1. 1 Barcodes and Zoocodes David J Patterson dpatterson@mbl.edu

2. 2 Barcodes and Zoocodes Outline Protistan issues What ICZN says (and what it doesn’t) Changing landscape How bar codes might fit in

3. 3 Barcodes 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

4. 4 Barcodes and Zoocodes Of the 30+ genera of heterotrophic euglenids Anisonema Astasia Atractonema Calkinsia Dinema Distigma Dolium Entosiphon Heteronema Metanema Peranema Phacus Urceolus have homonyms Then there’s the dinoflagellates, the stramenopiles, the cryptomonads, the …

5. 5 Barcodes 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

6. 6 Barcodes 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

7. 7 Barcodes 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

8. 8 Barcodes 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).

9. 9 Barcodes 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 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. 10 Barcodes and Zoocodes Not included in the Code as type material are Living material (such as cultures) Sequence information such as barcodes

11. 11 Barcodes and Zoocodes Relationship between barcodes and zoocode Nil

12. 12 Barcodes 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’)

13. 13 Barcodes 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

14. 14 Barcodes 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 embedded in on-line documents SO, which name to use in the index?

15. 15 Barcodes 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

16. 16 Barcodes 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

17. 17 Barcodes and Zoocodes All pieces of information about organisms Other organizational systems 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 TAXONOMIC INTELLIGENCE An architecture for managing biodiversity information on the web `

18. 18 Barcodes and Zoocodes KNOWLEDGE On the fly pages for all species customised for every user PORTAL Knowledge and aggregation technology deliver species pages Information becomes knowledge-rich statements Biology 2.0 WORKBENCH An on-line environment that allows experts to create knowledge All information within a unified navigable framework UNION A comprehensive, flexible, authoritative framework for knowledge Species information placed in evolutionary context CLASSIFICATION BANK Incorporating opinions about relationships Compilations of facts about species NAMES MANAGEMENT BY NAMEBANK SERVICES Fixing names problems with taxonomic intelligence Compendia of facts indexed by names NAMES – INDEXING TERMS – NAMEBANK DATABASE All names for all organisms - the means to index all content All content

19. 19 Barcodes 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

20. 20 Barcodes 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

21. 21 Barcodes 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

22. 22 Barcodes 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

23. 23 Barcodes and Zoocodes Thank you

24. 24 Barcodes and Zoocodes

25. 25 Barcodes and Zoocodes 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. 26 Barcodes 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

27. 27 Barcodes and Zoocodes RSS feed reader Some examples of taxonomic intelligence in action http://microscope.mbl.edu http://www.ubio.org

28. 28 Barcodes and Zoocodes Libraries Publishers Museums Federal Agencies Who is affected by these problems? Search engines Federated databases Students and researchers 106000 515 35800 33 712 155850 18700 Red spotted newt

29. 29 Barcodes and Zoocodes Where may barcodes fit into the picture All pieces of information about organisms Other organizational systems 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 TAXONOMIC INTELLIGENCE