1 barcodes and zoocodes david j patterson dpatterson@mbl.edu
Post on 16-Dec-2015
215 Views
Preview:
TRANSCRIPT
2Barcodes and Zoocodes
Outline
• Protistan issues
• What ICZN says (and what it doesn’t)
• Changing landscape
• How bar codes might fit in
3Barcodes and Zoocodes
Protists and ambiregnal problems –
Peranema trichophorum (Ehrenberg, 1830) Dujardin 1841
Pseudoperanema hyalinum Christen, 1962
• 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
4Barcodes and Zoocodes
Of the 30+ genera of heterotrophic euglenids
AnisonemaAstasiaAtractonemaCalkinsiaDinemaDistigmaDoliumEntosiphonHeteronemaMetanemaPeranemaPhacusUrceolus
have homonyms
Then there’s the dinoflagellates, the stramenopiles, the cryptomonads, the …
5Barcodes and Zoocodes
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
6Barcodes and Zoocodes
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
7Barcodes and Zoocodes
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
8Barcodes and Zoocodes
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).
9Barcodes and Zoocodes
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 useun-interpreted (photographic)type material, but this is notcode-compliant
• Absence of good types creates unstable (imprecise) concepts that cannot be resolved with current approaches
10Barcodes and Zoocodes
Not included in the Code as type material are
• Living material (such as cultures)
• Sequence information such as barcodes
12Barcodes and Zoocodes
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’)
13Barcodes and Zoocodes
Names offer a logical way to search for and index content
• 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
The significance of names
14Barcodes and Zoocodes
Indexes - what works in books doesn’t 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 embeddedin on-line documents
• SO, which name to use in the index?
15Barcodes and Zoocodes
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
16Barcodes and Zoocodes
Peranema – the fern
And for us, most significantly, are problems of homonyms
Peranema – the euglenid
14% plant generic names have also been used for non-plants
17Barcodes and Zoocodes
All pieces of information about organisms
Oth
er
orga
niza
tion
al
syst
ems
Compile all names
Fix names problems
Classifications & other opinions
Unified framework
Workbench to engage the experts
Applications – working with the complexity of biology
Semantic web for biology
TA
XO
NO
MIC
IN
TE
LL
IGE
NC
E
An architecture for managing biodiversity information on the web `
19Barcodes and Zoocodes
• 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
Where may barcodes fit into this picture
20Barcodes and Zoocodes
• 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.
What has to be done – concept reconciliation
21Barcodes and Zoocodes
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
22Barcodes and Zoocodes
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
26Barcodes and Zoocodes
• 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
Where may barcodes fit into the picture
27Barcodes and Zoocodes
RSS feed reader
Some examples of taxonomic intelligence in action
http://microscope.mbl.eduhttp://www.ubio.org
28Barcodes and Zoocodes
Libraries
Publishers
MuseumsFederal Agencies
Who is affected by these problems?
Search engines
Federated databases
Students and researchers
106000
515
35800
33
712
155850
18700Red spotted newt
29Barcodes and Zoocodes
Where may barcodes fit into the picture
All pieces of information about organisms
Oth
er
orga
niza
tion
al
syst
ems
Compile all names
Fix names problems
Classifications & other opinions
A unified framework
A 2.0 workbench to engage the experts
Applications – working with the complexity of biology
Semantic web for biology
TA
XO
NO
MIC
IN
TE
LL
IGE
NC
E
top related