Names are not sufficient: the challenge of documenting organism

identity R.K. Peet, J.B.Kennedy,

and N.M. Franz

and

The Ecological Society of America Vegetation PanelThe SEEK development team

Biodiversity data structure

Taxonomic database

Co-occurrence database

Occurrence database

Observation/Collection Event

Specimen or Object

Bio-Taxon

Locality

Community Type

Community type database

• Accurate identification and labelling of organisms is a critical part of collecting, recording and reporting biological data.

• Increasingly, research in biodiversity and ecology is based on the integration (and re-use) of multiple datasets.

• New tools are producing flawed results!

1. Biodiversity informatics depends on accurate and

precise taxonomy

High-elevation fir trees of western North America

AZ NM CO WY MT AB eBC wBC WA OR

Abies lasiocarpa

var. arizonica

Abies lasiocarpa var. lasiocarpa

Distribution

USDA - ITIS

Flora North America

Abies bifolia Abies lasiocarpa

R. plumosa

R. plumosa

R plumosav. intermedia

R. plumosav. plumosa

R. intermedia

R. plumosav. interrupta

R. pineticola

R. plumosa

R. sp. 1

R. plumosav. plumosa

R. plumosav. pineticola

Multiple concepts of Rhynchospora plumosa s.l.

Elliot 1816

Gray 1834

Kral 2003

Peet 2006?

1

2

3

Chapman1860

Multiple concepts of Andropogon virginicus L. sl

The Taxonomic database challenge:

Standardizing organisms and communities

The problem: Integration of data potentially

representing different times, places, investigators and taxonomic standards.

The traditional solution: A standard list of organisms /

communities.

Standardized taxon lists failto allow dataset integration

The reasons include:

• Taxonomic concepts are not defined (just lists),

• Multiple party perspectives on taxonomic concepts and names cannot be supported or reconciled,

• The user cannot reconstruct the database as viewed at an arbitrary time in the past.

This is the single largest impediment to large-scale synthesis in biodiversity & ecology.

Name ReferenceConcept

Taxonomic theory

A taxon concept represents a unique combination of a name and a reference.

Report -- name sec reference.

.

Name ConceptUsage

A usage represents an association of a concept with

a name.

• The name used in defining the concept need not be the same name used in your work.

e.g. Carya alba = Carya tomentosa sec. Gleason & Cronquist 1991.

• Usage can be used to apply multiple name systems to a concept

When reporting the identity of organisms in publications, data, or on specimens, provide not only the full scientific name of each kind of organism recognized, but also the reference that formed the basis of the taxonomic concept.

e.g., Abies lasiocarpa sec. Flora North America 1997.

2. Always report a taxon by reference to a concept

• Reference high-quality sources for taxon concepts such as a major compendium that provides its own defined concepts, or a source that references the concepts of others.

• Avoid checklists (e.g. ITIS) as they typically lack true taxonomic descriptions or circumscriptions

Choice of concepts

SEEK & GBIF are working to provide standards for concept

data• Several data models incorporate

taxon concepts. The IOPI, VegBank, and Taxonomer models are optimized for different uses.

• SEEK, GBIF, and TDWG developed TCS, which was adopted by TDWG in August 2005 and is being implemented by GBIF and SEEK

• A name in a publication could be either a concept or an identification.

• Identifications should include linkage to at least one concept, but need not be limited to a single concept.

Eg. --< Potentilla sec. Cronquist 1991 +~ Potentilla simplex sec Cronquist 1991 +~ Potentilla canadensis sec Cronquist 1991

3. Concepts and identifications are distinct.

4. Biodiversity informatics depends on standards and

connectivityDarwin Core and EML are widely used and

under continued development, but effectively obsolete.

• Names (Linnean Core)• Publications (Alexandrian core, etc)• Observations (proposed TDWG standard)• Identifications (proposed EML extension)• Taxonomic concepts (TCS)• GUIDS (under development by GBIF)

Step 1: Adoption of minimum standards and best practices by high-quality journals, funding agencies, and professional organizations.

Distributed information systems - and the way

ahead

Publishers, curators and data managers need to tag taxon

interpretations with concepts

• Precedence exists with tagging literature citations and GenBank accessions

• Presses are linking scientific names in many ejournals to ITIS (e.g. Evolution, Ecology)

Step 2: Creation, availability, and maintenance of databases that document core sets of taxonomic concepts and the relationships of these concepts to each other.

The way ahead

Relationships among concepts

• Exactly equal (identification)• Congruent, equal (=)• Includes (>)• Included in (<)• Overlaps (><)• Disjunct (|)

True concept-based checklists

• Equivalent of ITIS but with concept documentation and including how other concepts map onto the concepts accepted by the party.

• Several are operative or in development including EuroMed, IOPI-GPC, Biotics, VegBank. Concept documentation planned for ITIS/USDA.

Registration system and standard identifiers for names, references, and

concepts• Essential for data exchange

• GBIF is hosting a set of international workshops to design the GUID infrastructure.

Step 3: Development and provision of tools to facilitate mark-up of data and manuscripts with taxonomic concepts

The way ahead

Tools to develop and map concepts

• Taxonomists need mapping and visualization tools for relating concepts of various authors. SEEK will build prototypes for review and possible adoption.

• Aggregators need tools for mapping relationships among concepts.

• Users need tools for entering legacy concepts. Several are in development

Build on the infrastructure provided by

1) The VegBank data model2) The NVC peer review system3) GBIF & TDWG standards4) The Weakley concept dataset for

the Southeast

The Opportunity

Aus aus L.1758 Aus aus L.1758

(v) Aus L.1758

Xus Pargiter 2003

Xus beus (Archer) Pargiter 2003.

in Pargiter 2003

(ii) Aus L.1758

Aus bea Archer 1965

in Archer 1965

(i) Aus L.1758

Aus aus L.1758

in Linneaus 1758

Aus bea Archer 1965

Aus cea BFry 1989

(iii) Aus L.1758

in Fry 1989

Aus ceus BFry 1989

Aus aus L. 1758

A diligent nomenclaturist, Pyle (1990), notes that the species epthithets of Aus bea and Aus cea are of the wrong gender and publishes the corrected names Aus beus corrig. Archer 1965 and Aus ceus corrig. BFry 1989

Tucker publishes his revison without noting Pyle’s corrigendum of the name of Aus cea

Pargiter publishes his revison using Pyle’s corrigendum of the epithet bea to beus and Aus cea to Aus ceus.

Timeline showing taxonomic history (revisions and nomenclatural changes) pertaining to species comprising the imaginary genus Aus.

Aus aus L.1758

in Tucker 1991

(iv) Aus L.1758

Aus cea BFry 1989