Schindel CBOL Overview

Information about Schindel CBOL Overview

Published on January 14, 2008

Author: Raulo

Source: authorstream.com

Content

Overview of Consortium for the Barcode of Life (CBOL):  Overview of Consortium for the Barcode of Life (CBOL) David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution [email protected]; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938 Species Identification Matters:  Species Identification Matters Endangered/protected species Agricultural pests/beneficial species Invasive species Disease vectors/pathogens Hazards (e.g., bird strikes on airplanes) Environmental quality indicators Unsustainable harvesting Fidelity of cell lines/culture collections Global Taxonomy Initiative:  Global Taxonomy Initiative Established by Convention on Biological Diversity in 2002 (COP6) Purpose is to remove or reduce the ”taxonomic impediment” The taxonomic impediment:  The taxonomic impediment Knowledge gaps in our taxonomic system Shortage of trained taxonomists and curators Impact of these deficiencies on our ability to conserve, use and share the benefits of biological diversity Operational objectives of GTI:  Operational objectives of GTI Assess taxonomic needs and capacities Build and maintain human resources, systems and infrastructure Facilitate improved and effective infrastructure for access to taxonomic information Include taxonomic objectives in CBD work programmes and cross-cutting issues What is an effective infrastructure for taxonomy?:  What is an effective infrastructure for taxonomy? Taxonomists Training Access to information Literature Primary data Research tools Bandwidth Other computing resources Links to other biological web-based resources (e-biology/e-biodiversity) Infrastructure of Taxonomy: Fragmented, Disconnected:  Infrastructure of Taxonomy: Fragmented, Disconnected Collections and databases of specimens Seedbanks, culture/cell line collections Compilations of taxonomic names Floristic and faunistic surveys/inventories Monographs, Taxonomic revisions Data repositories (characters, gene sequences, images, trees) The (undigitized) Taxonomic Literature What do we mean by primary biodiversity data?:  What do we mean by primary biodiversity data? Associated notes, recordings, publications, etc. Observational data (e.g. bird banding data) Label data on ~ 1.5 - 3.0 billion specimens in natural history collections, herbaria, botanical gardens, etc. These data have been amassed over ~ 300 years; most not digital Big legacy data problem Biodiversity Informatics: Fragmented, Unconnected:  Biodiversity Informatics: Fragmented, Unconnected Growth of Biodiversity Databases:  Growth of Biodiversity Databases Authority files of taxonomic names Museum databases of associated data Databases of Species Distributions:  Databases of Species Distributions Authority files of taxonomic names Museum databases of associated data Databases of species occurrences and distribution DNA Barcodes: A Key Variable for Biodiversity Informatics:  DNA Barcodes: A Key Variable for Biodiversity Informatics Authority files of taxonomic names Museum databases of associated data Databases of species occurrences and distribution (OBIS) Some existing e-biodiversity resources:  Some existing e-biodiversity resources DNA sequence databases (GenBank et al.) (www.ncbi.nlm.nih.gov/Genbank) Protein Data Bank (www.rcsb.org/pdb) BOLD (www.barcodinglife.org) Catalogue of Life (spice.sp2000.org) Zoological Record (http://scientific.thomson.com/products/zr) GBIF (www.gbif.net) Cyber Infrastructure for Phylogenetic Research (CIPRES) (www.phylo.org) Long-Term Ecological Research (LTER) Network (www.lternet.edu) Emerging e-biodiversity resources:  Emerging e-biodiversity resources European Distributed Institute for Taxonomy (EDIT) Biodiversity Heritage Library: Digitizing Taxonomic Literature (www.bhl.si.edu) Encyclopedia of Life: Web pages for every species Uses of DNA Barcodes:  Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Uses of DNA Barcodes:  Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Uses of DNA Barcodes:  Uses of DNA Barcodes Research tool for improving species-level taxonomy: Associating all life history stages, genders Testing species boundaries, finding new variants Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasives Environmental indicators, protected species Using minimal samples, damaged specimens, gut contents, droppings “Triage” tool for flagging potential new species: Undescribed and cryptic species Using a Million Barcodes:  Using a Million Barcodes A critical mass of standardized data for: Biogeographic patterns, habitat dynamics Phylogeography Niche modelling Ecological relationships Dynamics of molecular evolution Complementing Tree of Life Long-term biodiversity monitoring Understanding and preserving biodiversity Consortium for the Barcode of Life: Major Points:  Mission: Promoting DNA barcoding as a global standard for species identification History of development Recent origin, rapid growth Mode of operation as an international initiative Compromise between bottom-up, democratic (slow) and top-down, centrally-managed (nimble) organization Distributed activity that seeks global participation Minimal bureaucracy, highly user-driven Focused on projects with near- and mid-term results Consortium for the Barcode of Life: Major Points CBOL Structure:  CBOL Structure Member Organizations Executive Committee Working Groups Scientific Advisory Board Secretariat Office Slide27:  CBOL Member Organizations: 2007 150+ Member organizations, 45 countries 30+ Member organizations from 20+ developing countries Consortium for the Barcode of Life (CBOL):  Consortium for the Barcode of Life (CBOL) First barcoding publications in 2002 Cold Spring Harbor planning workshops in 2003 Sloan Foundation grant, launch in May 2004 Secretariat opens at Smithsonian, September 2004 First international conference February 2005 Now an international affiliation of: Natural history museums, biodiversity organizations Users: e.g., government agencies Private sector biotech companies, database providers CBOL-Initiated Projects:  CBOL-Initiated Projects Fish Barcode of Life (FISH-BOL) 30,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI) 10,000 species by 2010 Tephritid fruit flies 2,000 pest/beneficial species and relatives by 2008 Mosquitoes 3,300 species by 2008 African scale insects, lake fish, stem-borers Logistical Issues:  Logistical Issues The Organization: By taxonomy? Geography? Application? The Taxonomic Framework: Consensus list of species The Sampling Strategy The Supply Chain The Data: Assembling and comparing data The Funding The Resulting Publications Projects initiated by others:  Projects initiated by others Marine zooplankton (CMarZ): Marine habitat, multiple taxa All-Leps: Multiple regions/habitats, single taxon BioCode, Moorea: Single location, multiple habitats, multiple taxa Major Challenges:  Major Challenges Lack of funding to acquire, identify, curate specimens Assembling, managing, editing, QA for BARCODE-compliant data are labor-intensive Technical problems with data transfer to BOLD, barcoding workbench at Guelph GenBank’s BarSTool is new Aversion to sharing data pre-publication Support from CBOL:  Support from CBOL ABBI, FISH-BOL, TBI, MBI get $50K per year Internships for data management Travel/consulting by taxonomists for specimen identification Assistance in proposal writing Interactions with Working Groups “Leading Lab” initiative to improve lab and data management protocols CBOL’s Working Groups:  CBOL’s Working Groups Database: Data standards and interoperability DNA: Lab protocols Data Analysis: New analytical methods; population genetics perspective Plants: Identify gene region(s) for barcoding Taipei Barcode Conference:  Taipei Barcode Conference Second International Barcode Conference Academia Sinica, week of 17 September Regional Barcode Meeting for South/East Asia CBOL Working Groups FISH-BOL/Marine Fisheries workshop Short course on lab and data protocols

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