title: Multigene molecular phylogeny and biogeographic diversification of the earth tongue fungi in the genera Cudonia and Spathularia (Rhytismatales, Ascomycota).
abstract: The family Cudoniaceae (Rhytismatales, Ascomycota) was erected to accommodate the "earth tongue fungi" in the genera Cudonia and Spathularia. There have been no recent taxonomic studies of these genera, and the evolutionary relationships within and among these fungi are largely unknown. Here we explore the molecular phylogenetic relationships within Cudonia and Spathularia using maximum likelihood and Bayesian inference analyses based on 111 collections from across the Northern Hemisphere. Phylogenies based on the combined data from ITS, nrLSU, rpb2 and tef-1α sequences support the monophyly of three main clades, the /flavida, /velutipes, and /cudonia clades. The genus Cudonia and the family Cudoniaceae are supported as monophyletic groups, while the genus Spathularia is not monophyletic. Although Cudoniaceae is monophyletic, our analyses agree with previous studies that this family is nested within the Rhytismataceae. Our phylogenetic analyses circumscribes 32 species-level clades, including the putative recognition of 23 undescribed phylogenetic species. Our molecular phylogeny also revealed an unexpectedly high species diversity of Cudonia and Spathularia in eastern Asia, with 16 (out of 21) species-level clades of Cudonia and 8 (out of 11) species-level clades of Spathularia. We estimate that the divergence time of the Cudoniaceae was in the Paleogene approximately 28 Million years ago (Mya) and that the ancestral area for this group of fungi was in Eastern Asia based on the current data. We hypothesize that the large-scale geological and climatic events in Oligocene (e.g. the global cooling and the uplift of the Tibetan plateau) may have triggered evolutionary radiations in this group of fungi in East Asia. This work provides a foundation for future studies on the phylogeny, diversity, and evolution of Cudonia and Spathularia and highlights the need for more molecular studies on collections from Europe and North America.
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China; Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America; Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Zai-Wei
authors.initials: ZW
authors.lastname: Ge
authors.affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
authors.forename: Zhu L
authors.initials: ZL
authors.lastname: Yang
authors.affiliation: Harvard University Herbaria and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
authors.forename: Donald H
authors.initials: DH
authors.lastname: Pfister
authors.affiliation: Via Don Luigi Sturzo 173, Genova, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Carbone
authors.affiliation: Institute of Mycology, Jilin Agriculture University, Changchun, Jilin, China.
authors.forename: Tolgor
authors.initials: T
authors.lastname: Bau
authors.affiliation: Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America.
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Smith
mesh_terms: D001203:Ascomycota / Q000145:classification* / Q000235:genetics*; D044822:Biodiversity; D002681:China; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005060:Europe; D019143:Evolution, Molecular; D005800:Genes, Fungal; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D009656:North America; D010641:Phenotype; D010802:Phylogeny; D058974:Phylogeography
chemical_list: D021903:DNA, Ribosomal Spacer
references.citation: Methods Mol Biol. 2009;537:39-64
references.pmid: 19378139
references.citation: Syst Biol. 2008 Oct;57(5):758-71
references.pmid: 18853362
references.citation: Mycopathologia. 2005 Feb;159(2):299-306
references.pmid: 15770457
references.citation: J Forensic Sci. 2002 Jul;47(4):811-8
references.pmid: 12136989
references.citation: Mycologia. 2006 Nov-Dec;98(6):1018-28
references.pmid: 17486977
references.citation: Mol Phylogenet Evol. 2006 Nov;41(2):295-312
references.pmid: 16837216
references.citation: Mycol Res. 2008 Apr;112(Pt 4):448-62
references.pmid: 18314317
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Am J Bot. 2004 Oct;91(10):1446-80
references.pmid: 21652303
references.citation: Am J Bot. 2011 Mar;98(3):426-38
references.pmid: 21613136
references.citation: Fungal Genet Biol. 2011 Mar;48(3):252-65
references.pmid: 20888422
references.citation: Mycol Res. 2008 Apr;112(Pt 4):425-36
references.pmid: 18314318
references.citation: PLoS One. 2011;6(12):e28161
references.pmid: 22174775
references.citation: Mycologia. 2011 Jan-Feb;103(1):57-74
references.pmid: 20943536
references.citation: Syst Biol. 2009 Apr;58(2):224-39
references.pmid: 20525580
references.citation: Nature. 2011 May 11;474(7350):200-3
references.pmid: 21562490
references.citation: Mycologia. 2006 Nov-Dec;98(6):838-49
references.pmid: 17486961
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Mol Phylogenet Evol. 2006 Nov;41(2):405-19
references.pmid: 16839785
references.citation: Mol Ecol. 2012 Apr;21(8):1864-77
references.pmid: 21883587
references.citation: Science. 1995 Jun 9;268(5216):1492-5
references.pmid: 7770775
references.citation: Am J Bot. 2012 Dec;99(12):2014-26
references.pmid: 23204485
references.citation: J Bacteriol. 1990 Aug;172(8):4238-46
references.pmid: 2376561
references.citation: Persoonia. 2009 Jun;22:129-38
references.pmid: 19915689
references.citation: Trends Plant Sci. 2005 Nov;10(11):550-8
references.pmid: 16226053
references.citation: Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):12002-6
references.pmid: 9342352
references.citation: Mycologia. 2009 Nov-Dec;101(6):810-22
references.pmid: 19927746
references.citation: Fungal Genet Biol. 2000 Oct;31(1):21-32
references.pmid: 11118132
references.citation: Mycologia. 2005 Jan-Feb;97(1):84-98
references.pmid: 16389960
references.citation: Mol Phylogenet Evol. 2010 Jul;56(1):294-304
references.pmid: 20159044
references.citation: Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19333-8
references.pmid: 23129628
references.citation: BMC Evol Biol. 2011 Aug 04;11:230
references.pmid: 21816066
references.citation: Mol Ecol. 1993 Apr;2(2):113-8
references.pmid: 8180733
references.citation: PLoS One. 2009;4(1):e4246
references.pmid: 19158947
references.citation: PLoS One. 2013;8(1):e52765
references.pmid: 23300990
references.citation: Mol Phylogenet Evol. 2008 Nov;49(2):495-502
references.pmid: 18817884
references.citation: Fungal Genet Biol. 2012 Jun;49(6):455-69
references.pmid: 22503770
references.citation: Evolution. 2003 Dec;57(12):2703-20
references.pmid: 14761051
references.citation: BMC Evol Biol. 2007 Nov 08;7:214
references.pmid: 17996036
references.citation: Science. 2001 Apr 27;292(5517):686-93
references.pmid: 11326091
references.citation: Syst Biol. 2008 Feb;57(1):58-75
references.pmid: 18275002
references.citation: Mol Ecol. 2006 Jan;15(1):225-39
references.pmid: 16367842
references.citation: Syst Biol. 2008 Feb;57(1):4-14
references.pmid: 18253896
references.citation: PLoS One. 2012;7(5):e37567
references.pmid: 22629418
references.citation: BMC Evol Biol. 2014 Jun 21;14:143
references.pmid: 24950598
references.citation: Nature. 2007 Feb 8;445(7128):635-8
references.pmid: 17287807
references.citation: Mol Biol Evol. 1999 Dec;16(12):1799-808
references.pmid: 10605121
references.citation: Mycol Res. 2006 Sep;110(Pt 9):1093-101
references.pmid: 16949808
references.citation: Mycologia. 2006 Nov-Dec;98(6):1065-75
references.pmid: 17486981
references.citation: Proc K Ned Akad Wet C. 1972;45(3):243-55
references.pmid: 4262225
references.citation: Mycologia. 2002 Jul-Aug;94(4):641-50
references.pmid: 21156537
references.citation: Mol Ecol. 2009 Mar;18(5):817-33
references.pmid: 19207260