Chapter 4 : Phylogenetics and Phylogenomics of the Fungal Tree of Life

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Phylogenetic trees, once restricted to studies on systematics, are now used throughout all disciplines of fungal biology and provide the evolutionary context for a broad suite of studies that include understanding the evolution of major life forms, description of complex biotic communities, and predictive experimental biology. This is especially true in the genomic era, where a rapid convergence of phylogenetics and genomics is occurring and is resulting in the emerging field of phylogenomics. This chapter provides a review of (i) the current status of fungal phylogenetics based on multigene phylogenies, (ii) current evolutionary hypotheses on the evolutionary relationships of organisms that are classified in the Kingdom Fungi, and (iii) the use of genome-scale sampling to infer evolutionary relationships of the fungi. The goal of the Deep Hypha Research Coordination Network was to accelerate the collection of multigene sequence data across the Fungal Tree of Life. By the Fungal Tree of Life, we explicitly refer to the monophyletic Kingdom Fungi (Fungi) and all of its subgroups. One of the more elusive areas of research in fungal phylogenetics has been the calibration of the Fungal Tree of Life to geologic time. Here we focus on the use of genome-scale data sets in phylogenetic analyses. Multigene analyses have had a major impact on phylogenetic studies of the Fungi, resulting in our most thorough understanding of evolutionary relationships of the Kingdom to date.

Citation: Spatafora J, Robbertse B. 2010. Phylogenetics and Phylogenomics of the Fungal Tree of Life, p 36-49. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch4

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RNA Polymerase II
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Image of FIGURE 1

Fungal Tree of Life. Phylogenetic tree depicting the major phyla and subphyla of the Kingdom Fungi. Hypotheses for major morphological transitions are depicted along the backbone of the tree. Lineages of zoosporic and zygosporangium-producing fungi are shown along the right of the tree with the symbols of stylized zoospores and zygosporangia, respectively. Dashed lines represent early-diverging lineages of uncertain placement (e.g., and Microsporidia) or internal nodes that are resolved in cited studies but with <70% bootstrap values (e.g., Blastocladiomycota and Glomeromycota). Phylogenetic relationships are based on , and .

Citation: Spatafora J, Robbertse B. 2010. Phylogenetics and Phylogenomics of the Fungal Tree of Life, p 36-49. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch4
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Image of FIGURE 2

Phylogeny and classification of Fungi: Basidiomycota. Dashed lines indicate taxa that are of uncertain placement. Reproduced with permission from .

Citation: Spatafora J, Robbertse B. 2010. Phylogenetics and Phylogenomics of the Fungal Tree of Life, p 36-49. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch4
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Image of FIGURE 3

Phylogeny and classification of Fungi: Ascomycota. Dashed lines indicate taxa that are of uncertain placement. Reproduced with permission from .

Citation: Spatafora J, Robbertse B. 2010. Phylogenetics and Phylogenomics of the Fungal Tree of Life, p 36-49. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch4
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Image of FIGURE 4

Different calibration points change estimated divergence dates. Ascomycota split from Basidiomycota after the origin of two phyla not shown, the Chytridiomycota and Glomeromycota. In the top diagram we assumed that the 400 million-year-old fossil represents Sordariomycetes as indicated by the letter “S.” This pushes the minimum age for the origin of the stem lineages of all five fungal phyla, including the Glomeromycota, to 1,489 million years ago, more than three times the age of the first fossil evidence of land plants. In the middle diagram we assumed that represents Pezizomycotina but not necessarily Sordariomycetes. Applying calibrations from plant and animal fossils in addition to assuming that represents Pezizomycotina gave an estimate of 792 million years ago for the origin of the fungal phyla, still almost twice the age of the first fossil evidence for vascular plants. In the bottom diagram, assuming that provided a minimum age for the Ascomycota, indicated by the letter “A,” at 400 million years resulted in the estimate that fungal phyla had been established by 452 million years ago, roughly the age of the first land plants. In this scenario, however, the ages for the divergences among vertebrates are far too recent given fossil data. This discrepancy might result from using fossils from one kingdom (Fungi) to calibrate events in the same kingdom and another kingdom (Animalia), as discussed in the text. Reproduced with permission from .

Citation: Spatafora J, Robbertse B. 2010. Phylogenetics and Phylogenomics of the Fungal Tree of Life, p 36-49. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch4
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Image of FIGURE 5

Maximum likelihood phylogeny reconstructed using a concatenated alignment of 153 universally distributed fungal genes. The concatenated alignment contains 42 taxa and exactly 38,000 amino acid positions. The optimum model according to ModelGenerator ( ) was found to be WAG+I+G. The number of rate categories was 4 (alpha 5 0.83), and the proportion of invariable sites was approximated at 0.20. Bootstrap scores for all nodes are displayed. is found at the base of the WGD node. Reproduced with permission from .

Citation: Spatafora J, Robbertse B. 2010. Phylogenetics and Phylogenomics of the Fungal Tree of Life, p 36-49. In Borkovich K, Ebbole D (ed), Cellular and Molecular Biology of Filamentous Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555816636.ch4
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1. Aime, M. C.,, P. B. Matheny,, D. A. Henk,, E. M. Frieders,, R. H. Nilsson,, D. J. McLaughlin,, L. J. Szabo, and, D. S. Hibbett. 2006. An overview of the higher-level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 98:896905.
2. Alexeyenko, A.,, I. Tamas,, G. Liu, and, E. L. L. Sonnhammer. 2006. Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22:e9e15.
3. Alexopoulos, C. J.,, C. W. Mims, and, M. Blackwell. 1986. Introductory Mycology. Wiley & Sons, New York, NY.
4. 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. 20:255266.
5. Baldauf, S. L., and, W. F. Doolittle. 1997. Origin and evolution of slime molds (Mycetozoa). Proc. Natl. Acad. Sci. USA 94:1200712012.
6. Baldauf, S. L., and, J. D. Palmer. 1993. Animals and fungi are each other’s closest relatives: congruent evidence from multiple proteins. Proc. Natl. Acad. Sci. USA 90:1155811562.
7. Barr, D. J. S. 1992. Evolution and kingdoms of organisms from the perspective of a mycologist. Mycologia 84:111.
8. Baurain, D.,, H. Brinkmann, and, H. Philippe. 2007. Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors? Mol. Biol. Evol. 24:69.
9. Begerow, D.,, M. Stoll, and, R. Bauer. 2006. A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data. Mycologia 98:906916.
10. Binder, M., and, D. S. Hibbett. 2006. Molecular systematics and biological diversification of Boletales. Mycologia 98:971981.
11. Blackwell, M.,, D. S. Hibbett,, J. W. Taylor, and, J. W. Spatafora. 2006. Research coordination networks: a phylogeny for Kingdom Fungi (Deep Hypha). Mycologia 98:829837.
12. Bruns, T. D.,, R. Vilgalys,, S. M. Barnes,, D. Gonzalez,, D. S. Hibbett,, D. J. Lane,, L. Simon,, S. Stickel,, T. M. Szaro,, W. G. Weisburg, and, M. L. Sogin. 1992. Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol. Phylogenet. Evol. 1:231241.
13. Bruns, T. D.,, T. J. White, and, J. W. Taylor. 1991. Fungal molecular systematics. Annu. Rev. Ecol. Syst. 22:525564.
14. Chen, F.,, A. J. Mackey,, J. K. Vermunt, and, D. S. Roos. 2007. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS ONE 2(4):e383.
15. Delsuc, R.,, H. Brinkmann, and, H. Philippe. 2006. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. 6:361375.
16. Drummond, A. J., and, A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
17. Eriksson, O. E., and, K. Winka. 1997. Supraordinal taxa of Ascomycota. Myconet 1:116.
18. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783791.
19. Fitzpatrick, D. A.,, M. E. Logue,, J. E. Stajich, and, G. Butler. 2006. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol. Biol. 6:99.
20. Fulton, D. L.,, Y. Y. Li,, M. R. Laird,, B. G. Horsman,, F. M. Roche, and, F. S. Brinkman. 2006. Improving the specificity of high-throughput ortholog prediction. BMC Bioinform. 7:270.
21. Geiser, D. M.,, C. Gueidan,, J. Miadlikowska,, F. Lutzoni,, F. Kauff,, V. Hofstetter,, E. Fraker,, C. L. Schoch,, L. Tibell,, W. A. Untereiner, and, A. Aptroot. 2006. Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. Mycologia98:10531064.
22. Gill, E. E., and, N. M. Fast. 2006. Assessing the microsporidia-fungi relationship: combined phylogenetic analysis of eight genes. Gene 375:103109.
23. Gunderson, J. H.,, H. Elwood,, A. Ingold,, K. Kindle, and, M. L. Sogin. 1987. Phylogenetic relationships between chlorophytes, chrysophytes, and oomycetes. Proc. Natl. Acad. Sci. USA 84:58235827.
24. Heckman, D. S.,, D. M. Geiser,, B. R. Eidell,, R. L. Stauffer,, N. L. Kardos, and, S. B. Hedges. 2001. Molecular evidence for the early colonization of land by fungi and plants. Science 293:11291133.
25. Hedges, S. B., and, S. Kumar. 2004. Precision of molecular time estimates. Trends Genet. 20:242247.
26. Hibbett, D. S.,, M. Binder,, J. F. Bischoff,, M. Blackwell,, P. F. Cannon,, O. E. Eriksson,, S. Huhndorf,, T. Y. James,, P. M. Kirk,, R. Lucking,, H. T. Lumbsch,, F. Lutzoni,, P. B. Matheny,, D. J. McLaughlin,, M. J. Powell,, S. Redhead,, C. L. Schoch,, J. W. Spatafora,, J. A. Stalpers,, R. Vilgalys,, M. C. Aime,, A. Aptroot,, R. Bauer,, D. Begerow,, G. L. Benny,, L. A. Castlebury,, P. W. Crous,, Y.-C. Dai,, W. Gams,, D. M. Geiser,, G. W. Griffith,, C. Gueidan,, D. L. Hawksworth,, G. Hestmark,, K. Hosaka,, R. A. Humber,, K. D. Hyde,, J. E. Ironside,, U. Koljag,, C. P. Kurtzman,, K.-H. Larsson,, R. Lichtwardt,, J. Longcore,, J. Miadlikowska,, A. Miller,, J.-M. Moncalvo,, S. Mozley-Standridge,, F. Oberwinkler,, E. Parmasto,, V. Reeb,, J. D. Rogers,, C. Roux,, L. Ryvarden,, J. P. Sampaio,, A. Schuβler,, J. Sugiyama,, R. G. Thorn,, L. Tibell,, W. A. Untereiner,, C. Walker,, Z. Wang,, A. Weir,, M. Weiss,, M. M. White,, K. Winka,, Y.-J. Yao, and, N. Zhang. 2007. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111:509547.
27. Hibbett, D. S.,, D. Grimaldi, and, M. J. Donoghue. 1995. Cretaceous mushrooms in amber. Nature 377:487.
28. Hibbett, D. S., and, P. B. Matheny. 2009. The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses. BMC Biol. 7:13.
29. Hibbett, D. S., and, M. Binder. 2002. Evolution of complex fruiting body morphologies in homobasidiomycetes. Proc. R. Soc. Lond. B 269:19631969.
30. Hibbett, D. S. 2006. A phylogenetic overview of the Agaricomycotina. Mycologia 98:917925.
31. Hibbett, D. S. 2004. Trends in morphological evolution in homobasidiomycetes. Syst. Biol.53:889903.
32. Hofstetter, V.,, J. Miadlikowska,, F. Kauff, and, F. Lutzoni. 2007. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Mol. Phylogenet. Evol. 44:412426.
33. James, T. Y.,, P. M. Letcher,, J. E. Longcore,, S. E. MozleyStandridge,, D. Porter, and, M. J. Powell. 2006a. A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98:860871.
34. James, T. Y.,, F. Kauff,, C. L. Schoch,, P. B. Matheny,, V. Hofstetter,, C. J. Cox,, G. Celio,, C. Gueidan,, E. Fraker,, J. Miadlikowska,, H. T. Lumbsch,, A. Rauhut,, V. Reeb,, A. E. Arnold,, A. Amtoft,, J. E. Stajich,, K. Hosaka,, G.-H. Sung,, D. Johnson,, B. O’Rourke,, M. Crockett,, M. Binder,, J. M. Curtis,, J. C. Slot,, Z. Wang,, A. W. Wilson,, A. Schuβler,, J. E. Longcore,, K. O’Donnell,, S. Mozley-Stan-dridge,, D. Porter,, P. M. Letcher,, M. J. Powell,, J. W. Taylor,, M. M. White,, G. W. Griffith,, D. R. Davies,, R. A. Humber,, J. B. Morton,, J. Sugiyama,, A. Y. Rossman,, J. D. Rogers,, D. H. Pfister,, D. Hewitt,, K. Hansen,, S. Hambleton,, R. A. Shoemaker,, J. Kohlmeyer,, B. VolkmannKohlmeyer,, R. A. Spotts,, M. Serdani,, P. W. Crous,, K. W. Hughes,, K. Matsuura,, E. Langer,, G. Langer,, W. A. Untereiner,, R. Lucking,, B. Budel,, D. M. Geiser,, A. Aptroot,, P. Diederich,, I. Schmitt,, M. Schultz,, R. Yahr,, D. S. Hibbett,, F. Lutzoni,, D. J. McLaughlin,, J. W. Spatafora, and, R. Vilgalys. 2006b. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818822.
35. James, T. Y.,, D. Porter,, C. A. Leander,, R. Vilgalys, and, J. E. Longcore. 2000. Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can. J. Bot. 78:336350.
36. Jeffroy, O.,, H. Brinkmann,, F. Delsuc, and, H. Philippe. 2006. Phylogenomics: the beginning of incongruence? Trends Genet. 22:225231.
37. Jothi, R.,, E. Zotenko,, A. Tasneem, and, T. M. Przytycka. 2006. COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics 22:779788.
38. Kauff, F.,, C. Cox, and, F. Lutzoni. 2007. WASABI: an automated sequence processing system for multi-gene phylogenies. Syst. Biol. 56:523531.
39. Kauff, F., and, F. Lutzoni. 2002. Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits. Mol. Phylogenet. Evol. 25:138156.
40. Keane, T. M.,, C. J. Creevey,, M. M. Pentomy,, T. J. Naughton, and, J. O. McInerney. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6:29.
41. Keeling, P. J., and, C. H. Slamovits. 2004. Simplicity and complexity of microsporidian genomes. Eukaryot. Cell 3:13631369.
42. Keeling, P. J., and, N. M. Fast. 2002. Microsporidia: biology and evolution of highly reduced intracellular parasites. Annu. Rev. Microbiol. 56:93116.
43. Keeling, P. J. 2003. Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet. Biol. 38:298309.
44. Kirk, P. M.,, P. F. Cannon,, D. W. Minter, and, J. A. Stalpers. 2008. Ainsworth and Bisby’s Dictionary of the Fungi. CAB International, Wallingford, United Kingdom.
45. Kuramae, E. E.,, V. Robert,, B. Snel,, M. Weiβ, and, T. Boekhout. 2006. Phylogenomics reveal a robust fungal tree of life. FEMS Yeast Res. 6:12131220.
46. Kuzniar, A.,, R. C. H., J. van Ham,, S. Pongor, and, J. A. M. Leunissen. 2008. The quest for orthologs: finding the corresponding gene across genomes. Trends Genet. 24:539551.
47. Lartillot, N., and, H. Philippe. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21:10951109.
48. Lee, S. C.,, N. Corradi,, E. J. Byrnes III,, S. Torres-Martinez,, F. S. Dietrich,, P. J. Keeling, and, J. Heitman. 2008. Microsporidia evolved from ancestral sexual fungi. Curr. Biol. 18:16751679.
49. Li, L.,, C. J. Stoeckert, Jr., and, D. S. Roos. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:21782189.
50. Liu, Y.,, J. W. Leigh,, H. Brinkmann,, M. T. Cushion,, N. Rodriguez-Ezpeleta,, H. Philippe, and, B. F. Lang. 2009. Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts. Mol. Biol. Evol. 26:2734.
51. Liu, Y. J.,, M. C. Hodson, and, B. D. Hall. 2006. Loss of the flagellum happened only once in the fungal lineage: phylo-genetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes. BMC Evol. Biol. 6:74.
52. Liu, Y. J., and, B. D. Hall. 2004. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc. Natl. Acad. Sci. USA 101:45074512.
53. Lumbsch, H. T.,, I. Schmitt,, R. Lindemuth,, A. Miller,, A. Mangold,, F. Fernandez, and, S. Huhndorf. 2005. Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta). Mol. Phylogenet. Evol. 34:512524.
54. Lutzoni, F.,, F. Kauff,, C. J. Cox,, D. McLaughlin,, G. Celio,, B. Dentinger,, M. Padamsee,, D. Hibbett,, T. Y. James,, E. Baloch,, M. Grube,, V. Reeb,, V. Hofstetter,, C. Schoch,, A. E. Arnold,, J. Miadlikowska,, J. W. Spatafora,, D. Johnson,, S. Hambleton,, M. Crockett,, R. Shoemaker,, G.-H. Sung,, R. Lücking,, T. Lumbsch,, K. O’Donnell,, M. Binder,, P. Diederich,, D. Ertz,, C. Gueidan,, K. Hansen,, R. C. Harris,, K. Hosaka,, Y.-W. Lim,, B. Matheny,, H. Nishida,, D. Pfister,, J. Rogers,, A. Rossman,, I. Schmitt,, H. Sipman,, J. Stone,, J. Sugiyama,, R. Yahr, and, R. Vilgalys. 2004. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am. J. Bot. 91:14461480.
55. Lutzoni, F.,, M. Pagel, and, V. Reeb. 2001. Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411:937940.
56. Matheny, P. B.,, Z. Wang,, M. Binder,, J. M. Curtis,, Y. W. Lim,, R. H. Nilsson,, K. W. Hughes,, V. Hofstetter,, J. F. Ammirati,, C. Schoch,, G. E. Langer,, D. J. McLaughlin,, A. W. Wilson,, T. Frøslev,, Z. W. Ge,, R. W. Kerrigan,, J. C. Slot,, E. C. Vellinga,, Z. L. Liang,, T. J. Baroni,, M. Fischer,, K. Hosaka,, K. Matsuura,, M. T. Seidl,, J. Vaura, and, D. S. Hibbett. 2007. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol. Phylogenet. Evol. 43:430451.
57. Matheny, P. B.,, J. M. Curtis,, V. Hofstetter,, M. C. Aime,, J.-M. Moncalvo,, Z. W. Ge,, Z. L. Yang,, J. C. Slot,, J. F. Ammirati,, T. J. Baroni,, N. L. Bougher,, K. W. Hughes,, D. J. Lodge,, R. W. Kerrigan,, M. T. Seidl,, D. K. Aanen,, M. DeNitis,, G. M. Daniele,, D. E. Desjardin,, B. R. Kropp,, L. L. Norvell,, A. Parker,, E. C. Vellinga,, R. Vilgalys, and, D. S. Hibbett. 2006. Major clades of Agaricales: a multi-locus phylogenetic overview. Mycologia 98:982995.
58. Miadlikowska, J.,, F. Kauff,, V. Hofstetter,, E. Fraker,, M. Grube,, J. Hafellner,, V. Reeb,, B. P. Hodkinson,, M. Kukwa,, R. Lücking,, G. Hestmark,, M. G. Otalora,, A. Rauhut,, B. Büdel,, C. Scheidegger,, E. Timdal,, S. Stenroos,, I. Brodo,, G. B. Perlmutter,, D. Ertz,, P. Diederich,, J. C. Lendemer,, P. May,, C. L. Schoch,, A. E. Arnold,, C. Gueidan,, E. Tripp,, R. Yahr,, C. Robertson, and, F. Lutzoni. 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylo- genetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98:10881103.
59. Philippe, H.,, F. Delsuc,, H. Brinkmann, and, N. Lartillot. 2005. Phylogenomics. Annu. Rev. Ecol. Evol. Syst. 36:541562.
60. Philippe, H.,, E. A. Snell,, E. Bapteste,, P. Lopez,, P. W. H. Holland, and, D. Casane. 2004. Phylogenomics of eukaryotes: impact of missing data on large alignments. Mol. Biol. Evol. 21:17401752.
61. Redecker, D.,, R. Kodner, and, L. E. Graham. 2000. Gloma-lean fungi from the Ordovician. Science 289:19201921.
62. Redecker, D., and, P. Raab. 2006. Phylogeny of the Glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. Mycologia 96:885895.
63. Reeb, V.,, F. Lutzoni, and, C. Roux. 2004. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol. Phylogenet. Evol. 32:10361060.
64. Remm, M.,, C. E. V. Storm, and, E. L. L. Sonnhammer. 2001. Automatic clustering of orthologs and inparalogs from pairwise species comparisons. J. Mol. Biol. 314:10411052.
65. Robbertse, B.,, J. Reeves,, C. Schoch, and, J. W. Spatafora. 2006. A phylogenomic analysis of the Ascomycota. Fungal Genet. Biol. 43:715725.
66. Rokas, A.,, B. L. Williams,, N. King, and, S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798804.
67. Ronquist, F., and, J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:15721574.
68. Sanderson, M. J. 2003. r8s; inferring absolute rates of evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301302.
69. Schoch, C. L.,, G.-H. Sung,, F. López-Giráldez,, J. P. Townsend,, J. Miadlikowska,, V. Hofstetter,, B. Robbertse,, P. B. Matheny,, F. Kauff,, Z. Wang,, R. Andrie,, K. Trippe,, L. M. Ciuffetti,, A. Amtoft,, E. Fraker,, B. P. Hodkinson,, G. Bonito,, F. Lutzoni,, J. Z. Groenewald,, M. Arzanlou,, S. de Hoog,, P. W. Crous,, D. Hewitt,, D. H. Pfister,, K. Peterson,, M. Gryzenhout,, M. J. Wingfield,, A. Aptroot,, S.-O. Suh,, M. Blackwell,, D. M. Hillis,, G. Griffith,, L. Castle-bury,, A. Rossman,, H. T. Lumbsch,, R. Lücking,, P. Diederich,, D. Ertz,, D. Geiser,, K. Hosaka,, P. Inderbitzin,, J. Kohlmeyer,, B. Volkmann-Kohlmeyer,, L. Mostert,, K. O’Donnell,, J. D. Rogers,, R. Shoemaker,, J. Sugiyama,, R. Summerbell,, W. Untereiner,, P. Johnston,, S. Stenroos,, A. Zuccaro,, P. Dyer,, P. Crittenden,, J. M. Trappe, and, J. W. Spatafora. 2009. The Ascomycota tree of life: a phylum wide phylogeny of the Ascomycota to address phylogenetic informativeness, ancestral character reconstruction and define novel lineages. Syst. Biol. 58:224239.
70. Schoch, C. L.,, R. A. Shoemaker,, K. A. Seifert,, S. Hambleton,, J. W. Spatafora, and, P. W. Crous. 2006. A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98:10411052.
71. Schüβler, A.,, D. Schwarzott, and, C. Walker. 2001. A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol. Res. 105:14131421.
72. Simon, L.,, J. Bousquet,, R. C. Levesque, and, M. Lalonde. 1993. Origin and diversification of endomycorrhizal fungi and coincidence with vascular land plants. Nature363:6769.
73. Smith, S. E., and, D. J. Read. 2008. Mycorrhizal Symbiosis, 3rd ed. Elsevier Ltd., New York, NY.
74. Spatafora, J. W.,, D. Johnson,, G.-H. Sung,, K. Hosaka,, B. O’Rourke,, M. Serdani,, R. Spotts,, F. Lutzoni,, V. Hofstetter,, E. Fraker,, C. Gueidan,, J. Miadlikowska,, V. Reeb,, H. T. Lumbsch,, R. Lücking,, I. Schmitt,, A. Aptroot,, C. Roux,, A. Miller,, D. Geiser,, J. Hafellner,, G. Hestmark,, A. E. Arnold,, B. Büdel,, A. Rauhut,, D. Hewitt,, W. Untereiner,, M. S. Cole,, C. Scheidegger,, M. Schultz,, H. Sipman, and, C. L. Schoch. 2006. A five-gene phylogenetic analysis of the Pezizomycotina. Mycologia 98:10201030.
75. Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:26882690.
76. Storm, C. E. V., and, E. L. L. Sonnhammer. 2002. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18:9299.
77. Sugiyama, J.,, K. Hosaka, and, S.-O. Suh. 2006. Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas. Mycologia 96:9961005.
78. Suh, S.-O.,, J. V. McHugh,, D. D. Pollock, and, M. Blackwell. 2005. The beetle gut: a hyperdiverse source of novel yeasts. Mycol. Res. 109:261265.
79. Sung, G.-H.,, G. O. Poinar, and, J. W. Spatafora. 2008. The oldest fossil evidence of animal parasitism by fungi supports a Cretaceous diversification of fungal-arthropod symbioses. Mol. Phylogenet. Evol. 49:495502.
80. Suzuki, Y.,, G. V. Glazki, and, M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:1613816143.
81. Tatusov, R. L.,, N. D. Fedorova,, J. D. Jackson,, A. R. Jacobs,, B. Kiryutin,, E. V. Koonin,, D. M. Krylov,, R. Mazumder,, S. L. Mekhedov,, A. N. Nikolskaya,, B. S. Rao,, S. Smirnov,, V. Sverdlov,, S. Vasudevan,, Y. I. Wolf,, J. J. Yin, and, D. A. Natale. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinform. 4:41.
82. Taylor, D. J., and, W. H. Piel. 2004. An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data. Mol. Biol. Evol. 21:15341537.
83. Taylor, J. W., and, M. L. Berbee. 2006. Dating divergences in the fungal tree of life: review and new analyses. Mycologia 98:838849.
84. Taylor, T. N.,, S. D. Klavins,, M. Krings,, E. L. Taylor,, H. Kerp, and, H. Hass. 2003. Fungi from the Rhynie chert: a view from the dark side. Trans. R. Soc. Edinb. Earth Sci. 94:457473.
85. Townsend, J. P. 2007. Profiling phylogenetic informativeness. Syst. Biol. 56:222231.
86. van der Heijden, R. T.,, B. Snel,, V. van Noort, and, M. A. Huynen. 2007. Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinform. 8:83.
87. van Dongen, S. 2000. Graph Clustering by Flow Simulation. University of Utrecht, Utrecht, The Netherlands.
88. White, M. M.,, T. Y. James,, K. O’Donnell,, M. J. Cafaro,, Y. Tanabe, and, J. Sugiyama. 2006. Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia96:872884.
89. Zmasek, C. M., and, S. R. Eddy. 2002. RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinform. 3:14.
90. Zwickl, D. J. 2008. GARLI manual (version 0.95). http://garli.nescent.org.

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