Aliwal Shoal Expedition Report

PhD (c): Jessica Escobar-Porras, University of KwaZulu-Natal, South Africa
Supervisor: Dr. Angus MacDonald
January 24th, 2013


Population genetics in South African elasmobranchs: Are they defined by the reproductive strategy of the species?

A difference to the first semester of 2012, the focus for the second semester was lab work and processing of samples. A lot has been accomplished for the Blacktip shark, Carcharhinus limbatus project, in the last six months. First, an optimize DNA extraction protocol was successfully obtained. Three methods to extract DNA from muscle tissue were tested, and after various test trials, a KAPA Express extraction kit with some modification on concentrations proved to be the most cost effective for Blacktip muscle tissue. Second, DNA material was extracted successfully from all forty samples as well as the isolation of the mitochondrial (mtDNA) control region. Since mtDNA is transferred only from mother to offsprings, it is very useful for identifying long term populations structures. Third, a preliminary analysis of 5 samples showed that there were at least two Blacktip populations contributing to the animals found at Aliwal Shoal. Additional analysis of 38 individuals, showed that: 1) Most blacktips are part of a separate lineage in the Indian Ocean, 2) a few come from Sierra Leone, 3) blacktips are creating sub-populations within the Indian Ocean, and 4) that at least 5 populations are contributing to the animals at Aliwal Shoal. In better words: Blacktip sharks at Aliwal Shoal are a city of sharks and not a family. Another achievement was securing collaboration with Dr. Vic Peddemors, who will facilitate samples from Australia, which will be used as the Outgroup, a requirement for genetic analysis.

Currently, data analysis and write-up of reports and articles are the main focus. Two samples did not produce sequences, so the problem still being investigated. Most importantly in progress is the confirmation of the results presented above. The confirming genetic models are being run using CLC Main Workbench 6 and 4Peaks software, which are free. Once all the results are confirmed, the write up of scientific paper and newsletters will be finalized. You will be the first ones to obtain these reports, which are scheduled to be completed by March 2013. Using these results the first conservation strategies would be drawn up and submitted to local authorities.
Future focus will on more lab work and write-up. Three months from March, the main goal is to obtain the population structure of the subpopulations found at Aliwal Shoal. Lab work will be carry out to isolate nuclear DNA, which is transferred from both parents on to offsprings, and perform PCR with 20 genetic markers. The more genetic markers used the more accurate the results, but also the more expensive. Twenty is a reliable number. Fragment analysis from these markers will be outsourced to speed up the process. Data will be then analyzed and results will be wrote up.

The project continues to move forward, and various issues are still being considered. First, it is the need to replicate the sampling in 2013, which will help to determinate if the same individuals are visiting Aliwal, or if they are different animals but from same subpopulations, or are different individuals from different subpopulations. The second issue is to find and sample the male population. This will revealed if mating is occurring within subpopulations or not, and the male contribution to the subpopulations of females at Aliwal. Most importantly, this will help to create a conservation plan for male blacktips.

The months ahead look challenging but very interesting and crucial to the well being of Blacktips at Aliwal Shoal. As a year approaches from the formation of this partnership, I want to tell you that I am immensely grateful for all the help, support and encouragement from THE WATERMEN PROJECT.