DNA Barcoding and the Consortium for the Barcode of Life

Katie Ferrell, Project ManagerKatie Ferrell, Project ManagerNational Museum of Natural HistoryNational Museum of Natural History

Smithsonian InstitutionSmithsonian Institutionferrellk@si.edu; ferrellk@si.edu; http://http://www.barcoding.si.eduwww.barcoding.si.edu

202/633-0810; fax 202/633-2938202/633-0810; fax 202/633-2938

Why are we here?Why are we here?

3 Main Goals of the All-Fungi Barcode 3 Main Goals of the All-Fungi Barcode Initiative WorkshopInitiative WorkshopWork towards a consensus on barcode Work towards a consensus on barcode

region(s) region(s) Come up with priorities for barcoding Come up with priorities for barcoding

project(s)project(s)Create steering committee charged withCreate steering committee charged with

presenting barcode region proposal if needed presenting barcode region proposal if needed developing strategies for barcode projects.developing strategies for barcode projects.

A DNA barcode is a A DNA barcode is a short gene sequence short gene sequence

taken from taken from standardized portions standardized portions

of the genome,of the genome, used to identify species used to identify species

What DNA Barcoding is NOTWhat DNA Barcoding is NOT

Barcoding is not DNA taxonomy;Barcoding is not DNA taxonomy; no single no single gene (or character) is adequategene (or character) is adequate

Barcoding is not Tree of Life;Barcoding is not Tree of Life; barcode barcode clusters are not phylogenetic treesclusters are not phylogenetic trees

Barcoding is not just COI;Barcoding is not just COI; standardizing on standardizing on one region has benefits and limitsone region has benefits and limits

Molecules in taxonomy is not new;Molecules in taxonomy is not new; but but large-scale and standardization large-scale and standardization are neware new

Associating Life Stages, Processed Parts, Associating Life Stages, Processed Parts, Dimorphic GendersDimorphic Genders

Uses of DNA BarcodesUses of DNA BarcodesApplied tool for identifying regulated species:Applied tool for identifying regulated species: Disease vectors, agricultural pests, invasivesDisease vectors, agricultural pests, invasives Environmental indicators, protected species Environmental indicators, protected species Using minimal samples, damaged specimens, gut Using minimal samples, damaged specimens, gut

contents, droppingscontents, droppings

Research tool for improving species-level taxonomy:Research tool for improving species-level taxonomy: Associating all life history stages, gendersAssociating all life history stages, genders Testing species boundaries, finding new variantsTesting species boundaries, finding new variants

““Triage” tool for flagging potential new species:Triage” tool for flagging potential new species: Undescribed and cryptic speciesUndescribed and cryptic species

Consortium for the Consortium for the Barcode of Life (CBOL)Barcode of Life (CBOL)

First barcoding publications around 2002 (Hebert, First barcoding publications around 2002 (Hebert, 2003)2003)

Cold Spring Harbor planning workshops in 2003Cold Spring Harbor planning workshops in 2003 Sloan Foundation 2-year grant for $800K May 2004Sloan Foundation 2-year grant for $800K May 2004 Secretariat opens at Smithsonian, September 2004Secretariat opens at Smithsonian, September 2004 First international conference February 2005First international conference February 2005 $1.55 million 2-year renewal in April 2006$1.55 million 2-year renewal in April 2006 Now an international affiliation of:Now an international affiliation of:

Natural history museums, biodiversity organizationsNatural history museums, biodiversity organizations Users: e.g., government agenciesUsers: e.g., government agencies Private sector biotech companies, database providersPrivate sector biotech companies, database providers

CBOL Member Organizations: 2007

• 150+ Member organizations, 45 countries

• 30+ Member organizations from 20+ developing countries

CBOL StructureCBOL Structure

Member Organizations

Executive Committee

Working Groups

Scientific Advisory Board

Secretariat Office

CBOL-Initiated ProjectsCBOL-Initiated Projects Fish Barcode of Life (FISH-BOL)Fish Barcode of Life (FISH-BOL)

30,000 marine/freshwater species by 201030,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI)All Birds Barcoding Initiative (ABBI)

10,000 species by 201010,000 species by 2010 Tephritid fruit fliesTephritid fruit flies

2,000 pest/beneficial species and relatives by 20082,000 pest/beneficial species and relatives by 2008 MosquitoesMosquitoes

3,300 species by 20083,300 species by 2008 African scale insects, lake fish, stem-borersAfrican scale insects, lake fish, stem-borers

CBOL’s Working GroupsCBOL’s Working GroupsDatabase:Database: Developing standards for the Developing standards for the

barcode data repository (INSDC)barcode data repository (INSDC)DNA:DNA: Protocols for formalin-fixed and old Protocols for formalin-fixed and old

museum specimens; Producing LIMS for museum specimens; Producing LIMS for disseminationdissemination

Data Analysis:Data Analysis: Beyond phenetic Beyond phenetic methods; population genetics perspectivemethods; population genetics perspective

Plants: Plants: Identify gene region(s) for Identify gene region(s) for barcodingbarcoding

Outreach ActivitiesOutreach ActivitiesRegional meetings in:Regional meetings in:

- Cape Town, South Africa, 7-8 April 2006, SANBICape Town, South Africa, 7-8 April 2006, SANBI- Nairobi, Kenya, 18-19 October 2006 Nairobi, Kenya, 18-19 October 2006 - Brazil, March 2007Brazil, March 2007- Taiwan, September 2007Taiwan, September 2007

Support from CBOL, host governments and Support from CBOL, host governments and international development agenciesinternational development agencies

Second International Barcode ConferenceSecond International Barcode Conference- Taiwan, September 2007Taiwan, September 2007

Goals of Regional MeetingsGoals of Regional Meetings

Raise awareness Raise awareness Explore potential applications in the regionExplore potential applications in the regionAssess greatest needs and opportunities Assess greatest needs and opportunities

in the regionin the region Identify highest priorities, construct Identify highest priorities, construct

national and regional action plans national and regional action plans Start intra-regional networks and Start intra-regional networks and

intercontinental partnershipsintercontinental partnerships

Tephritids (fruit flies)Tephritids (fruit flies)

Idea took shape in Stockholm in 2005Idea took shape in Stockholm in 2005Formed Steering CommitteeFormed Steering CommitteeCBOL supported planning of the Tervuren CBOL supported planning of the Tervuren

meeting in February 2006.meeting in February 2006.Meeting produced proposal for project Meeting produced proposal for project

(Demonstrator project).(Demonstrator project).Created networking opportunitiesCreated networking opportunities

Scale InsectsScale Insects

Initiative born out of the Cape Town regional Initiative born out of the Cape Town regional meeting in April 2006.meeting in April 2006.

Pest species worldwidePest species worldwide Formed a Steering CommitteeFormed a Steering Committee CBOL supported the planning of meeting held in CBOL supported the planning of meeting held in

February 2007 related to barcoding scale insectsFebruary 2007 related to barcoding scale insects Group faced dual challenges of coming up with Group faced dual challenges of coming up with

appropriate region and developing barcode appropriate region and developing barcode projects.projects.

Plant Working GroupPlant Working Group

Working towards finding plant barcode region(s)Working towards finding plant barcode region(s) Kress 2005 proposal for ITS and trnh-psbAKress 2005 proposal for ITS and trnh-psbA Kew Garden receives Sloan/Moore Foundation Kew Garden receives Sloan/Moore Foundation

support, early 2005support, early 2005 Phase 1 screens 100 genes across 50 sibling Phase 1 screens 100 genes across 50 sibling

species pairsspecies pairs Phase 2 tests of matK, rpcoC1, rpoB, ndhJ, and Phase 2 tests of matK, rpcoC1, rpoB, ndhJ, and

accDaccD Canadian proposal for rbcLCanadian proposal for rbcL CBOL protocols for approving barcode regionsCBOL protocols for approving barcode regions

All-Fungi Barcode InitiativeAll-Fungi Barcode InitiativeGoalsGoals

Work towards a consensus on appropriate Work towards a consensus on appropriate barcode region(s) for fungi.barcode region(s) for fungi.Develop priorities for future fungi barcoding Develop priorities for future fungi barcoding projects.projects.Select a steering committee charged with tasks Select a steering committee charged with tasks of presenting the barcode region proposal to of presenting the barcode region proposal to CBOL and of coordinating the planning of future CBOL and of coordinating the planning of future barcoding projects.barcoding projects.

CBOL will assist in the support of these planning CBOL will assist in the support of these planning efforts. efforts.