Biodiversity Research and DNA Barcoding in Korea

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Biodiversity Research and DNA Barcoding in Korea

• Won Kim
• School of Biological Sciences,
• Seoul National University, Seoul, Korea.

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Biodiversity
Number
Variety
Living Organisms
Systematics
Variability
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Systematics

• Systematics is the science dedicated to
  discovering, organizing, and interpreting
  biological diversity.
• Discovering, identifying, and describing species
  are the first step for biodiversity research.
• Phylogenetic analysis
• Classification
• Speciaton

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Biodivesity Research in Korea

• Biodivesity 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.
• Neverthless the major taxonomic works have been
  published in Illustrated Encyclopedia of Fauna
  Flora of Korea since 1959.

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Illustrated Encyclopedia of Fauna Flora of Korea
Total 41 encyclopedia 1959-2006
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Illustrated Encyclopedia of Fauna Flora of Korea

• Algae 2
  volumes
• Fungi 1
  volume
• Nonseed tracheophytes 2 volumes
• Higher plants 4 volumes
• Other plants 2
  volumes
• Planktons 2
  volumes
• Insects 10
  volumes
• Spiders 1
  volumes
• Invertebrates 10 volumes
• Fishes 2
  volumes
• Birds 2
  volume
• Amphibians Reptiles 1 volume
• Mammals 1 volume

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Illustrated Encyclopedia of Fauna Flora of Korea

• These encyclopedia are not enough, but
  fundamental materials for national biodiversity
  inventory.
• Unfortunately majority of the first generation
  taxonomists have retired without replacement
  36/41authors.
• About 30,000 species are known to occur in Korea.
• We estimate about 100,000 species living in
  Korea.

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Biological Resources

• The studies on the biodiversity are required to
  be comprehensive.
• The phylogenies and evolutionary processes of
  organisms as well as the identifications and
  descriptions of organisms should be studied.
• The detailed studies on the biological properties
  of each species are also required.
• However, majority of systematic studies in Korea
  are still remained in the level of identification
  and description of organisms and the study on
  their distributions through the faunal studies in
  most taxa.
• We have very insufficient taxonomic information
  owing to a lack of systematists and research
  funds.

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• Some data concerning marine invertebrates.
• Marine invertebrates are quite diverse and are
  found in every 34 phyla in animal Kingdom.

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Marine invertebrate fauna
Table 1. The estimated number of marine
invertebrate species reported from Korea
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Research Type

• Table 2. Papers concerning crustacean decapods
  published until now  in Korea

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Monitoring Studies

• There have been no real long term monitoring
  studies about marine invertebrate fauna so far,
  though marine systematists and the governmental
  agencies have conducted some regional surveys
  from time to time.

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Specimens

• There is no national Natural History Museum in
  Korea and there have been no reports at all on
  the list of the preserved specimens of marine
  invertebrates in Korea.

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Taxonomic Specialists

• Table 3. The estimated number of marine
  invertebrate taxonomist with Ph.D.

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Biological Resources

• 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.

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National Institute of Biological Resources, Korea

• Major Functions
• Storage of specimens
• Survey and Systematic research
• Education and Display
• Supporting Policymaking and Planning
• Two main extensive biodiversity researches
• are underway

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Two biodiversity researches

• Monographs

Survey and collecting organisms living in Korea
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?. Survey and collecting organisms living in Korea

• 6 groups
• Invertebrates I (insect)
• Invertebrates II
• Vertebrates
• Higher plants
• Lower plants (algae)
• Fungi Microorganisms
• About 90 researchers are involved.

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First Year Results

• Species unknown to Korea 616 species
• Invertebrates I (insect) 159
• Invertebrates II 111
• Vertebrates 13
• Higher plants 6
• Lower plants (algae) 148
• Fungi 62

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II. Monographs

• 5 groups
• Vertebrates
• Lower plant
• Invertebrates I (insect)
• Invertebrates II
• Fungi Microorganisms
• About 60 researchers are involved.
• First year results 20 volumes of monographs

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National Institute of Marine Biological
Resources, Korea

• The master plan is being promoted.
• Open in 2012
• Survey, Storage, and Systematic research
• Training taxonomic specialists for every marine
  taxa

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Molecular Systematics

• Spectacular achievements of molecular biology
  since 1953
• 18S Ribosomal RNA gene was used in the
  phylogenetic study in animal groups in late
  1980s.
• In Korea, molecular systematics was introduced in
  1989 by the present speaker.

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Traditional Taxonomy

• Monograph, Key, Description of new species, etc.
• The snapping shrimp genus Alpheus from the
  eastern Pacific (Decapoda Caridea Alpheidae). 
• (Kim, W., and L.G. Abele, 1988.
  Smithsonian Contribution to Zoology)
• The decapod crustaceans of the Panama Canal.
•   (Abele, L. G. and W. Kim, 1989.
  Smithsonian Contribution to Zoology)

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• Since 1986, my colleagues and I have studied the
  various aspects of nuclear rRNA genes and mtDNA
  of selected animal groups in terms of systematics
  and molecular evolution.

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(Abele, L.G, W. Kim, and B.E. Felgenhauer, 1989,
Mol. Biol. Evol)
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Phylum Pentastomida (tongue worm)

• Q phylogenetic position
• Data partial nucleotide sequences of 18S rRNA.
• Results the tongue worms are highly modified
  crustaceans closely related to fish lice
  (Branchiura, Crustacea, Arthropoda).
• (Abele, L.G, W. Kim, and B.E. Felgenhauer,
  1989, Mol. Biol. Evol.)

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(Kim, W. and L. G. Abele, 1990, J. Crustacean
Biol.)
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Selected Decapod Crustaceans

• Q relationships among infraorders within
  Decapoda
• Data Partial nucleotide sequences of 18S rRNA
• Results
• 1. Nucleotide sequences of 3 species of
  Procambarus are virtually identical (differ in
  only 3 of more than 1,500 nucleotides)
• 2. Variation is not evenly distributed
  across the molecule (conserved-variable-highly
  variable)
• 3. Variation is phylogenetically
  informative to infraorder or possibly superfamily
  level
• (Kim, W. and L. G. Abele, 1990, J.
  Crustacean Biol.)

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(Kim, W. and L. G. Abele, 1990, J. Crustacean
Biol.)
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Rapid progress in molecular systematics and
molecular evolution in 1990s

• Rate of nucleotide substitution differs among
• the different genes
• the different region of same gene
• different lineage
• Researchers began to search adequate molecular
  markers in their taxonomic groups.

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Nucleotide Analyses taxon specific
insertion/deletion of 18S rDNA nucleotide
sequences

• Sequence of the 18S ribosomal RNA-encoding gene
  of the crustacean Philyra pisum longer sequences
  of decapods in the V9 region
• (Moon, S.Y., G.S. Min, S.H. Kim, and W.
  Kim, 1994. Gene)
• Sequences of the 18S rDNAs from two Collembolan
  insects shorter sequences in the V4 and V7
  regions.
• (Hwang, U.W., B.H. Lee, and W. Kim, 1995.
  Gene)

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Combined Data Set morphological and molecular
characters

• Phylogenetic relationships of Annelids, Molluscs,
  and Arthropods evidenced from molecules and
  morphology.
• (Kim, C.B., S.Y. Moon, S.R. Gelder, and W. Kim,
  1996. J. Mol. Evol.)

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Molecular Phylogeny complete nucleotide sequence
of mitochondrial DNA

• Mitochondrial protein phylogeny joins myriapods
  with chelicerates
• (U.W. Hwang, M. Friedrich, D. Tautz, C.J.
  Park, and W. Kim, 2001. Nature)

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Molecular Identification (DNA
Barcode) Why?

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• Very similar species (species complex)
• Broken specimens
• Very small species
• Larvae, egg, young specimens
• Monitoring

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Meiobenthology?
Meiobenthology is the study of small benthic
metazoans that pass through a 0.500 mm sieve and
are retained on a 0.063 (or 0.045 mm) sieve. The
majority of recognized phyla have meiofaunal
representatives.
Porifera, Placozoa, Cnidaria, Ctenophora,
Platyhelminthes, Orthonectida, Rhombozoa,
Cycliophora, Acanthocephala, Nemertea,
Nematomorpha, Gnathostomulida, Kinorhyncha,
Loricifera, Nematoda, Rotifera, Gastrotricha,
Entoprocta, Priapulida, Pogonophora, Echiura,
Sipuncula, Annelida, Arthropoda, (Copepoda,
Halacaroidea, Ostracoda, Mystacocarida,
Tantulocarida), Tardigrada, Onychophora,
Mollusca, Phoronida, Bryozoa, Brachiopoda,
Echinodermata, Chaetognatha, Hemichordata,
Chordata
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Tardigrada
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Nematoda
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Campaign for DNA barcode In Korea

• 1989.3 After introduction of molecular
  systematics
• 1990s Spread of molecular systematics, study
  on the variability according to taxon,
  development of molecular makers for each taxon
• 2005.7 Symposium at Inha University DNA
  barcode and use of microsatellite
• 2005.11 13 papers under the title of molecular
  identification and diagnosis at the meeting of
  the Korean Society of Oceanography
• 2005.11 Organization of KABOL(Korean
  Association of Barcode of Life) (by Won Kim)
• 2006. 8 Symposium DNA taxonomy and biological
  barcode at the meeting of the Korean Society of
  Systematic Zoology

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Some messages in the DNA barcode symposiums

• Why DNA barcode?
• We need more complete species information.
• But we are lack of morphological taxonomists.
• There will be no person who can identify species.
  
• We need training taxonomic specialists.
• But it takes a lot of time.
• While we are training taxonomic specialists and
  doing continuous species inventories, we have to
  develop another tool for identifying and
  monitoring organisms.

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• Taxonomic specialist knows very well how
  difficult it is to identify very similar
  organisms, broken specimens or very tiny
  organisms by morphological characters.
• Even we do not know the species name, we need
  have some kind of unit such as a molecular
  taxonomic unit for monitoring.
• However, before doing massive DNA barcoding
  works, we must find an adequate molecular marker
  for each taxon and the range of variation
  defining species boundary.

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DNA Barcode Research Project

• A three year DNA barcode research project on all
  major groups of animals and plants has been
  finally launched this year.
• DNA barcode system for conservation and
  management of major organisms from Korea
• Funded by Korea Institute of Environmental
  Science and Technology
• 2007-2010

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Strategy and Goals

• Participating molecular systematists and
  classical taxonomist for each taxon
• Secure specimens and correct identification
• Application of the adequate molecular markers
  according to each taxon (COI, 18S, ITS,
  trnH-psbA, rbc L, etc.)
• Automation and standardization of entire protocol
  for collecting DNA barcode

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Strategy and Goals

• Development of various techniques for
  identification
• Identification based on different length of PCR
  product (Decapoda, Copepoda)
• Identification based on nucleotide similarities
  (Decapoda, Copepoda)
• Development of chip based on hybridization
  (birds, fishes)
• How to monitor organisms using DNA barcode system
• Multiplex PCR, cloning and sequencing

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DNA Proliferation (PCR)
DNA Extraction
Collection of specimens
Application of taxon specific primer
Barcode DB construction
Development of barcode and PCR marker
Determination of range of variation for species
identification
Morphological identification
Automatic, standardized techniques
Environmental monitoring, conservarion
Search for new resources
Gene bank
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Researchers
Molecular systematist
Selection of adequate molecular marker and
collection of DNA barcode
Morphological taxonomist
Developer of monitoring techniques
Development of monitoring techniques based on
DNA barcode
Providing voucher specimens with correct
identification
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Organization
Principal Investigator Group (11) Won Kim (Seoul
National University) Construction of DNA barcode
database, Molecular identification and
development of monitoring techniques
Total 54 researchers
A advisory committee
A steering committee
First Group (7) Chang Bae Kim (KRIBB) Development
of DNA barcode of Korean major vertebrates
Second Group (20) Gi Sik Min (In ha
university) Development of DNA barcode of Korean
major invertebrates
Third Group (16) Young-Bae Seo (Seoul National
University) DNA barcode and search for molecular
marker of Korean land tracheophytes and lower
plant
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Principal Investigator Group

• Construction of DNA barcode database
• Molecular identification system
• Development of monitoring techniques

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Construction of DNA Barcode DB
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Development of Identification System
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Molecular Identification System
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1st Group Development of DNA barcode of Korean
major vertebrates
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Goals

• Birds 135 species COI barcode
• Marine fishes 100 species COI barcode
• Mammals 30 species COI barcode
• Amphibians 20 species species COI 16S rRNA
  barcode
• Reptiles 20 species COI barcode
• No. of specimen 2-3/species

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2nd Group DNA barcode of Korean major
invertebrates
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Goals

• Invertebrates (except insect) 9 phyla, 11 taxa
  (5 subgroups)
• 75species 150 individuals/3 years/each taxon
• Total 675 species, 1,350 individuals
• Insects 5 orders Freshwater insects (5
  subgroups)
• 150-200 species, 500 individuals/3 years/each
  subgroup
• Total 900 species, 2,500 individuals

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3rd Group DNA barcode and searching for
molecular markers of Korean land tracheophytes
and lower plants
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Goals

• Searching for adequate molecular markers
• Multigene tiered approach
• Land Tracheophytes
• ITS (350 bp)
• trnH-psbA (450 bp)
• rbcL (1400 bp)
• Algae
• cox 1 (5-600 bp)
• rbcS (520 bp)
• Lichens
• rDNA
• DNA Barcoding of major plant species
• Automation of identifying plant species using DNA
  barcode
• Standardization of DNA barcoding according to
  international standard

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DNA Barcode Research Project

• If we have good results this year
• 2nd year ?
• 3rd year ?
• We hope for the current project to be continued
  as a National DNA Barcode Research Project.

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• Thank you.