The challenge of organism identity --- The flora of the Southeast as a case study

The challenge of organism The challenge of organism identityidentity

------ The flora of the Southeast The flora of the Southeast

as a case study as a case study

Robert K. PeetRobert K. PeetUniversity of North Carolina University of North Carolina

Ecological Society of America Vegetation Ecological Society of America Vegetation PanelPanel

SEEK development teamSEEK development teamSERNEC RTNSERNEC RTN

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

• Increasingly, research depends on Increasingly, research depends on the integration and re-use of the integration and re-use of multiple datasets.multiple datasets.

• Traditional Linnaean nomenclature is Traditional Linnaean nomenclature is insufficientinsufficient

Biodiversity documentation Biodiversity documentation depends on accurate depends on accurate

identification of organisms identification of organisms

USDA Plants & ITIS

Abies lasiocarpa

var. lasiocarpa

var. arizonica

One concept ofAbies lasiocarpa

Flora North America

Abies lasiocarpa

Abies bifolia

A narrower concept of Abies lasiocarpa

Partnership with USDA plants to provide plant concepts for data integration

High-elevation fir trees High-elevation fir trees of of

western North Americawestern North America AZ NM CO WY MT AB eBC wBC

WA OR

Abies lasiocarpa

var. arizonica

Abies lasiocarpa var. lasiocarpa

DistributionDistribution

USDA - ITISUSDA - ITIS

Flora North AmericaFlora North America

Abies bifolia Abies lasiocarpa

Minimal conceptsMinimal concepts

A B C

Andropogon virginicusAndropogon virginicus complex complex

9 elemental units; 17 base concepts, 27 9 elemental units; 17 base concepts, 27 scientific namesscientific names

The reasons include:The reasons include:• Taxonomic concepts are not defined Taxonomic concepts are not defined

(just lists of names),(just lists of names),

• Multiple party perspectives on taxon Multiple party perspectives on taxon concepts and names are not supportedconcepts and names are not supported

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

The single largest impediment to The single largest impediment to large-scale synthesis in large-scale synthesis in biodiversity & ecology.biodiversity & ecology.

Standardized taxon lists fail

to allow dataset integration

A Case Study:A Case Study:Flora of the Southeastern Flora of the Southeastern

USUS

1.1. Regional floras obsolete and Regional floras obsolete and incompleteincomplete

2.2. Need for an updated atlas of the Need for an updated atlas of the flora of the Southeastflora of the Southeast

3.3. Datasets with inconsistent Datasets with inconsistent taxonomic concepts have defied taxonomic concepts have defied integrationintegration

4.4. SERNEC has a goal of integrating SERNEC has a goal of integrating collections across the regioncollections across the region

5.5. 65,000 concept relationships 65,000 concept relationships already mappedalready mapped

How have things changed?How have things changed?Concept relationships of Southeastern Concept relationships of Southeastern US plants treated in different floras.US plants treated in different floras.

Based on > 65,000 concept Based on > 65,000 concept relationshipsrelationships

http://herbarium.unc.edu/flora.htm

Multiple groups are building IT Multiple groups are building IT tools but lack data to populate tools but lack data to populate the toolsthe tools

We have a critical mass of taxon We have a critical mass of taxon concepts and concept concepts and concept relationshipsrelationships

SERNEC organization provides a SERNEC organization provides a community approachcommunity approach

Potential for SERNEC to establish Potential for SERNEC to establish best practices and set standards best practices and set standards

The Opportunity

Toward a new AtlasToward a new Atlas

Carya carolinae-septentrionalisCarya carolinae-septentrionalis, Radford et al. , Radford et al. 19681968

How to How to integrate integrate new new sources sources of data??of data??

http://herbarium.unc.edu/seflora/firstviewer.htm

Carya carolinae-Carya carolinae-septentrionalisseptentrionalis

NCUNCU

RABRAB

USDAUSDA

CVSCVS

Add static database records & Add static database records & dynamic access to museum dynamic access to museum collectionscollections

But wait !!But wait !!There is a concept There is a concept

issueissue• According to Radford 1968, USDA According to Radford 1968, USDA PLANTS v 4.0, & Weakley 2005PLANTS v 4.0, & Weakley 2005–Carya carolinae-Carya carolinae-septentrionalisseptentrionalis

–Carya ovataCarya ovata

• According to Stone 1997 in FNAAccording to Stone 1997 in FNA–Carya ovata var australisCarya ovata var australis–Carya ovata var. ovataCarya ovata var. ovata

Carya carolinae-Carya carolinae-septentrionalisseptentrionalis

Some nominal occurrences might Some nominal occurrences might or or might notmight not represent the taxon represent the taxon

Software:Software:• Allow user to select a taxonomic Allow user to select a taxonomic

perspective (e.g., Weakley, PLANTS, perspective (e.g., Weakley, PLANTS, or FNA)or FNA)

• Allow user to select date-specific Allow user to select date-specific version of Databases.version of Databases.

• Data integration tools and servicesData integration tools and services

Data needs:Data needs:• Comprehensive map of relationships Comprehensive map of relationships

taxonomic conceptstaxonomic concepts• Identify observation records to Identify observation records to

conceptconcept

Next steps?Next steps?

• Publications, datasets, and Publications, datasets, and museums identify taxa to concepts.museums identify taxa to concepts.

• Databases and data services Databases and data services document core sets of taxonomic document core sets of taxonomic concepts and the relationships of concepts and the relationships of those concepts to each other. those concepts to each other.

The way aheadThe way ahead

We are pleased to We are pleased to acknowledge the support and acknowledge the support and

cooperation ofcooperation of

Ecological Society of America

Gap Analysis Program

National Center for Ecological Analysis and Synthesis

National Biological Information Infrastructure

Federal Geographic Data Committee

National Science Foundation