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

Cybertaxonomy and revisionary systematics

Dmitry Dmitriev

Illinois Natural History Survey, USAhttp://taxonworks.org/

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 • It stimulates further study and species discovery.• It quickly becomes outdated.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

PD

FH

TM

LX

ML

doi:10.3897/zookeys.50.539

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

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Sources Georeferences

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Collecting Events

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Collecting Events

SpecimensMedia

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Collecting Events

SpecimensMedia

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Collecting Events

SpecimensMedia

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Collecting Events

SpecimensMedia

People


Collecting Events

SpecimensMedia

People


Collecting Events

SpecimensMedia

People

Sources

Taxon Name

Georeferences

Collecting Events

SpecimensMedia

People

Sources

Alternative ClassificationTaxon Name

Georeferences

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SpecimensMedia

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Sources

Name Statuses


Georeferences

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Sources



Georeferences

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Taxon Name


Georeferences

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Matrices

Media


SpecimensMedia

SpecimensMedia

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Georeferences

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SpecimensMedia



Georeferences

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Sources

Taxon Name


Georeferences

Collecting Events

Taxon Concepts

Matrices

Media


SpecimensMedia

SpecimensMedia

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SpecimensMedia

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Collecting Events

SpecimensMedia

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SpecimensMedia

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SpecimensMedia

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SpecimensMedia

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SpecimensMedia

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SpecimensMedia

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SpecimensMedia

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SpecimensMedia

Taxon Name

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SpecimensMedia


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SpecimensMedia

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Georeferences

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SpecimensMedia



Georeferences

Collecting Events

SpecimensMedia

People

TaxonWorks: Nomen Ontology

https://github.com/SpeciesFileGroup/nomen



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.

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

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