Applied Marine Biology

The why of marine biology: a treatise

A few years ago, when my daughter was five years old, I was driving her to school and she asked me: “Daddy, what do you do for work?”

I told her that I was a scientist and that I study fish, to which she asked: “Why do you study them?”

It wasn’t the first time somebody had asked me that question, or one like it. I gave my daughter the same answer I give most people—I study fish because I think they are beautiful and interesting. But this answer, while being good enough for me, and my daughter, doesn’t seem to satisfy many others.

In recent years, as I’ve tried to advance in my career, that question has become more and more important. Why study fish, or marine biology? Why should anybody care?

For me the answer lies in the application of marine biology to issues of economics, politics, and public health. I believe that anybody willing to do a little research will quickly find that marine biology is able to contribute a lot to the well being of people around the globe.

Allow me to put forward six talking points, starting with this: fish are worth a lot of money.

1. Fish = $$$

Fish and fisheries are valuable natural resources. According to a 2014 FAO report, the global seafood industry has a total export value of about $129 Billion US dollars. And over half of the global seafood catch comes from developing countries and small scale fisheries.

Another FAO report (2012) suggests that the global marine catch is in decline, and that the state of the world’s fisheries is worsening. Overall, about 1/3 of all marine fisheries are over-fished and not well managed.

According to some sources, global fisheries management reform could result in over $50 Billion of increased seafood revenues per year (Sumalia et al. 2012. journal.pone.0040542; Costello et al. 2016. PNAS 113:5125-5129).  Therefore, there is a lot of incentive for societies and governments to improve the way they harvest the oceans.

2. It’s a fish-crazy world

In addition to the monetary value of fish, there are even higher cultural and social values.

Tsukiji Fish Market Holds First Auction For 2017
In 2016, a Japanese sushi chef bought a tuna at auction for $632,000.                                                                        

In Japan they have a yearly tuna auction, where it is considered a great honor to buy the first fish. Here, the sushi illuminati dole out obscene amounts of money to claim the notoriety. And most importantly—they cannot let a Chinese sushi chef outbid them!

Like sushi chefs, fishermen too can be a little crazy over fish. Once, while I was on Guam doing fieldwork, a bunch of local Chamorro fishermen began protesting the marine preserve at Tumon bay (a very touristy beach). There were about twenty people in the shallow water holding a large net, and another guy in a loin cloth, with a megaphone, taunting the law enforcement officers on the sand. “What are you waiting for?” he blasted through his megaphone. “They’re fishing. Arrest them!!!”

The madness of our fish-crazy world is widespread. Everywhere I’ve traveled—from Hawaii and other Pacific Islands, to Australia, Europe, and the Gulf of Mexico—people get very emotional about their fish, and their fishing.

3. Crime

Fish are so valuable, that there is a lot of crime surrounding the seafood industry. In 2011, it is estimated that between 1 and 2 Billion dollars of illegal seafood was imported into the United States (Pramod et al. 2014. Marine Policy 48:102-113). In recent years the international community has been trying to crack down on IUU fishing (illegal, unreported, and unregulated), but it remains a persistent problem, especially in the developing world.

Perhaps even more prevalent is the issue of seafood fraud:

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Seafood fraud is when a person orders red snapper, for example, at a restaurant and instead they’re brought tilapia. The reason for this is simple: red snapper retails at about $15 a pound, while tilapia is about $8 a pound. And most of the time the customer doesn’t know the difference.

I mention red snapper intentionally, because it is one of the most commonly mislabeled food fishes. If you buy a fillet of red snapper at a fish market, the odds of you actually getting something else approach 100% (

If you eat much seafood at all, you’ve probably been a victim of seafood fraud.

4. Political instability

I’ve already mentioned that over half of the global seafood catch comes from developing countries and small scale fisheries. In such parts of the world many people are subsistence fishers.

Notice I said fishers and not fishermen, because a suspected half of them are women:

Fishing is an important source of sustenance and income for many women in third-world countries.

Small scale fisheries in the developing world are deemed to be important to food security and poverty alleviation for millions of people (FAO 2011-2017).

We need to care about these small scale fisheries, because if we don’t, things like this can happen:

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In 1991 the government of Somalia collapsed and the country has not had a functioning government since. It also has over 1,000 miles of coastline (more than any other African country) and after the government was gone, foreign fishing fleets from Europe and Asia came and plundered Somali waters, stealing about $300 million of seafood every year.

The local subsistence fishermen just couldn’t compete, and some fishers even say that they were shot at by the foreign vessels becoming rich off of unregulated fishing. Eventually they armed themselves, for self-defense, and from there it was a small step to piracy.

At the height of the Somali pirate problem it is estimated that the cost to the global economy was between $6-8 Million US dollars per year.

Desperate people do desperate things, and if we don’t ensure the sustainable harvest of the world’s small-scale fisheries then we are going to have millions of desperate people in many parts of the world.

I might also mention that there is a very bad situation happening right now in the South China Sea:

Food Fight

5. Aquaculture

Why bother chasing down fish on the high seas when you can just raise them in captivity?

Between 1984 and 2016, global aquaculture production grew from about 11.4 million to 243.4 million USD per year, and from about 10 million tons to 110 million tons ( There is no doubt that people are starting to become farmers and ranchers of the sea, and making profitable business out of it. In the long-run, development of aquaculture will benefit global food and political stability. But it also comes with some environmental drawbacks.

It is unclear what the total environmental costs of aquaculture are, but loss of coastal habitat to shrimp farms, the accidental introduction of invasive species around the globe, and the irresponsible abuse of antibiotics, collectively, are becoming a huge burden on the environment.

6. Seafood poisoning

Marine toxins in seafood represent a significant threat to human health. Fish and shellfish can easily become contaminated with environmental toxins, many of which are derived from marine algae.

For example, the dinoflagellate Gambierdiscus produces a neurotoxic substance called ciguatoxin (Gaboriau et al. 2014. Toxicon 84: 41–50) that can contaminate seafood and cause permanent damage to human health, or even death. This small, unicellular algae lives on leafy macro-algae and thrives in warmer water conditions. Herbivorous fishes accidentally ingest the toxic algae when they are grazing and accumulate the toxin in their tissues. Predatory fish that eat the herbivores then become contaminated.

In tropical seas around the world, coral reef habitats are disappearing and being replaced by algae-dominated habitats. This makes more habitat for the toxic Gambierdiscus. Add in warmer water temperatures from climate change and you can expect cases to ciguatoxin to increase globally.

People will die.

How can genetics, genomics and biotechnology help improve ocean harvests and fish farming?

I am a fish biologist, but specifically I am a fish geneticist, conservation geneticist, and molecular ecologist. In short, I use DNA and RNA as tools to study all aspects of fish biology.

I mentioned above six different reasons why fish are important. I’d like to suggest six ways that DNA and RNA studies can help us manage our marine resources wisely.

1. Genetic stock assessments

The entire concept of sustainable fisheries is based on the assumption that fishermen are harvesting only a demographic surplus. As long as fishermen only take a surplus, the fishery is sustainable. If they take more than that, fish stocks will eventually collapse.

What is a stock? It is generally described as a group of fish that share the same geographic space, are inter-breeding, and have a unique demographic trajectory relative to other stocks. There are many fish stocks around the world that have been rendered unfishable by over-harvesting. And collapse is a real threat for many fish stocks around the globe today.

Collapse means that the numbers become so low that mature adult individuals become extremely rare. When red snapper stocks in the Gulf of Mexico collapsed in the 1990s, almost all the fish people caught were less than a year old. When that happens, you need to leave those fish in the water, and hope they grow up to replenish the population. And when stocks recover, they need to be sustainably managed. Management means less fishing equals more fish!

But before you can manage stocks, you first need to know what the geographic boundaries of the stocks are.

When I was a PhD student in Australia, I worked on two species of commercially important threadfin fishes: Polydactylus macrochir and Eleutheronema tetradactylum. At the time, both species were managed as single stocks across the northern coastline of Australia, from Western Australia to Queensland. Using just a small number of genetic markers, my work showed that there are many hundreds of stocks of these species in Australian waters, most associated with estuaries and genetically different at scales as small as 16 km (Horne et al. 2011. Molecular Ecology 20: 2291-2306; Horne et al. 2012. Marine Ecology Progress Series 449: 263-276; Horne et al. 2013. Fisheries Research 146:1-6).

One result from this work was that, in Western Australia, fish from the bay near the city of Broome were shown to be a different stock from those at the adjacent Eighty-mile beach. This discovery prompted the closure of the commercial threadfin fishery in Broome.

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This move was also meant to improve recreational fishing in Broome, and increase tourism to the city. I think it was a good management decision.


In the long run, managing threadfins at a small, local scale is going to result in much more sustainable harvests year after year for these fisheries than if the entire tropical coastline of Australia was considered one giant stock. These genetic stock assessments are the bread and butter of what I do as a scientist.

1b. Neutral vs. Adaptive genetic diversity

Traditionally, we use selectively neutral genetic variation to determine the genetic stock structure of fishes. Neutral here means that the genetic variants aren’t strongly affected by the influence of natural selection one way or the other. It makes sense to use neutral genetic variation because the patterns in the data then arise mostly out of demographic processes, such as migration between areas, and not environmental processes.

But sometimes, having genetic variation that reflects environmental processes can be useful. Sometimes environmental factors limit the geographic scale of fish stocks more than demographic ones. So as a category 1b, I’d like to submit that using adaptive, or putatively adaptive, genetic variation can reveal genetic differentiation and real stock limits that aren’t seen in neutral genetic markers.

The technology that allows us to do this us relatively new, but here is a figure from an upcoming red snapper paper, soon to be submitted, that shows the difference between adaptive and neutral genetic structure.

If you’re not familiar with either population structure indices, or multivariate analysis, just know that each little icon represents a population: colors are the sites where fish were sampled (Florida, Alabama, Texas, and North Carolina). Squares are the neutral genetic variation. Circles are the putatively adaptive genetic variation. The closer the icons are on the graph, the more genetically similar they are. The further away they are, the more genetically different. (Norell et al. in prep.)

For a long time red snapper populations across the Gulf of Mexico were thought to be genetically homogeneous, because people only looked at neutral genetic variation.  But as you can see, there is other genetic variation that distinguishes populations quite nicely. Some people I talk to say that Alabama was the epicenter of the fishery collapse during the 90’s. If so, the high differentiation of this population could represent fisheries induced evolution. But I think more work would be needed to make that conclusion.

Why does adaptive genetic variation show geographic population structure when the neutral variation doesn’t? Because it only takes a small number of migrants, every few generations, to spread neutral genetic diversity. But this level of connectivity isn’t demographically meaningful. That is, the number of migrants being exchanged between populations is so small that it has little to no effect on the size and persistence of each population.

In contrast, adaptive genetic diversity is not spread so readily. The fish that possess the best genes for any particular habitat are going to pass on those genes more successfully than migrants from other habitats. In the end, adaptive genetic diversity will accumulate in certain areas.

Red snapper in the Gulf of Mexico is currently managed as two stocks, east and west of the Mississippi River Delta. But according to the data I just showed you, this will need to be revised in the future.

2. Forensic Genetics

Once, back in 2004, when I was still at my undergraduate university, I was hanging out with two friends, talking. My first friend, was studying to be a dentist. He said:

“Man, when I’m a dentist, I’ll totally hook you guys up with free dental care.”

My second friend, was studying to be a lawyer. And he said:

“Yeah, and when I’m a lawyer, I’ll totally give both of you free legal advice.”

Then they both looked at me and asked: “So… how can you hook us up?”

I looked at them and said: “In the future, I’ll be able to tell you which of your children are actually yours.”

So far, neither of those friends have asked me to perform that service. But I could. Easily.

Everybody gets one set of genes from mom, and one from dad. We all share 50% of our DNA with each of our parents, and on average we share 50% of our DNA with each sibling (identical siblings share 100% of their DNA). Fish are no different. So I can use DNA to tell how far fish move from their relatives.

This is called relatedness, or kinship, analysis, and is a type of forensic genetics.

Unlike patterns of population structure, which can persist for a long time, patterns of genetic relatedness break down after only a few generations, which means they can be used to assess levels demographic exchange among populations.

Here’s a figure that uses relatedness analysis and spatial auto-correlation of Red snapper genotypes in the Carolinas.

A) Just a map. B) Group relatedness analysis. The null hypothesis here is that both populations are randomly mating. The p-values indicate that the possibility of falsely rejecting that null hypothesis is very small. C) Network of relatedness estimates. This is a good figure for anybody that isn’t a geneticist. Circles represent individual fish. And the length of the lines connecting them are negative relatedness values (relatedness values are correlations of genotypes, so, yes, they can be negative). In other words, the closer the circles are together, the more related they are. D) Spatial auto-correlation of individual genotypes. The global rtest assesses whether their are population breaks among individual genotypes. 

The most important part of this figure is quadrant C. In at least one way this is not a very good figure. The network should ideally be represented in three dimensions. But here I’ve flattened it into two, and I still think it gets the point across quite nicely: The blue dots are mostly more related to each other than they are to the red dots.

Here we see clear demographic discontinuities in red snapper, meaning that there is a lot more stock structure in this species than has been shown previously.

Ultimately, this research will lead to better management of this species, and more sustainable fishing.