Dear Donald,
Thanks for your e-mail. I agree with Richards reply, the used definition of taxon names and taxon concepts are a bit confusing and not directly matching the zoological point of view.
For a zoologist a taxon name is the naked name plus the authorship (author and year). At the species level this includes the epithet and authorship and often a link to the original genus. In the TCS I thought a naked taxon name is called a name-element. For botanists this part of nomenclature is rather implicit and the zoologist's (pre-)occupation on these details quite obscure.
When a species-group name (so the epithet/author/year) is linked to a genus-group name we obtain a scientific species name (so the actual binominal), often also called the species concept, but in general we understand as species concept the species name plus the associated subjective synonyms (although the semantics on this point are a bit fuzzy). I think your 'taxon name' is equivalent with the scientific species name.
The taxon concept is considered the use of a species concept in literature, so that equals your definition, however, the issue of taxon concepts is very much a botanic subject. This is caused by the fact that plants are sessile and have to adapt to local circumstances (animals run away from unfavorable environments). Due to local adaptation (phenotypic plasticity) each plant specimen can be considered as a crucial observation to verify a species concept. Another reason is that in contrast to plants asexuality is an exception in most non-sessile animal groups which provides a more randomly cross-breeding population and more morphological homogeneity. For zoologist the issue of taxon concept is more implicit and often merged to the issue of species concept, but of course this much depends on the taxonomic group.
The reason why zoologists are more focused on epithets compared to botanist is twofold:
(1) Zoologists (particularly entomologists) are not bookkeepers of nomenclatural history in a way botanist are. Especially objective synonymy is (i) not fully catalogued and (ii) solved at the generic level (as synonyms of genus names) if relevant. The historical reason to this practise is highly pragmatic: The -compared to botany- few entomologists have to deal with so many species names, so many parallel descriptive efforts in the past, and commonly incomplete taxonomic treatments that a nomenclatural bookkeeping sensu botany is out of question. Within Fauna Europaea we experienced that many entomologists even don't feel the slightest need to (as they call it) "maintain the trash of history".
(2) In zoology we have less homonomy compared to botany, especially when the authorship is taken into account. This could be partly due to the compared to botany extended authorship (also including year) and partly to other constraints (e.g. the fact that the zoological society is more divided and therefore more original in its naming). As a consequence zoologists are less drowning in a sea of homonyms and therefore there is less need to refer to identification anchors like for instance original publications. Thus I think taxon names in zoology are far more suitable for GUIDs compared to botany.
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How is Fauna Europaea organised?
- Basically we have a list of 'naked' taxon names (from the infraspecific level to Kingdom) including full authorship for at least the generic and (infra)specific levels. All those taxon names (read: name elements) have unique id's.
- All epithets are linked to their original genus, so original combinations can be reconstructed. This is nearly, but not completely similar to basionyms in botany because gender unequivalencies are not necessarily corrected.
- Species names are created by recursively linking species-group names to genus-group names. Genus names are parents of specific epithets, and specific epithets are parents of infraspecific epithets.
- Subjective synonyms are specific epithets recursively linked as childs to 'accepted' specific epithets. For objective synonymy genus names synonyms are recursively linked as childs to 'accepted' genus names.
- Conclusion: Names (=naked name element/author/year plus original genus for epithets) are for eternity. Species names (so your taxon names) are temporary concepts (if they are not basionyms) which don't have identifiers and which are not kept in the database after taxonomic changes else then by version control.
- However, an unique species name id can be easily artificially created by merging both generic and epithet id's (a trick we also use for Species2000).
- Taxon concepts are not explicitly covered.
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About TCS, GUIDs and nomenclators.
During the TDWG meeting at Christchurch I was happy the TCS did allow the flexibility of building up species and taxon concepts from scratch (so from the name elements). In St Petersburg I discovered that the adapted TCS had been botanized and the starting point moved to the binominal. Due to that zoologists evidently lose some nomenclatural playground and a possibility of 1:1 matching of their names to the schema. However, that's not a major problem because for most mappings zoological databases need to set up views anyway. The root for taxonomic modelling now is the original combination (= basionym) which is persistent, hence OK. My only remaining concern is the implementation of objective synonymy which is fundamentally different in entomology.
For practical reasons I think the starting point for assigning GUIDs should be basically nomenclatural. This mean that we should establish nomenclators and leave taxonomy out for the moment. With such nomenclators (plus GUIDs) we have the right tool to backlog scientific names in any database for unambiguous cross-linking. Taxonomy can be kept by the databases themselves and initiatives like the Catalogue of Life. Aside we should distinguish basionyms for unequivocal linking to type specimens and genetic resources.
Kind regards,
Yde de Jong Zoological Museum Amsterdam
[ Another topic for comments. Please keep the Topic number in responses. ]
Topic 3: GUIDs for Taxon Names and Taxon Concepts
Another key area in which TDWG has recognised the need for globally unique identifiers is in connection with taxon names and the various concepts associated with them. This issue actually also intersects with that of identifiers for taxonomic publications.
Definitions
In the following discussion, a "taxon name" is a scientific name string which simply identifies a name assigned in the taxonomic literature. In many cases such a name may have been applied in different ways by the original author and subsequent taxonomists. Each such application of a taxon name by a taxonomist to a set of organisms is here referred to as a "taxon concept". An understanding of the taxon concept adopted by a researcher is frequently essential if data are to be interpreted correctly. In its most basic form a "taxon concept" can be considered to be the use of a given "taxon name" in a given "taxonomic publication", in other words something that could be represented as, "Agenus aspecies Author1 Year1 sec. Author2 Year2". One possible approach to assigning identifiers to taxon concepts would therefore be to assign identifiers to taxon names and to taxonomic publications and to use a combination these identifiers to identify each taxon concept.
Note that a taxon concept may be defined at least in part by a set of assertions about the relationship between the present concept and the concepts adopted by earlier taxonomists. In addition it is possible for other researchers to make their own assertions about the relationships between the concepts published by different taxonomists. Much of the interest and value to be gained from modeling taxonomy relates to the interpretation of these asserted relationships.
Although the distinction between taxon names and taxon concepts may seem (over-)subtle, it is important that we should know whether we are referring simply to a nomenclaturally valid name, quite independently of any set of organisms to which it may be applied, or to a taxon concept which somehow applies such a name to such a set of organisms. Without this distinction, we will be restricted in our ability to develop biodiversity informatics, although of course there will be many cases in which all we can say is that a data set refers to some unspecified taxon concept associated with a given taxon name.
Identifiers
Clearly there are many situations in which a taxon name can itself be treated as a unique identifier without any apparent ambiguity about which name is being referenced (e.g. Turdus merula; Poa annua), but the existence of homonyms prevents this from being generally true. Even when taxon names include citations of the original publications (e.g. Turdus merula Linnaeus, 1758; Poa annua L.), they can be very difficult to compare since the form of the citations may vary greatly. Even where there is no ambiguity about which name is being referenced, such a name does not by itself serve to identify which associated concept is being referenced.
There are many different systems in place for associating other identifiers with either taxon names or taxon concepts. ITIS (http://www.itis.usda.gov/http://www.itis.usda.gov/, http://www.cbif.gc.ca/pls/itiscahttp://www.cbif.gc.ca/pls/itisca, http://siit.conabio.gob.mx/http://siit.conabio.gob.mx/) assigns Taxonomic Serial Numbers (TSNs) to each name in its system. Other species databases have their own identifiers for taxon concepts. Recording schemes often have their own identifiers for taxa (e.g. Bradley and Fletcher numbers for Lepidoptera in the UK, various systems of four-letter codes for North American bird species). These are often used to provide some stability and clarity in the taxonomy used by a given project.
Questions
I would like therefore to ask the following questions of any of you who use scientific names in your databases (either taxonomic databases recording a list of taxa, or databases recording information about taxa, specimens, observations, etc.):
Is your data organised using taxon names or to taxon concepts?Do you assign any reusable identifiers to taxon names orconcepts (i.e. identifiers used in more than one database)? 3. If so, what is the process in assigning new identifiers for additional taxa and for accommodating taxonomic change? 4. Where are these identifiers used (other organizations, databases, data exchange, recording forms, etc.)? 5. Do you use identifiers from any external classification within your database? 6. Would there be any social or technical roadblocks to replacing these identifiers with a single identifier that was guaranteed to be unique?
As before I am looking for information on existing practices and any requirements that would need to be accommodated within any general system of identifiers.
Thanks,
Donald
Donald Hobern (mailto:dhobern@gbif.orgdhobern@gbif.org) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480