Taxonomy
Linnaeus
ヒメアギトアリ(Anochetus  shohki)の画像一覧                    3
Fun with Latin•   Abracadabra     (abracadabra)•   Bahumbugi (ba humbug)•   Eurygenius      (youre a genius)•   Gelaebaen ...
Scatological fun with Latin•   Bugeranus•   Doryctes fartus•   Dyaria•   Eremobates inyoanus•   Pison eu•   Soranus       ...
Indri indriOften claimedname means“look!” or “there”in Malagasy(story is more complicated, see Wikipedia page http://en.wi...
Nomenclature has inherited aquaint view of the tree of life
Animals(International Code of Zoological         Nomenclature)
Plants and Fungi(International Code of Botanical         Nomenclature)
Bacteria (International Code ofNomenclature of Bacteria)
Evolutionary tree  for all of life    Constructed from    ribosomal RNA    sequences                       12
Unikonts                 BikontsThe Deep Roots of Eukaryotes, S. L. Baldauf, Science Jun 1                                ...
Fungi can could have two names   (anamorph and telomorph)     Anamorph is asexual phase,      telomorph is sexual stage[DN...
“Protists” (animal, plant, or both?)           (ambiregnal)
MicrosporidaOriginally regarded as protists and named underzoological code, they are now known to be fungi, butwill remain...
Homonyms Paris, Texas
Skull, mandible and tooth morphology of the holotype of L. melvillei MUSM 1676.O Lambert et al.Nature466, 105-108 (2010) d...
Leviathan melvillei
But Leviathan had already been    used as a genus name…
Oops…
Leviathan melvillei
Livyatanmelvillei
Why homonyms matter
Caeciliidae
Search GBIF in 2008 for “Caeciliidae”
Caeciliidae
Types of synonym  http://biostor.org/reference/17
HemihomonymsSame name, different code
MorusMulberry tree           Gannet                                 32
Agathis          33
Some plant and animal species have          the same name• Agathis montana (tree and wasp)• Abronia aurita (plant and liza...
Synonyms
@ryanschenk              http://synynyms.no.de/
All yourbase after1923 arebelong to us
Why do names change?
Opaque identifiers(you shouldn’t infer anything about  an object based on its identifier)
58D31D52-713D-44B4-9FE9-CB2D9249C422              versus          Homo sapiens
Opacity is a nice idea• Fundamental axiom of the web, but…• We invest identifiers with meaning  (even if we “shouldn’t”)• ...
Taxonomic names can indicate      relationship, and can be descriptive• Homo sapiens Linnaeus 1758 (modern man)• Homo nean...
Names can tell us about relationships              Cherie Booth                                        43
Name changes matterCherie Booth       Cherie Blair                                  44
Name changes matterJonathon Roughgarden   =   Joan Roughgarden                                              45
One reason taxonomic nameschange is because we invest them           with meaning (they are not opaque identifiers)
Drosophila
Type specimenSpeciesname
Genusname         Type speciesDrosophila   Drosophila funebris
Drosophila               Drosophila               funebris             Drosophila             melanogaster
How do make Drosophila taxonomy fit            the tree?• Make everything DrosophilaBig genus, have to rename lots of spec...
Asked ICZN: Can we change type    species of Drosophila?
ICZN says “no”
Problem is premise that names have           to match tree                              Drosophila                        ...
Types of synonym
Objective(no biology required)
Pithecanthropus erectus Dubois, 1894   = Homo erectus (Dubois, 1894)
Subjective(biology required)
Ioraniaconcordia&Rimicarisaurantiaca= Rimicarisexoculata  Genetic data show  small, orange, deep-vent  shrimps described a...
Classification ( ≠ phylogeny)
Classification can be contentious
Figure 32.12 Comparing the molecular based and grade-based trees of                         animal phylogeny
Coelomata(we should be looking at flies)         Coelomata     (true body cavity)
Ecdysozoa(flies and nematodes are both OK)                      Ecdysozoa
Viewing classifications
http://treevis.net
Voronitreemap
The End
Taxonomy
Taxonomy
Taxonomy
Taxonomy
Taxonomy
Taxonomy
Taxonomy
Taxonomy
Taxonomy
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Taxonomy

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  • 2007 was 300th anniversary of his birth
  • Coverage is not universal (ironically), different codes, leads to homonyms (give examples, e.g. Morus, Agathismontana,) Mention web sites that suffer from these problems
  • With the Melbourne 2011 code fungi will have a single name
  • Homonym, see http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=159975&lvl=3&lin=f&keep=1&srchmode=1&unlock name in insects has been suppressed since 1996
  • Homonym, see http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=159975&lvl=3&lin=f&keep=1&srchmode=1&unlock name in insects has been suppressed since 1996
  • http://diptera.info/forum/attachments/jf09-0798.jpg
  • http://diptera.info/forum/attachments/jf09-0798.jpg
  • Taxonomy

    1. 1. Taxonomy
    2. 2. Linnaeus
    3. 3. ヒメアギトアリ(Anochetus shohki)の画像一覧 3
    4. 4. Fun with Latin• Abracadabra (abracadabra)• Bahumbugi (ba humbug)• Eurygenius (youre a genius)• Gelaebaen (jelly bean)• Heerzlukenatcha (hurts lookin atcha)• Piezakake (piece a cake)• Ytubrutus (et tu Brutus) 4
    5. 5. Scatological fun with Latin• Bugeranus• Doryctes fartus• Dyaria• Eremobates inyoanus• Pison eu• Soranus 5
    6. 6. Indri indriOften claimedname means“look!” or “there”in Malagasy(story is more complicated, see Wikipedia page http://en.wikipedia.org/wiki/Indri ) 6
    7. 7. Nomenclature has inherited aquaint view of the tree of life
    8. 8. Animals(International Code of Zoological Nomenclature)
    9. 9. Plants and Fungi(International Code of Botanical Nomenclature)
    10. 10. Bacteria (International Code ofNomenclature of Bacteria)
    11. 11. Evolutionary tree for all of life Constructed from ribosomal RNA sequences 12
    12. 12. Unikonts BikontsThe Deep Roots of Eukaryotes, S. L. Baldauf, Science Jun 1 13
    13. 13. Fungi can could have two names (anamorph and telomorph) Anamorph is asexual phase, telomorph is sexual stage[DNA makes it possible to match the two]
    14. 14. “Protists” (animal, plant, or both?) (ambiregnal)
    15. 15. MicrosporidaOriginally regarded as protists and named underzoological code, they are now known to be fungi, butwill remain under zoological rules for naming.
    16. 16. Homonyms Paris, Texas
    17. 17. Skull, mandible and tooth morphology of the holotype of L. melvillei MUSM 1676.O Lambert et al.Nature466, 105-108 (2010) doi:10.1038/nature09067
    18. 18. Leviathan melvillei
    19. 19. But Leviathan had already been used as a genus name…
    20. 20. Oops…
    21. 21. Leviathan melvillei
    22. 22. Livyatanmelvillei
    23. 23. Why homonyms matter
    24. 24. Caeciliidae
    25. 25. Search GBIF in 2008 for “Caeciliidae”
    26. 26. Caeciliidae
    27. 27. Types of synonym http://biostor.org/reference/17
    28. 28. HemihomonymsSame name, different code
    29. 29. MorusMulberry tree Gannet 32
    30. 30. Agathis 33
    31. 31. Some plant and animal species have the same name• Agathis montana (tree and wasp)• Abronia aurita (plant and lizard) 34
    32. 32. Synonyms
    33. 33. @ryanschenk http://synynyms.no.de/
    34. 34. All yourbase after1923 arebelong to us
    35. 35. Why do names change?
    36. 36. Opaque identifiers(you shouldn’t infer anything about an object based on its identifier)
    37. 37. 58D31D52-713D-44B4-9FE9-CB2D9249C422 versus Homo sapiens
    38. 38. Opacity is a nice idea• Fundamental axiom of the web, but…• We invest identifiers with meaning (even if we “shouldn’t”)• In practice we rely on parsing identifiers (I trust “google.com” more than “givemeyourcreditcardnumberquick.com” )• Opacity ≠ obscurity (human readable identifiers not necessarily bad)
    39. 39. Taxonomic names can indicate relationship, and can be descriptive• Homo sapiens Linnaeus 1758 (modern man)• Homo neanderthalensis King, 1864 (Neanderthal man)• Homo erectus (Dubois, 1892) (upright man)• Pan troglodytes (Blumenbach, 1775) (chimpanzee) 42
    40. 40. Names can tell us about relationships Cherie Booth 43
    41. 41. Name changes matterCherie Booth Cherie Blair 44
    42. 42. Name changes matterJonathon Roughgarden = Joan Roughgarden 45
    43. 43. One reason taxonomic nameschange is because we invest them with meaning (they are not opaque identifiers)
    44. 44. Drosophila
    45. 45. Type specimenSpeciesname
    46. 46. Genusname Type speciesDrosophila Drosophila funebris
    47. 47. Drosophila Drosophila funebris Drosophila melanogaster
    48. 48. How do make Drosophila taxonomy fit the tree?• Make everything DrosophilaBig genus, have to rename lots of species• Restrict Drosophila to a monophyletic group that includes the type species (D. funebris)Drosophila melanogastercan’t be Drosophila melanogaster• Change the type species toDrosophilamelanogasterBut nomenclature is not taxonomy
    49. 49. Asked ICZN: Can we change type species of Drosophila?
    50. 50. ICZN says “no”
    51. 51. Problem is premise that names have to match tree Drosophila funebris Drosophila melanogaster
    52. 52. Types of synonym
    53. 53. Objective(no biology required)
    54. 54. Pithecanthropus erectus Dubois, 1894 = Homo erectus (Dubois, 1894)
    55. 55. Subjective(biology required)
    56. 56. Ioraniaconcordia&Rimicarisaurantiaca= Rimicarisexoculata Genetic data show small, orange, deep-vent shrimps described as new species are actually juvenile Rimicarisexoculata
    57. 57. Classification ( ≠ phylogeny)
    58. 58. Classification can be contentious
    59. 59. Figure 32.12 Comparing the molecular based and grade-based trees of animal phylogeny
    60. 60. Coelomata(we should be looking at flies) Coelomata (true body cavity)
    61. 61. Ecdysozoa(flies and nematodes are both OK) Ecdysozoa
    62. 62. Viewing classifications
    63. 63. http://treevis.net
    64. 64. Voronitreemap
    65. 65. The End

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