Genomic research, first pioneered in human health and medicine, is now being used to study the health of coral reef ecosystems and fisheries, providing new ways to protect and understand these important resources.
The Pan-Pacific Advanced Studies Institute on genomic applications to marine science in Southeast Asia concluded this week brought these advances to the Philippines. Sixty researchers and students from nine different countries met in Dumaguete, Philippines to discuss “next generation” DNA sequencing at the ten-day conference hosted by Silliman University and funded by the United States National Science Foundation.
“The purpose of this meeting is to initiate collaboration and transfer of technology,” said Dr. Mudjekeewis Santos at the National Fisheries Research & Development Institute.
Conference participants heard from experts in the field and discussed whether genomic technologies could help meet the challenges of managing marine species, such as climate change, harvest, and species ranges that span international boundaries. The meeting also offered hands-on tutorials on bioinformatics, cloud computing, and genetic simulations.
“Right now we are going through a transition from genetics to genomics,” says Dr. Santos. Traditional genetics involves studying a handful of genes, while genomics looks across thousands of markers in an organism’s entire complement of DNA.
When the human genome project was completed in 2003, it cost about $10,000 to sequence a million DNA base pairs. Since then, the cost of genomic sequencing has dropped precipitously/ With the advent of next generation technologies, the same amount is enough to fund a whole study on fishery stock structure or investigate the genes responding to bleaching in corals.
But now that obtaining the data is not the major obstacle, the challenge becomes when and how to use it.
“We plan to provide a ‘road map’ on how to navigate next gen research in marine ecosystems,” said conference organizer Dr. Demian Willette of Old Dominion University, USA.
The road map will walk researchers through pros and cons of different approaches and compile resources for designing effective studies, including the time and cost associated with each. “This will help scientists in the Philippines and South East Asia overcome many of the frustrations of moving into next gen and hasten the time it takes for hem to get data and information back to the policy makers and stakeholders.”
As the “center of the center” of marine biodiversity, the Philippines is an ideal host nation for PacASI. A number of presentation addressed how next generation sequencing approaches can test hypotheses on why the Coral Triangle and the Philippines in particular are so diverse.
Genomics is also incredibly powerful for studying adaptation, which may help guide the study of coral resilience in the face of climate change. By studying genes that are activated when corals undergo stress, and how these patterns vary across species and populations, we may gain insight into how corals can survive in a changing environment.
Marine protected areas and fisheries management may also benefit from these new tools. With more genetic markers, the hope is to have finer resolution data on how populations are connected across large areas. This may help fine-tune Marine Protected Areas to get the most benefit and also manage fishing stocks in a way that reflects their biology.
Tropical species were not the only ones under discussion at the recent PacASI.
The meeting attracted small contingent of salmon researchers who are currently exploring next generation sequencing applications to salmon management. Salmon is one of the only sustainable fisheries, and genetics has a large role in that success. This collaboration shared not only success stories, but also lessons learned.
Although next generation sequencing is a powerful tool, it is not likely to replace traditional genetics entirely. “Doctors have CAT scans and MRIs, but they still take your temperature and use a stethoscope,” said Dr. Paul Barber of the University of California Los Angeles, USA. The goal is to go forward as informed as possible, and use these techniques only when they are needed to answer research questions that cannot be addressed any other way.
Genetic and genomic tools are becoming increasingly available to marine scientists addressing some of the most pressing questions in food security, conservation of threatened marine species, and climate change. The PacASI has served as the first step in educating and training Philippine and regional marine scientists in applying these tools here.
