scott miller – sanbi, 7 april 2006 overview of dna barcoding and the barcode of life initiative...

Scott Miller – SANBI, 7 April 2006

Overview of DNA Barcoding and the Barcode of Life Initiative

Scott E. Miller, Chair, CBOL Executive Committee

National Museum of Natural HistorySmithsonian Institution

[email protected]; http://www.barcoding.si.edu


Poor representation of systematics infrastructure in Africa


Human resources also thinly distributed

• Stuckenberg (1964): most systematics done outside of Africa, but only 7% of world

entomologists working on Africa• Gaston & May (1992): only 4% of ecologists & 7%

of systematists in Africa• Surveys by CABI (1993), ICIPE (1996),

SAFRINET (1998) show same trends


Outreach to Africa

• South Africa and Kenya involved from beginning of CBOL in May 2004

• Southern African regional workshop now

• Eastern and Western regional workshops under discussion

• African involvement in global campaigns (e.g., birds, fish, mosquitos, fruit flies)


Reactions to Barcoding: 2004• From ecologists and other users:

“This is what we need! How soon can we get started?”

• From traditional taxonomists:“Species should be based on lots of characters, not just barcodes”

• From forward-looking taxonomists:“Using molecular data as species diagnostics isn’t

new, but standardization and broad implementation are great!”

• From barcoding practitioners:“I had my doubts at the beginning, but it really works

as a tool for identification (96% accurate in a recent mollusc paper) and it is at least as good as traditional approaches to discovering new species.”


A DNA barcode is a short gene sequence

taken from standardized portions

of the genome, used to identify species


The Mitochondrial Genome

Cyt bCyt b

D-Loop

ND5

H-strand

ND4

ND4LND3

COIII

COICOIL-strand

ND6

COI

ND2

ND1

COII

Small ribosomal RNA

Large ribosomal RNA

ATPase subunit 8

ATPase subunit 6


Uses of DNA Barcodes

Applied tool for identifying regulated species:• Disease vectors, agricultural pests, invasives• Environmental indicators, protected species

Research tool for assigning specimens to known species, including:

• Life history stages, damaged specimens, gut contents, droppings

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


Species Identification Matters• Endangered/protected species

• Agricultural pests

• Invasive species

• Disease vectors/pathogens

• Hazards (e.g., bird strikes on airplanes)

• Environmental quality indicators

• Unsustainable harvesting

• Fidelity of cell lines/culture collections


Uses of DNA Barcodes

Research tool for assigning specimens to known species, including:

• Life history stages, damaged specimens, gut contents, droppings


Uses of DNA BarcodesApplied tool for identifying regulated species:• Disease vectors, agricultural pests, invasives• Environmental indicators, protected speciesResearch tool for assigning specimens to known

species, including:• Life history stages, damaged specimens, gut

contents, droppings“Triage” tool for flagging potential new species:• Undescribed and cryptic species

23% marine species in Pearl Harbor are alien or cryptogenic


What DNA Barcoding is NOT• Barcoding is not DNA taxonomy; no

single gene (or character) is adequate• Barcoding is not Tree of Life; barcode

clusters are not phylogenetic trees• Barcoding is not just COI; standardizing

on one region has benefits and limits• Molecules in taxonomy is not new; but

large-scale and standardization are new• NEVERTHELESS, Barcoding is helping

to create a 21st century research environment for taxonomy


Wider Impacts of Barcoding: 2008• Catalyzing interoperability of databases

– Barcode data standards link sequences, specimens, species names and publications

• Renewing the mission of museums– DNA recovery from formalin-fixed specimens– Promoting the growth of DNA banks

• Expanding analytical toolbox for taxonomy

• Improving the information infrastructure– Digital library initiative in taxonomy


Digitizing Taxonomic Literature

• CBOL’s catalytic efforts:– Library-Laboratory meeting in London on

electronic access to taxonomic literature– Led to formation of Biodiversity Heritage

Library initiative– Proactive steps with PubMed to add

taxonomic journals to online abstracts– Aggressive negotiation with publishers of

barcoding papers


The Vision: Enabling research, product

development, and dissemination

Ideally, all data should be accessible:

• From any location• In formats appropriate to users• With a single query for each data type• Using simple links• Interoperable across data sets

… digitally


Species web pages


Collaborating with International Initiatives

• Global Biodiversity Information Facility (GBIF)• Global Taxonomy Initiative (GTI) of Convention on

Biological Diversity• BioNet International• Projects such as SABONET• Digital library• Genbank/EMBL/DDBJ• Leveraging “north” and “south” funding?


Planned Outreach • Regional meetings in:

– Cape Town, South Africa, 7-8 April 2006, SANBI– Brazil, 2nd quarter 2006– Southern Asia, mid-2007– Nairobi, Kenya, October 2006

• Second International Barcode Conference– Southeast Asia, February 2007

• Support from CBOL, host governments and international development agencies

scott miller – sanbi, 7 april 2006 overview of dna barcoding and the barcode of life initiative...

Documents