TY - JOUR AU - Baroni, T. J. AU - Beug, M. W. AU - Cantrell, S. A. AU - Clements, T. A. AU - Iturriaga, T. PY - 2018 DA - 2018// TI - Four new species of Morchella from the Americas JO - Mycologia VL - 110 ID - Baroni2018 ER - TY - JOUR AU - Brasier, C. M. AU - Kirk, S. A. AU - Pipe, N. D. AU - Buck, K. W. PY - 1998 DA - 1998// TI - Rare interspecific hybrids in natural populations of the Dutch elm disease pathogens Ophiostoma ulmi and O. novo-ulmi JO - Mycological Research VL - 102 ID - Brasier1998 ER - TY - JOUR AU - Burt, A. PY - 2000 DA - 2000// TI - Perspective: sex, recombination, and the efficacy of selection – was Weismann right? JO - Evolution VL - 54 ID - Burt2000 ER - TY - CHAP AU - Casselton, L. A. AU - Feldbrügge, M. ED - Borkovich, K. A. ED - Ebbole, D. J. PY - 2010 DA - 2010// TI - Mating and sexual morphogenesis in basidiomycete fungi BT - Cellular and molecular biology of filamentous Fungi PB - ASM Press CY - USA ID - Casselton2010 ER - TY - JOUR AU - Chase, T. E. AU - Ullrich, R. C. PY - 1990 DA - 1990// TI - Genetic basis of biological species in Heterobasidion annosum: Mendelian determinants JO - Mycologia VL - 82 ID - Chase1990 ER - TY - JOUR AU - Chen, X. J. AU - Butow, R. A. PY - 2005 DA - 2005// TI - The organization and inheritance of the mitochondrial genome JO - Nature Reviews Genetics VL - 6 ID - Chen2005 ER - TY - JOUR AU - Coppin, E. AU - Debuchy, R. AU - Arnaise, S. AU - Picard, M. PY - 1997 DA - 1997// TI - Mating types and sexual development in filamentous ascomycetes JO - Microbiology and Molecular Biology Reviews VL - 61 ID - Coppin1997 ER - TY - JOUR AU - Davin, A. A. AU - Tannier, E. AU - Williams, T. A. AU - Boussau, B. AU - Daubin, V. PY - 2018 DA - 2018// TI - Gene transfers can date the tree of life JO - Nature Ecology & Evolution VL - 2 ID - Davin2018 ER - TY - CHAP AU - Debuchy, R. AU - Berteaux-Lecellier, V. AU - Silar, P. ED - Borkovich, K. A. ED - Ebbole, D. J. PY - 2010 DA - 2010// TI - Mating systems and sexual morphogenesis in Ascomycetes BT - Cellular and molecular biology of filamentous Fungi PB - ASM Press CY - USA ID - Debuchy2010 ER - TY - JOUR AU - Degnan, J. H. AU - Rosenberg, N. A. PY - 2009 DA - 2009// TI - Gene tree discordance, phylogenetic inference and the multispecies coalescent JO - Trends in Ecology & Evolution VL - 24 ID - Degnan2009 ER - TY - JOUR AU - Du, X. H. AU - Wang, H. C. AU - Sun, J. J. AU - Xiong, L. Y. AU - Yu, J. J. PY - 2019 DA - 2019// TI - Hybridization, characterization and transferability of SSRs in the genus Morchella JO - Fungal Biology VL - 123 ID - Du2019 ER - TY - STD TI - Du XH, Wu DM, He GQ, Wei W, Xu N et al (2019b) Six new species and two new records of Morchella in China using phylogenetic and morphological analyses. Mycologia. https://doi.org/10.1080/00275514.2019.1640012 ID - ref12 ER - TY - JOUR AU - Du, X. H. AU - Zhao, Q. AU - O’Donnell, K. AU - Rooney, A. P. AU - Yang, Z. L. PY - 2012 DA - 2012// TI - Multigene molecular phylogenetics reveals true morels (Morchella) are especially species-rich in China JO - Fungal Genetics and Biology VL - 49 ID - Du2012 ER - TY - JOUR AU - Du, X. H. AU - Zhao, Q. AU - Xia, E. H. AU - Gao, L. Z. AU - Richard, F. PY - 2017 DA - 2017// TI - Mixed reproductive strategies, competitive mating-type distribution and life cycle of fourteen black morel species JO - Scientific Reports VL - 7 ID - Du2017 ER - TY - JOUR AU - Du, X. H. AU - Zhao, Q. AU - Xu, J. AU - Yang, Z. L. PY - 2016 DA - 2016// TI - High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China JO - Scientific Reports VL - 6 ID - Du2016 ER - TY - JOUR AU - Dujon, B. PY - 2005 DA - 2005// TI - Hemiascomycetous yeasts at the forefront of comparative genomics JO - Curr Opin Gen VL - 15 ID - Dujon2005 ER - TY - JOUR AU - Duong, T. A. AU - Beer, Z. W. AU - Wingfield, B. D. AU - Wingfield, M. J. PY - 2013 DA - 2013// TI - Characterization of the mating-type genes in Leptographium procerum and Leptographium profanum JO - Fungal Biology VL - 117 ID - Duong2013 ER - TY - CHAP AU - Fraser, J. A. AU - Hsueh, Y. P. AU - Findley, K. M. AU - Heitman, J. ED - Heitman, J. ED - Kronstad, J. W. ED - Taylor, J. W. ED - Casselton, L. A. PY - 2007 DA - 2007// TI - Evolution of the mating-type locus: the basidiomycetes BT - Sex in fungi: molecular determination and evolutionary implications PB - ASM Press CY - USA ID - Fraser2007 ER - TY - JOUR AU - Galtier, N. AU - Daubin, V. PY - 2008 DA - 2008// TI - Dealing with incongruence in phylogenomic analyses JO - Philosophical Transactions of the Royal Society B VL - 363 ID - Galtier2008 ER - TY - JOUR AU - Garbelotto, M. AU - Gonthier, P. PY - 2013 DA - 2013// TI - Biology, epidemiology, and control of heterobasidion species worldwide JO - Annual Review of Phytopathology VL - 51 ID - Garbelotto2013 ER - TY - JOUR AU - Gioti, A. AU - Mushegian, A. A. AU - Strandberg, R. AU - Stajich, J. E. AU - Johannesson, H. PY - 2012 DA - 2012// TI - Unidirectional evolutionary transitions in fungal mating systems and the role of transposable elements JO - Molecular Biology and Evolution VL - 29 ID - Gioti2012 ER - TY - JOUR AU - Gladieux, P. AU - Ropars, J. AU - Badouin, H. AU - Branca, A. AU - Aguileta, G. PY - 2014 DA - 2014// TI - Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes JO - Molecular Ecology VL - 23 ID - Gladieux2014 ER - TY - JOUR AU - Gladieux, P. AU - Vercken, E. AU - Fontaine, M. C. AU - Hood, M. E. AU - Jonot, O. PY - 2011 DA - 2011// TI - Maintenance of fungal pathogen species that are specialized to different hosts: allopatric divergence and introgression through secondary contact JO - Molecular Biology and Evolution VL - 28 ID - Gladieux2011 ER - TY - JOUR AU - Gogarten, J. P. PY - 2003 DA - 2003// TI - Gene transfer: gene swapping craze reaches eukaryotes JO - Current Biology VL - 13 ID - Gogarten2003 ER - TY - JOUR AU - Gonthier, P. AU - Nicolotti, G. AU - Linzer, R. AU - Guglielmo, F. AU - Garbellotto, M. PY - 2007 DA - 2007// TI - Invasion of European pine stands by a north American forest pathogen and its hybridization with a native interfertile taxon JO - Molecular Ecology VL - 16 ID - Gonthier2007 ER - TY - JOUR AU - Groenewald, M. AU - Barnes, I. AU - Bradshaw, R. E. AU - Brown, A. V. AU - Dlae, A. PY - 2007 DA - 2007// TI - Characterization and distribution of mating type genes in the Dothistroma needle blight pathogens JO - Mycology VL - 97 ID - Groenewald2007 ER - TY - JOUR AU - Groenewald, M. AU - Groenewald, J. Z. AU - Harrington, T. C. AU - Abeln, E. C. A. AU - Crous, P. W. PY - 2006 DA - 2006// TI - Mating type gene analysis in apparently asexual Cercospora species is suggestive of cryptic sex JO - Fungal Genetics and Biology VL - 43 ID - Groenewald2006 ER - TY - JOUR AU - Gross, B. L. AU - Rieseberg, L. H. PY - 2005 DA - 2005// TI - The ecological genetics of homoploid hybrid speciation JO - Journal of Heredity VL - 96 ID - Gross2005 ER - TY - JOUR AU - Heitman, J. PY - 2015 DA - 2015// TI - Evolution of sexual reproduction: a view from the fungal kingdom supports an evolutionary epoch with sex before sexes JO - Fungal Biology Reviews VL - 3 ID - Heitman2015 ER - TY - JOUR AU - Inderbitzin, P. AU - Harkness, J. AU - Turgeon, B. G. AU - Berbee, M. L. PY - 2005 DA - 2005// TI - Lateral transfer of mating system in Stemphylium JO - Proceedings of the National Academy of Sciences of the United States of America VL - 102 ID - Inderbitzin2005 ER - TY - JOUR AU - Katoh, K. AU - Misawa, K. AU - Kuma, K. AU - Miyata, T. PY - 2002 DA - 2002// TI - MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform JO - Nucleic Acids Research VL - 30 ID - Katoh2002 ER - TY - JOUR AU - Kauserud, H. AU - Schumacher, T. PY - 2001 DA - 2001// TI - Outcrossing or inbreeding: DNA markers provide evidence for type of reproductive mode in Phellinus nigrolimitatus (Basidiomycota) JO - Mycological Research VL - 105 ID - Kauserud2001 ER - TY - JOUR AU - Kohn, L. M. PY - 2005 DA - 2005// TI - Mechanisms of fungal speciation JO - Ann Rev Pytopathology VL - 43 ID - Kohn2005 ER - TY - JOUR AU - Kronstad, J. W. AU - Staben, C. PY - 1997 DA - 1997// TI - Mating types in filamentous fungi JO - Annual Review of Genetics VL - 31 ID - Kronstad1997 ER - TY - JOUR AU - Kucej, M. AU - Butow, R. A. PY - 2007 DA - 2007// TI - Evolutionary tinkering with mitochondrial nucleoids JO - Trends in Cell Biology VL - 17 ID - Kucej2007 ER - TY - JOUR AU - Kuo, M. AU - Dewsbury, D. R. AU - O’Donnell, K. AU - Carter, M. C. AU - Rehner, S. A. PY - 2012 DA - 2012// TI - Taxonomic revision of true morels (Morchella) in Canada and the United States JO - Mycologia VL - 104 ID - Kuo2012 ER - TY - JOUR AU - Leducq, J. B. AU - Nielly-Thibault, L. AU - Charron, G. AU - Eberlein, C. AU - Verta, J. P. PY - 2016 DA - 2016// TI - Speciation driven by hybridization and chromosomal plasticity in a wild yeast JO - Nature Microbiology VL - 1 ID - Leducq2016 ER - TY - JOUR AU - Lee, S. C. AU - Ni, M. AU - Li, W. AU - Shertz, C. AU - Heitman, J. PY - 2010 DA - 2010// TI - The evolution of sex: a perspective from the fungal kingdom JO - Microbiology and Molecular Biology Reviews VL - 74 ID - Lee2010 ER - TY - JOUR AU - Liu, L. AU - Wu, S. Y. AU - Yu, L. L. PY - 2015 DA - 2015// TI - Coalescent methods for estimating species trees from phylogenomic data JO - Journal of Systematics and Evolution VL - 53 ID - Liu2015 ER - TY - BOOK AU - Loizides, M. AU - Bellanger, J. M. AU - Clowez, P. AU - Richard, F. AU - Moreau, P. A. PY - 2016 DA - 2016// TI - Combined phylogenetic and morphological studies of true morels (Pezizales, Ascomycota) in Cyprus reveal significant diversity, including Morchella arbutiphila and M. disparilis spp. nov. mycological Progress 15: 39 ID - Loizides2016 ER - TY - JOUR AU - Lopes, A. AU - Linaldeddu, B. T. AU - Phillips, A. L. J. AU - Alves, A. PY - 2018 DA - 2018// TI - Mating type gene analyses in the genus Diplodia: from cryptic sex to cryptic species JO - Fungal Biology VL - 122 ID - Lopes2018 ER - TY - JOUR AU - Lopes, A. AU - Phillips, A. J. L. AU - Alves, A. PY - 2017 DA - 2017// TI - Mating type genes in the genus Neofusicoccum: mating strategies and usefulness in species delimitation JO - Fungal Biology VL - 121 ID - Lopes2017 ER - TY - JOUR AU - Maddison, W. P. PY - 1997 DA - 1997// TI - Gene trees in species trees JO - Systematic Biology VL - 46 ID - Maddison1997 ER - TY - JOUR AU - Mallet, J. PY - 2007 DA - 2007// TI - Hybrid speciation JO - Nature VL - 446 ID - Mallet2007 ER - TY - JOUR AU - Martin, S. H. AU - Steenkamp, E. T. AU - Wingfield, M. J. AU - Wingfield, B. D. PY - 2013 DA - 2013// TI - Mate-recognition and species boundaries in the ascomycetes JO - Fungal Diversity VL - 58 ID - Martin2013 ER - TY - JOUR AU - Martin, T. AU - Lu, S. W. AU - Tilbeurgh, H. AU - Ripoll, D. R. AU - Christina, D. PY - 2010 DA - 2010// TI - Tracing the origin of the fungala1 domain places its ancestor in the HMG-box superfamily: implication for fungal mating-type evolution JO - PLoS One VL - 5 ID - Martin2010 ER - TY - JOUR AU - Mbofung, G. Y. AU - Hong, S. G. AU - Pryor, B. M. PY - 2006 DA - 2006// TI - Phylogeny of Fusarium oxysporum f. sp. lactucae inferred from mitochondrial small subunit, elongation factor 1-α, and nuclear ribosomal intergenic spacer sequence data JO - Phytopathology VL - 97 ID - Mbofung2006 ER - TY - JOUR AU - Metzenberg, R. L. AU - Glass, N. L. PY - 1990 DA - 1990// TI - Mating type and mating strategies in Neurospora JO - Bioessays VL - 12 ID - Metzenberg1990 ER - TY - JOUR AU - Mirarab, S. AU - Bayzid, M. S. AU - Boussau, B. AU - Warnow, T. PY - 2014 DA - 2014// TI - Statistical binning enables an accurate coalescent based estimation of the avian tree JO - Science VL - 346 ID - Mirarab2014 ER - TY - JOUR AU - Newcombe, G. AU - Stirling, B. AU - McDonald, S. AU - Bradshaw, H. D. PY - 2000 DA - 2000// TI - Melampsora columbiana, a natural hybrid of M. medusae and M. occidentalis JO - Mycological Research VL - 104 ID - Newcombe2000 ER - TY - JOUR AU - Nichols, R. PY - 2001 DA - 2001// TI - Gene trees and species trees are not the same JO - Trends Ecol Evol VL - 16 ID - Nichols2001 ER - TY - JOUR AU - O’Donnell, K. PY - 2000 DA - 2000// TI - Molecular phylogeny of the Nectria haematococca-Fusarium solani species complex JO - Mycologia VL - 92 ID - O’Donnell2000 ER - TY - JOUR AU - O’Donnell, K. AU - Rooney, A. P. AU - Mills, G. L. AU - Kuo, M. AU - Weber, N. S. PY - 2011 DA - 2011// TI - Phylogeny and historical biogeography of true morels (Morchella) reveals an early cretaceous origin and high continental endemism and provincialism in the Holarctic JO - Fungal Genetics and Biology VL - 48 ID - O’Donnell2011 ER - TY - JOUR AU - Oakley, B. R. AU - Rinehart, J. E. PY - 1985 DA - 1985// TI - Mitochondria and nuclei move by different mechanisms in Aspergillus nidulans JO - The Journal of Cell Biology VL - 101 ID - Oakley1985 ER - TY - JOUR AU - O'Donnell, K. AU - Ward, T. J. AU - Geiser, D. M. AU - Kistler, H. C. AU - Aoki, T. PY - 2004 DA - 2004// TI - Genealogical concordance between the mating type locus and seven other genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade JO - Fungal Genetics and Biology VL - 41 ID - O'Donnell2004 ER - TY - JOUR AU - Osiewacz, H. D. PY - 2002 DA - 2002// TI - Aging in fungi: role of mitochondria in Podospora anserina JO - Mechanisms of Ageing and Development VL - 123 ID - Osiewacz2002 ER - TY - JOUR AU - Osiewacz, H. D. AU - Kimpel, E. PY - 1999 DA - 1999// TI - Mitochondrial-nuclear interactions and lifespan control in fungi JO - Experimental Gerontology VL - 34 ID - Osiewacz1999 ER - TY - JOUR AU - Palumbi, S. R. PY - 2009 DA - 2009// TI - Speciation and the evolution of gamete recognition genes: pattern and process JO - Heredity VL - 102 ID - Palumbi2009 ER - TY - JOUR AU - Pamilo, P. AU - Nei, M. PY - 1988 DA - 1988// TI - Relationships between gene trees and species trees JO - Molecular Biology and Evolution VL - 5 ID - Pamilo1988 ER - TY - JOUR AU - Paoletti, M. AU - Buck, K. W. AU - Brasier, C. M. PY - 2006 DA - 2006// TI - Selective acquisition of novel mating type and vegetative incompatibility genes via interspecies gene transfer in the globally invading eukaryote Ophiostoma novo-ulmi JO - Molecular Ecology VL - 15 ID - Paoletti2006 ER - TY - STD TI - Rambaut A (2009) FigTree version:1.4.2 Available at http://tree.bio.ed.ac.uk/software/figtree/ UR - http://tree.bio.ed.ac.uk/software/figtree/ ID - ref61 ER - TY - JOUR AU - Schumer, M. AU - Rosenthal, G. G. AU - Andolfatto, P. PY - 2014 DA - 2014// TI - How common is homoploid hybrid speciation? JO - Evolution VL - 68 ID - Schumer2014 ER - TY - JOUR AU - Shen, X. X. AU - Hittinger, C. T. AU - Rokas, A. PY - 2017 DA - 2017// TI - Contentious relationships in phylogenomic studies can be driven by a handful of genes JO - Nat Ecol Evol VL - 1 ID - Shen2017 ER - TY - JOUR AU - Sillo, F. AU - Gonthier, P. AU - Lockman, B. AU - Kasuga, T. AU - Garbelotto, M. PY - 2019 DA - 2019// TI - Molecular analyses identify hybridization-mediated nuclear evolution in newly discovered fungal hybrids JO - Ecology and Evolution VL - 00 ID - Sillo2019 ER - TY - JOUR AU - Silva, F. P. D. AU - Vechiato, M. H. AU - Harakava, R. PY - 2014 DA - 2014// TI - EF-1α gene and IGS rDNA sequencing of Fusarium oxysporum f. sp. Vasinfectum and F. oxysporum f. sp. phaseoli reveals polyphyletic origin of strains JO - Tropical Plant Pathology VL - 39 ID - Silva2014 ER - TY - JOUR AU - Spatafora, J. W. AU - Aime, M. C. AU - Grigoriev, I. V. AU - Martin, F. AU - Stajich, J. E. PY - 2017 DA - 2017// TI - The fungal tree of life: from molecular systematics to genome-scale phylogenies JO - Microbiology Spectrum VL - 5 ID - Spatafora2017 ER - TY - JOUR AU - Stamatakis, A. PY - 2006 DA - 2006// TI - RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models JO - Bioinformatics VL - 22 ID - Stamatakis2006 ER - TY - JOUR AU - Strandberg, R. AU - Nygren, K. AU - Menkis, A. AU - James, T. Y. AU - Wik, L. PY - 2010 DA - 2010// TI - Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora JO - Fungal Genetics and Biology VL - 47 ID - Strandberg2010 ER - TY - JOUR AU - Sun, S. AU - Heitman, J. PY - 2015 DA - 2015// TI - From two to one: unipolar sexual reproduction JO - Fungal Biology Reviews VL - 29 ID - Sun2015 ER - TY - JOUR AU - Swanson, W. J. AU - Vacquier, V. D. PY - 2002 DA - 2002// TI - The rapid evolution of reproductive proteins JO - Nature Reviews Genetics VL - 3 ID - Swanson2002 ER - TY - BOOK AU - Swofford, D. L. PY - 2002 DA - 2002// TI - Phylogenetic analysis using parsimony (*and other methods). Version 4 ID - Swofford2002 ER - TY - JOUR AU - Syvanen, M. PY - 1994 DA - 1994// TI - Horizontal gene transfer: evidence and possible consequences JO - Annual Review of Genetics VL - 28 ID - Syvanen1994 ER - TY - JOUR AU - Taşkın, H. AU - Büyükalaca, S. AU - Doğan, H. H. AU - Rehner, S. A. AU - O’Donnell, K. PY - 2010 DA - 2010// TI - A multigene molecular phylogenetic assessment of true morels (Morchella) in Turkey JO - Fungal Genetic and Biology VL - 47 ID - Taşkın2010 ER - TY - JOUR AU - Taylor, J. W. AU - Jacobson, D. J. AU - Kroken, S. AU - Kasuga, T. AU - Geiser, D. M. PY - 2000 DA - 2000// TI - Phylogenetic species recognition and species concepts in fungi JO - Fungal Genetics and Biology VL - 31 ID - Taylor2000 ER - TY - JOUR AU - Taylor, S. A. AU - Larson, E. L. PY - 2019 DA - 2019// TI - Insights from genomes into the evolutionary importance and prevalence of hybridization in nature JO - Nat Ecol Evol VL - 3 ID - Taylor2019 ER - TY - JOUR AU - Turgeon, B. G. PY - 1998 DA - 1998// TI - Application of mating type gene technology to problems in fungal biology JO - Annual Review of Phytopathology VL - 36 ID - Turgeon1998 ER - TY - JOUR AU - Waalwijk, C. AU - Mendes, O. AU - Verstappen, E. C. P. AU - Warrd, M. A. D. AU - Kema, G. H. J. PY - 2002 DA - 2002// TI - Isolation and characterization of the mating-type idiomorphs from the wheat septoria leaf blotch fungus Mycosphaerella graminicola JO - Fungal Genetics and Biology VL - 35 ID - Waalwijk2002 ER - TY - JOUR AU - Walters, J. R. AU - Harrison, R. G. PY - 2008 DA - 2008// TI - EST analysis of male accessory glands from Heliconius butterflies with divergent mating systems JO - BMC Genomics VL - 9 ID - Walters2008 ER - TY - CHAP AU - White, T. J. AU - Bruns, T. AU - Lee, S. AU - Taylor, J. ED - Innis, M. A. ED - Gelfand, H. H. ED - Sninsky, J. J. ED - White, T. J. PY - 1990 DA - 1990// TI - Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics BT - PCR protocols: a guide to methods and applications PB - Academic Press CY - USA ID - White1990 ER - TY - JOUR AU - Wik, L. AU - Karlsson, M. AU - Johannesson, H. PY - 2008 DA - 2008// TI - The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behavior of taxa JO - BMC Evolutionary Biology VL - 8 ID - Wik2008 ER - TY - JOUR AU - Yokoyama, E. AU - Arakawa, M. AU - Yamagishi, K. AU - Hara, A. PY - 2006 DA - 2006// TI - Phylogenetic and structural analyses of the mating-type loci in Clavicipitaceae JO - FEMS Microbiology Letters VL - 264 ID - Yokoyama2006 ER - TY - JOUR AU - Zerbino, D. R. AU - Birney, E. PY - 2008 DA - 2008// TI - Velvet: algorithms for de novo short read assembly using de Bruijn graphs JO - Genome Research VL - 18 ID - Zerbino2008 ER - TY - JOUR AU - Zhan, J. AU - Torriani, S. F. F. AU - McDonald, B. A. PY - 2007 DA - 2007// TI - Significant difference in pathogenicity between MAT1-1 and MAT1-2 isolates in the wheat pathogen Mycosphaerella graminicola JO - Fungal Genetics and Biology VL - 44 ID - Zhan2007 ER -