A Plan to Barcode All Fishes

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A Plan to Barcode All Fishes

• CSIRO Marine Research, Hobart, Tasmania

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Why barcode fish - 1

• Although the largest vertebrate group (about 50
  of all vertebrate species), they have a
  manageable number of species
• c. 20 000 marine (15 648 in Fish Base, 91 with
  subspecies)
• c. 15 000 freshwater (13 544 in Fish Base, 152
  with subspecies)
• (705 shared marine / freshwater species)
• c. 80 brackish only (82 in Fish Base, 1 with
  subspecies)

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Why barcode fish - 1

• Although the largest vertebrate group (about 50
  of all vertebrate species), they have a
  manageable number of species
• c. 20 000 marine (15 648 in Fish Base, 91 with
  subspecies)
• c. 15 000 freshwater (13 544 in Fish Base, 152
  with subspecies)
• (705 shared marine / freshwater species)
• c. 80 brackish only (82 in Fish Base, 1 with
  subspecies)
• Systematically very diverse
• Superclass Agnatha (jawless fish)
• Class Cyclostomata lampreys, hagfish
• Subphylum Gnathostomata (jawed vertebrates)
• Superclass Pisces (jawed fish)
• Class Chondrichthyes cartilaginous fish -
  chimaerids, sharks, rays
• Class Osteichthyes bony fish - coelacanths,
  lungfishes, eels, carps, tunas, salmons,
  flatfishes, sea horses etc

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Why barcode fish - 2

• Global value at first sale
• Capture fisheries in 2000 c. US 81 billion
• Aquaculture (excl. plants) in 2000 c. US 52
  billion
• Ornamental fish
• Retail trade in US alone in 2000 c. US 3
  billion
• Sports fishing
• In Australia in 1984, recreational fishers c.
  US 2 billion.

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Why barcode fish - 2

• Global value at first sale
• Capture fisheries in 2000 c. US 81 billion
• Aquaculture (excl. plants) in 2000 c. US 52
  billion
• Ornamental fish
• Retail trade in US alone in 2000 c. US 3
  billion
• Sports fishing
• In Australia in 1984, recreational fishers c.
  US 2 billion.
• Fisheries activities globally generate trade gt
  US 200 billion
• And employ 35 million people
• (65 marine capture, 15 inland capture, 20
  aquaculture)

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Applications of Fish Barcoding

• Identification of fish, fillets, fins, and
  fragments (marketing, substitutions, quota and
  bycatch management).

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Applications of Fish Barcoding

• Identification of fish, fillets, fins, and
  fragments (marketing, substitutions, quota and
  bycatch management).
• Identification of processed product e.g. canned
  fish, dried fish, mixtures (substitutions).

10
Applications of Fish Barcoding

• Identification of fish, fillets, fins, and
  fragments (marketing, substitutions, quota and
  bycatch management).
• Identification of processed product e.g. canned
  fish, dried fish, mixtures (substitutions).
• Identification of threatened, endangered and
  protected species (conservation).

11
Applications of Fish Barcoding

• Identification of fish, fillets, fins, and
  fragments (marketing, substitutions, quota and
  bycatch management).
• Identification of processed product e.g. canned
  fish, dried fish, mixtures (substitutions).
• Identification of threatened, endangered and
  protected species (conservation).
• Identification of fish eggs and fish larvae
  (ecosystem research, direct and indirect
  fisheries management).

12
Applications of Fish Barcoding

• Identification of fish, fillets, fins, and
  fragments (marketing, substitutions, quota and
  bycatch management).
• Identification of processed product e.g. canned
  fish, dried fish, mixtures (substitutions).
• Identification of threatened, endangered and
  protected species (conservation).
• Identification of fish eggs and fish larvae
  (ecosystem research, direct and indirect
  fisheries management).
• Identification of prey items in stomach contents
  (food webs and ecosystem research).

13
Applications of Fish Barcoding

• Identification of fish, fillets, fins, and
  fragments (marketing, substitutions, quota and
  bycatch management).
• Identification of processed product e.g. canned
  fish, dried fish, mixtures (substitutions).
• Identification of threatened, endangered and
  protected species (conservation).
• Identification of fish eggs and fish larvae
  (ecosystem research, direct and indirect
  fisheries management).
• Identification of prey items in stomach contents
  (food webs and ecosystem research).
• Identification of historical, archived and museum
  material (taxonomy).

14
Applications of Fish Barcoding

• Identification of fish, fillets, fins, and
  fragments (marketing, substitutions, quota and
  bycatch management).
• Identification of processed product e.g. canned
  fish, dried fish, mixtures (substitutions).
• Identification of threatened, endangered and
  protected species (conservation).
• Identification of fish eggs and fish larvae
  (ecosystem research, direct and indirect
  fisheries management).
• Identification of prey items in stomach contents
  (food webs and ecosystem research).
• Identification of historical, archived and museum
  material (taxonomy).
• Identification of new species and possible
  fusions, insights into phylogenetic relationships
  (fish biology, evolution).

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Applications of Fish Barcoding

• Identification of fish, fillets, fins, and
  fragments (marketing, substitutions, quota and
  bycatch management).
• Identification of processed product e.g. canned
  fish, dried fish, mixtures (substitutions).
• Identification of threatened, endangered and
  protected species (conservation).
• Identification of fish eggs and fish larvae
  (ecosystem research, direct and indirect
  fisheries management).
• Identification of prey items in stomach contents
  (food webs and ecosystem research).
• Identification of historical, archived and museum
  material (taxonomy).
• Identification of new species and possible
  fusions, insights into phylogenetic relationships
  (fish biology, evolution).
• Possible production of DNA microarrays from the
  sequence data

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What is needed?

• Specimens
• Relevant data per specimen
• Storage and taxonomic facilities
• Genetic facilities
• Database
• Organisation

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What is needed for Fish-BOL?

• Specimens
• One or more tissue specimens per
  species/subspecies
• Tissue samples not stored in formalin but in
  ethanol or frozen
• Accurate records for each specimen
• Use existing specimens where possible to reduce
  costs
• Collect new specimens by piggy-backing on
  existing cruises/collecting
• Consider a centralised tissue bank (at least per
  region)?

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What is needed for Fish-BOL?

• Specimens
• One or more tissue specimens per
  species/subspecies
• Tissue samples not stored in formalin but in
  ethanol or frozen
• Accurate records for each specimen
• Use existing specimens where possible to reduce
  costs
• Collect new specimens by piggy-backing on
  existing cruises/collecting
• Consider a centralised tissue bank (at least per
  region)?
• Relevant data per specimen
• Species identity, GPS location (including depth),
  names of collector identifier, date of
  collection, storage location
• Photograph of original specimen when possible

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What is needed for Fish-BOL?

• Storage and taxonomic facilities
• Storage of tissues and whole animals until
  sequencing completed (where possible)
• Storage of one or more voucher specimens per
  species (per region?)
• Specimens to be identified by expert taxonomist
• Undescribed species will require vouchers

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What is needed for Fish-BOL?

• Storage and taxonomic facilities
• Storage of tissues and whole animals until
  sequencing completed (where possible)
• Storage of one or more voucher specimens per
  species (per region?)
• Specimens to be identified by expert taxonomist
• Undescribed species will require vouchers
• Genetic facilities
• Sequencing will require access to automated
  sequencer
• Samples can be sent to a central sequencing
  facility (within region?)
• Each sample to be sequenced in both directions to
  get consensus sequence for database
• Electropherograms retained
• Each species to be represented by multiple
  specimens, preferably from different locations

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What is needed for Fish-BOL?

• Database
• Publicly-accessible (at least for search /
  specimen identification)
• Single database and a database manager
• Data input and correction simple (locally, or by
  database manager?)
• Outputs to include simple analyses and lists of
  species
• Links with other databases especially FishBase
• Probably will need to be mirrored in several
  locations
• Common names standardised to FishBase common
  names?

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What is needed for Fish-BOL?

• Database
• Publicly-accessible (at least for search /
  specimen identification)
• Single database and a database manager
• Data input and correction simple (locally, or by
  database manager?)
• Outputs to include simple analyses and lists of
  species
• Links with other databases especially FishBase
• Probably will need to be mirrored in several
  locations
• Common names standardised to FishBase common
  names?
• Organisation
• Scientific, taxonomy and database committees?
• Regional co-ordinators? What regions?
• Database manager
• Support funding

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FAO Statistical Areas with numbers of marine
species in blue (FishBase)
1042
128
1042
990
689
662
4795
1685
2297
3759
5738
4182
4182
1609
1735
1788
4295
2046
233
245
233
132
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Marine fish species by FAO areas

• Aim for 5 per species per FAO area?
• Aim to get the 5 samples from diverse parts of
  the area (but marine
• population differentiation ltlt freshwater
  population differentiation)

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Marine fish species by FAO areas

• Aim for 5 per species per FAO area?
• Aim to get the 5 samples from diverse parts of
  the area (but marine
• population differentiation ltlt freshwater
  population differentiation)

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A Possible Structure
There are many other possibilities of course,
e.g. having co-ordinators for each FAO area,
separate Indian Ocean and Pacific Ocean
co-ordinators, or North Pacific and South/Central
Pacific.. Each FAO area has a list of species
which the co-ordinator would be responsible for
updating, eg. species collected, barcoding
status, database entry Need to avoid / minimise
duplication of effort within an area.
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Barcoded Australian fish specimens in relation to
FAO areas
71
71
51
51
47
47
57
57
81
81
58
48
58
88
48
88
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Some of the questions that need answers

• Decide on an organisational structure

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Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)

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Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)
• Database structure - single overall, plus subsets
  per area?

31
Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)
• Database structure - single overall, plus subsets
  per area?
• Centralised tissue banks(s)?

32
Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)
• Database structure - single overall, plus subsets
  per area?
• Centralised tissue banks(s)?
• Import / export regulations of tissues

33
Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)
• Database structure - single overall, plus subsets
  per area?
• Centralised tissue banks(s)?
• Import / export regulations of tissues
• Identify experienced taxonomists for each
  area/region?

34
Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)
• Database structure - single overall, plus subsets
  per area?
• Centralised tissue banks(s)?
• Import / export regulations of tissues
• Identify experienced taxonomists for each
  area/region?
• Coping with taxonomic / identification
  uncertainty

35
Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)
• Database structure - single overall, plus subsets
  per area?
• Centralised tissue banks(s)?
• Import / export regulations of tissues
• Identify experienced taxonomists for each
  area/region?
• Coping with taxonomic / identification
  uncertainty
• Common names - standardise on English Fish Base
  names?

36
Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)
• Database structure - single overall, plus subsets
  per area?
• Centralised tissue banks(s)?
• Import / export regulations of tissues
• Identify experienced taxonomists for each
  area/region?
• Coping with taxonomic / identification
  uncertainty
• Common names - standardise on English Fish Base
  names?
• What funding agencies might support this push?

37
Some of the questions that need answers

• Decide on an organisational structure
• Sampling protocols (numbers of samples per
  species, identification, sample storage, data
  collection, sequencing strategies, database
  insertion)
• Database structure - single overall, plus subsets
  per area?
• Centralised tissue banks(s)?
• Import / export regulations of tissues
• Identify experienced taxonomists for each
  area/region?
• Coping with taxonomic / identification
  uncertainty
• Common names - standardise on English Fish Base
  names?
• What funding agencies might support this push?
• Time frame - is five years realistic?