. 38:253-269.
4. ARMALEO, D., AND P. CLERC. 1995. A rapid and inexpensive method for the purification of DNA from lichens and their symbionts. Lichenologist 27:207-213.
5. BIGELOW, H. E. 1974. The Clitocybe pyxidata group. Bull. Soc. Linn. Lyon 1974(n.s.):39-46.
6. BOUCHER, D. H. 1985. The idea of mutualism, past and future. Pages 1-28 in The biology of mutualism: Ecology and evolution (D. H. Boucher, ed.). Oxford Univ. Press, New York.
7. BRONSTEIN, J. L. 1991. Mutualism studies and the study of mutualism. Bull. Ecol. Soc. Am. 72:6-8.
8. BULL, J. J., J. P. HUELSENBECK, C. W. CUNNINGHAM, D. L. SWOFFORD, AND P. J. WADDELL. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384-397.
9. CLÉMENCON, H. 1982. Kompendium der Blätterpilze Europäische omphalinoide Tricholomataceae. Z. Mykol. 48:195-239.
10. COOKE, R. 1977. The biology of symbiotic fungi. Wiley and Sons, New York.
11. CUMMINGS, M. P., S. P. OTTO, AND J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
12. CUNNINGHAM, C. W. 1997. Can three inference tests predict when data should be combined? Mol. Biol. Evol. 14:733-740.
13. DE QUEIROZ, A., M. J. DONOGHUE, AND J. KIM. 1995. Separate versus combined analysis of phylogenetic evidence. Annu. Rev. Ecol. Syst. 26:657-681.
14. DEVEREUX, J., P. HAEBERLI, AND O. SMITHIES. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
15. FAITH, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Syst. Zool. 40:366-375.
16. FAITH, D. P., AND P. S. CRANSTON. 1991. Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure. Cladistics 7:1-28.
17. FELSENSTEIN, J. 1981a. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
18. FELSENSTEIN, J. 1981b. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol. J. Linn. Soc. 16:183-196.
19. FELSENSTEIN, J. 1985. Confidence intervals on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
20. FELSENSTEIN, J. 1993. PHYLIP: Phylogeny inference package, version 3.53c. Department of Genetics, Univ. Washington, Seattle.
21. GATESY, J., R. DESALLE, AND W. WHEELER. 1993. Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol. Phylogenet. Evol. 2: 152-157.
22. GUADET, J., J. JULIEN, J. F. LAFAY, AND Y. BRYGOO. 1989. Phylogeny of some Fusarium species, as determined by large subunit rRNA sequence comparison. Mol. Biol. Evol. 6:227-242.
23. GULDEN, G., AND K. M. JENSSEN. 1988. Arctic and alpine fungi - 2. Soppkonsulenten, Oslo.
24. GULDEN, G., K. M. JENSSEN, AND J. STORDAL. 1985. Arctic and alpine fungi - 1. Soppkonsulenten, Oslo.
25. HAMMERSTEIN, P., AND R. F. HOEKSTRA. 1995. Mutualism on the move. Nature 376:121-122.
26. HIBBETT, D. S., AND R. VILGALYS. 1993. Phylogenetic relationships of Lentinus (Basidiomycotina) inferred from molecular and morphological characters. Syst. Bot. 18:409-433.
27. HIGGINS, D. G., AND P. M. SHARP. 1988. CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244.
28. HILLIS, D. M. 1995. Approaches for assessing phylogenetic accuracy. Syst. Biol. 44:3-16.
29. HILLIS, D. M., AND J. P. HUELSENBECK. 1992. Signal, noise, and reliability in molecular phylogenetic analyses. J. Hered. 83:189-195.
30. HOPPLE, J. S., AND R. VILGALYS. 1994. Phylogenetic relationships among coprinoid taxa and allies based on data from restriction site mapping of nuclear rDNA. Mycologia 86:96-107.
31. HUELSENBECK, J. P., J. J. BULL, AND C. W. CUNNING-HAM. 1996. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11:152-157.
32. JANSEN, D. H. 1985. The natural history of mutualisms. Pages 40-99 in The biology of mutualism: Ecology and evolution (D. H. Boucher, ed.). Oxford Univ. Press, New York.
33. JØRGENSEN, P. M., AND S. RYMAN. 1989a. The correct names of the lichenized Omphalina species in Scandinavia. Graphis Scripta 3:138-143.
34. JØRGENSEN, P. M., AND S. RYMAN. 1989b. Proposal to conserve Omphalina Quélet over Phytoconis Bory and Botrydina Brébisson (Basidiomycetes). Taxon 38:305-308.
35. KÄLLERSJÖ, M., J. S. FARRIS, A. G. KLUGE, AND C. BULT. 1992. Skewness and permutation. Cladistics 8:275-287.
36. KISHINO, H., AND M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29: 170-179.
37. KLUGE, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.
38. KUHNER, M. K., AND J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
39. KÜHNER, R. 1980. Les Hyménomycètes agaricoïdes. Bull. Soc. Linn. Lyon 49:1-1027.
40. KUMAR, S., K. TAMURA, AND M. NEI. 1993. MEGA: Molecular evolutionary genetics analysis, version 1.01. Pennsylvania State Univ., University Park.
41. KUYPER, T. W. 1986. Generic delimitation in European omphalinoid Tricholomataceae. Atti Cent. Stud. Flora Mediterr. 6:83-104.
42. LAKE, J. A. 1991. The order of sequence alignment can bias the selection of tree topology. Mol. Biol. Evol. 8:378-385.
43. LAMOURE, D. 1979. Caractères morphologiques, caryologiques et culturaux des mycéliums de trois espèces de Rickenella (Agaricales). Ann. Mycol. II 8: 251-254.
44. LANGE, M. 1981. Typification and delimitation of Omphalina Quél. Nord. J. Bot. 1:691-696.
45. LAW, R., AND D. H. LEWIS. 1983. Biotic environments and the maintenance of sex - Some evidence from mutualistic symbioses. Biol. J. Linn. Soc. 20:249-276.
46. LEWIS, D. H. 1985. Symbiosis and mutualism: Crisp concepts and soggy semantics. Pages 29-39 in The biology of mutualism: Ecology and evolution (D. H. Boucher, ed.). Oxford Univ. Press, New York.
47. LUTZONI, F., AND M. PAGEL. 1997. Accelerated evolution as a consequence of transitions to mutualism. Proc. Natl. Acad. Sci. USA. 94 (in press).
48. LUTZONI, F., AND R. VILGALYS. 1995a. Integration of morphological and molecular data sets in estimating fungal phytogenies. Can. J. Bot. 73(suppl. 1): S649-S659.
49. LUTZONI, F., AND R. VILGALYS. 1995b. Omphalina (Basidiomycota, Agaricales) as a model system for the study of coevolution in lichens. Cryptogam. Bot. 5: 71-81.
50. MADDISON, W. P., AND D. R. MADDISON. 1992. MacClade: Analysis of phylogeny and character evolution, version 3.0. Sinauer, Sunderland, Massachusetts.
51. MALLOCH, D. W., K. A. PIROZYNSKI, AND P. H. RAVEN. 1980. Ecological and evolutionary significance of mycorrhizal symbioses in vascular plants (a review). Proc. Natl. Acad. Sci. USA 77:2113-2118.
52. MARGULIS, L., AND R. FESTER. 1991. Symbiosis as a source of evolutionary innovation: Speciation and morphogenesis. MIT Press, Cambridge, Massachusetts.
53. MONCALVO, J. M., S. A. REHNER, AND R. VILGALYS. 1993. Systematics of Lyophyllum section Difformia based on evidence from culture studies and ribosomal DNA sequences. Mycologia 85:788-794.
54. MORITZ, C., C. J. SCHNEIDER, AND D. B. WAKE. 1992. Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Syst. Biol. 41:273-291.
55. MOSER, M. 1983. Keys to agarics and boleti (Polyporales, Boletales, Agaricales, Russulales). Roger Phillips.
56. NORVELL, L. L., S. A. REDHEAD, AND J. F. AMMIRATI. 1994. Omphalina sensu lato in North America. 1. Omphalina wynniae and the genus Chrysomphalina. 2. Omphalina sensu Bigelow. Mycotaxon 50:379-407.
57. OLSEN, G. J., H. MATSUDA, R. HAGSTROM, AND R. OvERBEEK. 1994. FastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10:41-48.
58. PENNY, D., AND M. D. HENDY. 1985. The use of tree comparison metrics. Syst. Zool. 34:75-82.
59. PIROZYNSKI, K. A., AND D. L. HAWKSWORTH. 1988. Coevolution of fungi with plants and animals: Introduction and overview. Pages 1-30 in Coevolution of fungi with plants and animals (K. A. Pirozynski and D. L. Hawksworth, eds.). Academic Press, New York.
60. PIROZYNSKI, K. A., AND D. W. MALLOCH. 1975. The origin of land plants: A matter of mycotrophism. BioSystems 6:153-164.
61. PRYER, K. M., A. R. SMITH, AND J. E. SKOG. 1995. Phylogenetic relationships of extant ferns based on evidence from morphology and rbcL sequences. Am. Fern J. 85:205-282.
62. QUÉLET, L. 1886. Enchiridion fungorum in Europa media. Paris.
63. RAITHELHUBER, J. 1973. Zur Abgrenzung der Gattung Gerronema, Omphalia, Ciitocybe und Haasiella. Metrodiana 4:61-72.
64. REDHEAD, S. A. 1984. Arrhenia and Rimbachia, expanded generic concepts, and a reevaluation of Leptoglossum with emphasis on muscicolous North American taxa. Can. J. Bot. 62:865-892.
65. REDHEAD, S. A. 1986. Mycological observations: 17-20. Nomenclatural notes on some omphalioid genera in Canada: Chrysomphalina, Rickenella, Gerronema, Omphalina. Acta Mycol. Sinica Suppl. 1:297-304.
66. REDHEAD, S. A. 1989. A biogeographical overview of the Canadian mushroom flora. Can. J. Bot. 67:3003-3062.
67. REDHEAD, S. A., AND T. W. KUYPER. 1987. Lichenized agarics: Taxonomic and nomenclatural riddles. Pages 319-348 in Arctic and alpine mycology II (G. A. Laursen, J. F. Ammirati, and S. A. Redhead, eds.). Plenum, New York.
68. REDHEAD, S. A., AND T. W. KUYPER. 1988. Phytoconis, the correct generic name for the basidiolichen Botrydina. Mycotaxon 31:221-223.
69. REDHEAD, S. A., AND L. K. WERESUB. 1978. On Omphalia and Omphalina. Mycologia 70:556-568.
70. REHNER, S. A., AND G. J. SAMUELS. 1994. Taxonomy and phytogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycol. Res. 98:625-634.
71. RISCH, S., AND D. BOUCHER. 1978. What ecologists look for. Bull. Ecol. Soc. Am. 57:8-9.
72. RODRIGO, A. G., M. KELLY-BORGES, P. R. BERGQUIST, AND P. L. BERGQUIST. 1993. A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. N.Z. J. Bot. 31:257-268.
73. SIMON, L., J. BOUSQUET, R. C. LÉVESQUE, AND M. LALONDE. 1993. Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants. Nature 363:67-69.
74. SINGER, R. 1962. The Agaricales in modern taxonomy, 2nd edition. J. Cramer, Weinheim, Germany.
75. SINGER, R. 1964. Die Gattung Gerronema. Nova Hedwigia 7:53-92.
76. SINGER, R. 1975. The Agaricales in modern taxonomy, 3rd edition. J. Cramer, Vaduz, Liechtenstein.
77. SINGER, R. 1986. The Agaricales in modern taxonomy, 4th edition. Koeltz Scientific Books, Koenigstein, Germany.
78. SWOFFORD, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? Pages 295-333 in Phylogenetic analysis of DNA sequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford Univ. Press, New York.
79. SWOFFORD, D. L. 1993. PAUP: Phylogenetic analysis using parsimony, version 3.1.1. Smithsonian Institution, Washington, D.C.
80. TEMPLETON, A. R., AND L. E. GILBERT. 1985. Population genetics and the coevolution of mutualism. Pages 128-144 in The biology of mutualism: Ecology and evolution (D. H. Boucher, ed.). Oxford Univ. Press, New York.
81. VILGALYS, R., AND M. HESTER. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172:4238-4246.
82. VILGALYS, R., AND B. L. SUN. 1994. Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences. Proc. Natl. Acad. Sci. USA 91:4599-4603.
83. WHEELER, W. C. 1990. Combinatorial weights in phylogenetic analyis: A statistical parsimony procedure. Cladistics 6:269-275.
84. WHITE, T. J., T. BRUNS, S. LEE, AND J. W. TAYLOR. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Pages 315-322 in PCR protocols: A guide to methods and applications (J. J. Gelfand, J. J. Sninsky, and T. J. White, eds.). Academic Press, New York.