1. Transition to taxon concepts from a world of legacy data --- R.K. Peet 1, A.S. Weakley 1,2, X. Liu 1,3, & N. Franz 4,5 1 The University of North Carolina at Chapel Hill 2 The North Carolina Botanical Garden 3 National Evolutionary Synthesis Center 4 National Center for Ecological Anal. & Synthesis 5 University of Puerto Rico, Mayagüez

2. Taxonomic database challenge The well-known problem: Integration of data from different times & places, by multiple investigators using varied taxonomic standards. The well-known solution: Identifications to taxon concepts that have mapped relationships to related concepts (within and across authorities).

3. NameReferenceConcept Taxonomic theory A taxon concept represents a unique combination of a name and a reference. Report -- name sec. reference..

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

5. USDA Plants & ITIS Abies lasiocarpa var. lasiocarpa var. arizonica One concept ofAbies lasiocarpa

6. Flora North America Abies lasiocarpa Abies bifolia A narrow concept of Abies lasiocarpa Partnership with USDA plants to provide plant concepts for data integration

7. 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 Minimal concepts ABC

8. Andropogon virginicus complex in the Carolinas 9 elemental units; 17 base concepts, 27 scientific names

9. Relationships among concepts Exactly equal (identification)Exactly equal (identification) Congruent, equal (=)Congruent, equal (=) Includes (>)Includes (>) Included in (<)Included in (<) Overlaps (> <) Disjunct (|)Disjunct (|)

10. CategoryExplanation Original Appears in the reference where the new name/type association was established. Example: Andropogon virginicus L. sec. Linnaeus (1753). Revisional Appears in a comprehensive revision of an existing Taxonomic name and lineage, e.g. a monograph. Example: Andropogon virginicus L. sec. Campbell (1983). Relational Appears in a comprehensive compilation without descriptions); meaning may be inferred from the list of mutually exclusive concepts. Example: Andropogon virginicus L. sec. ITIS (2006). Informal Appears in a taxonomic treatment yet is poorly specified, being outside of the focal names and taxa. Example: Andropogon hallii Hackel sec. Weakley (2006). (“a Midwestern species”) Nominal Appears outside of the context of a particular source; indirectly links to all other concepts with the name. Example: Andropogon virginicus L. Types of Concepts

11. The good news: TDWG has embraced taxonomic concepts and adopted TCS. TDWG has embraced taxonomic concepts and adopted TCS. Multiple organizations are developing tools for concept use and integration. Multiple organizations are developing tools for concept use and integration. The challenge: Few large-scale compilations of concepts and their relationships are available. Few large-scale compilations of concepts and their relationships are available. Legacy data lacking concept annotation will be around forever. Legacy data lacking concept annotation will be around forever.

12. A Case Study: Flora of the Southeastern US 1. Regional floras were badly obsolete and incomplete 2. No flora covered the Atlantic SE 3. Ecological datasets with multiple taxonomic authorities and inconsistent taxonomic concepts defied integration 4. Need for an updated atlas of the flora of the Southeast 5. Good candidate for a demonstration

13. Massive Import Scanned indices -- OCRScanned indices -- OCR Spreadsheets for preliminary concept documentationSpreadsheets for preliminary concept documentation Import into software tool for managing concepts and relationshipsImport into software tool for managing concepts and relationships

14. ConceptMapper Document and manage taxon concepts from multiple sourcesDocument and manage taxon concepts from multiple sources Document and manage concept relationships from multiple sourcesDocument and manage concept relationships from multiple sources Input data files as txt, xls, mdb, or TCSInput data files as txt, xls, mdb, or TCS Export data as txt, mdb, or TCSExport data as txt, mdb, or TCS

15. Concept mapper

16. Critical SE floristic works 1.Weakley 2005-. Flora of the Carolinas, Virginia, Georgia, and Surrounding Areas 2.Small 1933. Manual of the southeastern flora 3.Fernald 1950. Gray's manual of botany 4.Gleason 1952. Britton and Brown illustrated flora 5.Radford, Ahles & Bell 1968. Manual of the vascular flora of the Carolinas 6.Gleason & Cronquist 1991. Manual of vascular plants of northeastern United States and adjacent Canada 7.1993-2005. Flora of North America north of Mexico 8.Kartesz 1999. A synonymized checklist for the vascular flora of the United States, Canada, and Greenland 9.Wofford 1989. Vascular Plants of the Blue Ridge 10.Godfrey & Wooton 1979. Aquatic and Wetland Plants of Southeastern United States 11.1980-1990. Vascular Flora of the Southeastern United States 12. Recent monographs and revisions (>800)

17. Concept mapping progress ~ 65000 relationships of taxon concepts to Weakley 2005 concepts~ 65000 relationships of taxon concepts to Weakley 2005 concepts Based on ~ 800 taxonomic references.Based on ~ 800 taxonomic references.

18. “Index of Taxonomic Unscathedness” Only 16.9% of the flora of the Carolinas has gone from Small (1933) to modern treatment without changes in Only 16.9% of the flora of the Carolinas has gone from Small (1933) to modern treatment without changes in –concept (lumping and splitting), and/or –name (taxonomic rank, orthography, basionym, generic placement), and/or –family placement

19. Splittiness and lumpiness – or “there and back again” The Age of Split – 1900-1955The Age of Split – 1900-1955 The Age of Lump – 1956-1990The Age of Lump – 1956-1990 The Second Age of Split – 1991-presentThe Second Age of Split – 1991-present Comparison of this work to major eastern North American floras in CONCEPT lumping/splittingComparison of this work to major eastern North American floras in CONCEPT lumping/splitting

20. Toward a new Atlas Carya carolinae-septentrionalis, Radford et al. 1968 How to integrate new sources of data?? http://herbarium.unc.edu/seflora/firstviewer.htm

21. Add dynamic access to NCU collection Carya carolinae-septentrionalis NCURAB

22. NCURABUSDACVS Add USDA PLANTS records & CVS vegetation plot data

23. But wait !! There is a concept issue According to Radford 1968, USDA PLANTS v 4.0, & Weakley 2005According to Radford 1968, USDA PLANTS v 4.0, & Weakley 2005 –Carya carolinae-septentrionalis –Carya ovata According to Stone 1997 in FNAAccording to Stone 1997 in FNA –Carya ovata var australis –Carya ovata var. ovata

25. Carya carolinae-septentrionalis Some nominal occurrences might or might not represent the taxon

26. All specimens of Carya ovata must be identified to nominal concepts

27. Consider Cleistes Cleistes bifaria was split off C. divaricata after Radford et al. was published.Cleistes bifaria was split off C. divaricata after Radford et al. was published. Radford et al. records must be mapped as ambiguous.Radford et al. records must be mapped as ambiguous. Kartesz incorrectly maps all Cleistes in the Carolinas as C. divaricata owing to uncritical import of records from Radford.Kartesz incorrectly maps all Cleistes in the Carolinas as C. divaricata owing to uncritical import of records from Radford.

30. Data layers SpecimensSpecimens –NCU (~80,000 - nominal) –NCSU (~10,000 - nominal) –Weymouth Woods (~2,000 - Weakley) –UNC-C (in process, ~43,000 - Weakley) High-quality databasesHigh-quality databases –Sorrie’s SE Costal Plain endemics (Weakley) –NC Natural Heritage Program (Weakley) –Harmon et al. 2006 West Virginia atlas (US) –Selected literature records (idiosyncratic)

31. Data layers – 2 Other databasesOther databases –Radford et al. 1968 (Radford) –USDA PLANTS (US) Site recordsSite records –Carolina Vegetation Survey (~300,000) Total county records in database ~1,500,000Total county records in database ~1,500,000 Coming soon: Atlases - TN, VA, SC, KY Collections: UNC-W, Western Carolina, UNC-CComing soon: Atlases - TN, VA, SC, KY Collections: UNC-W, Western Carolina, UNC-C

33. Specimens matching the name

34. ..\..\New Folder\Snap32.jpg Images matching the name

35. Community types with the concept

36. Link to Vegetation plots with the taxon

37. Design: Allow user to select date-specific version of Weakley.Allow user to select date-specific version of Weakley. Allow user to select a Weakley, PLANTS, or FNA perspective (or others?).Allow user to select a Weakley, PLANTS, or FNA perspective (or others?). Data needs: Map relationships to PLANTS v 4.0Map relationships to PLANTS v 4.0 Map relationships between PLANTS and FNAMap relationships between PLANTS and FNA Date-stamp changes in WeakleyDate-stamp changes in Weakley More distribution layersMore distribution layers Next steps?

38. LinksConceptMapper http://152.2.14.231/conceptmapper/ Weakley flora http://herbarium.unc.edu/flora.htm NCU Atlas of the SE flora http://herbarium.unc.edu/seflora/firstviewer.htmThanks NSF (SEEK, VegBank), NC Bot. Garden