IOTC-2017-SC20-INF08

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IOTC-2017-SC20-INF08 Population Structure of IOTC species and sharks of interest in the Indian Ocean Principal Investigator: Campbell Davies (CSIRO) Co-investigators: Hilario Murua (AZTI ), Francis Marsac (IRD), Fahmi Zulkarnaen (CFR-RITF) IOTC Scientific Committee Meeting, Seychelles, December, 2017

Aim Describe the population structure and connectivity of a range of tuna and tuna-like species within the Indian Ocean (and adjacent Pacific and Atlantic waters as appropriate), as well as some of the key shark species that interact with Indian Ocean Tuna Commission (IOTC) fisheries. Methods Genetics using Single-Nucleotide-Polymorphisms (SNPs) Otolith/vertebrae microchemistry (elemental &/or isotopes) Participation and capacity building with coastal states

Phase 1 study species Neritic tunas Longtail tuna (Thunnus tongol) Kawakawa (Euthynnus affinis) Narrow-barred Spanish mackerel (Scomberomorus commerson) Tropical tunas Skipjack tuna (Katsuwonus pelamis) Yellowfin tuna (Thunnus albacares) Bigeye tuna (Thunnus obesus) Temperate tunas Albacore (Thunnus alalunga) Billfish Swordfish (Xiphias gladius) Striped marlin (Tetrapturus audax) Indo-Pacific sailfish (Istiophorus platypterus) Sharks Scalloped hammerhead shark (Sphyrna lewini) Blue shark (Prionace glauca)

PROJECT ADMINISTRATION COMMITTE IOTC- (ES/deputy + Accountant) + PI (Campbell) FAO (Nicolas) Reporting and accounting Contracting arrangement PROJECT MANAGEMENT PRINCIPAL INVESTIGATOR PROJECT LEADERSHIP TEAM PROJECT TECHNICAL COMMITTE IOTC-> SC/WP Chairs and vicechairs Peer-review and advisory Committee. TASK LEADERS Cross-cutting Species

Project schedule and status Deliverable Original Schedule Status Signed LoA, IOTC/FAO-CSIRO 03-Jan-17 03-Jan-17 2 complete Partner contracts 04-Feb-17 1 to finalise Literature search 14-Feb-17 Complete Draft Standard Operating Procedure (SOP) 04-Mar-17 Complete Detailed genetic methods comparison plan 03-May-17 Complete Progress report; initial methods comparison for swordfish (then ongoing updates) 03-Jul-17 In progress Confirm that 1st round of sampling has been completed 03-Sep-17 Nov 17 Mar 18 1st round of genetic analysis has been completed (50/species x 5 sites) 03-Jan-18 June 2018

Project SharePoint site

Literature review OCEANS AND ATMOSPHERE Literature search of peer reviewed and grey literature Population Structure of IOTC on population structure: species and sharks of Methods interest in the Indian Ocean Case studies Literature Search: Summary Report Campbell Davies, Jessica Farley and Ruth Sharples 5 May 2017 460 references initially Population structure of IOTC species in the Indian Ocean -EU Funded Project (GCP/INT/233/EC) Compiled in the freeware, Principal Investigator: Campbell Davies (CSIRO) Co-investigators: Hilario Murua (AZTI ), Francis Marsac (IRD), Zulkarnaen Fahmi ZOTERO (www.zotero.org) (RCFMC-TRIF) Living bibliography to be updated throughout the project Available through SharePoint site.

Standard Operating Procedures for field sampling Population Structure of IOTC species and sharks of interest in the Indian Ocean: Estimation with Next Generation Sequencing Technologies and Otolith Microchemistry SAM PLING PROTOCOLS FOR POPULATION STRUCTURE STUDY Overview of sampling plan for field sampling of young of the year and spawning adults of target species Standard methods for planning, data recording, collection, preserving and transporting of tissue samples and otoliths/vert. Detailed descriptions for each target species Sampling kits distributed to partners

Detailed plan for genotyping methods comparison Objective: To provide direct comparison of two main genotyping-by-sequencing approaches Radseq and ddrad SWO, LOT, SKJ SWO dependent on quality of samples from historical study Factor No levels Description Sequencing method 2 DArT(94), RADseq (94) (RADseq, ddrad) Species 3 SWO (?), SKJ, LOT Location 2 2 distant locations/species n 24 24 fish/location Total 288

Participation and capacity building Opportunities for participation and capacity building: Field sampling (design, sampling and preservation methods etc) Collaboration and/or training in genetics lab and population genetics analysis methods Collaboration and/or training in otolith microchemistry lab and population discrimination methods Collaboration and training in scientific writing (reports and peer review articles)

Participation

Kawakawa (Euthynnus affinis, KAW) Target Size = Young of year <25 cm, Adults >40 cm Area Spawning Adult/ Juvenile Country Source Fishery, Port Sampling SW -Mozambique Port sampling [TBC with José] W J/A -Seychelles Purse Seine Oct-Nov, Apr-May J/A -Kenya Artisanal Fishers, Kenyan LL, Sports Fishing Contact for sample collection Mr José Halafo -Fisheries Research Institute of Mozambique Iñigo Krug, -AZTI Anaïs Médieu -IRD Mr Ndegwa Stephen -Kenya Fisheries Service A -Tanzania 35-84 cm Dr Johnson Grayson -Department of Animal, Aquaculture and Ranges Sciences NW J/A? -Iran Dr Farhad Kaymaram -Iranian Fisheries Research Organization A Spanish? Purse Seine bycatch 47-70 cm N/Centr -India al A -Maldives 25-55 cm FL

List of people and addresses to send samples to: Species Muscle tissue Otolith/vertebrae Longtail CSIRO CSIRO Narrow-barred Spanish mackerel CSIRO CSIRO Kawakawa Indonesia? Indonesia Skipjack Naiara Rodríguez-Ezpeleta (AZTI) Igaratza Fraile (AZTI) Yellowfin Jessica Farley (CSIRO) Igaratza Fraile (AZTI) Bigeye Naiara Rodríguez-Ezpeleta (AZTI) Jessica Farley (CSIRO) Mayliss Labonne / Albacore Swordfish Natacha Nikolic (IRFEMER) Jessica Farley (CSIRO) Sophie Arnaud-Haond (IFREMER) Audrey Darnaude (IRD) Mayliss Labonne / Audrey Darnaude (IRD) Blue shark Jessica Farley (CSIRO) Scalloped hammerhead Jessica Farley (CSIRO) Jessica Farley (CSIRO) Striped marlin CSIRO NA Indo-Pacific sailfish CSIRO NA

Key Contacts Project Leader: Campbell Davies, campbell.davies@csiro.au Co-investiagtors: Hilario Murura, hmurua@azti.es Francis Marsac, francis.marsac@ird.fr Fahmi Zulkarnaen, fahmi.p4ksi@gmail.com

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