Barcodes and Zoocodes

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

2. Outline • Protistan issues • What ICZN says (and what it doesn’t) • 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 Distigma Dolium Entosiphon Heteronema Metanema Peranema Phacus Urceolus have homonyms Then there’s 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 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

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 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?

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. Semantic web for biology Applications – working with the complexity of biology Workbench to engage the experts Unified framework Classifications & other opinions Fix names problems Other organizational systems Compile all names TAXONOMIC INTELLIGENCE All pieces of information about organisms An architecture for managing biodiversity information on the web `

18. 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

19. 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.

20. 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

21. 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

22. Thank you

24. 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

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

26. Who is affected by these problems? Search engines Libraries Students and researchers Publishers Museums Federated databases Federal Agencies Red spotted newt

27. Semantic web for biology Applications – working with the complexity of biology A 2.0 workbench to engage the experts A unified framework Classifications & other opinions Fix names problems Other organizational systems Compile all names TAXONOMIC INTELLIGENCE All pieces of information about organisms Where may barcodes fit into the picture