1 Barcodes and Zoocodes David J Patterson [email protected]

1Barcodes and Zoocodes

Barcodes and Zoocodes

David J Patterson

[email protected]


Outline

• Protistan issues

• What ICZN says (and what it doesn’t)

• Changing landscape

• How bar codes might fit in


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


Of the 30+ genera of heterotrophic euglenids

AnisonemaAstasiaAtractonemaCalkinsiaDinemaDistigmaDoliumEntosiphonHeteronemaMetanemaPeranemaPhacusUrceolus

have homonyms

Then there’s the dinoflagellates, the stramenopiles, the cryptomonads, the …


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


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


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


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).


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


Not included in the Code as type material are

• Living material (such as cultures)

• Sequence information such as barcodes


Relationship between barcodes and zoocode

• Nil


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’)


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


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?


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


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


All pieces of information about organisms

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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

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An architecture for managing biodiversity information on the web `


• 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


• 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


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


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


Thank you



• 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


RSS feed reader

Some examples of taxonomic intelligence in action

http://microscope.mbl.eduhttp://www.ubio.org


Libraries

Publishers

MuseumsFederal Agencies

Who is affected by these problems?

Search engines

Federated databases

Students and researchers

106000

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712

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18700Red spotted newt


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

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Documents

1 Barcodes and Zoocodes David J Patterson [email protected]