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Barcodes and Zoocodes

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(Ehrenberg, 1830) Dujardin 1841. Pseudoperanema hyalinum Christen, 1962 ... Red spotted newt. 29. Barcodes and Zoocodes. Where may barcodes fit into the picture ... – PowerPoint PPT presentation

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Title: Barcodes and Zoocodes


1
Barcodes and Zoocodes
David J Patterson dpatterson_at_mbl.edu
2
Outline
  • Protistan issues
  • What ICZN says (and what it doesnt)
  • Changing landscape
  • How bar codes might fit in

3
Protists and ambiregnal problems
  • Protists are neither plants nor animals
  • Nomenclaturally, they can be treated as either
  • or both
  • Leading to interesting consequences
  • Such as Peranema / Pseudoperanema
  • - and its 2 type species

Pseudoperanema hyalinum Christen, 1962
Peranema trichophorum (Ehrenberg, 1830) Dujardin
1841
4
Of the 30 genera of heterotrophic euglenids
Anisonema Astasia Atractonema Calkinsia Dinema D
istigma Dolium Entosiphon Heteronema Metanema Pera
nema Phacus Urceolus have homonyms
Then theres the dinoflagellates, the
stramenopiles, the cryptomonads, the
5
What is covered by the Zoo code
  • A name, being a label or a flag for the concept
    criteria are set by the code
  • The species is nebulous we do not know what
    species are, otherwise we would not be able to
    bring a meeting to its knees by asking the
    question, So, what do YOU think a species is?
  • Concept, a precise but inaccurate model of a
    species
  • Type material criteria are set by the code
  • Description in a publication criteria are set
    by the code
  • Observations

6
Imprecise relationships between concepts and
species
  • May be separated from the species (bad
    descriptions)
  • May overlap with the concept
  • May be part of the range of the species (most
    common)
  • Indeed more than one concept may be included
    within the species (subjective synonyms)
  • Or a concept may be much broader than the
    species
  • Or embrace more than one species
  • The concept ? reality
  • Concepts may be precise but are always inaccurate

7
Types reference points for the concept
  • There are many kinds of types
  • For species, types are specimens
  • Holotype, a singular entity
  • Type series, comprised of syntypes, from which a
    lectotype may be selected
  • Neotype offers a device to create a new type

8
What can be a type
  • An animal, or part of an animal, or the
    fossilized work of an animal or the work of an
    animal for names established before 1931
  • A colony or part of a colony (e.g. corals)
  • A natural replacement, impression, mould or part
    thereof
  • (72.5.4) in extant species of protistans, one or
    more preparations of directly individuals
    representing different stages of the life cycle
    (a hapantotype)
  • A microscopic preparation in which the relevant
    type-material is clearly indicated
  • (72.5.6) In the case of a nominal species-group
    taxon based on an illustration or description, or
    a bibliographic reference to an illustration or
    description, the name-bearing type is the
    specimen or specimens illustrated (and not the
    illustration or description itself).

9
How well typified are protozoa
  • Very poorly
  • Foraminifera are the most speciose group, they
    form shells, and these are used as types
  • Ciliates are reasonably speciose, and many recent
    descriptions have type material in the form of
    silver-stained preparations on glass slides but
    these fade
  • For most protists, only interpreted illustrations
    are available
  • We have tended to use un-interpreted
    (photographic) type material, but this is
    not code-compliant
  • Absence of good types creates unstable
    (imprecise) concepts that cannot be resolved
    with current approaches

10
Not included in the Code as type material are
  • Living material (such as cultures)
  • Sequence information such as barcodes

11
Relationship between barcodes and zoocode
  • Nil

12
Why pluralize Zoocodes
  • The nature and role of systematics is changing
    to embrace informatics
  • Zoology has begun a new phase, with the first
    version of an on-line names registry
  • This will survive because nomenclature is
    fundamental to the management of biological
    information
  • Informatics needs a unified nomenclatural
    foundation (i.e. no more of the parochiality of
    plants and animals)

13
The significance of names
  • Names annotate data objects
  • All names annotate all data objects
  • A compilation of all names ever used is the
    foundation of a universal index for biology
  • or for a semantic web for biology

Names offer a logical way to search for and
index content
14
Indexes - what works in books doesnt necessarily
work on the internet
  • Because names of organisms change over time
  • or can be mis-spelled
  • or have vernacular versions
  • All of which will be embedded in on-line
    documents
  • SO, which name to use in the index?

15
Reconciliation linking alternative names for
the same organism
A query initiated with any name, can be expanded
to all names and will unify data associated with
each
16
And for us, most significantly, are problems of
homonyms
Peranema the fern
14 plant generic names have also been used for
non-plants
Peranema the euglenid
17
An architecture for managing biodiversity
information on the web
18
All content
19
Where may barcodes fit into this picture
  • NOT compliant with the code
  • BUT
  • Acting as surrogates for type material
    overcoming the lack of type material problem. As
    they have no validity under the code, they need
    to be chained to something that can be associated
    with traditional taxonomy a kind of vouchering
  • Acting as a taxonomic concept anything with
    100 similarity to this barcode is the same
    entity (the uncertain relationships between the
    concept and species remain)
  • As the flag, a replacement for a conventional
    name that can tie into an informatics environment

20
What has to be done concept reconciliation
  • Barcode-concepts are precise and low cost
    identifiers for taxa
  • The relationship among barcode concepts and
    traditional concepts will need to be assessed
  • The most discriminating barcode will be more
    helpful in this regard
  • Would benefit from an (automated) protocol that
    will assess on a case by case basis the
    relationship with phylogenetic trees.

21
What has to be done informatics links
Barcode
Phylogenetic analysis - concept reconciliation
links barcode to names (cultures have a role
here)
Taxonomic intelligence chains barcode to name and
to local and distributed content
22
In sum
  • The code is not relevant
  • Favor the most discriminatory barcode
  • Concept reconciliation is important but not an
    overwhelming challenge
  • Embed the processes within the emergent
    informatics structure

23
  • Thank you

24
(No Transcript)
25
Disambiguation distinguishing spelled alike
names for different things
  • Clues ( rulesets) that allow automated tools to
    discriminate the euglenid from the fern
  • Peranema Dons (the fern) Peranema Dujardin (the
    euglenid)
  • Peranema and Pteridophyta vs Peranema and
    Euglenida
  • Peranema trichophorum, or Peranema, Anisonema
    and Urceolus

26
Where may barcodes fit into the picture
  • This troika is potentially very powerful
  • The use of barcodes is inevitable
  • They offer an accelerated mechanism to catalog
    and identify (map to concepts) and instantly
    engage the informatics structure

27
Some examples of taxonomic intelligence in action
RSS feed reader
http//microscope.mbl.edu http//www.ubio.org
28
Who is affected by these problems?
Search engines
Libraries
Publishers
Students and researchers
Museums
Federated databases
Federal Agencies
106000
515
35800
33
712
155850
18700
Red spotted newt
29
Where may barcodes fit into the picture
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