Validating taxonomic names (BITW 2013)

Validating taxonomic names (BITW 2013)

A presentation on the complications of name validation.

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Gaurav Vaidya

June 24, 2013
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  1. VALIDATING TAXONOMIC NAMES Victoria Tersigni (Dartmouth) Gaurav Vaidya (CU Boulder)

  2. Taxonomic checklists

  3. Taxonomic checklists Homo sapiens Felis tigris Delphinus orca Magnifera indica

    Linnaea borealis
  4. Nomenclatural codes

  5. Nomenclatural codes

  6. Nomenclatural codes

  7. Components of a name Felis tigris Linnaeus, 1758 [=> Panthera

    tigris (Linnaeus, 1758)] (Animalia) Linnaean/taxonomic name (and the result of taxon reconciliation later!)
  8. Components of a name Felis tigris Linnaeus, 1758 [=> Panthera

    tigris (Linnaeus, 1758)] (Animalia) Canonical/binomial name (not in Darwin Core!)
  9. Components of a name Felis tigris Linnaeus, 1758 [=> Panthera

    tigris (Linnaeus, 1758)] (Animalia) Authority (dwc:scientificNameAuthorship)
  10. Components of a name Felis tigris Linnaeus, 1758 [=> Panthera

    tigris (Linnaeus, 1758)] (Animalia) Accepted name (dwc:acceptedNameUsage)
  11. Components of a name Felis tigris Linnaeus, 1758 [=> Panthera

    tigris (Linnaeus, 1758)] (Animalia) Higher taxonomy (dwc:higherClassification)
  12. Taxonomic checklists

  13. Online taxonomic checklists

  14. Online taxonomic checklists

  15. Online taxonomic checklists

  16. Online taxonomic checklists

  17. Online taxonomic checklists Lists of names and accepted names.

  18. Online taxonomic checklists Lists of names and accepted names. Formatted

    according to the nomenclatural codes.
  19. Online taxonomic checklists Lists of names and accepted names. Formatted

    according to the nomenclatural codes. Downloadable?
  20. Integrated Taxonomic Information System (ITIS) http://www.itis.gov/

  21. ITIS meets Darwin Core http://gaurav.github.com/itis-dwca/

  22. GBIF Checklist Bank (beta)

  23. TaxRefine http://www.github.com/gaurav/taxrefine

  24. Summary the First 1. Names are ridiculously awesome.

  25. Summary the First 1. Names are ridiculously awesome. 2. Different

    nomenclatural codes work differently.
  26. Summary the First 1. Names are ridiculously awesome. 2. Different

    nomenclatural codes work differently. 3. Names have parts, all of which can be important.
  27. Summary the First 1. Names are ridiculously awesome. 2. Different

    nomenclatural codes work differently. 3. Names have parts, all of which can be important. 4. Multiple checklists may disagree on which is the correct accepted name (synonymy).
  28. Junius Henderson b. 1865 – d. 1937

  29. None
  30. http://bit.ly/jhfnblog

  31. http://bit.ly/henderson-simplified

  32. Two kinds of names Scraped Name: what Henderson wrote in

    his notebook. Annotator Name: what our (mysteriously anonymous annotators) thought the correct accepted taxonomic name for that species was.
  33. Validating common names

  34. Validating common names Can be confusing: “limpet”: http://en.wikipedia.org/wiki/Limpet “fish”: http://en.wikipedia.org/wiki/Fish

    “water snakes”: eh?
  35. Validating common names Can be confusing: “limpet”: http://en.wikipedia.org/wiki/Limpet “fish”: http://en.wikipedia.org/wiki/Fish

    “water snakes”: eh? But sometimes very specific: “English sparrow”: Passer domesticus “American goldfinch”: Carduelis tristis “Say phoebe”: Sayornis saya “robin”: Turdus migratorius
  36. Names when correct What does a scientific name look like

    when it’s correct?
  37. Names when correct What does a scientific name look like

    when it’s correct? Zonitoides arboreus
  38. Names when correct What does a scientific name look like

    when it’s correct? Zonitoides arboreus O. congesta
  39. Names when correct What does a scientific name look like

    when it’s correct? Zonitoides arboreus O. congesta Succinea cf. avara
  40. Names when correct What does a scientific name look like

    when it’s correct? Zonitoides arboreus O. congesta Succinea cf. avara Junco sp.
  41. Names when correct What does a scientific name look like

    when it’s correct? Zonitoides arboreus O. congesta Succinea cf. avara Junco sp. Gymnorhinus cyanocephalus Wied-Neuwied 1841
  42. Names when correct What does a scientific name look like

    when it’s correct? Zonitoides arboreus O. congesta Succinea cf. avara Junco sp. Gymnorhinus cyanocephalus Wied-Neuwied 1841 Carpodacus mexicanus (Statius Muller, 1776)
  43. Names when wrong What does a scientific name look like

    when it’s wrong?
  44. Names when wrong What does a scientific name look like

    when it’s wrong? “Limnaea” (misspelling of Lymnaea)
  45. Names when wrong What does a scientific name look like

    when it’s wrong? “Limnaea” (misspelling of Lymnaea) “Tyrranus verticalis” (misspelling of Tyranus verticalis)
  46. Names when wrong What does a scientific name look like

    when it’s wrong? “Limnaea” (misspelling of Lymnaea) “Tyrranus verticalis” (misspelling of Tyranus verticalis) Boulder, Colorado
  47. Synonymy Henderson records “housefinches -- singing in town”

  48. Synonymy Henderson records “housefinches -- singing in town” Original description:

    Fringi!a mexicana Statius Müller, 1776
  49. Synonymy Henderson records “housefinches -- singing in town” Original description:

    Fringi!a mexicana Statius Müller, 1776 By 1900, known as Carpodacus mexicanus.
  50. Synonymy Henderson records “housefinches -- singing in town” Original description:

    Fringi!a mexicana Statius Müller, 1776 By 1900, known as Carpodacus mexicanus. In 2012, renamed to Haemorhous mexicanus.
  51. Cross-code homonymy

  52. Cross-code homonymy

  53. Cross-code homonymy

  54. Cross-code homonymy

  55. Changing meanings Henderson wrote (at “Boulder, Feby 13, 1909”): “Saw

    only usual number of magpies and long crested jays, one buzzard, a few chickadees, one canyon or winter wren and one pine squirrel” What did he mean by “winter wren”?
  56. Changing meanings Henderson wrote (at “Boulder, Feby 13, 1909”): “Saw

    only usual number of magpies and long crested jays, one buzzard, a few chickadees, one canyon or winter wren and one pine squirrel” What did he mean by “winter wren”? 1909: Nannus hiemalis
  57. Changing meanings Henderson wrote (at “Boulder, Feby 13, 1909”): “Saw

    only usual number of magpies and long crested jays, one buzzard, a few chickadees, one canyon or winter wren and one pine squirrel” What did he mean by “winter wren”? 1909: Nannus hiemalis 1944: Combined into Troglodytes troglodytes.
  58. Changing meanings Henderson wrote (at “Boulder, Feby 13, 1909”): “Saw

    only usual number of magpies and long crested jays, one buzzard, a few chickadees, one canyon or winter wren and one pine squirrel” What did he mean by “winter wren”? 1909: Nannus hiemalis 1944: Combined into Troglodytes troglodytes. 2010: Split into three species, including Troglodytes hiemalis.
  59. Summary the Second It’s hard for computers to read and

    make sense of names (but OpenRefine can make this easier).
  60. Summary the Second It’s hard for computers to read and

    make sense of names (but OpenRefine can make this easier). It’s hard to know which of several names is currently accepted.
  61. Summary the Second It’s hard for computers to read and

    make sense of names (but OpenRefine can make this easier). It’s hard to know which of several names is currently accepted. It’s hard to know what someone meant by a name.
  62. Summary the Second It’s hard for computers to read and

    make sense of names (but OpenRefine can make this easier). It’s hard to know which of several names is currently accepted. It’s hard to know what someone meant by a name. Patience, diligence and a good search engine.
  63. http://tinyurl.com/bitw-taxon

  64. Images used Wikimedia Commons: Systema naturae, 10th edition: http://commons.wikimedia.org/wiki/File:Linnaeus1758-title-page.jpg Species

    Plantarum: http://commons.wikimedia.org/wiki/File:Species_plantarum_002.JPG Junius Henderson: http://commons.wikimedia.org/wiki/File:Junius_Henderson.jpg Crucibulum (fungi): http://commons.wikimedia.org/wiki/File:2012-08-13_Crucibulum_laeve_%28Huds.-_Relh %29_Kambly_248884_crop.jpg Crucibulum (gastropod): http://en.wikipedia.org/wiki/File:Crucibulum_deformis_01.JPG Ficus (gastropod): http://en.wikipedia.org/wiki/File:Ficus_gracilis_01.JPG Ficus (plant): http://commons.wikimedia.org/wiki/File:Ra%C3%ADces_superficiales.JPG Screenshots of the following websites: http://www.eol.org/ http://www.antweb.org/ http://www.cites.org/ “Darwin Core” image from http://www.canadensys.net/wp-content/uploads/darwin-core-unofficial-logo.jpg Book covers from: http://www.andrewisles.com/assets/Bookmine/BMImg_26493_26493_Christidis_syst_web.jpg http://www.nhbs.com/images/jackets_resizer_large/17/172431.jpg http://www.nhbs.com/world_catalogue_of_insects_volume_10_psychidae_lepidoptera_tefno_177350.html Clements checklist: http://www.birds.cornell.edu/clementschecklist/images/BookCover.jpg