Taxonomic data issues: Taxonomic data issues:

An ecologist’s experienceAn ecologist’s experience

R.K. PeetR.K. Peet

The University of North Carolina

Adapted by J KennedyAdapted by J Kennedy

Taxonomic database Taxonomic database challenge:challenge:

Standardizing organisms and Standardizing organisms and communitiescommunities

The problem:The problem: Integration of data potentially Integration of data potentially

representing different times, places, representing different times, places, investigators and taxonomic standards.investigators and taxonomic standards.

The traditional solution:The traditional solution: A standard list of organisms / A standard list of organisms /

communities.communities.

Standard lists are available for Taxa

Representative examples for higher plants in Representative examples for higher plants in North America / USNorth America / US

USDA PlantsUSDA Plants http://plants.usda.gov ITIS http://www.itis.usda.gov NatureServe http://www.natureserve.org BONAP Flora North America

These are intended to be checklists wherein the taxa These are intended to be checklists wherein the taxa recognized perfectly partition all plants. The lists can recognized perfectly partition all plants. The lists can be dynamic.be dynamic.

Abies lasiocarpa

Abies bifolia

Abies lasiocarpa

sec. Littlesec. USDA PLANTS

sec. Flora North America

Three concepts of subalpine firThree concepts of subalpine fir

Splitting one species into two illustrates the ambiguity often associated with scientific names.

USDA Plants & ITIS

Abies lasiocarpa

var. lasiocarpaabove the red line

var. arizonicabelow the red line

One concept ofAbies lasiocarpa

Flora North America

Abies

Abies lasiocarpa

Abies bifolia

A narrow concept of Abies lasiocarpa

Andropogon virginicusAndropogon virginicus complex in the complex in the CarolinasCarolinas

9 elemental units; 17 base concepts9 elemental units; 17 base concepts

Standardized taxon lists Standardized taxon lists failfail

to allow dataset integrationto allow dataset integration

The reasons include:The reasons include:

• Taxonomic concepts are not defined (just Taxonomic concepts are not defined (just lists), lists),

• Relationships among concepts are not Relationships among concepts are not defineddefined

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

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

Name ReferenceConcept

Taxonomic conceptsTaxonomic concepts

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

Relationships among concepts

allow comparisons and conversions

• Congruent, equal (=)• Includes (>)• Included in (<)• Overlaps (><)• Disjunct (|)• and others …

High-elevation fir trees of western US

AZ NM CO WY MT AB eBC wBC WA OR

var. arizonica

Abies lasiocarpa

Distribution

USDA & ITIS

Flora North America

Abies bifolia Abies lasiocarpa

A. lasiocarpa sec USDA > A. lasiocarpa sec FNA

A. lasiocarpa sec USDA > A. bifolia sec FNA

A. lasiocarpa v. lasiocarpa sec USDA > A. lasiocarpa sec FNA

A. lasiocarpa v. lasiocarpa sec USDA | A. bifolia sec FNA

A. lasiocarpa v. arizonica sec USDA < A. bifolia sec FNA

var. lasiocarpa

When reporting the identity of organisms in publications, data, or on specimens, provide the full scientific name of each kind of organism and the reference that provided the taxonomic concept.

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

Best practice: Report taxa by reference to concepts.

• 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 as they typically lack true taxonomic descriptions or circumscriptions.

Best practice: Choose high-quality concepts

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

• An annotation is an identification.

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

Concepts and identifications

are distinct.

Documenting identifications

Relationships added for identification= Indicates identification ~ (or aff.) Indicates similarity≡ Indicates identity, or defined as

Example of complex identification< Potentilla sec. Cronquist 1991 +~ Potentilla simplex sec Cronquist 1991 +~ Potentilla canadensis sec Cronquist 1991

Fuzzy logic qualification

1 = Absolutely wrong2 = Understandable but wrong3 = Reasonable or acceptable 4 = Good answer5 = Absolutely correct

Demonstration ProjectsConcept relationships of Southeastern US

plants treated in different floras.

Based on > 50,000 mapped concepts