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Exciting strides for eDNA: Insights into whale shark population genetics

Paper: Sigsgaard, E. E., Nielsen, I. B., Bach, S. S., Lorenzen, E. D., Robinson, D. P., Knudsen, S. W., Pedersen, M. W., Jaidah, M. A., Orlando, L., Willerslev, E., Moller, P.R, and Thomsen, P. F. (2016). Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nature Publishing Group, 1(November), 1–4. http://doi.org/10.1038/s41559-016-0004


DNA: the great mystery solver. You’ve seen it on countless TV shows- the criminal is caught because there was DNA in saliva left at the crime scene. Over the past few decades, genetic sequencing using DNA has become a powerful tool in our lives, impacting the judicial system, medicine, and scientific research.

Biologists can determine a lot about an animal just by analyzing the DNA contained in a tiny piece of tissue (skin, scales, hair, etc).  However, there are some drawbacks to obtaining that DNA from animal tissue samples. You have to get up close and personal with the study organism, which can be expensive, require a lot of equipment, and may even be impossible from rare or elusive animals.

Figure 1: a whale shark glides through the water. Image source: mentalfloss.com

Figure 1: a whale shark glides through the water. Image source: mentalfloss.com

For example, the mysterious whale shark (Rhincodon typhus, Fig.1). Although it is the largest fish on the planet (growing up to 40 feet long, larger than a school bus!), scientists know very little about the biology of these gentle, plankton-eating giants. Most of the information we have is gathered when the whale sharks are near land, but time spent near humans only accounts for a small portion of a whale shark’s life.

Traditionally, scientists have only been able to use DNA to answer key biological questions about whale sharks by getting near enough to groups of whale sharks and taking pieces of tissue from individuals (much like a tissue biopsy used for medicine. Haven’t had one of those? Think of taking a straw and coring out a small piece of a potato- the whale shark is the potato). While using this technique can ensure a more reliable source of DNA for a single individual, it is expensive and has left a myriad of questions scientists are unable to answer.

But now, scientists may be able to get that valuable DNA without having to find a desired animal and chunk out a piece of its flesh. Scientists have been experimenting with using environmental DNA (eDNA) as a new way to gather insights into whale shark biology.

So what is eDNA?

Your DNA is everywhere. Every time you scratch an itch you slough off dead skin cells. Every time you blow your nose, wipe your hands, brush your hair, or even sit on a couch, you leave cells that contain DNA behind. Slightly disgusting, but true.

Animals do the same thing, and constantly lose bits of tissue in their environment. For animals living in the ocean, that leaves their tissue (and unique DNA) behind floating around in the water. These tiny bits of DNA floating around in the water are known as “environmental DNA”, or eDNA. Scientists have been working on ways to use this eDNA to answer questions that have previously only been answered by getting a solid tissue sample from an individual.

The process:

Essentially, scientists collect a water sample from a given area and filter it to concentrate all of those dirty floating bits of DNA. They can then analyze it much the same as they would a piece of tissue to figure out what kinds of animals have been in the environment shedding tissue. This is an exciting new technique that has a huge potential to answer a wide range of questions – but it is still new and scientists need to discover exactly what they can and can’t use it for. So far, eDNA has been used primarily to identify microorganisms in an area, and has not been widely applied to larger organisms, let alone to entire groups or populations of those organisms. While eDNA can show what animals may have been in the area, it cannot tell scientists if that animal was alive or dead (possibly it was just a meal for another animal in the area), how old the animal is,  or if an animal lives in the area or was just passing through. Oceanic currents further complicate the technique by possibly washing an animal’s DNA into an area it has never been before. However, these shortcomings do not mean the process cannot shed light on some previously unanswerable questions; scientists just need to identify the limitations of the method.

In this study, scientists took water samples from an area in the Arabian Gulf where at least 300 whale sharks aggregate seasonally. They compared the genetic sequences obtained from the water samples (eDNA) to tissue samples taken from some of the whale sharks in this aggregation. They also tested surrounding water where whale sharks were not directly seen by scientists. Their goal was to determine if eDNA is a reliable method that can give comparable data to that of the currently utilized tissue sampling methods for studying population genetics.

Does eDNA pass the test?

Fig 2: The eDNA (shown in white boxes) samples from this study found the same genetic diversity (called “haplotypes”) that were found from tissue samples (“Qatar tissue”, blue circles) and found a larger range of diversity (i.e. more haplotypes) than were found from the tissue samples. The red triangles show the genetic diversity recorded in databases from other studies, showing that the diversity found with the eDNA sequences makes sense based on our knowledge of other whale shark populations.

Figure 2: The eDNA (shown in white boxes) samples from this study found the same genetic diversity (called “haplotypes”) that were found from tissue samples (“Qatar tissue”, blue circles) and found a larger range of diversity (i.e. more haplotypes) than were found from the tissue samples. The new haplotypes, however, did match with other known whale shark genetic sequences (red triangles).

Researchers found that the eDNA was a more cost effective, faster, and a less invasive method compared to the traditional tissue sampling procedures. The eDNA sequences matched with those from the tissue samples but also found a larger degree of genetic diversity than had been indicated by the tissue samples. This suggests that the eDNA gives an accurate picture of the genetic diversity for a population and may actually give scientists better insight into population structures than traditional tissue sampling by allowing scientists to sample a larger number of individuals in the area (Fig. 2).

The researchers were also able to compare their eDNA sequences to libraries of genetic sequences from other whale shark populations around the world (red triangles in Fig 2). Using the eDNA, researchers found that the Arabian Sea population was connected to a population in the Indo-Pacific, but was genetically different than populations in the Atlantic Ocean. This can give scientists an idea of where whale sharks may be migrating and/or if groups of whale sharks are breeding with, or isolated from other populations.

Finally, the researchers used the eDNA to try to answer an ecological question. It is currently unknown why the whale sharks aggregate in the Arabian Sea, but it has been hypothesized that they gather to feed on the eggs of spawning tuna mackerels. The researchers were able to analyze the eDNA to see if there was any correlation between the presence of whale sharks and tuna mackerels. Sure enough, where there was more tuna mackerel eDNA, there was also more whale shark DNA. Of course, this does not unequivocally prove why whale sharks are aggregating, but it does support the hypothesis.


This study just scratches the surface. After seeing how well the results from eDNA compared to those from conventional DNA sampling, it is a definite possibility that this technique will become more mainstream- acting as a more effective method that may be able to answer key questions previously beyond our reach. How effective do you think this method is and what sorts of questions would you like to answer with eDNA? Tell us in the comment section below.


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