Molecular methods as ways of dealing with terminological difficulties in fungal ecology

Julia Budziszewska, Joanna Piątkowska



Many ecological terms are very difficult to define, or to apply to some groups of organisms. In the case of fungi, it is unclear how to speak of individuals, populations and species. Relying on morphological characters often gives ambiguous results. However, in recent years new techniques have been developed, techniques that provide us with robust tools, helpful in recognizing specific groups in nature. This paper aims to give a short overview of how molecular methods are used to delimitate species, individuals and populations in fungi.


molecular ecology; species; population; individual

Full Text:



Baldauf S. L., 2003, Phylogeny for the faint of heart: a tutorial, Trends in Genetics 19 (6): 345-351. DOI:

Bombik M., 1985, O rodzajach definicji [About types of definitions], Miscellanea Logica 2: 17-239.

Bujakiewicz A., 1992, Badania mikosocjologiczne w zespole Ficario - Ulmetum campestris w rezerwacie "Wielka Kępa Ostromecka" nad Wisłą [Mycosociological research in the Ficario-Ulmetum campestris association in the "Wielka Kępa Ostromecka" reserve on the Vistula river], Acta Mycologica 27 (2): 277-290.

Carle G. F. & Olson M. V., 1985, An electrophoretic karyotype for yeast, Proceedings of the National Academy of Science USA 82: 3756-3760. DOI:

Cracraft J., 1992, Species Concepts and Speciation Analysis, [in:] The Units of Evolution: Essays on the Nature of Species, MIT Press: 93.

Fiore-Donno A. M. & Martin F., 2001, Populations of ectomycorrhizal Laccaria amethystina and Xerocomus spp. show contrasting colonization patterns in a mixed forest, New Phytologist 152: 533-542. DOI:

Freeland J. R., 2005, Molecular Ecology, John Wiley & Sons, West Sussex.

Guidot A., Debaud J. C. & Marmeisse R., 2001, Correspondence between genet diversity and spatial distribution of above- and below-ground populations of the ectomycorrhizal fungus Hebeloma cylindrosporum, Molecular Ecology 10 (5): 1121-1131. DOI:

Harper J. L. & White J., 1974, The demography of plants, Annual Review of Ecology and Systematics 5: 419-463. DOI:

Hartl D. L. & Jones E. W., 2005, Genetics: Analysis of Genes and Genomes, 6th edition, Jones & Bartlett Publisher, Sudbury.

Hawksworth D., 2004, Limitation of dual nomenclature in pleomorphic fungi, Taxon 53(2): 596-598. DOI:

Hennig W., 1965, Phylogenetic Systematics, Annual Review of Entomology 10: 97-116. DOI:

Kellner M., Burmester A., Wöstermeyer A. & Wöstermeyer J., 1993, Transfer of genetic information from the mycoparasite Parasitella parasitica to its host Absidia glauca, Current Genetics 23: 334-337. DOI:

Koide R. T., Shumway D. L., Xu B. & Sharda J. N., 2007, On temporal partitioning of a community of ectomycprrhizal fungi, New Phytologist 174 (2): 420-429. DOI:

Landis F. C. & Gargas A., 2007, Using ITS2 secondary structure to create species-specific oligonucleotide probes for fungi, Mycologia 99 (5) : 681-692.

Mayden R. L., 1997, A hierarchy of species concepts: The denoument in the saga of the species problem, [in:] M. F. Claridge, A. H. Dawah, M. R. Wilson (eds.), Species: The Units of Biodiversity, Systematics Association Special Volumes Series 54, Chapman & Hall, London: 382-424.

Mayr E., 1940, Speciation phenomena in birds, American Naturalist 74: 249-278. DOI:

Mueller V. G. & Wolfenbarger L. L., 1999, AFLP genotyping and fingerprinting, Trends in Ecology and Evolution 14: 389-394.

Muyzer G., de Waal E. C. & Uitterlinden A. G., 1993, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA, Applied and Environmental Microbiology 59: 695-700.

Odum E., 1982, Podstawy ekologii, wyd. 3 [Fundamentals of ecology, third. edition], Państwowe Wydawnictwo Rolnicze i Leśne, Warszawa.

Okada G., Seifert K. A., Takematsu A., Yamaoka Y., Miyazaki S. & Tubaki K., 1998, A molecular phylogenetic reappraisal of the Graphium complex based on 18S rDNA sequences, Canadian Journal of Botany 76: 1495-1506.

Paszko B., 2002, Hybridization as a cause of taxonomic problems in the genus Calamagrostis in Poland, Ecological Questions 2: 151-157.

Queiroz K. de, 2007, Species Concepts and Species Delimitation, Systematic Biology 56 (6): 879-886. DOI:

Rieseberg L. H., Wood T. E., Back E., 2006, The nature of plant species, Nature 440: 524-527.

Santelices B., 1999, How many kinds of individual are there?, Trends in Ecology and Evolution 14 (4): 152-155.

Schwartz D. C. & Cantor C. R., 1984, Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis, Cell 37 (1): 67-75. DOI:

Scrosati R., 2002, An updated definition of genet applicable to clonal seaweeds, bryophytes, and vascular plants, Basic and Applied Ecology 3: 97-99. DOI:

Slot J. C., & Hibett D. S., 2007, Horizontal Transfer of a Nitrate Assimilation Gene Cluster and Ecological Transitions in Fungi: A Phylogenetic Study, PLoS ONE 2 (10): e1097.

Sung G. H., Hywel-Jones N. L., Sung J. M., Luangsa-Ard J. J., Shrestha B. & Spatafora J. W., 2007, Phylogenetic classification of Cordyceps and the clavicipitaceous fungi, Studies in Mycology 57: 5-59. DOI:

Tagou D. & Moussard C., 2003, Principes des techniques de biologie moléculaire, INRA éditions, Paris, 2003: 152-170.

Taylor J. W., Jacobson D. J. & Fisher M. C., 1999, The Evolution of Asexual Fungi: Reproduction, Speciation and Classification, Annual Review of Phytopathology 37: 197-246. DOI:

Taylor J. W., Jacobson D. J., Kroken S., Kasuga T., Geiser T. M., Hibbet D. S. & Fisher M. C., 2000, Phylogenetic species recognition and species concept in fungi, Fungal Genetics and Biology 31: 21-32. DOI:

Wiley E. O., 1978, The evolutionary species concept reconsidered, Systematic Zoology 27: 17-26. DOI:

Williams J. G. K., Kubelik A. R., Livak K. J., Rafalski J. A. & Tingey S. V., 1990, DNA polymorphisms amplified by arbitrary primers are useful as genetic markers, Nucleic Acids Research 18: 6531-6535. DOI:

Wittgenstein L., 1953, Philosophical Investigations, Blackwell Publishers, Oxford.

Partnerzy platformy czasopism