Cybertaxonomy and revisionary systematics Dmitry Dmitriev Illinois Natural History Survey, USA

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Presentation transcript:

Cybertaxonomy and revisionary systematics Dmitry Dmitriev Illinois Natural History Survey, USA

Taxonomy During last 255 years since Linnaeus about 1,800,000 species have been described Descriptive taxonomy remains very slow and labor intensive process

Species accumulation curve Catalogue of Life provides records for ~1,350,000 species names Total estimated at 1,800,000 species

Number of species described in 10 years periods Estimated 10,000-15,000 species described each year

Species accumulation curve in Cicadellidae

Species accumulation curve in Cicadellidae: Typhlocybinae

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

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.

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.

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

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 It quickly becomes outdated. 2006: First record of the tribe Erythroneurini from South America.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

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.

Available applications 3i SpeciesFile MX Scratchpads

3i - Interactive keys

3i – Pictorial keys

3i - Dichotomous Keys

3i - Taxonomic pages

Publications based on 3i

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

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.

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

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.

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.

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.

MX (MatriX) Dichotomous and matrix based keys.

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

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)

Article publishing Paper assembled from Scratchpad database XML submission, peer review & marked-up publication by Pensoft Published in Zookeys & Phytokeys PDF HTML XML doi: /zookeys

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 Specimens Media People Sources Collecting Events Specimens Media People SourcesGeoreferences Collecting Events Specimens Media People SourcesGeoreferences Collecting Events Specimens Media People SourcesGeoreferences Collecting Events Specimens Media People SourcesGeoreferences Collecting Events Specimens Media People SourcesGeoreferences Collecting Events Specimens Media People SourcesGeoreferences Collecting Events Specimens Media People SourcesGeoreferences Collecting Events Specimens Media People SourcesGeoreferences Collecting Events Specimens Media People Sources Taxon Name Georeferences Collecting Events Specimens Media People Sources Alternative Classification Taxon Name Georeferences Collecting Events Specimens Media People Sources Name Statuses Alternative Classification Taxon Name Georeferences Collecting Events Specimens Media People Sources RelationshipsName Statuses Alternative Classification Taxon Name Georeferences Collecting Events Specimens Media People Sources Taxon Name RelationshipsName Statuses Georeferences Collecting Events Taxon Concepts Matrices Media Alternative Classification Specimens Media Specimens Media Collecting Events Specimens Media Georeferences Collecting Events Specimens Media Georeferences Collecting Events Specimens Media Georeferences Collecting Events Specimens Media Georeferences Collecting Events Specimens Media Georeferences Collecting Events Specimens Media Georeferences Collecting Events Specimens Media Georeferences Collecting Events Specimens Media Georeferences Collecting Events Specimens Media Taxon Name Georeferences Collecting Events Specimens Media Alternative Classification Taxon Name Georeferences Collecting Events Specimens Media Name Statuses Alternative Classification Taxon Name Georeferences Collecting Events Specimens Media RelationshipsName Statuses Alternative Classification Taxon Name Georeferences Collecting Events Specimens Media People

TaxonWorks: Nomen Ontology

TaxonWorks: Nomen Ontology

TaxonWork: new development

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.