Rob Jennings University of Connecticut, USA

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Barcoding for CoML Assessing Zooplankton
Diversity
Rob Jennings University of Connecticut,
USA Photos by R.R. Hopcroft University of
Alaska, USA L.P. Madin Woods Hole Oceanographic
Institution, USA N. Copley Woods Hole
Oceanographic Institution, USA
CMarZ Steering Group Meeting 6 November Ocean
Research Institute, University of Tokyo
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CoML Ocean Realm Field Projects

• Natural Geography in Shore Areas NaGISA
• Gulf of Maine Area Program GOMA
• Pacific Ocean Shelf Tracking POST
• Census of Diversity of Abyssal Marine Life
  CeDAMar
• Tagging of Pacific Pelagics TOPP
• Patterns and Processes of Ecosystems in the
  Northern
• Mid-Atlantic MAR-ECO
• Biogeography of Chemosynthetic Ecosystems ChEss
• Arctic Ocean Diversity ArcOD
• International Census of Marine Microbes ICOMM
• Census of Marine Zooplankton - CMarZ
• Global Census of Marine Life on Seamounts
  CenSeam
• Global Census of Coral Reef Ecosystems CREEFS
• Continental Margin Ecosystems on a Worldwide
  Scale
• CoMargE
• Census of Antarctic Marine Life CAML

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What is DNA Barcoding?

• Definition Derivation of short DNA sequence(s)
  that enables species identification or
  recognition in a particular domain of life (e.g.,
  eucaryotes).
• Focus to date For animals, a 658 base-pair
  fragment of the mitochondrial gene, cytochrome
  oxidase subunit I (mtCOI).
• Barcode of Life Initiative (BOLI) will resolve
  barcodes for named species and use a barcoding
  approach to assess undescribed biological
  diversity.

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What isnt DNA Barcoding?

• It is not intended to, in any way, supplant or
  invalidate existing taxonomic practice.
• It is not DNA taxonomy it does not equate
  species identity, formally or informally, with a
  particular DNA sequence.
• It is not intended to duplicate or compete with
  efforts to resolve deep phylogeny (e.g.,
  Assembling the Tree of Life, ATOL).

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Why Barcode Zooplankton?

• DNA is particularly useful to study animal
  plankton, because the organisms are frequently
  rare, fragile, and/or small.
• Evolutionarily-conserved body plans for some
  groups (e.g., copepods) makes morphological
  identification difficult and mistakes likely.
• Many species are widespread or circumglobal DNA
  can be used to evaluate taxonomic significance of
  geographic variation.
• DNA-based species identification will speed
  analysis of samples for known species.
• Zooplankton will test barcode protocols, since 15
  animal groups (phyla) are represented.

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Barcoding Goals for CMarZ

• Link morphological / molecular systematic
  analysis for global zooplankton assemblage
• DNA barcode 7,000 described species in 15 phyla
• Submit DNA, specimen collection data
• - Barcode section of GenBank
• - CMarZ database with environmental data
• - Searchable from OBIS portal
• Reveal cryptic species within circumglobal
  species by population genetic analysis
• Discover new species by sampling biodiversity
  hotspots, unexplored ocean regions, deep sea
• Assess zooplankton diversity by environmental
  sequencing of unsorted samples
• Develop automatable DNA chip-based approaches and
  protocols to identify and quantify species

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Barcoding Ostracods (Crustacea)

• Ostracod species differed in mtCOI sequence by
  15 to 38 for 19 species (15 more completed).
• Barcoding for Ostracods
• Good species identification
• Cryptic variation within species

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Barcoding Euphausiids (Crustacea)

• Fourteen of 86 euphausiid species were identified
  by Peter Wiebe.
• 50 euphausiids ? including 19 species of
  Euphausia ? have been barcoded to date.
• Barcoding for Euphausiids
• Good at species identification
• Can reveal cryptic species

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Barcoding Planktonic Gastropods

• MtCOI barcodes for 17 species of gastropods
  (pteropods and heteropods) differed by 1.4 to
  44.
• Barcoding for Gastropods
• Good at species identification
• Less consistent species phylogeny

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Barcoding Medusozoans (Cnidaria)

• Barcoding is done by Brian Ortman (UConn/USA).
• 13 species of siphonophores
• greatly expanded, much of siphonophore diversity
  (160 spp.)

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Barcoding Arctic Zooplankton

• ArcOD (Arctic Ocean Diversity) sends identified
  specimens of Arctic zooplankton for barcoding by
  CMarZ.
• Comprehensive DNA database of 210 species of the
  Central Arctic assemblage is underway.
• DNA obtained from 50 species already, comprising
  several dates and locations work in progress at
  UConn

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CMarZ Barcoding Structure and Operations

• Barcoding cruises
• DNA sensitive collection protocols- anyone can
  collect
• Standardized and web-available sampling and
  processing protocols
• Taxonomic training ? Molecular training
• Increased ability to use preserved (e.g.
  formalin) samples
• Distributed network of barcoding centers
• Local taxonomic expertise
• Care of specimens
• Capacity-building

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CMarZ Barcoding Centers

• Existing barcoding centers
• UConn, USA ? Oviedo, Spain ? ORI, Japan
• Emergent barcoding centers
• Qingdao, China ? Goa, India

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Results and Conclusions

• Global-scale analysis of zooplankton species
  diversity integrated morphological and molecular
  analysis.
• DNA barcodes for all 6,800 known species of 15
  phyla in the zooplankton.
• Species discovery by CMarZ will double number of
  zooplankton species
• - sampling new ocean regions (deep sea)
• - cryptic species within circumglobal species

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Got specimens? CMarZ encourages and challenges
the CoML community to provide identified
specimens of holozooplankton groups for
barcoding. A DNA barcode (700 base-pair region of
mtCOI with replicates / metadata) will be
determined for appropriately preserved (i.e.,
frozen or in alcohol) and identified
holozooplankton specimens. Contact Rob Jennings
(rob.jennings_at_uconn.edu). Got data? DNA
barcodes for zooplankton should be submitted to
1. BARCODE section of GenBank
(www.ncbi.nlm.nih.gov/BankIt/barcode) 2.
Barcode of Life Database (BOLD see
www.barcodinglife.org.
UCONN address for specimen shipment Ann
BucklinDepartment of Marine Sciences University
of Connecticut - Avery Point 1080 Shennecossett
Road, Groton, CT 06340 USA Email
ann.bucklin_at_uconn.edu
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Acknowledgements CMarZ Steering Group Members
Demetrio Boltovskoy (Arg.) Janet Bradford-Grieve
(NZ) Ann Bucklin (USA) Colomban de Vargas
(France) Ruben Escribano (Chile) Steven Haddock
(USA) Steve Hay (UK) Russell R. Hopcroft
(USA) Ahmet Kideys (Turkey) Laurence P. Madin
(USA) Webjørn Melle (Norway) Vijayalakshmi Nair
(India) Shuhei Nishida (Japan) Mark D. Ohman
(USA) Francesc Pagés (Spain) Annelies
Pierrot-Bults (Netherlands) Chris Reid
(UK) Sigrid Schiel (Germany) Sun Song
(China) Erik Thuesen (USA) Hans Verheye (South
Africa) Peter Wiebe (USA)
CoML Zooplankton Workshop Portsmouth, NH USA,
March 2004
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Acknowledgements UConn Team DNA
Brian Ortman (Univ. Conn. Ph.D. student) Leo
Blanco Bercial (Univ. Oviedo, Spain) Ebru
Unal (Univ. Conn. Ph.D. student) Paola Batta
Lona (Univ. Conn. Res. Assist.) Lisa Nigro
not shown (Univ. Conn. Lab Manager) CJ
Sweetman not shown (Univ. Conn. Guest
Researcher)
UConn Team DNA on the RV Ron Brown April 2006