DNA Barcodes and Biodiversity

DNA Barcoding – Rationale

Conventional Genomics - All Genes, One Species

Gaining Barcode Closure for Animals Horizontal Genomics - One Gene, All Species

Horizontal Genomics for Biodiversity Identifying Life: conservation, management, bioprospecting Discovering Life: new species, species ages, geographic patterns Evolutionary Rules: rate variation, shifts in nucleotide usage, protein diversification

DNA Barcode: short standardized sequence enabling species discrimination in a large block of life Horizontal Genomics for Biodiversity - DNA Barcoding

4 15 = 1 Billion10 11 = 100 Billion DNA Barcoding – Prospects Barcoding Products and Life

Prospects for Diagnosing Species with DNA Barcodes Average species lifespan in fossil record: 4 million years Rate of sequence change: 1% per million years Amount of sequence change: 40 changes per 1000 bp DNA Barcoding – Prospects

Gaining Barcode Closure for Animals An Internal ID System for All Animals DNA Barcoding in Animals Typical Animal Cell Mitochondrion DNA mtDNA D-Loop ND5 H-strand ND4 ND4L ND3 CO III L-strand ND6 ND2 ND1 CO II Small ribosomal RNA ATPase subunit 8 ATPase subunit 6 Cytochrome b CO I The Mitochondrial Genome

DNA Barcoding in Animals Barcode Target: 648 bp of COI

The Analytical Chain: From Specimen to Database DNA Barcoding in Animals

Barcode of Life Database

“ It’s not science.” - Rodman, June 2003 “Too bad it won’t deliver.” - Sperling, October 2003 “DNA barcoding is wanting in rationale, methodology and interpretation of results.” - Will and Rubinoff, June 2004 “There is nothing fundamentally new in barcoding, except scale and proposed standardization.” - Moritz & Cicero, September 2004

“ This pioneering effort in DNA barcoding will set in motion the single most significant project in biology that I know today.” - Janzen, July 2003 “Fashionable DNA-barcoding methods are a breakthrough for identification.” - Wheeler, Raven & Wilson, January 2004 “I believe that the problem of species numbers will be solved by taking small pieces of organisms and sticking them in a hand-held machine which analyses their DNA.” - Lord May, April 2004 “There is little doubt that large-scale and standardized sequencing, when integrated with existing taxonomic practice, can contribute significantly to the challenges of identifying individuals and increasing the rate of discovering biological diversity.” - Moritz & Cicero, September 2004

Resolving Species Through DNA Barcoding Humans and Our Relatives

Proportion of Species Pairs n = 13320x = 11.2% Sequence Divergence COI Divergences (%) in Closely Related Animals Resolving Species Through DNA Barcoding

Sensitivity Analysis on Large Phyla Resolving Species Through DNA Barcoding

Rates of EvolutionG + C (3rd position) 1x2x3x4x5x6x7x8x9x10x Ephemeroptera Lepidoptera Hymenoptera 1x2x3x4x5x Aves Mammals Osteichthyes Hymenoptera Lepidoptera Ephemeroptera Aves Mammals Osteichthyes Sensitivity Analysis Resolving Species Through DNA Barcoding

Bird Identification Through DNA Barcodes

Resolving Species Through DNA Barcoding Bird Identification Through DNA Barcodes

Resolving Species Through DNA Barcoding Birds of North America

Resolving Species Through DNA Barcoding Decapod Identification Through DNA Barcodes

Resolving Species Through DNA Barcoding Tropical Biodiversity

Resolving Species Through DNA Barcoding

COI Divergences (%) Resolving Species Through DNA Barcoding

Effective in varied geographic settings Effective in varied taxonomic groups >99.99% resolution Resolving Species Through DNA Barcoding Barcoding Animals (10 million species)

Resolving Species Through DNA Barcoding Barcode Repository ( data pits)

Resolving Species Through DNA Barcoding

COI Divergence in Eukaryotes Eubacteria Ciliata Apicomplexa Dinoflagellata Euglenophyta Kinetoplastida Chloroarachniophyta Animalia Chlorophyceae Fungi Xanthophyceae Phaeophyceae Eustigmatophyceae Bacillarioophyceae Cryptophyta Prymnesiophyta Chlorophyceae Rhodophyta Land Plants 20 % aa Resolving Species Through DNA Barcoding

Algae Identification Through DNA Barcodes Resolving Species Through DNA Barcoding

Barcodes: Developing a Reference Library for Known Species Master key ID all life stages IDs cheap & fast Residual taxonomic uncertainty low Alpheus heterochelis

There is a close correspondence between species recognized by sequence thresholds and those revealed by traditional taxonomic approaches. DNA Barcodes: Can We Use Them to Recognize New Species?

Automating Species Discovery: Moths

Sequence thresholds reveal >95% of species Barcode counts = counts through conventional taxonomy Rapid draft counts through barcodes Total evidence is the goal Barcodes: A Lead Role in Species Discovery?

DNA Barcoding – Toward Global Acivation Taxonomy, DNA, and the Barcode of Life Imagine a world in which any person, anywhere, at any time can identify any species at little or no cost. That world is techno- logically upon us. This report addresses the formative stages of an Initiative to bring this to society sooner rather than later.

DNA Barcoding – Towards Global Activation First International Barcode of Life Conference: Feb 5-8, 2005

Guelph DNA Barcoding – Toward Global Activaion CBOL launched April, Active memberships in 25 countries (and growing). Projects to barcode all birds and all fishes on Earth. Estimated cost to barcode all animal life: $1 billion.

Gaining Barcode Closure for Animals 10 million species x 10 barcodes each = 100 million barcodes Gaining Closure for All Animals The Future of DNA Barcoding

Barcoding: A Field Guide for the Third Millenium

Global Bio-ID System Evolutionary Rules Conserving Life Bio-Management

Acknowledgements Laboratory Database Collaborators Funders Jeremy DeWaard Sujeevan Ratnasingham 45 colleagues in Gordon and Betty Moore Foundation NSERC CFI OIT Canada Research Chairs Program Rob Dooh Janet Topan Nataly Ivanova Angela Holliss Stephanie Kirk 8 nations Pia Marquardt