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Ocean Genome Legacy Newsletter
March 2013

banner 600pixel    exploring, preserving and protecting the genetic diversity of the world's oceans

In This Issue
The World of Conservation Genomics
What did this fish have for dinner?
Coming Soon...
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Imagine that you have a box over your head and you are trying to find your way around with just a small hole to look through.  The world around you becomes a hand, a floor tile, a light switch, or any number of disembodied objects from which you must make sense of your surroundings.  Now take the box off your head and see the whole world around you, how everything comes together to create your complete environment.


This month, we'll show you how Next Generation Sequencing (NGS) has enabled conservationists to take the boxes off their heads and see the world of marine genomics.


And, as always, follow our expeditions and other news from the marine world on our Facebook and Twitter pages!

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Conservation Genomics - Opening the window on the environment
We recognize the diversity of life through species. To study nature we count and compare species and observe where they occur and how their numbers change. Without the species concept, we would be hard pressed to understand or manage the diversity of nature.  But how can we recognize and define species? It turns out that this is surprisingly difficult. In the past we used physical characteristics to identify species. But many species look deceptively similar, and sometimes members of a single species can look deceptively different. With the advent of DNA sequencing, scientists found a new way to identify species - by the differences in the sequences of their genes. DNA sequencing not only helps to sort out species, but also can help to tell apart different populations within a species. This kind of information has been essential to conservation biologists in their efforts to identify groups that may be threatened with extinction.

New developments in sequencing technology are now letting scientists go beyond individual genes to simultaneously look at ALL the genes in an individual (genomes). Seeing all the genes not only tells us that species are different, but also tells why and how they are different. This gives scientists new insights into the ways that species, individuals or populations respond to their environments, helping conservationists to understand not only which species are endangered, but what to do to help them survive.
genetics vs genomics
The conceptual difference between a conservation genetics and conservation genomics research approach
(modified after Ouborg et al. 2010, Trends in Genetics 26: 177-187)
The technology that has enabled this kind of in-depth genomic analysis is Next Generation Sequencing (NGS). Rather than sequencing one molecule of DNA at a time, NGS methods break the genome into many small pieces and sequence many (up to 600 million) DNA molecules in parallel. Computer programs are then used to reassemble these short DNA sequences to obtain the complete genome sequence. The sequencing process may take anywhere from a few hours to 2 weeks depending on the particular method, and the costs have decreased phenomenally with time. Scientists hope the cost of sequencing the human genome (3 billion base pairs) will soon drop below $1000. Compare this to the $3 billion and ten years required for the first human genome project completed just ten years ago. 
Genomic Sequencing
Courtesy of
Marine biologists are currently making use of this new technology in their research. For example, Morin et al. (2010) used NGS methods to sequence the complete mitochondrial genomes of 139 Killer Whales to show that this one species has genetically and geographically distinct populations (ecotypes) with different behaviors and prey preferences. Information like this is invaluable for species conservation managers because it shows them that saving just one population might miss much of the diversity needed for the species to survive. 


As policy makers struggle to justify commercial regulations and restricted access to marine protected environments, genomic studies like this one will become a critical part of decision making.



For a more in-depth description of conservation genomics, read this report from the European Science Foundation


Want to find out more about how NGS works?  Take a look at this brochure from Illumina.  


For an overview of the role genomics is (and will be) playing in marine conservation, read this article by E.E. Nielsen et al

mtDNA Barcoding: It's Not Just for FDA Compliance!
Since OGL began offering it's SpeciesCheckTM seafood DNA barcode service in the spring of 2012, we have had a number of interesting requests. One came from Rachel Brewton, a Research Assistant working under the direction of Dr. Stephen Szedlmayer in the Fisheries and Allied Aquacultures department at Auburn University.  Rachel wanted to know what red snapper (Lutjanus campechanus) eats in the wild, so she sent us tissue samples from the stomach contents of wild caught specimens. OGL helped Rachel to unambiguously identify numerous prey species using DNA sequences from this partially digested and otherwise unidentifiable material. OGL is proud to assist in Auburn University's work to improve fisheries sustainability by giving fishery mangers greater insight into the role of red snapper in marine food webs. The work may even aid aquaculturists in improving the diets of farmed fish, thereby helping to improve our own diets!

Food for thought? Let us know how we can help you with your own seafood identification project!

 Coming Soon...

Conservation in the Sargasso Sea       

A number of groups have been working together recently to establish a Marine Protected Area (MPA) in the Sargasso Sea - a vast area in the middle of the Northwestern Atlantic Ocean bounded by the Gulf Stream and the Canary Current.  The Sargasso Sea supports a unique marine community associated with its namesake, the vast mats of floating Sargassum seaweed that provide habitat, spawning ground, nursery, and migratory routes for many ecologically and commercially important marine species. Like many areas of the Ocean, the Sargasso Sea is under serious threat from overexploitation, pollution and climate change. Read next month about these new efforts to protect the "Blue Halo."


Sargasso Sea


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Dan Distel
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