A Plan to Barcode All Fishes by cus77764

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									                A Plan to Barcode All Fishes




CSIRO Marine Research, Hobart, Tasmania
                      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)
                          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
                    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.
                       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 > US$ 200 billion

And employ 35 million people
(65% marine capture, 15% inland capture, 20% aquaculture)
             Applications of Fish Barcoding
• Identification of fish, fillets, fins, and fragments (marketing,
  substitutions, quota and bycatch management).
             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).
             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).
             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).
             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).
             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).
             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).
             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
                   What is needed?

•   Specimens
•   Relevant data per specimen
•   Storage and taxonomic facilities
•   Genetic facilities
•   Database
•   Organisation
                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)?
                 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
                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
                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
                 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?
                 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
             FAO Statistical Areas
with numbers of marine species in blue (FishBase)
1042
                           128

                                                          1042




                                          990
                             689

                    4795                                           662

                                          2297     1685

                    5738    3759

  4182                                                              4182

             4295                  1788         1609        1735
                           2046
       233                                                245
                                                                         233
                             132
           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 << freshwater population differentiation)
                   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 << freshwater population differentiation)


Number of species per FAO area
Pacific Arctic         128     Med. / Black Seas        662
Pacific NW            4795     Atlantic NW              990
Pacific NE             689     Atlantic NE              1042
Pacific CW            5738     Atlantic CW              2297     Indian W              4182
Pacific CE            3759     Atlantic CE              1685     Indian E              4295
Pacific SW            2046     Atlantic SW              1609
Pacific SE            1788     Atlantic SE              1735
Pacific Antarctic      132     Atlantic Antarctic       248      Indian Antarctic      233
                     19075                             10268                           8710

Total across the 19 FAO areas = 37,391              Total barcodes @ 5 per species = 190,265
Total number of marine species = 15,648             Total barcodes @ 5 per species = 78,240

Antarctic across 3 FAO areas = 613
Total number in Antarctic = 369
                                         A Possible Structure
                                                     Board of Directors

                                                     Scientific Steering
                                                         Committee

                            Taxonomy Committee       DataBase Manager            FishBase
                                                    Database Committee

              Atlantic Co-ordinator               SubAntarctic Co-ordinator            Indo-Pacific Co-ordinator
                  9358 species                          613 species                         27420 species
                  7 FAO areas                           3 FAO areas                          9 FAO Areas

                                                   Pacific         etc etc      Arctic        SW Pacific           etc etc
 Mediterranean/   NE Atlantic         etc etc
                                                 132 species       2 areas    128 species    5738 species          7 areas
   Black Sea      1042 species        5 areas
  662 species

                    Taxonomist(s)

                     Collector(s)

                     Geneticist(s)


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.
Barcoded Australian fish specimens in relation to FAO areas




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    Some of the questions that need answers


• Decide on an organisational structure
    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)
    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?
    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)?
    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
    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?
    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
    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?
    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?
    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?

								
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