Post on 12-Feb-2016
description
EcoInformatics &
Vegetation Science
The symposium messagePlant community ecology is on the brink of a dramatic transformation that will be made possible by the emergence of the new field of ecoinformatics.
An important role for IAVS is to encourage, facilitate, and direct this transformation.
The challenge“… ecology is a science of contingent generalizations, where future trends depend (much more than in the physical sciences) on past history and on the environmental and biological setting.”
Robert May 1986.
Traditional Community Ecology
The questions:• How are communities structured?• How do taxa interact?
The solutions :• Simple observations.• Simple experiments.
The scale:• Stand or landscape.
Major data types• Site data: climate, soils, topography, etc.• Taxon attribute data: identification,
phylogeny, distribution, life-history, functional attributes, etc.
• Occurrence data: attributes of individuals (e.g., size, age, growth rate) and taxa (e.g., cover, biomass) that co-occur at a site.
EcoInformatics opportunitiesThe availability of massive quantities of data (and co-occurrence data in particular) has the potential to create new directions and allow critical syntheses in ecology.
•Theoretical community ecology. Who occurs together, and where, and following what rules?
•Vegetation & species modeling. Where should we expect species & communities to occur after environmental changes?
•Remote sensing. What is really on the ground?•Monitoring & restoration. What changes are
really taking place in the communities?
How do we get there?
• Standard data structures. • Public data archives (deposit, withdraw,
cite, annotate).• Standard exchange formats.• Standard protocols.• Tools for semantic mediation & data
discovery.
What next? 1. International data exchange standard –
IAVS 2. Requirement for data archiving – JVS and
other journals3. Requirement for documentation of
taxonomic concepts4. Linked system of international databases
2003 Charge to the Working Group
1. Develop international data exchange standard including XML schema.
2. Recommend standards and requirements for archiving plot data.
3. Communicate with TDWG, IOPI, GBIF, ITIS and others regards our taxonomic database needs.
4. Address issues related to requirements for extended queries, intellectual property rights, & confidentiality.
IAVS EcoInformatics Working Group website: http://www.bio.unc.edu/faculty/peet/vegdata/
An information infrastructure for
vegetation science in North America
Robert K. PeetUniversity of North Carolina
in collaboration with Don Faber-Langendoen, Michael Jennings, Dennis Grossman, Michael Lee, & Mark Anderson
I am pleased to acknowledge the support and cooperation
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
The North American Initiative• Ecological Society of America – Development
of standards and implementation of peer review; maintenance of VegBank archive.
• US Federal Geographic Data Committee – Establishment of US government standards.
• NatureServe – Maintenance and distribution of the “International Classification of Ecological Communities.”
• USDA PLANTS & ITIS – Maintenance of a standard taxonomic database for organisms.
Physiognomic categoriesCategory ExampleClass . . . . . . . . . . Woodlands Subclass . . . . . . .Mainly Evergreen Woodlands Group . . . . . . . . .Evergreen Needle‑leaved Woodlands Subgroup . . . . . Natural/Seminatural Formation . . . . Evergreen Coniferous Woodland with Rounded Crowns
Floristic categories Alliance . . . . . . Juniperus occidentalis Association . . . . Juniperus occidentalis /
Artemesia tridentata
• Requirements for vegetation field plots.• Documentation & description of floristic
types.• Submission & peer review of proposed
types.• Management, citation, & archiving of
vegetation data.
Guidelines for Vegetation Classification
The ESA Vegetation Panel and its partners have collaborated to develop guidelines for the floristic levels of the classification covering:
Guidelines for describing the associations and alliances of the
U.S. National Vegetation Classification. Michael Jennings, Don Faber-Langendoen, Robert Peet, Orie
Loucks, David Glenn-Lewin, Antoni Damman, Michael Barbour, Robert Pfister, Dennis Grossman, David Roberts, David Tart,
Marilyn Walker, Stephen Talbot, Joan Walker, Gary Hartshorn, Gary Waggoner, Marc Abrams, Alison Hill, Marcel Rejmanek
The Ecological Society of America Vegetation Classification Panel. Version 4.0. July, 2004
http://www.esa.org/vegweb/Under review by FGDC as a U.S. federal standard
Overview of online resources
Stores plots and makes them publicly accessible
Stores current communities in the NVC
Stores current plant taxonomy
Allows people to change and update NVC and plants
vegbank.org natureserve.org
plants.usda.govTBA
NatureServe Biotics
Classification Mgt.
US-NVC Panel
Revision Proposal
Analysis & Synthesis
VegBank & other plot archives
US-NVC---
Proposed data flowExtraction
NatureServe Explorer
Peer Review
NVC Proceedings
Legend
External Action
Internal Action
Entity
VegBank
• The ESA Vegetation Panel is developing a public archive for vegetation plots known as VegBank (http://vegbank.org).
• VegBank is expected to function for vegetation plot data in a manner analogous to GenBank.
• Primary data will be deposited for reference, novel synthesis, and reanalysis.
• The database architecture is generalizable to most types of species co-occurrence data.
Challenges• Distributed databases and data
exchange formats • Data ownership, intellectual property
rights, & confidentiality• Multiple classifications of organsms and
communities• Multiple plot types (relevés & Hubbell
plots)• Data entry & submission tools• Perfect archiving• Plot and taxon interpretation
Biodiversity data structure
Taxonomic databases
Plot/Inventory databases
Specimen databases
Observation/CollectionEvent
Object or specimen
BioTaxon
Locality
SynTaxon
Community type databases
Project
Plot PlotObservation
Taxon / Individual Observation
Taxon Interpretation
PlotInterpretation
Core elements of VegBank
http://www.vegbank.org
VegBank Interface Tools
• Desktop client (VegBranch) for data preparation and local use.
• Flexible XML data import supporting VegBranch & TurboVeg formats.
• Flexible data export.• Easy web access to central archive
VegBranch can be used for converting legacy data, entering data, and
maintaining a local plot database.
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.
Most standardized taxon lists fail to allow effective integration of datasets
The reasons include:• The user cannot reconstruct the database as
viewed at an arbitrary time in the past, • Taxonomic concepts are not defined (just lists),• Multiple party perspectives on taxonomic concepts
and names cannot be supported or reconciled.The single largest impediment to large-scale
synthesis in community ecology
Carya ovata(Miller)K. Koch
Carya carolinae-sept.(Ashe) Engler & Graebner
Carya ovata(Miller)K. Kochsec. Gleason
1952sec. Radford et al. 1968
Three concepts of shagbark hickory
Splitting one species into two illustrates the ambiguity often associated with scientific names. If you encounter the name “Carya ovata (Miller) K. Koch” in a database, you cannot be sure which of two meanings applies.
Name ReferenceConcept
A taxonon concept represents a unique combination of a name and
a reference
“taxon concept” is equivalent to “Potential taxon” & “taxonomic assertion”
NamesCarya ovata Carya carolinae-septentrionalisCarya ovata v. ovataCarya ovata v. australis
Taxon concepts(One shagbark)C. ovata sec Gleason ’52C. ovata sec FNA ‘97
(Southern shagbark)C. carolinae-s. sec Radford ‘68C. ovata v. australis sec FNA ‘97
(Northern shagbark)C. ovata sec Radford ‘68C. ovata (v. ovata) sec FNA ‘97
ReferencesGleason 1952 Britton & BrownRadford et al. 1968 Flora CarolinasStone 1997 Flora North America
Six shagbark hickory assertionsPossible taxonomic synonyms are listed
together
Party Perspective
The Party Perspective on an Assertion includes:
•Status – Standard, Nonstandard, Undetermined• Correlation with other assertions –
Equal, Greater, Lesser, Overlap, Undetermined.• Lineage – Predecessor and Successor assertions.• Start & Stop dates.
http://www.natureserve.org/explorer
Coming soon – direct links to views of
typal and occurrence plots in VegBank
Concluding remarks• Much of what we are doing in the US is
common to the vegetation classification enterprise worldwide, but much is also novel. We need and encourage greater international communication and collaboration.
• Public plot archives, initially driven by the classification enterprise, have the potential to radically change the development of vegetation science in general.