Reconciliation of conflicting phenotypic and rRNA gene phylogenies of fungi in glomeromycota based on underlying patterns and processes

Mycorrhizas - Functional Processes and Ecological Impact

Volumn , Issue , 2009, Pages 137-154

  Morton, Joseph B ^a  

^a WEST VIRGINIA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77956922201     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-540-87978-7_10     Document Type: Chapter

References (61)

1. Clapp JP, Rodriguez A, Dodd JC (2001) Inter- and intra-isolate rRNA large subunit variation in Glomus coronatum spores. New Phytol 149:539-554
2. Corradi N, Sanders IR (2006) Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices. BMC Evol Biol 6:21
3. Corradi N, Hijri M, Fumagalli L, Sanders IR (2004) Arbuscular mycorrhizal fungi (Glomeromycota) harbour ancient fungal tubulin genes that resemble those of the chytrids (Chytridiomycota). Fungal Genet Biol 41:1037-1045
4. de la Providencia IEF, de Souza D, Fernandez F, Séjalon-Delmas N, Declerck S (2005) Arbuscular mycorrhizal fungi reveal distinct patterns of anastomosis formation and hyphal healing mechanisms between different phylogenetic groups. New Phytol 165:261-271
5. de Queiroz A, Donoghue MJ, Kim J (1996) Separate versus combined analysis of phylogenetic evidence. Annu Rev Ecol Syst 26:657-681
6. de Silva GA, Lumini E, Maia LC, Bonfante P, Bianciotto V (2006) Phylogenetic analysis of Glomeromycota by partial LSU rDNA sequences. Mycorrhiza 16:183-189
7. Doyle JJ (1992) Gene trees and species trees: molecular systematics as one-character taxonomy. Syst Bot 17:144-163
8. Doyle JJ (1997) Trees within trees: genes and species, molecules and morphology. Syst Biol 46:537-553
9. Eickbush TH, Eickbush DG (2007) Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175:477-485
10. Gandolfi A, Sanders IR, Rossi V, Menozzi P (2003) Evidence of recombination in putative ancient asexuals. Mol Biol Evol 20:754-761
11. Gianinazzi-Pearson V, Lemaine MC, Arnould C, Gollotte A, Morton JB (1994) Localization of β (1-3)-Glucans in spore and hyphal walls of fungi in the Glomales. Mycologia 86:478-485
12. Giovannetti M, Azzolini D, Citernesi AS (1999) Anastomosis formation and nuclear and protoplasmic exchange in arbuscular mycorrhizal fungi. Appl Environ Microbiol 65:5571-5575
13. Giovannetti M, Sbrana E, Strani P, Agnolucci M, Rinaudo V, Avio L (2003) Genetic diversity of isolates of Glomus mosseae from different geographic areas detected by vegetative compatibility testing and biochemical and molecular analysis. Appl Environ Microbiol 69:616-624
14. Hart MM, Reader RJ (2002) Taxonomic basis for variation in the colonization strategy of arbuscular mycorrhizal fungi. New Phytol 153:335-344
15. Helgason T, Watson IJ, Young PW (2003) Phylogeny of the Glomerales and Diversisporales (Fungi: Glomeromycota) from actin and elongation factor 1-alpha sequences. FEMS Microbiol Lett 229:127-132
16. Hijri M, Sanders IR (2005) Low gene copy number shows that arbuscular mycorrhizal fungi inherit genetically different nuclei. Nature 433:160-163
17. Hosny M, Gianinazzi-Pearson V, Dulieu H (1998) Nuclear DNA content of 11 fungal species in Glomales. Genome 41:422-428
18. James TY, Kauff F, Schoch CL et al. (2006) Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443:818-822
19. Klironomos JN, Hart MM (2002) Colonization of roots by arbuscular mycorrhizal fungi using different sources of inoculum. Mycorrhiza 12:181-184
20. Kuhn G, Hijri M, Sanders IR (2001) Evidence for the evolution of multiple genomes in arbuscular mycorrhizal fungi. Nature 414:745-748
21. Lanyon SM (1988) The stochastic mode of molecular evolution: what consequences for systematic investigations. Auk 105:565-573
22. Liao D (1999) Concerted evolution: molecular mechanism and biological implications. Am J Hum Genet 64:24-30
23. Long EO, IB Dawid (1980) Repeated genes in eukaryotes. Annu Rev Biochem 49:727-764
24. Lutzoni F, Kauff F, Cox CJ, McLaughlin D et al. (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot 91:1446-1480
25. Lyons-Weiler J, Milinkovitch MC (1997) A phylogenetic approach to the problem of differential lineage sorting. Mol Biol Evol 14:968-975
26. Maddison WP (1997) Gene trees in species trees. Syst Biol 46:523-536
27. Merryweather J, Fitter AH (1998) The arbuscular mycorrhizal fungi of Hyacinthoides non-scripta I. Diversity of fungal taxa. New Phytol 138:117-129
28. Morton JB (1990a) Species and clones of arbuscular mycorrhizal fungi (Glomales, Zygomycetes): Their role in macro- and microevolutionary processes. Mycotaxon 37:493-515
29. Morton JB (1990b) Evolutionary relationships among arbuscular mycorrhizal fungi in the Endogonaceae. Mycologia 82:192-207
30. Morton JB, Benny GL (1990) Revised classificationofarbuscularmycorrhizal fungi (Zygomycetes): a new order, Glomales, two new suborders, Glomineae and Gigasporineae, and two new families, Acaulosporaceae and Gigasporaceae, with an emendation of Glomaceae. Mycotaxon 37:471-491
31. Morton JB, Redecker D (2001) Two new families of Glomales, Archaeosporaceae and Paraglomaceae, with two new genera Archaeospora and Paraglomus, based on concordant molecular and morphological characters. Mycologia 93:181-195
32. Morton J, Franke M, Bentivenga S (1994) Developmental foundations for morphological diversity among endomycorrhizal fungi in Glomales (Zygomycetes). In: Varma A, Hock B (eds) Mycorrhiza: structure, function, molecular biology, and biotechnology. Springer, Berlin, pp 669-683
33. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
34. Oehl F, Sieverding E (2005) Pacispora, a new vesicular arbuscular mycorrhizal fungal genus in the Glomeromycetes. J Appl Bot 78:72-82
35. Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5:568-583
36. Patterson C (1982) Morphological characters and homology. In: Joysey KA, Friday AE (eds) Problems of phylogenetic reconstruction. Academic, New York, pp 21-74
37. Patterson C, Williams DM, Humphries CJ (1993) Congruence between molecular and morphological phylogenies. Annu Rev Ecol Syst 24:153-188
38. Pawlowska T (2005) Genetic processes in arbuscular mycorrhizal fungi. FEMS Microbiol Lett 251:185-192
39. Pawlowska TE, Taylor JW (2004) Organization of genetic variation in individuals of arbuscular mycorrhizal fungi. Nature 427:733-737
40. Redecker D, Raab P (2006) Phylogeny of the Glomeromycota (arbuscular mycorrhizal fungi): Recent developments and new gene markers. Mycologia 98:885-895
41. Redecker D, Kodner R, Graham LE (2000) Glomalean fungi from the Ordovician. Science 289:1920-1921
42. Rodriguez A, Clapp JP, Robinson L, Dodd JC (2004) Ribosomal RNA gene sequence diversity in arbuscular mycorrhizal fungi (Glomeromycota). J Ecol 92:986-989
43. Rodriguez A, Clapp JP, Robinson L, Dodd JC (2005) Studies on the diversity of the distinct phylogenetic lineage encompassing Glomus claroideum and Glomus etunicatum. Mycorrhiza 15:33-46
44. Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
45. Rooney AP, Ward TJ (2005) Evolution of a large ribosomal RNA multigene family in filamentous fungi: birth and death of a concerted evolution paradigm. Proc Natl Acad Sci USA 102:5084-5089
46. Sanderson MJ, Donoghue MJ (1989) Patterns of variation in levels of homoplasy. Evolution 43:1781-1795
47. Schlichting CD, Pigliucci M (1998) Phenotypic evolution: a reaction norm perspective. Sinauer Associates, Inc., Sunderland, MA
48. Schüßler A, Kluge M (2001) Geosiphon pyriforme, an endosymbiosis between fungus and cyanobacteria, and its meaning as a model system for arbuscular mycorrhizal research. In: Hock B (ed) The Mycota IX: fungal associations. Springer, London/Berlin, pp. 151-161
49. Schüßler A, Gehrig H, Schwartzott D, Walker C (2001a) A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol Res 105:1413-1421
50. Schüßler A, Gehrig H, Schwartzott D, Walker C (2001b) Analysis of partial Glomales SSU rRNA gene sequences: implications for primer design and phylogeny. Mycol Res 105:5-15
51. Schwartzott D, Walker C, Schüßler A (2001) Glomus, the largest genus of the arbuscular mycorrhizal fungi (Glomales) is nonmonophyletic. Mol Syst Evol 21:190-107
52. Smith SE, Read DJ (1997) Mycorrhizal symbiosis, 2nd edition. Academic, London UK
53. Spain JL, Sieverding E, Oehl F (2006) Appendicispora: a new genus in the arbuscular mycorrhizaforming Glomeromycetes, with a discussion of the genus Archaeospora. Mycotaxon 97:163-182
54. Stukenbrock EH, Rosendahl S (2005) Clonal diversity and population genetic structure of arbuscular mycorrhizal fungi (Glomus spp.) studied by multilocus genotyping of single spores. Mol Ecol 14:743-752
55. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fishe MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21-32
56. Trappe JM (1987) Phylogenetic and ecological aspects of mycotrophy in the angiosperms from an evolutionary standpoint. In: Safir GR (ed) Ecophysiology of VA mycorrhizal plants. CRC Press, Boca Raton, FL, pp. 5-25
57. Trouvelot S, van Tuinen D, Hijri M, Gianinazzi-Pearson V (1999) Visualization of ribosomal DNA loci in spore interphasic nuclei of glomalean fungi by fluorescence in situ hydridization. Mycorrhiza 8:203-206
58. Voegele RT, Mendgen K (2003) Rust haustoria: nutrient uptake and beyond. New Phytol 159:93-100
59. Walker C, Schüßler A (2004) Nomenclatural clarifications and new taxa in the Glomeromycota. Mycol Res 108:981-982
60. Walker C, Vestberg M, Demircik F, Stockinger H, Saito M, Sawaki H, Nishmura I, Schüßler A (2007) Molecular phylogeny and new taxa in the Archaeosporales (Glomeromycota): Ambispora fennica gen. sp. nov., Ambisporaceae fam. nov., and emendation of Archaeospora and Archaeosporaceae. Mycol Res 111:137-153
61. Wheeler WC, Honeycutt RL (1988) Paired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implications. Mol Biol Evol 5:90-96