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Validating taxonomic names (BITW 2013)

Validating taxonomic names (BITW 2013)

A presentation on the complications of name validation.

Gaurav Vaidya

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

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  2. Taxonomic checklists

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

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  4. Nomenclatural codes

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  5. Nomenclatural codes

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  6. Nomenclatural codes

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

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

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

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

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

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  12. Taxonomic checklists

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  13. Online taxonomic checklists

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  14. Online taxonomic checklists

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  15. Online taxonomic checklists

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  16. Online taxonomic checklists

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

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

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

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  20. Integrated Taxonomic
    Information System (ITIS)
    http://www.itis.gov/

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

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  22. GBIF Checklist Bank (beta)

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

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

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

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  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.

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  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).

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  28. Junius Henderson
    b. 1865 – d. 1937

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  29. http://bit.ly/jhfnblog

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

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  31. 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.

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  32. Validating common names

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

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  34. 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

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

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

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

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

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

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  40. 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

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  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
    Carpodacus mexicanus (Statius Muller, 1776)

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

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

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

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  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)
    Boulder, Colorado

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  46. Synonymy
    Henderson records “housefinches -- singing in town”

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

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

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  49. 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.

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  50. Cross-code homonymy

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  51. Cross-code homonymy

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  52. Cross-code homonymy

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  53. Cross-code homonymy

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  54. 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”?

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  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”?
    1909: Nannus hiemalis

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  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
    1944: Combined into Troglodytes troglodytes.

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  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.
    2010: Split into three species, including Troglodytes hiemalis.

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

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  59. 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.

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  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.
    It’s hard to know what someone meant by a name.

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  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.
    Patience, diligence and a good search engine.

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  62. http://tinyurl.com/bitw-taxon

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  63. 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

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