Cybertaxonomy and revisionary systematics Dmitry Dmitriev Illinois Natural History Survey, USA
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Transcript of Cybertaxonomy and revisionary systematics Dmitry Dmitriev Illinois Natural History Survey, USA
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Cybertaxonomy and revisionary systematics
Dmitry Dmitriev
Illinois Natural History Survey, USAhttp://taxonworks.org/
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Taxonomy
• During last 255 years since Linnaeus about 1,800,000 species have been described
• Descriptive taxonomy remains very slow and labor intensive process
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Species accumulation curve
•Catalogue of Life provides records for ~1,350,000 species names
•Total estimated at 1,800,000 species
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Number of species described in 10 years periods
•Estimated 10,000-15,000 species described each year
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Species accumulation curve in Cicadellidae
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Species accumulation curve in Cicadellidae: Typhlocybinae
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Number of species of Typhlocybinae described in 10 year periods
•Beamer•Edwards•Osborn•Ribaut•Matsumura
•Knull•Zachvatkin•Ross•Young
•Dworakowska•Anufriev•Ross
•Dworakowska•Dietrich•Dmitriev
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Taxonomic impediment
• Despite our best efforts, the vast majority (perhaps 90% or more) of the species remain undocumented.
• Taxonomists currently describe 15,000 new species per year.
• Recent estimates suggest that between 27,000 and 130,000 species are being lost each year to extinction.
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Taxonomic revision challenges
• A taxonomic revision summarizes knowledge about a group of organisms (morphology, distribution patterns, ecological preferences, bioacoustics, molecular variation, synonyms, new species, tools for identifications, etc.)
• Efficient management and synthesis of large amounts of nomenclatural, morphological, and distributional data is required.
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Number of species of Typhlocybinae described in 10 year periods
•Beamer•Edwards•Osborn•Ribaut•Matsumura
•Knull•Zachvatkin•Ross•Young
•Dworakowska•Anufriev•Ross
•Dworakowska•Dietrich•Dmitriev
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Taxonomic revision challenges• When published, a revision provides a snap-shot of the modern
knowledge on a group of organisms. • It stimulates further study and species discovery.• It quickly becomes outdated.
• 2006: First record of the tribe Erythroneurini from South America. Description of the genus Zyginama
• 2008: Revision of the genus Zyginama (70 species)
•2013: Three new species of the genus Zyginama from Argentina
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What is cybertaxonomy?• Technological advances, including relational
databases, digital imaging, and Internet dissemination, provide taxonomists with tools to increase both the quality and quantity of such studies.
• Cybertaxonomy aims to develop information processing tools that enable taxonomists both to produce traditional taxonomic revisions more rapidly and to develop new models for managing and disseminating taxonomic information.
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Available applications
• 3i• SpeciesFile• MX• Scratchpads
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3i - Interactive keys
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3i – Pictorial keys
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3i - Dichotomous Keys
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3i - Taxonomic pages
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Publications based on 3i
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3i - Data Sharing
• Catalogue of Life (CoL)• Encyclopedia of Life (EoL)• Global Biodiversity Information Facility (GBIF)• Discover Life• Global Name Architecture (GNA)
• Biodiversity Heritage Library
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SpeciesFile
•Designed by David Eades and colleagues in the Illinois Natural History Survey (USA)
•Supported by International Orthoptera Society
•Online application based on SQL Server database and Visual Basic.net.
•Originally designed for the insect order Orthoptera, but later was adopted by researchers working on other insect groups.
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Species File
•System allows storage and retrieval of taxonomic and nomenclatural information with associated images, distribution, and bibliography information.
•System strictly enforces the rules of the International Code of Zoological Nomenclature.
•Data shared with Catalogue of Life, GBIF
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MX (MatriX)
•Designed by Matt Yoder in Texas A&M University (USA)
•Based on MySQL and Ruby on Rails online application.
•Originally designed for the insect order Hymenoptera, but later was adopted by researchers working on other insect groups.
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MX (MatriX)
•The system could be used for storage and manipulation of different types of data: bibliographies, images, specimen records, distribution, molecular and morphological information.
•Dichotomous and matrix based keys.
•Images could be linked to MorphBank.
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MX (MatriX)
•Significant part of MX is an integrated morphological ontology builder which allows to link vocabulary terms to each other, as well as their definitions and illustrations.
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MX (MatriX)
•Dichotomous and matrix based keys.
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Scratchpads• Based on Drupal content
management system• Online application which
provides users with templates to enter taxonomy related information in uniform way
• Support for classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies
• Data could be exported in various formats
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Publishing observations and taxon data
Specimen records & species pages on Scratchpads
Pushed to GBIF & EOL(requires site registration with
GBIF & EOL)
Darwin Core
Archive (DwCA)
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Article publishing
Paper assembled from Scratchpad database
XML submission, peer review & marked-up publication by Pensoft
Published in Zookeys & Phytokeys
PD
FH
TM
LX
ML
doi:10.3897/zookeys.50.539
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TaxonWork: new development
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TaxonWork: new development
Taxon Name
RelationshipsName Statuses
Georeferences
Collecting Events
Taxon Concepts
Interactive Keys
Matrices
Sources
Media
People
Alternative Classification
Specimens
Sources
People
Sources
Media
People
Sources
SpecimensMedia
People
Sources
Collecting Events
SpecimensMedia
People
Sources Georeferences
Collecting Events
SpecimensMedia
People
Sources Georeferences
Collecting Events
SpecimensMedia
People
Sources Georeferences
Collecting Events
SpecimensMedia
People
Sources Georeferences
Collecting Events
SpecimensMedia
People
Sources Georeferences
Collecting Events
SpecimensMedia
People
Sources Georeferences
Collecting Events
SpecimensMedia
People
Sources Georeferences
Collecting Events
SpecimensMedia
People
Sources Georeferences
Collecting Events
SpecimensMedia
People
Sources
Taxon Name
Georeferences
Collecting Events
SpecimensMedia
People
Sources
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
People
Sources
Name Statuses
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
People
Sources
RelationshipsName Statuses
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
People
Sources
Taxon Name
RelationshipsName Statuses
Georeferences
Collecting Events
Taxon Concepts
Matrices
Media
Alternative Classification
SpecimensMedia
SpecimensMedia
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Taxon Name
Georeferences
Collecting Events
SpecimensMedia
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
Name Statuses
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
RelationshipsName Statuses
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
People
Sources
Taxon Name
RelationshipsName Statuses
Georeferences
Collecting Events
Taxon Concepts
Matrices
Media
Alternative Classification
SpecimensMedia
SpecimensMedia
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Georeferences
Collecting Events
SpecimensMedia
Taxon Name
Georeferences
Collecting Events
SpecimensMedia
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
Name Statuses
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
RelationshipsName Statuses
Alternative ClassificationTaxon Name
Georeferences
Collecting Events
SpecimensMedia
People
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TaxonWorks: Nomen Ontology
https://github.com/SpeciesFileGroup/nomen
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TaxonWorks: Nomen Ontology
https://github.com/SpeciesFileGroup/nomen
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TaxonWork: new development
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Acknowledgements
•Collaborators: Christopher Dietrich, Roman Rakitov, Daniela Takia, Sindhu Krishnankutti, Doris Lagos, David Eades, Matt Yoder, Edward DeWalt, Alexey Solodovnikov, Yalin Zhang, Richard Pile, and many others.
•Grant support: NSF, EoL.