Thursday, November 10, 2016

Natural Tags

Natural Tags

By: Julie Vecchio
PhD Student
University of South Florida

Many researchers and anglers know about tagging fish, sharks, or even other organisms to learn about their movements. Anglers enjoy participating in these programs because they can help with science and learn something new about the fish in their area. However, an emerging topic in ecology is the use of “natural tags.” Essentially, using natural tags means using the internal chemistry of an organism to learn about its genetics, origin, movements, or even chemical exposure levels. Currently there are three main types of natural tags that are commonly used. These are genetic signatures, otolith microchemistry, and tissue isotopes.

Genetic Signatures

In Florida, the primary species that has been studied on a large scale using genetic signatures is the tarpon, Megalops atlanticus, a popular sportfish. Currently the Florida tarpon fishery is entirely catch-and-release. During this project, citizen scientists collected DNA samples from their catch. Before releasing the fish, the angler would take a swab of the outer jaw, picking up a few skin cells. These cells were then processed for the genetic signature.

Each individual has a unique genetic code.  Using the genetic signature, researchers are able to determine whether that particular individual has been sampled genetically before. Based on the numbers of different individuals captured, and the number of times a particular individual has been re-sampled, the researchers can then get an idea of the total size of the tarpon population in Florida’s waters. If the individual had been captured previously, the researchers can also determine how far that fish has moved since the last time it was captured. During the 10-year project, researchers analyzed over 22,000 genetic samples from tarpon.

DNA sampling has a few distinct advantages over conventional tagging techniques. First, it is relatively inexpensive. Since anglers are already capturing the fish, additional research time is not needed to collect samples. Second, it is relatively non-invasive. The fish barely feels the scrape as the skin cells are collected. Finally, all organisms maintain their DNA signature throughout their lives, negating the need to factor in tag-shedding.

To learn more about tarpon genetic signatures visit this website.

Otolith Microchemistry

Just like people, fish have three small bones in their ears, used primarily for balance, but fish also use theirs for hearing. In fish they are called otoliths. Fish otoliths are made of calcium carbonate, the same material that makes up oyster shells. Each day of the fish’s life, it deposits a miniscule new layer of calcium carbonate on the outside of the otolith.  As these tiny rings accumulate, they form seasonal patterns. These patterns can be counted to find out how old the fish is.

However, otoliths are not made of 100% calcium carbonate. Other elements, especially metals like aluminum, strontium, and many others are also incorporated into the otolith matrix, and the signature of these elements can reveal where a particular individual was living at some period during its life. This can be especially useful for finding out where individuals were living as juveniles, to better understand what habitats produce the most successful adults.

What the above graphic shows is that juvenile gag grouper living in each of Florida’s major west coast estuaries contains a unique chemical signature. This information can be used to determine the locations adults, which live offshore in mixed populations, had spent their juvenile period. This information can help managers determine which specific nursery areas are most important to protect.

Otolith microchemistry can also be used to determine whether, and even when, an individual was exposed to environmental toxins, such as an oil spill. This technique is currently being used to evaluate the impact of the Deepwater Horizon oil spill on both estuarine and reef fish species in the northern Gulf of Mexico.

Tissue isotope analysis

As a fish lives, eats, and grows within a particular environment, the chemistry of the surroundings are incorporated into all of its tissues. Many of the most common elements such as carbon and nitrogen exist in the environment in a variety of forms, usually light (normal) or heavy (rare), and sometimes radioactive (such as C-14). By chemically analyzing the ratio of heavy to light versions of these elements, or counting the number of radioactive atoms, we can learn information about where the fish has been living and what it has been eating at various time-scales. We can even tell the age of very old fish using this method.

Different body tissues recycle their cells at varying rates, resulting in our ability to infer movement at different timescales. For example, liver cells are recycled quickly (1-3 weeks) and muscle cells are recycled much more slowly (1-3 months).  A recent pilot study of juvenile red grouper on the West Florida Shelf showed that all of these 1-year old fish had traveled to their location from the north over the previous month or so. Since liver values equilibrate with their environment much faster, the graph shows that most of these individuals had been living to the north, but then moved southward. Specimen 5 had probably arrived to the area within the past week, while specimens 6 and 12 had probably been in the area for at least 1 month.

One tissue which never turns over is the eye lens. Like otoliths, a fish will add material to the eye lens as it grows. We can then peel back the layers of the lens, just like peeling an onion, and analyze the chemistry to reveal not only where a fish has been living, but also what it has been eating throughout its entire lifespan. This is particularly useful for long-lived fish or species which use a variety of habitats.

In most species, the ratio of heavy to light nitrogen can tell researchers that the individual fish eat larger prey as they grow in size. In the graph below, the shorter lines represent younger fish. Longer lines are older fish. All fish display the same pattern of eating larger prey as they grow throughout their lives.

A final use for the isotopes in the eye lenses of fishes is to find out the age of very old fish or fish that don’t have a good record of growth within their otoliths. A recent study measured the radioactive carbon in the eye lenses of Greenland sharks and found them to be up to 200 years old.

Nielsen et al. 2016. Eye lens radiocarbon reveals centuries of longevity in the Greenland shark (Somniosus microcephalus). Science. 353 (6300): 702-704


In short, the use of chemical signatures embedded in the cells of fish has become an invaluable tool to understand the movements, living habits, and food preferences of a variety of important fish species. These techniques are expanding our understanding of fish in many directions that were not possible just a few years ago. Using genetic signatures, microchemistry of otoliths, tissue isotopes, and even yet-to-be developed chemical techniques will continue to expand our knowledge of important fisheries species, improving our ability to manage and conserve them for generations to come.

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