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
2020-09-25
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 Hist39:217–233 [CrossRef]
    [Google Scholar]
  4. Ashlock P. D.. 1971; Monophyly and associated terms. Syst Zool20:63–69[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 Evol7:2885–2895 [CrossRef][PubMed]
    [Google Scholar]
  6. Barnett J. A.. 2004; A history of research on yeasts 8: taxonomy. Yeast21:1141–1193 [CrossRef][PubMed]
    [Google Scholar]
  7. Brummitt R. K.. 1997; Taxonomy versus cladonomy, a fundamental controversy in biological systematics. Taxon46:723–734 [CrossRef]
    [Google Scholar]
  8. Brummitt R. K.. 2003; Further dogged defense of paraphyletic taxa. Taxon52:803–804[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 Contrib12:1–9
    [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 Microbiol52:7–76 [CrossRef][PubMed]
    [Google Scholar]
  12. Crisp M., Chandler G.. 1996; Paraphyletic species. Telopea6:813–844 [CrossRef]
    [Google Scholar]
  13. Cronquist A.. 1987; A botanical critique of cladism. Bot Rev53:1–52 [CrossRef]
    [Google Scholar]
  14. Donoghue M. J.. 1985; A critique of the biological species concept and recommendations for a phylogenetic alternative. Bryologist88:172–181 [CrossRef]
    [Google Scholar]
  15. Donoghue M. J., Cantino P. D.. 1988; Paraphyly, ancestors, and the goals of taxonomy: a botanical defense of cladism. Bot Rev54:107–128 [CrossRef]
    [Google Scholar]
  16. Farris J. S.. 1974; Formal definitions of paraphyly and polyphyly. Syst Zool23:548–554 [CrossRef]
    [Google Scholar]
  17. Felsenstein J.. 2001; The troubled growth of statistical phylogenetics. Syst Biol50:465–467 [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 Syst34:397–423 [CrossRef]
    [Google Scholar]
  19. Ghiselin M. T.. 1985; Mayr versus darwin on paraphyletic taxa. Syst Zool34:460–462 [CrossRef]
    [Google Scholar]
  20. Giribet G., Hormiga G., Edgecombe G. D.. 2016; The meaning of categorical ranks in evolutionary biology. Org Divers Evol16:427–430 [CrossRef]
    [Google Scholar]
  21. Gupta R. S.. 2000; The natural evolutionary relationships among prokaryotes. Crit Rev Microbiol26:111–131 [CrossRef][PubMed]
    [Google Scholar]
  22. Hennig W.. 1965; Phylogenetic systematics. Ann Rev Entomol10:97–116 [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. Taxon55:564–570 [CrossRef]
    [Google Scholar]
  25. Hörandl E., Stuessy T. F.. 2010; Paraphyletic groups as natural units of biological classification. Taxon59:1641–1653
    [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 Carlsberg7:273–278
    [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. Yeast7:61–72 [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. Mycoscience51:2–14 [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 Leeuwenhoek105:541–550 [CrossRef][PubMed]
    [Google Scholar]
  31. Lachance M. A., Hurtado E., Hsiang T.. 2016; A stable phylogeny of the large-spored Metschnikowia clade. Yeast33:261–275 [CrossRef][PubMed]
    [Google Scholar]
  32. Marriott H., Allers T.. 2016; Archaea and the meaning of life. Microbiol Today43:74–77
    [Google Scholar]
  33. Mayr E.. 1981; Biological classification: toward a synthesis of opposing methodologies. Science214:510–516 [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. Science276:734–740 [CrossRef][PubMed]
    [Google Scholar]
  36. Rieseberg L. H., Brouillet L.. 1994; Are many plant species paraphyletic?. Taxon43:21–32 [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. Nature521:173–179 [CrossRef][PubMed]
    [Google Scholar]
  38. Stuessy T. F., Hörandl E.. 2014; Evolutionary systematics and paraphyly: introduction. An Mo Bot Gard100:2–5[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 Direct4:30 [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 Fungus6:65–68
    [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). Persoonia32:25–51 [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 Mycol81:55–83 [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. Nature504:231–236 [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 USA74:5088–5090 [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 USA87:4576–4579 [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 Most Cited RSS feed

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