The Use of DNA Testing to Monitor Illegal Whaling

A conversation with Stephen Palumbi

From the January 1995 issue of the Environmental Review


     In 1982 the International Whaling Commission imposed a moratorium on all commercial whale hunting but allowed countries to kill a limited number of certain whale species under scientific permit or for indigenous use. In their paper in Science Professors Baker and Palumbi ask, "Are whale products available today exclusively from species hunted or traded in accordance with international treaties? A spot check of Japanese retail markets shows that they are not and suggests the existence of legal whaling serves as a cover for the sale of illegal whale products."

     The authors analyzed the DNA of sixteen whale meat products purchased in Japanese markets and found that seven were South Pacific minke whales presumably taken legally under scientific permit. The remaining nine samples were either North Atlantic minke, fin whale, North Pacific humpback whale or from the dolphin family, which includes pilot whales, orcas and dolphins. This paper provides additional evidence that  illegal international trade in whale products continues, despite a moratorium on commercial whaling.

     We discussed this paper with one of the authors, Stephen Palumbi. He received the Ph.D. in marine ecology from the University of Washington. Dr. Palumbi uses DNA analytical techniques to study population biology of marine animals and is currently a professor in the zoology department at the Kewalo Marine Laboratory at the University of Hawaii.

ER: Dr. Palumbi, who funded this study, the lab analysis and the trip to Japan?

SP: The study was initiated by Earth Trust, which is an international conservation organization that works on marine conservation issues like whaling and drift net fisheries. They approached us with this basic conservation question about whether or not we could tell what a species of whale was on a retail market. We were interested in that mostly because of the broader conservation context; that is, do legal markets serve as potential covers for the sale of illegal products?

So Earth Trust provided the funds for the field work - sending Dr. Baker to Japan and obtaining the samples there. And then we were also supported by the MJ Research Company that makes the small portable PCR machine that we took with us. They gave us the PCR machine. [PCR, Polymerase Chain Reaction, copies a small amount of DNA repetitively, to get enough DNA to sequence. ed.]

     Dr. Baker came back from Japan with those whale meat samples and then they were analyzed in Hawaii in my lab. Those analyses were not supported by Earth Trust. We collected the data and analyzed it independently of them. We then informed them about six months later what we had found. And they have been great allies in all of this; they were quite surprised by what we found.

ER: Didn't they suspect that illicit whale meat was going to be found in the Japanese market?

SP:: They did. In fact, the reason they were so interested in this subject was they had for years been getting reports and eye witness accounts of that happening and they could never gather any evidence about it. But it is a normal human response; you might expect something but when you finally get independent corroboration of it, you tend to be excited.

     In any case, Earth Trust's interest in the work really sparked it off. They are much more used to dealing with the diplomacy and politics of conservation issues; we simply do genetics. So it has been a good collaboration.

ER: Why did you copy the whale DNA in Japan rather than bringing the samples to your lab in Hawaii?  

SP: The reason for that was that these whale meat samples were purchased in Japan, and because of the Convention for the International Trade of Endangered Species (CITES) those whale meat samples could not be exported from Japan.

ER: Even though the meat was imported illegally, in some cases?

SP: Yes. Of course at that point, we could not have known that. And CITES does not recognize that kind of nuance. We needed to go to Japan and amplify the DNA we wanted to analyze, and then bring back only the synthetic copies. So that allowed us to do the analysis here. It did mean that those samples had to stay in Japan. We pretty much had a one-shot opportunity to get information out of the samples and bring them back.

     The idea was to see whether the PCR technique would work and whether the information we got out of it was interesting and useful.

ER: What did your DNA analysis show?

SP: We showed that out of the sixteen samples we brought back and analyzed, about half of them were from the expected animals - that is, minke whales taken in the southern hemisphere.

ER: Which would be legal?

SP: Which would be legal under a permit that the Japanese government maintains for scientific whaling of minke whales in the southern hemisphere. They have taken about 300 animals a year for the last three to five years. And that is the primary source of legal whale meat going into the Japanese retail market.

     So the basic conservation question we wanted to ask was whether or not that legal market was serving as a cover for the sale of other products. Whale meat is very poorly labeled; you cannot tell what species it is when you purchase the meat in a grocery store. And it is very difficult to tell one piece of whale meat from another.      So given that difficulty, and given that some whale meat is legal - does that mean that illegal sources of whale meat are also potentially getting into the market?

     We found the samples that were not southern hemisphere minke whales fell into two main categories: there were three samples which were not baleen whales at all; they were either dolphins or some kind of small toothed whale; the others were baleen whales but they were baleen whales that were unexpected in that market. [Baleen whales use a straining device to collect food, toothed whales catch larger prey. ed]. There were four samples that were fin whales, and there was a Northern Atlantic minke whale, and there was also one sample that had humpback whale meat in it. Those samples are not expected out of the Japanese retail market, and they have been covered by international protection, in the case of the humpback whales, since 1966.

ER: And so the fin whale and the North Atlantic minke - is there any way that meat could have been taken legally?

SP: Oh, yes. There are several scenarios under which they could have been taken legally. For example, both species have been hunted in scientific operations in the 1980s by North Atlantic Nations. In the case of North Atlantic minke whales, Norway has been taking them. But the national policies of Norway have been that those animals are for domestic use only, not for international trade. So in this case it is not a question of whether they were taken legally but whether they were moved into Japan legally.

     In any case, it is possible the samples were in Japan prior to protection going on for these last couple species. And in this case, the samples would have had to have been in storage for between four and seven years, and that is possible. We do not have any evidence for or against that, and no one has come to us from Japan saying, "see, here is this freezer full of meat we have been keeping for seven years and are doling it out in a small way." We have been waiting for someone to come up and say that is what is going on, but no one has so far.

ER: What response to this paper have you gotten from Japan?

SP: We have had different kinds of responses. There was an international symposium on marine mammal genetics held in La Jolla a few weeks ago sponsored by the National Marine Fisheries Service and the Marine Mammal Commission and the International Whaling Commission. Mr. Iagi from the Japanese Fishery Agency came to that, and Dr. Baker went as well; they had a discussion about our results.      There were some legitimate questions that the fisheries agency people had that we were able to clear up, so there was a good interchange of ideas. Our best news was that the Japanese Fishery Agency has decided to repeat our work. They are going to establish a DNA reference library for all the cetaceans in coastal Japan, and they are going to establish a DNA testing facility for the retail market. [Cetaceans include whales, dolphins and porpoises. ed.]

     There have been less productive interchanges. The Japanese Whaling Association and a number of people working in consultation with them have been writing letters to various newspapers around the country complaining about our results and calling it a misuse of science for cynical purposes. I was just reading a letter in the Wall Street Journal today from the Japanese Whaling Association. That has been a misinformation policy - taking aspects of our work and making misleading statements about it.

ER: How much uncertainty is there in the DNA analysis? How did you do convince yourselves you had good information?

SP: The DNA can be represented by a long string of letters and you obtain those letters by sequencing the DNA. The sequences are aligned to one another and then you look for similarities. There are computer programs available that make this task easier, but with species as different as baleen and toothed whales, it is very clear that those are different DNA sequences. And you can very easily, even by eye, divide them up into two groups - the baleen whales on one side and the toothed whales on the other side. Once you have done that, you can ask, how reliable is that division into baleen and toothed whales?

     One source of error is the DNA sequence itself. Suppose you did not have that exact sequence? Suppose you had a slightly different sequence? Would you still make that same division? A bootstrap technique is a computer resampling of the original data. The computer chooses from the data set at random, creates a new data set smaller than the first and then the machine asks, do you still get the same division? - in this case, between baleen and toothed whales. If you do that hundreds of times, with random sampling of the original DNA data, you come up with an estimate of reliability. How many times out of one hundred did you get the division between baleen and toothed whales that you had seen in the original data set? If it turns out that you only got that division say in fifty out of one hundred times, then the reliability of the DNA sequence is low. If, however, you got that same division all of the time, or ninety-nine times out of one hundred, then the reliability of the DNA data is quite high.

     So because the DNA sequences are very long strings of information, you can afford to throw some of it away to see how good that data base is. Now beyond that, to go from knowing it is a baleen whale to knowing what species it is, then you essentially do the same thing over and over at finer and finer levels of resolution.

ER: The result of that process is in your figure in your paper. It has 100% for the minke whales, 98% for the humpback and 92% for the fin whales. Are those numbers probabilities?

SP: Studies show that those numbers are very conservative estimates of probability.

ER: So the accusations by industry representatives haven't challenged your analysis?

SP: No. They have never challenged the bootstrap analysis. In this case, the statistical analysis has remained unchallenged. And, in fact, I think part of the problem is that the technologies that we have been using have been very well developed and used very commonly in some branches of biology - but not fisheries so much. And so the idea of the statistical reliability of those data really does not seem to have penetrated.

     Instead, for example, complaints about the study have said, "Well, how could you tell, that this was a fin whale when you don't have every sequence from every small dolphin around coastal Japan?" And that just demonstrates a lack of understanding of the basic procedures. We can tell right off that the DNA is not from a dolphin because it is not from a toothed whale. Once we know a sample is a baleen whale - and we have an excellent reference library for baleen whales - then knowing the species is much easier.

ER: Are baleen whales covered under the CITES moratorium?

SP: Yes. Baleen whales are regulated now under the IWC's moratorium on commercial whaling. So coastal whales, humpback whales around Japan, would be covered by that moratorium.

     Are they making it into the market place as well? We do not know that yet. There are not that many coastal baleen whales around Japan. The existence, though, of fin whales and North Atlantic minkies in that market suggests it is not just coastal by-catch in Japan that is going on, but in fact there is a very active international trade in these protected species.

     This does not come as a great surprise. People have noted a long history of attempts to ship illegal products into Japan. We talk about some of them in the Science paper - a shipment of products labeled shrimp that was investigated in Oslo on its way to Korea, and it turned out to be whale meat.

ER: So its origin was North Atlantic?

SP: Yes, presumably. We do not have any sample from that particular shipment, but one presumes its origin was within the North Atlantic.

ER: So someone was taking that three and a half tons of whale meat and trying to get it into Korea labelled as shrimp meat?

SP: That is what the customs inspectors in Oslo had concluded. So this type of trade is apparently going on quite commonly. And the fact that we discovered these animals in the retail market then serves not just as a single note out there about the existence of these activities, but in fact confirms a very different kind of evidence - evidence from customs inspectors around the world - that these illegal shipments have been going on.

ER: DNA analysis is a powerful tool and it's encouraging that the Japanese authorities seem to be opening up to its use.

SP: We found it encouraging too. And of course, any kind of tool, any kind of evidence, can be used in various ways. It would be possible, I am sure, to go into a Japanese market and just pick the whale meat that was completely legal.

     Whether or not the DNA testing provides an accurate view of what is actually in the market to a large extent, does not depend on the DNA testing procedures; it depends upon the procedures used to actually collect the samples. You can imagine in our own country, a state inspector going into a market would be greeted with a much different spectrum of choices than just somebody else.

ER: If they knew he was coming.

SP: Exactly. So it depends upon the willingness of the people doing the testing to actually discover what is there, rather than simply show that everything is OK. And at that point then, details of the DNA testing are not as important as the details of the market sampling itself. So in this case, we can move away from worrying too much about how the genetic testing is done and  concentrate more on how the sampling is done. Although, it seems there is little real appreciation - and understandably - among people about how a sequence of DNA can be identified. I get it especially these days with forensic DNA popping up in so many different areas.

ER: Is the preservation of the DNA good enough in a package of pickled whale meat to get usable DNA?

SP: There probably is degradation because of the way that we had to deal with the samples. We chose a small piece of DNA - about 250 base pairs long - because the smaller the bit of DNA you try to amplify or copy, the more successful you are likely to be. For example, when people have used these techniques to get little bits of DNA out of mummies, or out of fossils or out of preserved samples that have been around for a very long time - insects in amber or remains that come out of a peat bog - the smaller the piece of DNA, the more likely it is you will be able to amplify it, because the DNA in the sample has been cut up into small pieces. So probably those samples have been degraded, but vinegar or just drying or salting a bit of material fixes it or cures it. The same thing that preserves the meat preserves the DNA.

ER: So what is the basis for the criticism of your work?

SP: The work has been criticized by the Japanese Whaling Association as being sponsored by the anti-whaling organization, Earth Trust. There is not much I can say about that.

ER: It's true.

SP: It is true, yes. I am not ashamed of it either.

ER: As long as the science is done right.

SP: Earth Trust has been very good about the need for the data to be strong and independent. There have been times though, when we were working on the publication of the Science paper and because of that, we were being very quiet about the results. We would make no press announcements until the paper was published. And there were times when they could just barely contain themselves, but they did. They recognized that the strength of publishing the results in Science - very severely peer reviewed before they came out - would mean they would be taken more seriously, and that makes a big difference. So Earth Trust deserves a great deal of credit for biding their time and waiting for what can be a frustrating and slow academic process to grind through.

ER: How reproducible is this DNA analysis?

SP: We were also concerned about the issue of replication. Our biggest problem with replication is that the samples are in Japan, and after sitting there for a year and a half, we are not sure we can go back and repeat the work with those same samples. And our focus for replication was on that humpback whale sequence because that, locally anyway, had the most political implications. So we were much more careful about that than we were about - well, we were careful about everything - but that one, we went back over and over again. And with amplified products that we had, we verified many times that the humpback whale sequence was there.

ER: So you'd go back to the same test tube and pull out a little more sample and analyze it again?

SP: Yes. Normally what we would want to do is go back to the sample. And if we got two differing sequences out of the sample, we would probably go back to the sample and much more carefully try to get something which was a single piece of tissue. But we did not have that opportunity in this particular case.

ER: You tied one hand behind your back in abiding by the CITES rules so scrupulously.

SP: There was not anything to be done about it. Those are good regulations. They do a good job of protecting many species around the world and there is no point in claiming that you should not have to be bound by them because you are doing research. We delayed the whole project many months in order to work out a practical way of amplifying DNA from those samples, then scrubbing it clean of all of the whale's original DNA and bringing back just the synthetic copies.

ER: How does this result address your concern that the legal whale meat market may be used to cover up illegal activity?

SP: It is clear that Japan's is a very heterogenous market - it has a lot of products from many different places in it. And because it is a legal market, a lot of meat can be sold on it. Very expensive and valuable material can be sold on it without - until now - the ability to tell what was what. Those meat samples are quite expensive. The average price is $50 to $100 per kilogram; there is a lot of economic pressure to put products on that market.

     It is important to point out that the smaller toothed whales are unregulated and that means there will be a legal market. The issue is not just baleen whales, but can you tell the difference between toothed and baleen whales? And how do you regulate such a market?

ER: What is known about the extent of illegal whaling?

SP: It is not very well documented, although the documentation is getting stronger from Russia and from those involved in what was the former Soviet fishing fleet. That paper referenced in our paper is a scientific correspondence to Nature which describes the relatively large takes the Soviet fleet was engaging in during the 1960s and 70s. Even after the humpback whales went on the international protected list, thousands of them were taken by the Soviet fleet. And so we do not know the magnitude of that catch right now. [Soviet whalers took 48,477 humpback whales in the South Pacific between 1948 and 1973. ed.]

     We have a very difficult time knowing how that catch has affected the ability of those populations to recover. But one lesson you can take from that is that there was a fleet operating in the middle of the ocean taking thousands of animals, and no one knew. How does that happen? The answer is, the ocean is a very big place. To my mind, that incident shows the extent of illegal whaling that can go on without the international community having any idea about it. We cannot tell what is going on in every square mile of an open ocean all of the time. Illegal whaling can be going on quite commonly without anyone knowing about it except the people doing it themselves, and it is going on.

ER: Has the humpback whale population in the South Pacific not recovered the way other whale populations have?

SP: It is thought that the heavy take of some species - particularly blue whales - in the southern hemisphere has resulted in much smaller population increases after the hunting moratorium than were predicted. An important caveat is that numbers of those whales in various places around the world are very difficult to determine. And the numbers of whales that were present when protection went into effect are difficult to know. So in general, what you are dealing with there is a feeling that certain populations are not recovering well, although hard data are particularly difficult to come by. It has been frustrating, I think, to whale biologists all over the world that it is so difficult to get a good idea of the numbers of whales that are there and that has hampered efforts to understand whale populations.

Literature Cited

Which Whales are Hunted? A Molecular Approach to Monitoring Whaling. 1994 Science 265:1538-1539.

Copyright 1995 Environmental Review