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Abstract

Yeast systematics has wholeheartedly embraced the phylogenetic approach. Central to this has been the unspoken convention that taxa at all ranks be strictly monophyletic. This can result in a proliferation of small genera and instances of nomenclatural instability, counter to the expected benefit of phylogenetic systematics. But the literature abounds with examples, at all taxonomic levels, where paraphyly is a reality that can no longer be ignored. The very concepts of Bacteria or Archaea, under the constraint of monophyly, are in peril. It is therefore desirable to effect a shift in practices that will recognize the existence of paraphyletic taxa.

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2016-12-01
2021-07-24
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References

  1. Ackery P. R., Vane-Wright R. I. 1984 Milkweed Butterflies: The Cladistics and Biology p. 425. Ithaca, New York: Cornell University Press;
    [Google Scholar]
  2. Albert J. S., Petry P., Reis R. E. 2011; Major biogeographic and phylogenetic patterns. In Historical Biogeography of Neotropical Freshwater Fishes pp. 21–57 Edited by Albert J. S., Reis R. E. University of California Press; [CrossRef]
    [Google Scholar]
  3. Archibald J. D. 2012; Darwin's two competing phylogenetic trees: marsupials as ancestors or sister taxa?. Arch Nat Hist 39:217–233 [View Article]
    [Google Scholar]
  4. Ashlock P. D. 1971; Monophyly and associated terms. Syst Zool 20:63–69 [CrossRef]
    [Google Scholar]
  5. Austin C. M., Tan M. H., Croft L. J., Hammer M. P., Gan H. M. 2015; Whole genome sequencing of the Asian Arowana (Scleropages formosus) provides insights into the evolution of ray-finned fishes. Genome Biol Evol 7:2885–2895 [View Article][PubMed]
    [Google Scholar]
  6. Barnett J. A. 2004; A history of research on yeasts 8: taxonomy. Yeast 21:1141–1193 [View Article][PubMed]
    [Google Scholar]
  7. Brummitt R. K. 1997; Taxonomy versus cladonomy, a fundamental controversy in biological systematics. Taxon 46:723–734 [View Article]
    [Google Scholar]
  8. Brummitt R. K. 2003; Further dogged defense of paraphyletic taxa. Taxon 52:803–804 [CrossRef]
    [Google Scholar]
  9. Cantino P. D., de Queiroz K. 2010; Phylocode, International code of phylogenetic nomenclature, version 4c. https://www.ohio.edu/phylocode/PhyloCode4c.pdf
  10. Carter J. G., Altaba C. R., Anderson L. C., Campbell D. C., Fang Z., Harries P. J., Skelton P. W. 2015; The paracladistic approach to phylogenetic taxonomy. Paleontol Contrib 12:1–9
    [Google Scholar]
  11. Cavalier-Smith T. 2002; The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52:7–76 [View Article][PubMed]
    [Google Scholar]
  12. Crisp M., Chandler G. 1996; Paraphyletic species. Telopea 6:813–844 [View Article]
    [Google Scholar]
  13. Cronquist A. 1987; A botanical critique of cladism. Bot Rev 53:1–52 [View Article]
    [Google Scholar]
  14. Donoghue M. J. 1985; A critique of the biological species concept and recommendations for a phylogenetic alternative. Bryologist 88:172–181 [View Article]
    [Google Scholar]
  15. Donoghue M. J., Cantino P. D. 1988; Paraphyly, ancestors, and the goals of taxonomy: a botanical defense of cladism. Bot Rev 54:107–128 [View Article]
    [Google Scholar]
  16. Farris J. S. 1974; Formal definitions of paraphyly and polyphyly. Syst Zool 23:548–554 [View Article]
    [Google Scholar]
  17. Felsenstein J. 2001; The troubled growth of statistical phylogenetics. Syst Biol 50:465–467 [View Article][PubMed]
    [Google Scholar]
  18. Funk D. J., Omland K. E. 2003; Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann Rev Ecol Evol Syst 34:397–423 [View Article]
    [Google Scholar]
  19. Ghiselin M. T. 1985; Mayr versus darwin on paraphyletic taxa. Syst Zool 34:460–462 [View Article]
    [Google Scholar]
  20. Giribet G., Hormiga G., Edgecombe G. D. 2016; The meaning of categorical ranks in evolutionary biology. Org Divers Evol 16:427–430 [View Article]
    [Google Scholar]
  21. Gupta R. S. 2000; The natural evolutionary relationships among prokaryotes. Crit Rev Microbiol 26:111–131 [View Article][PubMed]
    [Google Scholar]
  22. Hennig W. 1965; Phylogenetic systematics. Ann Rev Entomol 10:97–116 [View Article]
    [Google Scholar]
  23. Hennig W. 1966 Phylogenetic Systematics p. 263 Urbana: University of Illinois Press;
    [Google Scholar]
  24. Hörandl E. 2006; Paraphyletic versus monophyletic taxa-evolutionary versus cladistic classifications. Taxon 55:564–570 [View Article]
    [Google Scholar]
  25. Hörandl E., Stuessy T. F. 2010; Paraphyletic groups as natural units of biological classification. Taxon 59:1641–1653
    [Google Scholar]
  26. Judd W. S., Campbell C. S., Kellogg E. A., Steves P. F. 1999 Plant Systematics, a Phylogenetic Approach , p. 464 Sunderland, MA: Sinauer;
    [Google Scholar]
  27. Klöcker A. 1909; Deux nouveaux genres de la famille des Saccharomycètes. CR Trav Lab Carlsberg 7:273–278
    [Google Scholar]
  28. Kurtzman C. P., Robnett C. J. 1991; Phylogenetic relationships among species of Saccharomyces, Schizosaccharomyces, Debaryomyces and Schwanniomyces determined from partial ribosomal RNA sequences. Yeast 7:61–72 [View Article][PubMed]
    [Google Scholar]
  29. Kurtzman C. P., Suzuki M. 2010; Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces . Mycoscience 51:2–14 [View Article]
    [Google Scholar]
  30. Lachance M. A., Fedor A. N. 2014; Catching speciation in the act: Metschnikowia bowlesiae sp. nov., a yeast species found in nitidulid beetles of Hawaii and Belize. Antonie Van Leeuwenhoek 105:541–550 [View Article][PubMed]
    [Google Scholar]
  31. Lachance M. A., Hurtado E., Hsiang T. 2016; A stable phylogeny of the large-spored Metschnikowia clade. Yeast 33:261–275 [View Article][PubMed]
    [Google Scholar]
  32. Marriott H., Allers T. 2016; Archaea and the meaning of life. Microbiol Today 43:74–77
    [Google Scholar]
  33. Mayr E. 1981; Biological classification: toward a synthesis of opposing methodologies. Science 214:510–516 [View Article][PubMed]
    [Google Scholar]
  34. Mount S. M. 2010; Can we now speak of fish?. http://ongenetics.blogspot.ca/2010/05/can-we-not-speak-of-fish.html
  35. Pace N. R. 1997; A molecular view of microbial diversity and the biosphere. Science 276:734–740 [View Article][PubMed]
    [Google Scholar]
  36. Rieseberg L. H., Brouillet L. 1994; Are many plant species paraphyletic?. Taxon 43:21–32 [View Article]
    [Google Scholar]
  37. Spang A., Saw J. H., Jørgensen S. L., Zaremba-Niedzwiedzka K., Martijn J., Lind A. E., van Eijk R., Schleper C., Guy L., Ettema T. J. 2015; Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521:173–179 [View Article][PubMed]
    [Google Scholar]
  38. Stuessy T. F., Hörandl E. 2014; Evolutionary systematics and paraphyly: introduction. An Mo Bot Gard 100:2–5 [CrossRef]
    [Google Scholar]
  39. Valas R. E., Bourne P. E. 2009; Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life. Biol Direct 4:30 [View Article][PubMed]
    [Google Scholar]
  40. Vellinga E. C., Kuyper T. W., Ammirati J., Desjardin D. E., Halling R. E., Justo A., Laessøe T. E., Lebel T., Lodge D. J. et al. 2015; Six simple guidelines for introducing new genera of fungi. IMA Fungus 6:65–68
    [Google Scholar]
  41. Verkley G. J., Dukik K., Renfurm R., Göker M., Stielow J. B. 2014; Novel genera and species of coniothyrium-like fungi in Montagnulaceae (Ascomycota). Persoonia 32:25–51 [View Article][PubMed]
    [Google Scholar]
  42. Wang Q. M., Begerow D., Groenewald M., Liu X. Z., Theelen B., Bai F. Y., Boekhout T. 2015; Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina. Stud Mycol 81:55–83 [View Article][PubMed]
    [Google Scholar]
  43. Wiley E. O., Lieberman B. S. 2011 Phylogenetics: Theory and Practice of Phylogenetic Systematics, 2nd edn. , pp. 432 Wiley; [CrossRef]
    [Google Scholar]
  44. Williams T. A., Foster P. G., Cox C. J., Embley T. M. 2013; An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504:231–236 [View Article][PubMed]
    [Google Scholar]
  45. Woese C. R., Fox G. E. 1977; Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090 [View Article][PubMed]
    [Google Scholar]
  46. Woese C. R., Kandler O., Wheelis M. L. 1990; Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579 [View Article][PubMed]
    [Google Scholar]
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