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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 Barcoding for CoML: Assessing Zooplankton Diversity

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Page 1: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

Rob Jennings – University of Connecticut, USA

Photos by R.R. Hopcroft – University of Alaska, USAL.P. Madin – Woods Hole Oceanographic Institution, USAN. Copley – Woods Hole Oceanographic Institution, USA

CMarZ Steering Group Meeting6 November – Ocean Research Institute, University of Tokyo

Barcoding for CoML: Assessing Zooplankton Diversity

Page 2: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

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 - CMarZCensus 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

CoML Ocean Realm Field ProjectsCoML Ocean Realm Field Projects

Page 3: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

What What isis DNA Barcoding? 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.

Page 4: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

What isn’t 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).

Page 5: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

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.

Why Barcode Zooplankton?Why Barcode Zooplankton?

Page 6: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

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

Barcoding Goals for CMarZBarcoding Goals for CMarZ

Page 7: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

Barcoding Ostracods (Crustacea)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

Page 8: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

Barcoding Euphausiids (Crustacea)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

Page 9: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

Barcoding Planktonic GastropodsBarcoding 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

Page 10: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

Barcoding Medusozoans (Cnidaria)Barcoding Medusozoans (Cnidaria)

• Barcoding is done by

Brian Ortman (UConn/USA).

• 13 species of

siphonophores• greatly expanded, much

of siphonophore diversity

(160 spp.)

Page 11: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

Barcoding Arctic Zooplankton 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

Page 12: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

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

CMarZ Barcoding Structure CMarZ Barcoding Structure and Operationsand Operations

Page 13: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

CMarZ Barcoding CentersCMarZ Barcoding CentersCMarZ Barcoding CentersCMarZ Barcoding Centers

• Existing barcoding centers• UConn, USA Oviedo, Spain ORI, Japan

• Emergent barcoding centers• Qingdao, China Goa, India

Page 14: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

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

Results and ConclusionsResults and Conclusions

Page 15: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

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 ([email protected]).

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 SciencesUniversity of Connecticut - Avery Point1080 Shennecossett Road, Groton, CT 06340 USAEmail: [email protected]

Page 16: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

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

AcknowledgementsCMarZ Steering Group Members

Page 17: Rob Jennings – University of Connecticut, USA Photos by R.R. Hopcroft – University of Alaska, USA L.P. Madin – Woods Hole Oceanographic Institution, USA

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

AcknowledgementsAcknowledgementsUConn Team DNAUConn Team DNA


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