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Taxonomic data issues: An ecologist’s experience

Taxonomic data issues: An ecologist’s experience. R.K. Peet The University of North Carolina Adapted by J Kennedy. Taxonomic database challenge: Standardizing organisms and communities

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Taxonomic data issues: An ecologist’s experience

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  1. Taxonomic data issues: An ecologist’s experience • R.K. Peet • The University of North Carolina • Adapted by J Kennedy

  2. 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.

  3. Standard lists are available for Taxa Representative examples for higher plants in North America / US USDA 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 recognized perfectly partition all plants. The lists can be dynamic.

  4. Three concepts of subalpine fir Splitting one species into two illustrates the ambiguity often associated with scientific names. Abies bifolia Abies lasiocarpa Abies lasiocarpa sec. Little sec. USDA PLANTS sec. Flora North America

  5. One concept ofAbieslasiocarpa • USDA Plants & ITIS • Abies lasiocarpa • var. lasiocarpa • above the red line • var. arizonica • below the red line

  6. A narrow concept of Abies lasiocarpa Flora North America Abies Abies lasiocarpa Abies bifolia

  7. Andropogon virginicus complex in the Carolinas 9 elemental units; 17 base concepts

  8. Standardized taxon lists fail • to allow dataset integration • The reasons include: • Taxonomic concepts are not defined (just lists), • Relationships among concepts are not defined • The user cannot reconstruct the database as viewed at an arbitrary time in the past, • Multiple party perspectives on taxonomic concepts and names cannot be supported or reconciled.

  9. Taxonomic concepts A taxon concept represents a unique combination of a name and a reference. Report -- name sec reference. . Name Concept Reference

  10. A usage represents an association of a concept with a name. Name Usage Concept • 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

  11. Relationships among conceptsallow comparisons and conversions • Congruent, equal (=) • Includes (>) • Included in (<) • Overlaps (><) • Disjunct (|) • and others …

  12. High-elevation fir trees of western US AZ NM CO WY MT AB eBC wBC WA OR Distribution Abies lasiocarpa var. arizonica var. lasiocarpa USDA & ITIS Abies bifolia Abies lasiocarpa Flora North America A. lasiocarpasec USDA > A. lasiocarpasecFNA A. lasiocarpasecUSDA > A. bifoliasecFNA A. lasiocarpa v. lasiocarpasecUSDA > A. lasiocarpasecFNA A. lasiocarpa v. lasiocarpasecUSDA|A. bifoliasecFNA A. lasiocarpa v. arizonicasecUSDA < A. bifoliasecFNA

  13. Best practice: Report taxa by reference to concepts. 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.

  14. Best practice: Choose high-quality 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.

  15. Concepts and identifications are distinct. • 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.

  16. 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

  17. Fuzzy logic qualification 1 = Absolutely wrong 2 = Understandable but wrong 3 = Reasonable or acceptable 4 = Good answer 5 = Absolutely correct

  18. Demonstration Projects Concept relationships of Southeastern US plants treated in different floras. Based on > 50,000 mapped concepts

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