Chapter 2.9 References and further reading

Chapter 2.9 References and further reading

As a gentle introduction you might like to read on-line this chapter taken from the book Slayers, Saviors, Servants, and Sex: An Exposé of Kingdom Fungi by David Moore; published by Springer-Verlag, New York: 2001, ISBN 0387950982. VIEW on Amazon. VIEW on publisher's website.

Chapter 8: The old Kingdom in time and space  [CLICK HERE to download]

Adl, S.M., Simpson, A.G.B., Farmer, M.A., Andersen, R.A., Anderson, O.R. and 23 others. (2005). The new higher level classification of Eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology, 52: 399-451. DOI: https://doi.org/10.1111/j.1550-7408.2005.00053.x.

Adl, S.M., Simpson, A.G.B., Lane, C.E., Lukeš, J., Bass, D. and 20 others. (2012). The revised classification of Eukaryotes. Journal of Eukaryotic Microbiology, 59: 429-493. DOI: https://doi.org/10.1111/j.1550-7408.2012.00644.x.

Aravind, L. & Subramanian, G. (1999). Origin of multicellular eukaryotes — insights from proteome comparisons. Current Opinion in Genetics & Development, 9: 688–694. DOI: https://doi.org/10.1016/S0959-437X(99)00028-3.

Arthur, M.A. (2009). Biogeochemistry: Carbonate rocks deconstructed. Nature, 460: 698-699. DOI: https://doi.org/10.1038/460698a.

Beakes, G.W., Honda, D. & Thines, M. (2014). Systematics of the Straminipila: Labyrinthulomycota, Hyphochytriomycota, and Oomycota. In: The Mycota Systematics and Evolution, VII part A: (2nd ed.), (eds D.J. McLaughlin & J.W. Spatafora), pp 39-97. Berlin, Heidelberg: Springer-Verlag. ISBN 978-3-642-55317-2. DOI: https://doi.org/10.1007/978-3-642-55318-9_3.

Benny, G.L., Humber, R.A. & Voigt, K. (2014). Zygomycetous fungi: Phylum Entomophthoromycota and Subphyla Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoopagomycotina. In: The Mycota Systematics and Evolution, VII part A: (2nd ed.), (eds D.J. McLaughlin & J.W. Spatafora), pp. 209-250. Berlin, Heidelberg: Springer-Verlag. ISBN 978-3-642-55317-2. DOI: https://doi.org/10.1007/978-3-642-55318-9_8.

Blackwell, M. (2000). Terrestrial life - fungal from the start? Science, 289: 1884-1885. DOI: https://doi.org/10.1126/science.289.5486.1884.

Boyce, C.K., Hotton, C.L., Fogel, M.L., Cody, G.D., Hazen, R.M., Knoll, A.H. & Hueber, F.M. (2007). Devonian landscape heterogeneity recorded by a giant fungus. Geology, 35: 399-402. DOI: https://doi.org/10.1130/G23384A.1.

Bruns, T. (2006) A kingdom revised. Nature 443, 758-760. DOI: https://doi.org/10.1038/443758a.

Burger, W.C. (2002). Perfect Planet, Clever Species: How Unique Are We? Amherst, New York: Prometheus Books. 345 pp. ISBN: 1591020166.

Burki, F. (2014). The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harbor Perspectives in Biology, 6: article a016147. DOI: https://doi.org/10.1101/cshperspect.a016147.

Burnett, J. (2003). Fungal Populations and Species. Oxford, UK: Oxford University Press. 348 pp. ISBN-10: 0198515537, ISBN-13: 978-0198515531.

Cardona, T., Murray, J.W. & Rutherford, A.W. (2015). Origin and evolution of water oxidation before the last common ancestor of the Cyanobacteria. Molecular Biology and Evolution, 32: 1310-1328. DOI: https://doi.org/10.1093/molbev/msv024. VIEW on Amazon.

Casadevall, A. (2005). Fungal virulence, vertebrate endothermy, and dinosaur extinction: is there a connection? Fungal Genetics and Biology, 42: 98–106. DOI: https://doi.org/10.1016/j.fgb.2004.11.008.

Cavalier-Smith, T. (2006). Cell evolution and Earth history: stasis and revolution. Philosophical Transactions of the Royal Society of London, series B, 361: 969-1006. DOI: https://doi.org/10.1098/rstb.2006.1842.

Cavalier-Smith, T. (2010a). Deep phylogeny, ancestral groups and the four ages of life. Philosophical Transactions of the Royal Society of London, series B, 365: 111-132. DOI: https://doi.org/10.1098/rstb.2009.0161.

Cavalier-Smith, T. (2010b). Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biology Letters, 6: 342-345. DOI: https://doi.org/10.1098/rsbl.2009.0948.

Cavalier-Smith, T. & Chao, E.E-Y. (2006). Phylogeny and megasystematics of phagotrophic heterokonts (Kingdom Chromista). Journal of Molecular Evolution, 62: 388-420. DOI: https://doi.org/10.1007/s00239-004-0353-8.

Choi, J.-J. & Kim, S.-H. (2017). A genome Tree of Life for the fungi kingdom. Proceedings of the National Academy of Sciences of the United States of America, 114: 9391-9396. DOI: https://doi.org/10.1073/pnas.1711939114.

Didier, E.S., Becnel, J.J., Kent, M.L., Sanders, J.L. & Weiss, L.M. (2014). Microsporidia. In: The Mycota Systematics and Evolution, VII part A: (2nd ed.), (eds D.J. McLaughlin & J.W. Spatafora), pp. 115-140. Berlin, Heidelberg: Springer-Verlag. ISBN 978-3-642-55317-2. DOI: https://doi.org/10.1007/978-3-642-55318-9_5.

Doolittle, W.F. (1999). Lateral genomics. Joint millennium issue of Trends in Cell Biology, 9, Trends in Biochemical Science, 24, Trends in Genetics, 15: M5-M8. DOI: https://doi.org/10.1016/S0168-9525(99)01877-6.

Doolittle, W.F. (2000). The nature of the universal ancestor and the evolution of the proteome. Current Opinion in Structural Biology, 10: 355–358. DOI: https://doi.org/10.1016/S0959-440X(00)00096-8.

Doolittle, R. F., Feng, D. F., Tsang, S., Cho, G. & Little, E. (1996). Determining divergence times of the major kingdoms of living organisms with a protein clock. Science, 271: 470-477. DOI: https://doi.org/10.1126/science.271.5248.470.

Dörfelt, H. & Schmidt, A.R. (2005). A fossil Aspergillus from Baltic amber. Mycological Research, 109: 956-960. DOI: https://doi.org/10.1017/S0953756205003497.

Edwards, D., Kenrick, P. & Dolan, L. (2018). History and contemporary significance of the Rhynie cherts - our earliest preserved terrestrial ecosystem. Philosophical Transactions of the Royal Society of London, series B, 373: article number 20160489. DOI: https://doi.org/10.1098/rstb.2016.0489.

Embley, T.M. & Hirt, R.P. (1998). Early branching eukaryotes? Current Opinion in Genetics & Development, 8: 624–629. DOI: https://doi.org/10.1016/S0959-437X(98)80029-4.

Flemming, H-C. & Wingender, J. (2010). The biofilm matrix. Nature Reviews Microbiology, 8: 623–633. DOI: https://doi.org/10.1038/nrmicro2415.

Gardner, A. (2014). Life, the universe and everything. Biology & Philosophy, 29: 207-215. DOI: https://doi.org/10.1007/s10539-013-9417-8.

Hand, E. (2009). When Earth greened over. Nature, 460: 161. DOI: https://doi.org/10.1038/460161a.

Hawksworth, D.L., Hibbett, D.S., Kirk, P.M. & Lücking, R. (2016). Proposals to permit DNA sequence data to serve as types of names of fungi. Taxon, 65: 899–900. DOI: https://doi.org/10.12705/654.31.

Hawksworth, D.L. & Lücking, R. (2017). Fungal diversity revisited: 2.2 to 3.8 million species. In: The Fungal Kingdom, (eds J. Heitman, B. Howlett, P. Crous, E. Stukenbrock, T. James & N. Gow), pp. 79-95. Washington, DC: ASM Press. DOI: https://doi.org/10.1128/microbiolspec.FUNK-0052-2016.

Hawksworth, D.L., May, T.W. & Redhead, S.A. (2017). Fungal nomenclature evolving: changes adopted by the 19th International Botanical Congress in Shenzhen 2017, and procedures for the Fungal Nomenclature Session at the 11th International Mycological Congress in Puerto Rico 2018. IMA Fungus, 8(2): 211–218. https://doi.org/10.5598/imafungus.2017.08.02.01.

Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., Kirk, P.M., Lücking, R., Thorsten Lumbsch, H., Lutzonig, F., Matheny, P.B., McLaughlin, D.J., Powell, M.J. Redhead, S., Schoch, C.L. Spatafora, J.W., Stalpers, J.L., Vilgalys, R., Aime, M.C., Aptroot, A., Bauer, R., Begerow, D., Benny, G.L., Castlebury, L.A., Crous, P.W., Dai, Y-C., Gams, W. Geiser, D.M., Griffith, G.W., Gueidan, C., Hawksworth, D.L., Hestmark, G., Hosaka, K., Humber, R.A., Hyde, K.D., Ironside, J.E., Kõljalg, U., Kurtzman, C.P., Larsson, K-H., Lichtwardt, R., Longcore, J., Miądlikowska, J., Miller, A., Moncalvo, J-M., Mozley-Standridge, S., Oberwinkler, F., Parmasto, E., Reeb, V., Rogers, J.D., Roux, C., Ryvarden, L., Sampaio, J.P., Schüßler, A., Sugiyama, J., Thorn, R.G., Tibell, L., Untereiner, W.A., Walker, C., Wang, Z., Weir, A., Weiss, M., White, M.M., Winka, K., Yao, Y-J. & Zhang, N. (2007). A higher-level phylogenetic classification of the Fungi. Mycological Research, 111: 509-547. DOI: https://doi.org/10.1016/j.mycres.2007.03.004.

Hibbett, D.S., Grimaldi, D. & Donoghue, M.J. (1995). Cretaceous mushrooms in amber. Nature, 377: 487. DOI: https://doi.org/10.1038/377487a0.

Hueber, F.M. (2001). Rotted wood-alga-fungus: the history and life of Prototaxites Dawson 1859. Review of Paleobotany and Palynology, 116: 123-148. DOI: https://doi.org/10.1016/S0034-6667(01)00058-6.

Hyde, K.D., Maharachchikumbura, S.S.N., Hongsanan, S. et al. (2017). The ranking of fungi: a tribute to David L. Hawksworth on his 70th birthday. Fungal Diversity, 84: 1-23. DOI: https://doi.org/10.1007/s13225-017-0383-3.

James, T.Y., Kauff, F., Schoch, C.L., Matheny, P.B., Hofstetter, V., Cox, C.J. and 65 others. (2006). Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature, 443: 818-822. DOI: https://doi.org/10.1038/nature05110.

Jones, M.D.M., Richards, T.A., Hawksworth, D.L., Bass, D. (2011). Validation and justification of the phylum name Cryptomycota phyl. nov. IMA Fungus, 2: 173-175. DOI: https://doi.org/10.5598/imafungus.2011.02.02.08.

Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. & Gray, M.W. (2005). The tree of eukaryotes. Trends in Ecology and Evolution, 20: 670 – 676. DOI: https://doi.org/10.1016/j.tree.2005.09.005.

Keeling, P.J, Leander, B.S. & Simpson, A. (2009). Eukaryotes. Eukaryota, organisms with nucleated cells. Version of 28 October 2009. URL: http://tolweb.org/Eukaryotes/3/2009.10.28 in The Tree of Life Web Project, http://tolweb.org/.

Knauth, L.P. & Kennedy, M.J. (2009). The late Precambrian greening of the Earth. Nature, 460: 728-732. DOI: https://doi.org/10.1038/nature08213.

Krings, M., Harper, C.J. & Taylor, E.L. (2018). Fungi and fungal interactions in the Rhynie chert: a review of the evidence, with the description of Perexiflasca tayloriana gen. et sp. nov. Philosophical Transactions of the Royal Society of London, series B, 373: article number 20160500. DOI: https://doi.org/10.1098/rstb.2016.0500.

Margulis, L. (2004). Serial endosymbiotic theory (SET) and composite individuality. Transition from bacterial to eukaryotic genomes. Microbiology Today, 31: 172-174. http://www.socgenmicrobiol.org.uk/pubs/micro_today/pdf/110406.pdf.

Martin, W. Rotte, C., Hoffmeister, M., Theissen, U., Gelius-Dietrich, G., Ahr, S. & Henze, K. (2003). Early cell evolution, eukaryotes, anoxia, sulfide, oxygen, fungi first (?), and a Tree of Genomes revisited. International Union of Biochemistry and Molecular Biology: Life, 55: 193-204. DOI: https://doi.org/10.1080/1521654031000141231.

McCarthy, C.G.P. & Fitzpatrick, D.A. (2017). Multiple approaches to phylogenomic reconstruction of the fungal kingdom. Advances in Genetics, 100: 211-266. DOI: https://doi.org/10.1016/bs.adgen.2017.09.006.

McLaughlin, D.J., Hibbett, D.S., Lutzoni, F., Spatafora, J.W. & Vilgalys, R. (2009). The search for the fungal tree of life. Trends in Microbiology, 17: 488-497. DOI: https://doi.org/10.1016/j.tim.2009.08.001.

McLaughlin, D.J. & Spatafora, J.W. (eds) (2014). The Mycota Systematics and Evolution, VII part A: (2nd ed.). Berlin, Heidelberg: Springer-Verlag. Pp. 461. ISBN 978-3-642-55317-2. DOI: https://doi.org/10.1007/978-3-642-55318-9.

McLaughlin, D.J. & Spatafora, J.W. (eds) (2015). The Mycota Systematics and Evolution, VII part B: (2nd ed.). Berlin, Heidelberg: Springer-Verlag. Pp. 311. ISBN 978-3-662-46010-8. DOI: https://doi.org/10.1007/978-3-662-46011-5.

Moore, D. (2013). Fungal Biology in the Origin and Emergence of Life. Cambridge, UK: Cambridge University Press. 230 pp. ISBN-10: 1107652774, ISBN-13: 978-1107652774. VIEW on Amazon.

Moore, D. & Novak Frazer, L. (2002). Essential Fungal Genetics. New York: Springer-Verlag Inc. ISBN-10: 0387953671, ISBN-13: 978-0387953670. VIEW on Amazon.

Nakayashiki, H., Nishimoto, N., Ikeda, K., Tosa, Y. & Mayama, S. (1999). Degenerate MAGGY elements in a subgroup of Pyricularia grisea: a possible example of successful capture of a genetic invader by a fungal genome. Molecular and General Genetics, 261: 958-966. DOI: https://doi.org/10.1007/s004380051044.

Penny, D. & Poole, A. (1999). The nature of the last universal common ancestor. Current Opinion in Genetics & Development, 9: 672–677. DOI: https://doi.org/10.1016/S0959-437X(99)00020-9.

Petersen, H. (2013). The Kingdom of Fungi. New Jersey, USA: Princeton University Press, Pp. 272. ISBN-10: 0691157545, ISBN 13: 978-0691157542.

Philippe, H., Germot, A. & Moreira, D. (2000). The new phylogeny of eukaryotes. Current Opinion in Genetics & Development, 10: 596–601. DOI: https://doi.org/10.1016/S0959-437X(00)00137-4.

Pirozynski, K.A. (1976). Fossil Fungi. Annual Review of Phytopathology, 14: 237-246. DOI: https://doi.org/10.1146/annurev.py.14.090176.001321.

Poinar, G. Jr. (2016). Fossil fleshy fungi (‘mushrooms’) in amber. Fungal Genomics & Biology, 6: 142 (5 pages). DOI: https://doi.org/10.4172/2165-8056.1000142.

Powell, M.J. & Letcher, P.M. (2014). Chytridiomycota, Monoblepharidomycota, and Neocallimastigomycota. In: The Mycota Systematics and Evolution, VII part A: (2nd ed.), (eds D.J. McLaughlin & J.W. Spatafora), pp. 141-176. Berlin, Heidelberg: Springer-Verlag. ISBN 978-3-642-55317-2. DOI: https://doi.org/10.1007/978-3-642-55318-9_6.

Ramsdale, M. (2003). Fungi and the bare necessities of life. Mycologist, 17: 14. DOI: https://doi.org/10.1017/S0269-915X(03)00109-5.

Redecker, D., Kodner, R., & Graham, L.E. (2000). Glomalean fungi from the Ordovician. Science, 289: 1920-1921. DOI: https://doi.org/10.1126/science.289.5486.1920.

Ren, R., Sun, Y., Zhao, Y., Geiser, D., Ma, H. & Zhou, X. (2016). Phylogenetic resolution of deep eukaryotic and fungal relationships using highly conserved low-copy nuclear genes. Genome Biology and Evolution, 8: 2683–2701. DOI: https://doi.org/10.1093/gbe/evw196.

Retallack, G.J. & Landing, E. (2014). Affinities and architecture of Devonian trunks of Prototaxites loganii. Mycologia, 106: 1143-1158. DOI: https://doi.org/10.3852/13-390.

Reynolds, N.K., Smith, M.E., Tretter, E.D., Gause, J., Heeney, D., Cafaro, M.J., Smith, J.F., Novak, S.J., Bourland, W.A. & White, M.M. (2017). Resolving relationships at the animal-fungal divergence: A molecular phylogenetic study of the protist trichomycetes (Ichthyosporea, Eccrinida). Molecular Phylogenetics and Evolution,109: 447-464. DOI: https://doi.org/10.1016/j.ympev.2017.02.007.

Richards, T.A., Leonard, G., Soanes, D.M. & Talbot, N.J. (2011). Gene transfer into the fungi. Fungal Biology Reviews, 25: 98-110. DOI: https://doi.org/10.1016/j.fbr.2011.04.003.

Rikkinen, J., Dörfelt, H., Schmidt, A.R. & Wunderlich, J. (2003). Sooty moulds from European Tertiary amber, with notes on the systematic position of Rosaria (‘Cyanobacteria’). Mycological Research, 107: 251-256. DOI: https://doi.org/10.1017/S0953756203007330.

Sage, R.F., Sage, T.L. & Kocacinar, F. (2012). Photorespiration and the evolution of C4 photosynthesis. Annual Review of Plant Biology, 63: 19-47. DOI: https://doi.org/10.1146/annurev-arplant-042811-105511.

Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., Chen, W. & the Fungal Barcoding Consortium. (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America, 109: 6241-6246. DOI: https://doi.org/10.1073/pnas.1117018109.

Sipiczki, M. (2000). Where does fission yeast sit on the tree of life? Genome Biology, 1: reviews1011.1–1011.4. http://genomebiology.com/2000/1/2/reviews/1011/.

Spatafora, J.W., Chang, Y., Benny, G.L., Lazarus, K., Smith, M.E., Berbee, M.L., Bonito, G., Corradi, N., Grigoriev, I., Gryganskyi, A., James, T.Y. O’Donnell, K., Roberson, R.W., Taylor, T.N., Uehling, J., Vilgalys, R., White, M.M. & Stajich, J.E. (2016). A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia, 108: 1028-1046. DOI: https://doi.org/10.3852/16-042.

Taylor, T.N., Krings M. & Taylor, E.L. (2015). Fossil Fungi. San Diego: Academic Press. 398 pp. ISBN-10: 0123877318, ISBN-13: 978-0123877314. DOI: https://doi.org/10.1016/B978-0-12-387731-4.00014-1.

Truong, C., Mujic, A.B., Healy, R., Kuhar, F., Furci, G., Torres, D., Niskanen, T., Sandoval-Leiva, P.A., Fernández, N., Escobar, J.M., Moretto, A., Palfner, G., Pfister, D., Nouhra, E., Swenie, R., Sánchez-García, M., Matheny, P.B. & Smith, M.E. (2017). How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity. New Phytologist, 214: 913–919. DOI: https://doi.org/10.1111/nph.14509.

Vajda, V. & McLoughlin, S. (2004). Fungal proliferation at the Cretaceous-Tertiary boundary. Science, 303: 1489. DOI: https://doi.org/10.1126/science.1093807.

Visscher, H., Brinkuis, H., Dilcher, D.L., Elsik, W.C., Eshet, Y., Looy, C.V., Rampino, M.R. & Traverse, A. (1996). The terminal Paleozoic fungal event: evidence of terrestrial ecosystem destabilization and collapse. Proceedings of the National Academy of Sciences of the United States of America, 93: 2155-2158. Stable URL: http://www.jstor.org/stable/38482.

Walton, J. D. (2000). Horizontal gene transfer and the evolution of secondary metabolite gene clusters in fungi: An hypothesis. Fungal Genetics and Biology, 30: 167–171. DOI: https://doi.org/10.1006/fgbi.2000.1224.

Wellman, C.H. & Gray, J. (2000). The microfossil record of early land plants. Philosophical Transactions of the Royal Society of London, Series B, 355: 717-732. [see section 3, which starts on page 725]. Stable URL: http://www.jstor.org/stable/3066802.

Williams, B.P., Johnston, I.G., Covshoff, S. & Hibberd, J.M. (2013). Phenotypic landscape inference reveals multiple evolutionary paths to C₄ photosynthesis. eLife 2: e00961. DOI: https://doi.org/10.7554/eLife.00961.

Woese, C.R. (1987). Bacterial evolution. Microbiological Reviews, 51: 221-271. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC373105/pdf/microrev00049-0051.pdf.

Woese, C.R., Kandler, O. & Wheels, M.L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proceedings of the National Academy of Sciences of the United States of America, 87: 4576-4579.  Stable URL: http://www.jstor.org/stable/2354364.

Wolf, Y.I., Kondrashov, A.S. & Koonin, E.V. (2000). Interkingdom gene fusions. Genome Biology, 1: research0013.1–0013.13. http://genomebiology.com/2000/1/6/research/0013.

Xu, J. (ed.) (2005). Evolutionary Genetics of Fungi. Norfolk, UK: Horizon Bioscience. 350 pp. ISBN-10: 1904933157. ISBN-13: 978-1904933151.

Yarza, P., Yilmaz, P., Panzer, K., Glöckner, F.O. & Reich, M. (2017). A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences. Marine Genomics, 36: 33-39. DOI: https://doi.org/10.1016/j.margen.2017.05.009.

Zalasiewicz, J. & Williams, M. (2013). The Goldilocks Planet: The 4 billion year story of Earth’s climate. Oxford: Oxford University Press. ISBN-10: 0199683506, ISBN-13: 978-0199683505. VIEW on Amazon.

Zhang, J. (2000). Protein-length distributions for the three domains of life. Trends in Genetics, 16: 107-109. DOI: https://doi.org/10.1016/S0168-9525(99)01922-8.

Updated July, 2018