OVERVIEW

Short course on DNA barcoding methodsNovember 29, 2011

Overview of this training session

9:00 – 10:00. Module I: Introduction to Barcoding and its pipeline -Brief introduction to barcoding and the current goals, iBOL working groups and campaigns (Darío Lijtmaer) -The barcoding pipeline (Amy Driskell) -Barcode Data Standard compliance (David Schindel)

Overview of this training session

10:00 – 12:30. Module II: Acquisition and Handling of specimens and tissue samples - Pros and cons of collecting specimens for barcoding vs. sampling existing collections (Sally Adamowicz) - Field Collection (Sally Adamowicz)

- Museum Harvesting (Jeremy deWaard)

- Front-end processing (Michelle Van der Bank)

Overview of this training session

14:00 – 15:30. Module III: Brief description of laboratory methods and information management for small, medium and large-scale facilities -DNA Extraction (Darío Lijtmaer) -PCR Amplification (Darío Lijtmaer) -Information management and data quality (Amy Driskell)

Overview of this training session

16:00 – 17:30. Module IV: Taxon-specific aspects of the barcoding pipeline -Short talks about taxon-specific key elements

-Plants (Dave Erickson)- Algae (Gary Saunders)- Fungi (Benjamin Stielow)- Marine invertebrates (Dirk Steinke)- Terrestrial invertebrates (Julie Stahlhut)- Vertebrates (Bob Ward)

- Round table for Q&A and discussions about taxon-specific aspects of the pipeline

Brief introduction to barcoding and the current goals, iBOL working groups and campaigns

Darío LijtmaerMuseo Argentino de Ciencias Naturales “Bernardino Rivadavia”

Short course on DNA barcoding methodsNovember 29, 2011

Problems with traditional, morphology-based identification

Genetic-based identification (DNA barcodes) can help

overcoming these problems

Species are variable

There are 10 -100 million species in our planet

There are cryptic species

Sometimes we can only access fragments

The ideal genetic marker

Universal application Good recoverability Efficiency (smallest read necessary) Easy to align Easy to analyze The Mitochondrial Genome

D-Loop

H-strandCOIII

L-strand

ND6

ND2

COII

Small ribosomal RNA

COI

Cytb

Organization of the project: CBOL

CBOL was established in 2004. Goals:

- help organizing the project.

- connect the members of the barcoding community.

- establish barcoding as a standard proceduree for species identification.

Distribution of CBOL institutions

NMNH, Washington

Organization of the project: iBOL

iBOL was officially launched in 2009.

Main goal: to generate 5 million barcodes from 500,000 species by 2014.

Central nodes Regional nodes National nodes

iBOL organization

Theme 1:DNA Barcode Library

WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life

iBOL organization

Theme 2: Methodologies

WG2.1 Barcoding Biotas

WG2.2 Museum Life

WG2.3 Methodological Innovation

WG2.4 Paleobarcoding

iBOL organizationiBOL organization

WG2.3 Methodological Innovation

WG2.4 Paleobarcoding: Surveying the Past

WG3.1 Core Functionality

WG3.2 Mirrors

iBOL organization

Theme 3: Informatics

WG4.1 Environmental Barcoding

WG4.2 Handheld Barcoder

Theme 4: Technologies

iBOL organization

WG4.1 Environmental Barcoding:Species identifications from ‘slurries’

Agrawal et al 2007. A Pocket-Sized Convective PCR Thermocycler.

WG5.1 Project management

WG5.2 Communications

iBOL organization

Theme 5: Administration

Genomics and its Ethical,

Environmental, Economic, Legal

and Social aspects

iBOL organization

Theme 6: GE3LS

iBOL organization

Theme 1:DNA Barcode Library

WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life

iBOL organization

iBOL organization

Theme 1:DNA Barcode Library

WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life

iBOL organization

iBOL organization

Theme 1:DNA Barcode Library

WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life

iBOL organization

iBOL organization

Theme 1:DNA Barcode Library

WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life

iBOL organization

iBOL organization

Theme 1:DNA Barcode Library

WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life

iBOL organization

iBOL organization

Theme 1:DNA Barcode Library

WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life

iBOL organization

iBOL organization

Theme 1:DNA Barcode Library

WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life

iBOL organization

Specimen

Sample

Extract Amplify Sequence

Photographs

Collection data

Why are we here today?

Thank you!

Questions?