Activity 3.1: Sampling to evaluate genetic make-up and zonation of selected flagship species.
Billfish tissue samples (pectoral fin clippings and muscle tissue) will be taken using two sources: (1) Collected by sports fishermen operating as members of billfish tagging programs and New South Wales fisheries. Assistance by recreational fishers is valuable as it promotes citizen science, and in turn sustainable catch and release practices enabling non-lethal sampling to be undertaken. (2) Muscle tissue will be collected from artisanal fishery catches at fish markets in Somalia, Kenya, Tanzania, Mozambique, Madagascar and Mauritius. The samples will be fixed in 20% DMS0 in a 5M NaCl solution and frozen at -20oC until used. About 200 individuals to be sampled from primary regions, targeting about 50 individuals in each location.
Activity 3.2: Molecular Analysis
To determine the stock structure, the DaRT DD-RAD Sequencing technique will be employed to develop Single Nucleotide polymorphisms (SNP’s). Recently, this NGS approach has been used to identify population structure in a number of highly migratory species that were previously thought to be panmictic. To facilitate development of SNPs using DD-RAD seq, genomic DNA will first be extracted from the tissue samples using the Bioline Isolate Spin Column method. High quality tissue will be sent for DD-RAD Sequencing and the DaRT-Soft bioinformatics pipeline will be used to find and filter SNP’s that may contain genetic signatures of population differentiation. SNPs discovered using RAD-sequencing will be used to evaluate both broad- scale genetic structure throughout the Indian Ocean and finer scale connectivity in the WIO.
Geographic description: Regional Time Frame: Two and half years Responsible partner/s: Team leaders Dr. Sam Williams, Dr. Julian Pepperrell and Dr. Nina Wambiji assisted by all contributing collaborators.