Plunging hands into the mushroom jar: a phylogenetic framework for Lyophyllaceae (Agaricales, Basidiomycota)
详细信息 查看全文
- 作者：J. -M. Bellanger (1)
P. -A. Moreau (2)
G. Corriol (3)
A. Bidaud (4)
R. Chalange (5)
Z. Dudova (6)
F. Richard (7)
1. UMR 5175 CEFE - INSERM - Campus CNRS ; 1919 Route de Mende ; 34293 ; Montpellier ; France
2. EA 4483 ; Facult茅 des sciences pharmaceutiques et biologiques ; Universit茅 de Lille ; BP 83 ; 59006 ; Cedex Lille ; France
3. Conservatoire botanique national des Pyr茅n茅es et de Midi-Pyr茅n茅es ; Vallon de Salut ; BP 70315 ; 65203 ; Bagn猫res de Bigorre Cedex ; France
4. 2436 ; route de Brailles ; 38510 ; V茅zeronce-Curtin ; France
5. 45 ; rue du docteur Calmette ; 91170 ; Viry-Chatillon ; France
6. Department of Botany ; Charles University ; Prague ; Czech Republic
7. UMR 5175 CEFE - Universit茅 de Montpellier 鈥?Campus CNRS ; 1919 Route de Mende ; 34293 ; Montpellier ; France - 关键词：Lyophyllaceae ; Phylogeny ; Species limits ; Barcoding
- 刊名：Genetica
- 出版年：2015
- 出版时间：April 2015
- 年：2015
- 卷：143
- 期：2
- 页码：169-194
- 全文大小：2,421 KB
- 参考文献：1. Abarenkov, K, Henrik Nilsson, R, Larsson, KH, Alexander, IJ, Eberhardt, U, Erland, S (2010) The UNITE database for molecular identification of fungi鈥攔ecent updates and future perspectives. New Phytol 186: pp. 281-285 CrossRef
2. Alvarado, P, Moreno, G, Vizzini, A, Consiglio, G, Manj贸n, JL, Setti, L (2014) Atractosporocybe, Leucocybe and Rhizocybe: three new clitocyboid genera in the Tricholomatoid clade (Agaricales) with notes on Clitocybe and Lepista. Mycologia 106: pp. 13-369
3. Anisimova, M, Gil, M, Dufayard, J-F, Dessimoz, C, Gascuel, O (2011) Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 60: pp. 685-699 CrossRef
4. Baroni, TJ, Franco-Molano, AE, Lodge, J, Linder, DL, Horak, E, Hofstetter, V (2007) Arthromyces and Blastosporella, two new genera of conidia-producing lyophylloid agarics (Agaricales, Basidiomycota) from the neotropics. Mycol Res 111: pp. 572-580 CrossRef
5. Bon, M. (1992) Cl茅 monographique des esp猫ces gal茅ro-naucorio茂des. Association d鈥櫭ヽologie et de mycologie
6. Bon, M (1994) Deux Lyophylloideae int茅ressantes et le genre Gerhardtia st. et nom. nov. Doc Mycol 24: pp. 65-68
7. Bon M (1999). Flore mycologique d鈥橢urope 5. Collybio-marasmio茂des et ressemblants. Documents Mycologiques, M茅moire hors s茅rie n掳5. Lille
8. Castresana, J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: pp. 540-552 CrossRef
9. Chevenet, F, Brun, C, Ba帽uls, A-L, Jacq, B, Christen, R (2006) TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinform 7: pp. 439 CrossRef
10. Consiglio, G, Contu, M (2002) Il genere Lyophyllum P. Karst. emend. K眉hner, in Italia. Rivista di Micologia 45: pp. 99-181
11. Contu M, Consiglio G (2005) 鈥?004鈥?Il genere / Gerhardtia ( / Lyophyllaceae) in Europa, con osservazioni sulle rimanenti specie conosciute. Micologia e Vegetazione Mediterranea 19(2): 151鈥?62
12. Cooper, JA (2014) New species and combinations of some New Zealand agarics belonging to Clitopilus, Lyophyllum, Gerhardtia, Clitocybe, Hydnangium, Mycena, Rhodocollybia and Gerronema. Mycosphere 5: pp. 263-288 CrossRef
13. Courtecuisse R, Duhem B (2012) Champignons de France et d鈥橢urope. 2e 茅dition. Delachaux & Niestl茅, Lausanne
14. Dereeper, A, Guignon, V, Blanc, G, Audic, S, Buffet, S, Chevenet, F (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36: pp. 465-469 CrossRef
15. Donk, MA (1962) The generic names proposed for Agaricaceae. Beihefte zur Nova Hedwigia 5: pp. 320
16. Du, X-H, Zhao, Q, Yang, ZL, Hansen, K, Ta艧k谋n, H, B眉y眉kalaca, S (2012) How well do ITS rDNA sequences differentiate species of true morels (Morchella)?. Mycologia 104: pp. 1351-1368 CrossRef
17. Edgar, RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: pp. 1792-1797 CrossRef
18. Fr酶slev, TG, Jeppesen, TS, Laess酶e, T, Kj酶ller, R (2007) Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe. Mol Phylogenet Evol 44: pp. 217-227 CrossRef
19. Gardes, M, Bruns, TD (1993) ITS primers with enhanced specificity for basidiomycetes鈥攁pplication to the identification of mycorrhizae and rusts. Mol Ecol 2: pp. 113-118 CrossRef
20. Giraud, T, Refr茅gier, G, Gac, M, Vienne, DM, Hood, ME (2008) Fungal Genet Biol 45: pp. 791-802 CrossRef
21. Guindon, S, Dufayard, J-F, Lefort, V, Anisimova, M, Hordijk, W (2010) New algorithms and methods to estimate maximum likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: pp. 307-321 CrossRef
22. Harder, CB, Laess酶e, T, Fr酶slev, TG, Ekelund, F, Rosendhal, S, Kj酶ller, R (2013) A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification. Fungal Biol 117: pp. 764-775 CrossRef
23. Hibbett, DS (2007) After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century. Mycol Res 111: pp. 1001-1018 CrossRef
24. Hofstetter, V, Cl茅men莽on, H, Vilgalys, R, Moncalvo, JM (2002) Phylogenetic analyses of the Lyophylleae (Agaricales, Basidiomycota) based on nuclear and mitochondrial rDNA sequences. Mycol Res 106: pp. 1043-1059 CrossRef
25. Hofstetter, V, Redhead, SA, Kauff, F, Moncalvo, J-M, Matheny, PB, Vilgalys, R (2014) Taxonomic revision and examination of ecological transitions of the Lyophyllaceae (Basidiomycota, Agaricales) based on a multigene phylogeny. Cryptogam Mycol 35: pp. 399-425 CrossRef
26. Holec, J, Kola艡铆k, M (2013) Ossicaulis lachnopus (Agaricales, Lyophyllaceae), a species similar to O. lignatilis, is verified by morphological and molecular methods. Mycol Prog 12: pp. 589-597 CrossRef
27. James, TY, Kauff, F, Schoch, CL, Matheny, PB, Hofstetter, V, Cox, CJ (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443: pp. 818-822 CrossRef
28. Jargeat, P, Martos, F, Carriconde, F, Gryta, H, Moreau, P-A, Gardes, M (2010) Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota). Mol Ecol 19: pp. 5216-5230 CrossRef
29. J眉lich, W (1982) Lyophyllaceae. Bibl Mycol 85: pp. 378
30. Karsten, PA (1881) Hymenomycetes Fennici. Acta Societatis pro Fauna et Flora Fennica 2: pp. 40
31. Kiss, L (2012) Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi. Proc Natl Acad Sci USA 109: pp. E1811 CrossRef
32. Knudsen H, Vesterholt J, (eds) (2012) Funga Nordica. Nordsvamp, Copenhagen
33. K眉hner, R (1938) Utilisation du carmin ac茅tique dans la classification des Agarics leucospor茅s. Bulletin Mensuel de la Soci茅t茅 Linn茅enne de Lyon 7: pp. 204-211
34. K眉hner, R (1980) Les Hym茅nomyc猫tes agaricoides. Bulletin Mensuel de la Soci茅t茅 Linn茅enne de Lyon 49: pp. 1-1027
35. K眉hner, R, Romagnesi, H (1953) Flore analytique des champignons sup茅rieurs (agarics, bolets, chanterelles). Masson & Cie, Paris
36. Larsson, E, Sundberg, H (2011) Lyophyllum shimeji, a species associated with lichen pine forest in northern Fennoscandia. Mycoscience 52: pp. 289-295 CrossRef
37. Liu, YJ, Whelen, S, Hall, BD (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Mol Biol Evol 16: pp. 1799-1808 CrossRef
38. Matheny, PB (2005) Improving phylogenetic inference of mushrooms with RPB1 and RPB2 nucleotide sequences (Inocybe, Agaricales). Mol Phylogenet Evol 35: pp. 1-20 CrossRef
39. Matheny, PB, Curtis, JM, Hofstetter, V, Aime, MC, Moncalvo, JM, Ge, ZW (2006) Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98: pp. 982-995 CrossRef
40. Moreau P-A, Vila J, Aime MC, Antonin V, Horak E, P茅rez-Butron JL, Richard F, Urban A, Welti S, Vizzini A (2015) Cibaomyces and Cyptotrama, two new genera for Europe, and an emendation of / Rhizomarasmius (Basidiomycota, Physalacriaceae). Mycol Prog (in press)
41. Neville, P, Poumarat, S (1997) Premiere r茅colte fran莽aise de Tephrocybe gibberosa et sa position par rapport aux Tephrocybe carbonicoles. Bollettino del Gruppo Micologico Bresadola 40: pp. 347-366
42. Norvell, LL (2010) Report of the nomenclature committee for fungi: 15. Taxon 59: pp. 291-293
43. O鈥橠onnell, K, Rooney, AP, Mills, GL, Kuo, M, Weber, NS, Rehner, SA (2011) Phylogeny and historical biogeography of true morels (Morchella) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic. Fungal Genet Biol 48: pp. 252-265 CrossRef
44. Osmundson, TW, Robert, VA, Schoch, CL, Baker, LJ, Smith, A, Robich, G (2013) Filling gaps in biodiversity knowledge for macrofungi: contributions and assessment of an herbarium collection DNA barcode sequencing project. PLoS One 8: pp. e62419 CrossRef
45. R Core Team (2014) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. http://www.R-project.org/
46. Redhead, SA (1981) Parasitism of bryophytes by agarics. Can J Bot 59: pp. 63-67 CrossRef
47. Redhead, SA (2014) Nomenclatural novelties. Index Fungorum 202: pp. 1
48. Redhead, SA, Hofstetter, V, Cl茅men莽on, H, Moncalvo, J-M (2006) 1742) Proposal to conserve the name Lyophyllum with a conserved type (Basidiomycota. Taxon 55: pp. 1034-1036 CrossRef
49. Ronquist, F, Huelsenbeck, JP (2003) MrBayes聽3: bayesian phylogenetic inference under mixed models. Bioinformatics 19: pp. 1572-1574 CrossRef
50. Schoch, CL, Seifert, KA, Huhndorf, S, Robert, V, Spouge, JL, Levesque, CA, Chen, W (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109: pp. 6241-6246 CrossRef
51. Seifert, KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Res 9: pp. 83-89 CrossRef
52. Singer, R (1986) The agaricales in modern taxonomy. Koeltz Scientific Books, Koenigstein
53. Talavera, G, Castresana, J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: pp. 564-577 CrossRef
54. Taylor, JW, Jacobson, DJ, Kroken, S, Kasuga, T, Geiser, DM, Hibbett, DS, Fisher, MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31: pp. 21-32 CrossRef
55. Vesterholt J, Ludwig E (2012) / Lyophyllum. In: Knudsen H, Vesterholt J, (eds): 583
56. Wang, X-Q, Zhou, D-Q, Zhao, Y-C, Zhang, X-L, Li, L, Li, S-H (2013) Lyophyllum rhombisporum sp. nov. from China. Mycotaxon 123: pp. 473-477 CrossRef - 刊物类别：Biomedical and Life Sciences
- 刊物主题：Life Sciences
Life Sciences
Animal Genetics and Genomics
Plant Genetics and Genomics
Human Genetics
Microbial Genetics and Genomics - 出版者：Springer Netherlands
- ISSN：1573-6857
文摘
During the last two decades, the unprecedented development of molecular phylogenetic tools has propelled an opportunity to revisit the fungal kingdom under an evolutionary perspective. Mycology has been profoundly changed but a sustained effort to elucidate large sections of the astonishing fungal diversity is still needed. Here we fill this gap in the case of Lyophyllaceae, a species-rich and ecologically diversified family of mushrooms. Assembly and genealogical concordance multigene phylogenetic analysis of a large dataset that includes original, vouchered material from expert field mycologists reveal the phylogenetic topology of the family, from higher (generic) to lower (species) levels. A comparative analysis of the most widely used phylogenetic markers in Fungi indicates that the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and portions of the genes for RNA polymerase II second largest subunit (RPB2) is the most performing combination to resolve the broadest range of taxa within Lyophyllaceae. Eleven distinct evolutionary lineages are identified, that display partial overlap with traditional genera as well as with the phylogenetic framework previously proposed for the family. Eighty phylogenetic species are delineated, which shed light on a large number of morphological concepts, including rare and poorly documented ones. Probing these novel phylogenetic species to the barcoding method of species limit delineation, indicates that the latter method fully resolves Lyophyllaceae species, except in one clade. This case study provides the first comprehensive phylogenetic overview of Lyophyllaceae, a necessary step towards a taxonomical, ecological and nomenclatural revision of this family of mushrooms. It also proposes a set of methodological guidelines that may be of relevance for future taxonomic works in other groups of Fungi.