title: Data partitions, Bayesian analysis and phylogeny of the zygomycetous fungal family Mortierellaceae, inferred from nuclear ribosomal DNA sequences.
abstract: Although the fungal order Mortierellales constitutes one of the largest classical groups of Zygomycota, its phylogeny is poorly understood and no modern taxonomic revision is currently available. In the present study, 90 type and reference strains were used to infer a comprehensive phylogeny of Mortierellales from the sequence data of the complete ITS region and the LSU and SSU genes with a special attention to the monophyly of the genus Mortierella. Out of 15 alternative partitioning strategies compared on the basis of Bayes factors, the one with the highest number of partitions was found optimal (with mixture models yielding the best likelihood and tree length values), implying a higher complexity of evolutionary patterns in the ribosomal genes than generally recognized. Modeling the ITS1, 5.8S, and ITS2, loci separately improved model fit significantly as compared to treating all as one and the same partition. Further, within-partition mixture models suggests that not only the SSU, LSU and ITS regions evolve under qualitatively and/or quantitatively different constraints, but that significant heterogeneity can be found within these loci also. The phylogenetic analysis indicated that the genus Mortierella is paraphyletic with respect to the genera Dissophora, Gamsiella and Lobosporangium and the resulting phylogeny contradict previous, morphology-based sectional classification of Mortierella. Based on tree structure and phenotypic traits, we recognize 12 major clades, for which we attempt to summarize phenotypic similarities. M. longicollis is closely related to the outgroup taxon Rhizopus oryzae, suggesting that it belongs to the Mucorales. Our results demonstrate that traits used in previous classifications of the Mortierellales are highly homoplastic and that the Mortierellales is in a need of a reclassification, where new, phylogenetically informative phenotypic traits should be identified, with molecular phylogenies playing a decisive role.
authors.affiliation: Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
authors.forename: Tamás
authors.initials: T
authors.lastname: Petkovits
authors.forename: László G
authors.initials: LG
authors.lastname: Nagy
authors.forename: Kerstin
authors.initials: K
authors.lastname: Hoffmann
authors.forename: Lysett
authors.initials: L
authors.lastname: Wagner
authors.forename: Ildikó
authors.initials: I
authors.lastname: Nyilasi
authors.forename: Thasso
authors.initials: T
authors.lastname: Griebel
authors.forename: Domenica
authors.initials: D
authors.lastname: Schnabelrauch
authors.forename: Heiko
authors.initials: H
authors.lastname: Vogel
authors.forename: Kerstin
authors.initials: K
authors.lastname: Voigt
authors.forename: Csaba
authors.initials: C
authors.lastname: Vágvölgyi
authors.forename: Tamás
authors.initials: T
authors.lastname: Papp
mesh_terms: D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D019143:Evolution, Molecular; D005658:Fungi / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D012270:Ribosomes / Q000235:genetics
chemical_list: D004271:DNA, Fungal; D004275:DNA, Ribosomal
references.citation: Mycologia. 2004 Jan-Feb;96(1):143-9
references.pmid: 21148836
references.citation: Mol Biol Evol. 2011 Jan;28(1):523-32
references.pmid: 20801907
references.citation: Biochimie. 2004 Nov;86(11):807-15
references.pmid: 15589690
references.citation: Curr Protoc Bioinformatics. 2002 Aug;Chapter 2:Unit 2.3
references.pmid: 18792934
references.citation: Syst Biol. 2010 Jan;59(1):108-17
references.pmid: 20525623
references.citation: Syst Biol. 2005 Jun;54(3):373-90
references.pmid: 16012105
references.citation: Biotechnol Lett. 2005 Feb;27(3):149-53
references.pmid: 15717122
references.citation: Syst Biol. 2007 Aug;56(4):564-77
references.pmid: 17654362
references.citation: Bioinformatics. 2001 Dec;17(12):1246-7
references.pmid: 11751242
references.citation: Bioinformatics. 2010 Jun 15;26(12):1569-71
references.pmid: 20421198
references.citation: Mycol Res. 2007 May;111(Pt 5):509-47
references.pmid: 17572334
references.citation: Syst Biol. 2004 Jun;53(3):448-69
references.pmid: 15503673
references.citation: Biol Rev Camb Philos Soc. 1998 Aug;73(3):203-66
references.pmid: 9809012
references.citation: Mol Biol Evol. 2008 Jul;25(7):1253-6
references.pmid: 18397919
references.citation: Syst Biol. 2002 Oct;51(5):754-60
references.pmid: 12396589
references.citation: Mycol Res. 2006 May;110(Pt 5):501-10
references.pmid: 16769506
references.citation: Syst Biol. 2010 Mar;59(2):145-61
references.pmid: 20525627
references.citation: Syst Biol. 2001 Nov-Dec;50(6):913-25
references.pmid: 12116640
references.citation: Bioinformatics. 2001 Aug;17(8):754-5
references.pmid: 11524383
references.citation: Syst Biol. 2002 Jun;51(3):492-508
references.pmid: 12079646
references.citation: Syst Biol. 2007 Oct;56(5):837-56
references.pmid: 17934998
references.citation: Gene. 2001 May 30;270(1-2):113-20
references.pmid: 11404008
references.citation: Mycologia. 2006 Nov-Dec;98(6):872-84
references.pmid: 17486964
references.citation: Syst Biol. 2011 Jul;60(4):541-61
references.pmid: 21436107
references.citation: Mol Biol Evol. 2001 Jun;18(6):1001-13
references.pmid: 11371589
references.citation: Syst Biol. 2004 Feb;53(1):47-67
references.pmid: 14965900
references.citation: Syst Biol. 2011 May;60(3):303-17
references.pmid: 21368323
references.citation: Nat Prod Rep. 2001 Apr;18(2):171-81
references.pmid: 11336287
references.citation: Mol Phylogenet Evol. 2008 Oct;49(1):59-68
references.pmid: 18672078
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Mycol Res. 2003 Mar;107(Pt 3):339-50
references.pmid: 12825503
references.citation: Syst Biol. 2004 Aug;53(4):571-81
references.pmid: 15371247
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Syst Biol. 2000 Jun;49(2):369-81
references.pmid: 12118412
references.citation: Methods Mol Biol. 2000;132:115-30
references.pmid: 10547834
references.citation: J Clin Microbiol. 1999 Dec;37(12):3957-64
references.pmid: 10565914
references.citation: Nature. 2006 Oct 19;443(7113):818-22
references.pmid: 17051209
references.citation: Evol Bioinform Online. 2008 May 26;4:193-201
references.pmid: 19204817
references.citation: New Phytol. 2011 Aug;191(3):789-794
references.pmid: 21453289
references.citation: Bioinformatics. 2006 Nov 15;22(22):2715-21
references.pmid: 16954142