Poster Abstracts

161 Pages·2007·2 MB·English

Second International Barcode of Life Conference 18-20 September 2007
1
Conference Abstracts
Welcome
Dear Conference Participants,
The Local Organizing Committee and the Consortium for the Barcode of Life welcome you to Taipei,
to Academia Sinica, and to the Second International Barcode of Life Conference. The First
Barcoding Conference was held more than two years ago at the Natural History Museum in London
and momentum and participation in the Barcode of Life Initiative has increased remarkably since
then. At the time of this writing, more than 350 people from more than 45 countries have registered
for the conference. Over the course of the three-day conference, you will receive presentations from
34 speakers from 14 countries and see 125 poster displays presented by researchers from 38 countries.
These numbers confirm that DNA barcoding has become a truly global enterprise.
The Scientific Program Committee has designed the agenda to provide a broad overview of the latest
developments in DNA barcoding science and technology. We will learn the “state-of-the-art” of
barcoding lab protocols, data management, and data analysis. Presenters will bring us up to date on
their progress on global barcoding projects and the application of barcoding to applied problems that
face society. Panelists will discuss the future of barcoding and its relation to other fields of research.
We hope that each of you will learn more about what interests you, and will become interested in the
new things you will learn.
The conference will include four types of presenters: Keynote Speakers (their presentations will be
30 minutes each), Invited Speakers (20 minutes each), Contributed Speakers selected through
committee evaluation (15 minutes each), and Discussion Panelists. Almost every session includes
time for discussion and questions from the audience. The sessions with Panel Discussions have been
organized to stimulate discussion with the conference participants. We hope that you will take
advantage of these opportunities for interaction with the speakers and each other.
You will also see that the agenda includes 90-minute lunch breaks and 20-30 minute coffee breaks
each morning and afternoon. We hope that you will use these opportunities to visit the poster
presentations and exhibit booths and to interact with the presenters. The latest software for DNA
barcoding will be demonstrated at several of the exhibit booths and we urge you to take a look.
The Local Organizing Committee has arranged for meeting staff to be available at the registration
desk throughout the meeting if you have any questions. You will also see Conference Assistants
circulating around the meeting and we hope that you will ask them for help if you need anything.
Thank you all for coming to Taipei to take part in this event. We hope that you find the conference
stimulating and productive!

David E. Schindel Kwang-Tsao Shao Scott E. Miller
Executive Secretary, Conference Chair CBOL Chair
CBOL Academia Sinica Smithsonian Institution

Second International Barcode of Life Conference 18-20 September 2007
2
Conference Abstracts
Table of Contents
Welcome Letter …2

Sponsors…4

Agenda…5

Plenary Session Abstracts…8

Posters by Subject…62

Posters Floorplan…67

Poster Abstracts…68

Index…155

Second International Barcode of Life Conference 18-20 September 2007
3
Conference Abstracts
Sponsors
We would like to thank the following sponsors who have made this
Conference possible:
Academia Sinica
National Science Council
Forestry Bureau, Council of Agriculture
Fisheries Agency, Council of Agriculture
Bureau of Animal and Plant Health Inspection and Quarantine, Council of
Agriculture
Taipei City Government
National Taiwan Museum
Ministry of the Interior
Ichthyological Society Taiwan
Taiwan Forestry Research Institute
National Sun Yat-Sen University
National Museum of Natural Science
Taiwan Seed Improvemnet and Propagation Station
Consortium for the Barcode of Life
Smithsonian Institution
Genome Canada
BioNET International
Swiss Agency for Development and Cooperation
The Alfred P. Sloan Foundation

Special Thanks to
Local Organizing Committee
General Innovation Service (GIS)
CBOL Secretariat

Second International Barcode of Life Conference 18-20 September 2007
4
Conference Abstracts
AAggeennddaa
DAY ONE: TUESDAY 18 SEPTEMBER 2007

SESSION 1: GLOBAL ACTIVITIES OF THE BARCODE OF LIFE INITIATIVE (BOLI)
8:00 - 9:00 Conference Registration
9:00-9:30 Conference Opening - Kwang-Tsao Shao, Conference Chair, Academia Sinica
9:30 - 10:00 Keynote I -DNA Barcoding in the Genome Era - Ya-Ping Zhang, Kuming Institute of Zoology,
Chinese Academy of Science
10:00 - 10:30 Keynote II – Biodiversity Research and DNA Barcoding in Korea - Won Kim, Seoul National
University
10:30 - 11:00 Keynote III: Barcoding in Applied Taxonomic Challenges- Helida Oyieke, National
Museums of Kenya
11:00 - 11:30 COFFEE BREAK
SESSION 2: DIVERSE APPLICATIONS OF DNA BARCODING
11:30 - 11:45 Progress by CBOL since London Conference - Scott Miller, Smithsonian Institution
(CBOL)
11:45 - 12:45 Brief presentations and panel discussion of major barcoding projects
• Yvonne Linton, Natural History Museum London, CBOL Demonstrator Project 1: Mosquito Barcoding
Initiative
• Marc De Meyer, Royal Museum of Central Africa, Belgium, CBOL Demonstrator Project 2: Tephritid
Barcode Initiative
• Mark Stoeckle, The Rockefeller University, All Birds Barcoding Initiative (ABBI) Update
• Robert Hanner, University of Guelph, The Fish Barcode of Life (FISH-BOL) Campaign
• Mark Bagley, US Environmental Protection Agency, DNA Barcodes for Assessment of the Biological
Integrity of Aquatic Ecosystems
• Ann Bucklin, University of Connecticut, DNA Barcoding of the Global Marine Zooplankton Assemblage
12:45 - 1:00 Open discussion between audience and panel
1:00 - 2:30 LUNCH
SESSION 3: HOW DOES BARCODING WORK AND HOW WELL DOES IT WORK?
2:30 - 3:00 Keynote Address- Toward a Barcoded World- Paul Hebert, University of Guelph
3:00 - 3:15 The BARCODE Data Standard: Enabling Molecular Diagnostics for Biodiversity-Bob Hanner,
University of Guelph
3:15 - 3:30 Barcoding in an all-species inventory – The Moorea Biocode Project- Chris Meyer, University
of California Berkeley
3:30 - 3:45 Barcodes bridge the old and the new: use of museum specimens to identify molecular
operational taxonomic units in larvae of scarab beetles (Coleoptera: Scarabaeoidea)
Andrew Mitchell, NSW Department of Primary Industries, Australia
3:45 - 4:00 DNA barcode, type specimens and species delimitation in the genus Eumunida
Sarah Samadi, Museum National d'Histoire Naturel, Paris
4:00 - 4:30 COFFEE BREAK
SESSION 4: HOW CLOSE ARE WE TO HAND-HELD, FIELD-FRIENDLY, OR TABLE-TOP BARCORDERS?
4:30 - 4:45 In vitro repair enhances amplicon recovery and accuracy from damaged DNA -Tom Evans,
New England Biolabs
4:45 - 5:00 Express Barcodes: Racing from Bugs to Identifications -Natalia Ivanova, University of Guelph
5:00 - 5:15 Development of a DNA barcode-based DNA chip for identification of marine organisms in
the East Sea of Korea -Youn-Ho Lee, Korea Ocean Research and Development Institute
5:15 - 5:30 Fish and Chips: microarray-based DNA-barcoding of European Marine Fishes -
Kochzius Marc, University of Bremen
5:30 - 5:45 Portable Pyrosequencing device for DNA sequencing -Mostafa Ronaghi, Stanford
University
5:45 - 6:00 Open discussion between audience and speakers

Second International Barcode of Life Conference 18-20 September 2007
5
Conference Abstracts
Agenda
DAY 2: WEDNESDAY, 19 SEPTEMBER 2007

SESSION 5: ANALYTICAL METHODS FOR BARCODE DATA.
8:30 – 8:45 Introduction-Michel Veuille, Museum National d’Histoire Naturel Paris
8:45 - 9:00 Comparing phylogenetic and statistical classification methods for DNA barcoding – Frederic
Austerlitz, CNRS/AgroParisTech/Universite Paris Sud
9:00 - 9:15 Fast Barcode-Based Species Identification Using String Kernels –Vladimir Pavlovic,
Rutgers University
9:15 - 9:30 Species Classification with Optimized Logic Formulas – Giovanni Felici, Consiglio
Nazionale delle Ricerche
9:30 - 9:45 DNA Barcode sequence identification incorporating taxonomic hierarchy and
within taxon variability – Damon Little, The New York Botanical Garden
9:45 - 10:00 A Comparison of Algorithms for Species Identification based on DNA barcodes –
Bogdan Pasaniuc, University of Connecticut
10:00 - 10:30 Open discussion between audience and speakers
10:30 - 11:00 COFFEE BREAK
SESSION 6: CASE STUDIES I. INTEGRATIVE TAXONOMIC STUDIES USING DNA BARCODING
11:00 - 11:20 Barcoding, Biogeography and Evolution in the Tropics of the New World – Eldredge
Bermingham, STRI, Panama
11:20 - 11:40 The role of DNA Barcoding in the broader context of Integrative Taxonomy - Benoit Dayrat,
University of California, Merced
11:40 - 12:00 Sphingids and Barcodes- The New Taxonomy- Rodolphe Rougerie, University of Guelph
12:00 - 12:20 Bamboozled by bloodsuckers: barcoding backs biodiversity- Mark Siddall, American Museum
of Natural History
12:10 - 12:30 Open discussion between audience and speakers
12:30 - 2:00 LUNCH/ Group Photo at Front Gate
SESSION 7: WHAT NEW SCIENCE WILL WE SEE AT THE THIRD BARCODE CONFERENCE?
2:00 - 2:20 Barcoding and biodiversity research - Les Christidis, Australian Museum
2:20 - 2:40 "Ecological inventory with a barcorder, the ecological taxascope: who eats what in a
complex tropical forest" - Dan Janzen, University of Pennsylvania
2:40 - 3:40 Panel discussion: What new research can we do with a MILLION Barcode records?
• Paul De Barro, CSIRO, Australia
• Peter Ng, National University of Singapore
• Axel Meyer, University of Konstanz
• Robert Andersen, Bigelow Laboratory for Ocean Sciences
3:40 - 4:00 COFFEE BREAK
SESSION 8: CASE STUDIES II. DNA BARCODING IN DEVELOPING COUNTRIES.
4:00 - 4:20 DNA Barcoding: considerations for vectors of neglected diseases
- Daniel Masiga, ICIPE, Nairobi, Kenya
4:20 - 4:40 All Birds Barcoding Initiative in the Neotropics: Identifying and discovering bird species in
the richest avifauna of the World - Pablo Tubaro,
National Museum of Natural History, Argentina
4:40 - 5:00 FISH-BOL and Barcoding in India - Wazir Lakra,
National Bureau of Fish Genetic Resources, India
5:00 - 5:15 Transforming taxonomy for effective biodiversity assessment of arthropods in Madagascar
-Brian Fisher, California Academy of Sciences
5:15 - 5:30 Construction of A DNA Barcode System for Amphibians and Reptiles in Taiwan –
Si-Min Lin, Chinese Culture University, Taiwan
5:30 - 5:45 Open discussion between audience and speakers

Second International Barcode of Life Conference 18-20 September 2007
6
Conference Abstracts
Agenda
DAY 3: THURSDAY, 20 SEPTEMBER 2007

SESSION 9: BARCODING IN THE WIDER EVOLUTIONARY CONTEXT
8:30 - 9:30 Panel discussion: Barcoding and other initiatives in evolutionary research
• Michael Donoghue, Yale University, Barcoding and the Tree of Life
• Masaki Miya, Natural History Museum, Chiba University, Evolutionary History of Fishes: An overview
based on >1000 whole mitochondrial genome sequences
• Dan Faith, The Australian Museum, How large-scale barcoding promotes large-scale biodiversity
assessment
• Richard Lane, Natural History Museum London, Barcoding and the practice of systematics
9:30 - 10:00 Open discussion between audience and panel
10:00 - 10:30 COFFEE BREAK
SESSION 10: STATE-OF-THE-ART PRACTICES: HOW TO MANAGE YOUR BARCODE DATA.
10:30 - 10:50 BOLD, the Barcoding Workbench - Sujeevan Ratnasingham, University of Guelph
10:50 - 11:50 Panel discussion: How are the BAROCDE data standards being implemented?
• Scott Federhen, NCBI/NIH, BARCODE records in GenBank
• Simon Tillier, Museum National d’Histoire Naturel, Paris, BARCODE data, museum catalogs and GBIF
• Andrew Polaszek, ICZN, London, Zoobank- the open-access animal name registry-working with CBOL
towards the new taxonomy
11:50 - 12:10 The Encyclopedia of Life: A website for every species - James Edwards, Smithsonian
Institution (EOL)
12:10 - 12:30 Open discussion between audience and speakers
12:30 - 2:00 LUNCH

SESSION 11: STATE-OF-THE-ART PRACTICES: HOW DO THE BEST BARCODE LABS DO THEIR WORK?
2:00 - 2:20 Technology Transfer, an efficient DNA barcoding workflow: how we do it and more
importantly to you, how we can help you do it- Lee Weigt, Chair, CBOL DNA Working Group,
Smithsonian Institution
2:20 - 2:40 African Wildlife Tissue Banking - Paul Bartels, BioBank, South Africa
2:40 - 3:00 Recovering historic DNA (HDNA) and ancient DNA (ADNA): Implications for DNA barcoding -
David Lambert, Allan Wilson Centre, New Zealand
3:00 - 3:20 Exploring archival and environmental samples through minimalist barcodes- Mehrdad
Hajibabaei, University of Guelph
3:20 - 3:30 Open discussion between audience and speakers
3:30 - 4:00 COFFEE BREAK
SESSION 12: BARCODING WITH NON-COI GENE REGIONS.
4:00 - 4:20 Optimising selection of DNA barcode regions and CBOL’s guidelines for non-CO1 selection
Freek Bakker, University of Wageningen, Netherlands Herbarium
4:20 - 4:40 Standardized land plant barcoding requires a multi-loci approach - Robyn Cowan,
Royal Botanic Gardens, Kew
4:40 - 5:00 Using DNA barcodes to test the identity and purity of plant-based medicines and
herbals - John Kress, Smithsonian Institution
5:00 - 5:20 DNA-barcoding on a different scale: Challenges within Coccoidea - Lyn Cook,
University of Queensland
5:20 - 5:40 Canadian plant barcoding results with some global implications - Sean Graham, University
of British Columbia
5:40 - 6:00 Progress toward DNA barcoding the vast diversity of fungi-
Amy Rossman,USDA Beltsville
6:00 Closing remarks and adjournment - Kwang-Tsao Shao, Conference Chair, Academia Sinica

Second International Barcode of Life Conference 18-20 September 2007
7
Conference Abstracts
Plenary Session Abstracts
(By Speaker Order)
Session 1: Global activities of the Barcode of Life Iniative (BOLI)

KEYNOTE ADDRESS

DNA BARCODING IN NEW GENOME ERA

YA-PING ZHANG

State Key Laboratory of Genetic Resource and Evolution, Kunming Institute of Zoology, Chinese Academy of Science,
Kunming 650223
Laboratory for Conservation and Utilization of Bioresource, Yunnan University, Kunming 650091

Both the identification and the knowledge of evolutionary position of species are very important
for all biological studies. The new identification systems based on DNA sequence diversity have
been developed in recent years. The ideal core barcode DNA fragments should not only enable
accurate, rapid and cost-effective identification of species, but can also provide high phylogenetic
resolution. A 648-bp fragment of the cytochrome c oxidase I (COI) gene has been selected as the
core barcode DNA marker for animals. We sequenced the entire mitochondrial genome of the
Ursidae family, which represents a typical example of rapid evolutionary radiation, to evaluate the
individual mitochondrial gene performance in supporting the complete mtDNA-based phylogeny.
Among single gene trees, only the CYTB and ND5 trees have the same branching order as that
from the combined all gene analysis. With more and more genome sequence data from animals, we
will be able to evaluate the effect of mitochondrial pseudogenes on DNA barcoding, and develop
additional markers for DNA barcoding.

Zhang Ya-Ping

Dr. Zhang Ya-Ping held a B.S. in Biochemistry from Fudan University in 1986
and a Ph.D. in Genetics Zoology in 1991 from Kunming Institute of Zoology
(KIZ), Chinese Academy of Sciences. He completed post-doctoral studies at
the Center for Research of Endangered Species (CRES), the Zoological Society
of San Diego during 1992-1995. He has been working in KIZ Since 1995. He
was appointed as an Academician of CAS in 2003 and the director of KIZ in
2005.

His major research interests are Conservation genetics, molecular evolution,
and population genetics. The Laboratory’s current research interests can be
summarized into following areas: (1) adaptive evolution, (2) molecular
phylogeny of animals, (3) population genetics and conservation genetics of
animal species in China, (3) genetic diversity and origin of domesticated
animals, (4) genetic diversity and evolution history of human populations in
East Asia, (5) genome evolution.

The results of all above fields have been published more than 170 papers in peer review journals, including
Nature, Science, PNAS, Mol. Biol. Evol., Mol. Phylogen.Evol., Am. J. Hum. Genet., Genetics, Genomics
and et al.

Second International Barcode of Life Conference 18-20 September 2007 8
Conference Abstracts
Plenary Session Abstracts
KEYNOTE ADDRESS

BIODIVERSITY RESEARCH AND DNA BARCODING IN KOREA

WON KIM

School of Biological Sciences, Seoul National University

Biodiversity research in Korea has been far from comprehensive. Even the biota has not been
systematically well surveyed or documented owing to a lack of taxonomic specialists and research
funds. Nevertheless the major taxonomic works have been published in “Illustrated Encyclopedia
of Fauna & Flora of Korea” since 1959 (1959-2006; vol.1-vol.41). After the Rio meeting in 1992,
numbers of systematists have consistently emphasized the importance of systematics along with
biological resources in public. On years of efforts, “National Institute of Biological Resources,
Korea” is scheduled to be open in October, 2007. A master plan of the tentatively named “National
Institute of Marine Biological Resources, Korea” is also being promoted. These two institutes will
be the central units managing biological resources in Korea. The molecular systematics was first
introduced to Korea in 1989. Since then, the majority of Korean systematists have adopted
molecular methods, with developments of technology, in their researches. While a few systematists
have individually conducted DNA barcoding researches, the necessity of national undertaking
DNA barcording project has been invoked through several symposiums. A three year DNA
barcode research project on all major groups of animals and plants, sponsored by Korea Institute of
Environmental Science and Technology, has been finally launched this year. We hope for this
project to be continued.

Won Kim

Dr. Won Kim received a B.S. and a M.S. from the Dept. of Zoology, Seoul National
University in 1977 and 1981, respectively. He received a Ph.D. from the Dept. of
Biological Sciences, Florida State University in 1985 and worked as a research
associate at the same department during 1986-1989. He has been working in Seoul
National University since 1989. He served as a chairperson of the Dept. of
Molecular Biology during 1995-1999 and an associate dean of College of Natural
Science during 1999-2000. He is a member of the Korean Academy of Science and
Technology since 2004. His major research interests are classical taxonomy,
molecular systematics, molecular ecology and biogeography, and molecular
evolution and bioinformatics.

The current research interests can be summarized into following areas: (1) classical
taxonomy of various marine invertebrates, (2) molecular systematic studies of selected invertebrates, (3)
molecular identification based on various molecular markers and DNA barcoding, (4) microsatellite search
and studying population structure, (5) evolution of genes based on nucleotide analysis, (6) pattern search for
finding candidate genes. About 150 papers have been published in various journals, including Smithoni.
Contrib. Zool., J. Crustacean. Biol., Korean J. Syst. Zool., Mol. Biol. Evol., Mol. Phylogen. Evol., J. Mol.
Evol., Nature, Mol. Ecol. Notes, Computat. Biol. Chem., etc.

Second International Barcode of Life Conference 18-20 September 2007 9
Conference Abstracts
Plenary Session Abstracts
KEYNOTE ADDRESS

BARCODING IN APPLIED TAXONOMIC CHALLENGES

HELIDA OYIEKE

National Museums of Kenya

Taxonomy plays a very important function in the scientific and socio-economic arenas by
facilitating species classification and identification. Millions of species have been discovered in
both aquatic and terrestrial systems while many more are yet to be. Traditional taxonomy has in the
past met human needs in biodiversity conservation and management, agricultural production and
human health. However, as the demand for taxonomic services increases, traditional taxonomy is
becoming inadequate in coping with the demand. The issue is aggravated by the fact that the
number of taxonomists is significantly getting reduced globally. It is currently clear that DNA
barcoding technique is increasingly complimenting the efforts made by taxonomists. It is becoming
a tool that could settle conflicts arising among taxonomists on species identities. The technique
becomes handy in cases where only parts of specimens are available such as in the identification of
wildlife and their products in illegal trade. Barcoding can be used as a tool for flagging new species
that have not yet been described as well as cryptic species. The neotropical skipper butterfly,
Astrapes fulgerator, acryptic species complex found in north-western Costa Rica, was found to
consist of 10 different species through DNA barcoding by Herbet et al. Associating all life history
stages of a specific species have been a challenge to traditional taxonomy and there is great
potential in surmounting this huddle through barcoding. Much as DNA barcoding technique is
becoming a possible solution to problems that traditional taxonomy has delayed or failed to solve
in good time, a lot of mileage will be gained if experts from the two divide work together to
complement one another.

Dr. Helida A. Oyieke

Dr. Helida Oyieke is the Director for Research and Collections at the National
Museums of Kenya, a natural history based museum centered in Nairobi, where she
oversees and provides general leadership on research programmes in the institutions.
She holds a B.Ed, M.Sc and Ph.D degrees in biological sciences all from the
University of Nairobi and is specialized in the Marine Botanical Sciences. Helida
started her research career in 1984 at the Kenyan Marine and Fisheries Research
Institute in Mombasa where she rose to the rank of Senior Research Scientist. In 1994
she joined her current institution as a Senior Research Scientist, rose to Principal
Scientist position before finally being appointed to her current position in 2004.

Throughout her research career she has mobilized grants for research in the fields of taxonomy, ecology,
biodiversity conservation and collection management, and serves in several technical national and regional
committees. Dr. Oyieke is currently serving as a member of CBOL Executive Committee, representing
Africa, and also chairs the steering committee for the eastern Africa Barcode Initiative where she is making
efforts to popularize barcoding technology as a tool for taxonomy in the region.

Second International Barcode of Life Conference 18-20 September 2007 10
Conference Abstracts