1887

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.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001474
2016-12-01
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/12/4924.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001474&mimeType=html&fmt=ahah

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. [CrossRef]
    [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. [CrossRef] [PubMed]
    [Google Scholar]
  6. Barnett J. A..( 2004;). A history of research on yeasts 8: taxonomy. . Yeast 21: 1141–1193. [CrossRef] [PubMed]
    [Google Scholar]
  7. Brummitt R. K..( 1997;). Taxonomy versus cladonomy, a fundamental controversy in biological systematics. . Taxon 46: 723–734. [CrossRef]
    [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. [CrossRef] [PubMed]
    [Google Scholar]
  12. Crisp M., Chandler G..( 1996;). Paraphyletic species. . Telopea 6: 813–844. [CrossRef]
    [Google Scholar]
  13. Cronquist A..( 1987;). A botanical critique of cladism. . Bot Rev 53: 1–52. [CrossRef]
    [Google Scholar]
  14. Donoghue M. J..( 1985;). A critique of the biological species concept and recommendations for a phylogenetic alternative. . Bryologist 88: 172–181. [CrossRef]
    [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. [CrossRef]
    [Google Scholar]
  16. Farris J. S..( 1974;). Formal definitions of paraphyly and polyphyly. . Syst Zool 23: 548–554. [CrossRef]
    [Google Scholar]
  17. Felsenstein J..( 2001;). The troubled growth of statistical phylogenetics. . Syst Biol 50: 465–467. [CrossRef] [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. [CrossRef]
    [Google Scholar]
  19. Ghiselin M. T..( 1985;). Mayr versus darwin on paraphyletic taxa. . Syst Zool 34: 460–462. [CrossRef]
    [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. [CrossRef]
    [Google Scholar]
  21. Gupta R. S..( 2000;). The natural evolutionary relationships among prokaryotes. . Crit Rev Microbiol 26: 111–131. [CrossRef] [PubMed]
    [Google Scholar]
  22. Hennig W..( 1965;). Phylogenetic systematics. . Ann Rev Entomol 10: 97–116. [CrossRef]
    [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. [CrossRef]
    [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. [CrossRef] [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. [CrossRef]
    [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [PubMed]
    [Google Scholar]
  36. Rieseberg L. H., Brouillet L..( 1994;). Are many plant species paraphyletic?. Taxon 43: 21–32. [CrossRef]
    [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [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. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001474
Loading
/content/journal/ijsem/10.1099/ijsem.0.001474
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error