Molecular taxonomy

Molecular taxonomy and ITS Trematodes of marine fish Jousson et al. (2000)... 

Klutzman CP Molecular taxonomy of the fungi in Benett JW, Lasure LL (eds) Gene Manipulations in Fungi. Orlando, Academic Press, 1985, pp 35-63. 

Roeijmans HJ, de Hoog GS, Tan CS, Figge MJ Molecular taxonomy and GC/MS of metabolites of Scytalidium hyalinum and Nattrassia mangiferae (Hendersonula toniloidea). J Med Vet Mycol 1997 35 181-188. 

Sterflinger K, Prillinger H Molecular taxonomy and biodiversity of rock fungal communities in an urban environment (Vienna, Austria). Antonie van Leeuwenhoek 2001 80 275-286. 

Prior to the early 1980s, life was considered to reside in five kingdoms, four of which were eukaryotic, and the Monera, containing the very small, anucleate cells, called prokaryotes (Figure 1(a)). However, with the advent of molecular taxonomy (sequence comparisons of... 

Molecular taxonomy. In ways never before possible, we can compare the sequences not just from existing organisms but also, when DNA is available from fossil specimens, from extinct ancestors of living organisms. Within given genetic families of limited... 

On the one hand, molecular taxonomy helps morphological taxonomy to reveal species complexes and potentially identify the correct units of diversity (e.g. Pons et al., 2006 Burns et al., 2008) on the other hand, environmental sequencing by cloning PCR products but mostly by ultrasequencing, is providing distributional data of many taxa otherwise unrecorded or undistinguished (e.g. Robeson et al., 2009 Creer et al., 2010). 

The debate over cosmopolitan vs. limited endemism in free-living microorganisms has mostly focused on the question of taxonomy defenders of cosmopolitanism are usually lumpers while defenders of endemism are usually splitters (see Finlay et al., 2004 and answer by Mitchell and Meisterfeld, 2005 for an example). Recent developments in taxonomy and especially in molecular taxonomy have provided several examples showing that the splitters may be right and that we have even underestimated the true diversity of testate amoebae (Lara et al., 2008). However, this debate is only one part of the whole story. Several other important factors influence the distribution of free-living microorganisms and all of these suffer from a clear lack of data or conceptual framework ... 

This paper benefited from discussions with J. Archie, R. Cann, D. Irwin, T. Kocher, M. Mickevich, S. Paabo, D. Swofford, K. Thomas, A.C. Wilson and many participants in the NATO Advanced Studies Institute in Molecular Taxonomy. I thank J. Archie, A. Martin and D. Swofford for comments on the manuscript and C. McIntosh for help with the figure. Financial support for data collection and for the author during the writing of this paper were provided by NSF BSR 88-22710. 

Application of molecular taxonomy methods has changed the quantitative and qualitative composition of the genus and made it possible to find close and distant relatives. High levels of DNA homology between representatives of some species resulted in the reduction of the number of classical species from 11 to 5 P. freudenreichii, P. thoenii, P. Jensenii, P. acidipropionici and P. cyclohexanicum. 

On the other hand, the boundaries of the genus were extended by including four species of anaerobic corynebacteria that inhabit human skin. Using the methods of traditional, numerical and molecular taxonomy, anaerobic corynebacteria were shown to be different from the other members of the genus Corynebacterium by a number of essential characteristics and to have genomic similarities with propionic acid bacteria. The anaerobic corynebacteria have been reclassified as P. acnes, P. avidum, P. granulosum and P. lymphophilum and are called cutaneous propionibacteria now. 

Erdtman H 1973 Molecular taxonomy. In Miller L P (ed) Phytochemistry. Vol III. Inorganic elements and special groups of chemicals. Van Nostrand Reinhold New York, 327-350... 

To overcome these difficulties, researchers have developed a molecular taxonomy over the last 15 years based on the following tests DNA recombination the similarity of DNA base composition the similarity of enzymes ultrastructure characteristics and cell wall composition. The DNA recombination tests have proven to be effective for delimiting yeast species. They measure the recombination percentages of denatured nuclear DNA (mono-stranded) of different strains. An elevated recombination rate between two strains (80-100%) indicates that they belong to the same species. A low recombination percentage (less than 20% of the sequences in common) signifies that the strains belong to different and very distant species. Combination rates between these extremes are more difficult to interpret. 

The latest yeast classification (Barnett etal., 2000) is based on recent advances in genetics and molecular taxonomy—in particular, DNA recombination tests reported by Vaughan Martini and Martini (1987) and hybridization experiments... 

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