Barcode of Life

I've written a lot about the fish collection process (and about the reservations I have had with it), but not that much about why it's being done. The samples that have been collected here are part of the much larger "Barcode of Life" project. The idea is to catalog every living species in the world with a genetic "barcode." Once it's complete, you will be able to take a sample of any living organism, run it through the barcode process, and get a positive taxonomic identification output. It is different from a genome (where the entire genetic code of an organism is sequenced). Instead, only enough genes to identify the organism are sequenced (saving time and money). But what good is it to be able to identify species in this way? The benefit of having a database of genetic "barcodes" may not be obvious (it wasn't for me).


The truth is, I'm not really all that familiar with the project. I can, however, share some of what I've learned about it in the last few days. First of all, it will be useful in the enforcement of some environmental regulations. Enforcement agencies can (and actually already are) using it to crack down on the illegal fish and "bush meat" trade. For example, just before our Smithsonian visitors came here the director of the project was sent a fillet of fish by the government body that regulates the fish trade (the EPA or FDA?), seized from a distributor suspected of selling an endangered species. By running a sample through the test, he identified the species from an otherwise indistinguishable fillet and informed the regulators whether or not any laws were being broken. In that particular case, it turned out that endangered fish was not being sold (though, I think some labeling laws were probably broken).

Also, the barcode project has been extraordinarily effective if identifying new species. Currently, most taxonomic identification is a visual process. Humans have to physically look at organisms and distinguish them by their anatomy and markings. And humans, of course, make a lot of mistakes. Species can look the same, but be genetically very different. An example is the recently discovered species of Soapfish I mentioned in an earlier post.

Rypticus subbifrenatus

Rypticus sp.

Both of these photos are from the same field ID guide, improperly listed as color variations of the same species. Actually, they are genetically quite different.

Another area where it has been helpful is in the identification of species throughout their lifecycles. Fishes, in particular, can vary dramatically as they transition from larval, through juvenile, intermediate, and terminal phases. I always wondered how anybody ever knew, for example, a juvenile Smooth Trunkfish was actually a Smooth Trunkfish. They don't look anything alike. In the past it required identifying enough specimens in transition to reveal the link or (believe it or not) raising them in captivity and observing the transition! I was told that they are finding that numerous species previously thought to be unique are simply juvenile phases of other known fish. Since genetic code remains the same no matter what phase the species is in, they can always be identified by their genetic barcode.

Juvenile Phase

Terminal Phase

Okay, they resemble each other a little in the photos, but in real life making the connection is much more difficult.

Probably the most exciting application for the barcode of life (at least in my opinion) is still many years from actually being available. I think of it as sort of a field ID "iPhone application," or something like a Star Trek "tri-corder" for identifying species. It would be a handheld genetic sequencer that could instantly pull up all sorts of pertinent information on whatever living thing you can manage to get your hands on (probably easier to use with plants than most animals). I imagine amateur naturalists of the future carrying around these things in place of the visual ID books we use now. It sounds like something that belongs in science fiction, but it turns out that small field sequencers already exist for scientists, and the director of the Smithsonian lab predicts that a consumer friendly version is probably only 10 years away. Once this technology is out there, its potential is huge (Imagine you're a researcher interested in a rare insect. You flag it in the barcode database to be notified each time the record is accessed, an amateur naturalist finds it in the field an runs it through the sequencer out of curiosity, he or she gets all the information they are interested in as well as a personal message from you asking them to collect the data necessary for your research. It's collaborative research taken to a whole new level. It's like wikipedia on steroids).

The Barcode project promises a lot of very exciting things, the extent of which has probably yet to be conceived. Knowing just some of its potential makes me glad that I got the chance to be part of it, if even in the smallest way.

Fish Collection

It has been a non-stop endeavor working with the Smithsonian group. This morning, however, I'm taking some time off from it. Ever since it arrived, the focus has been on using their other chemical, rotenone (the one that kills the fish rather just anesthetizing them). It hugely more effective. Almost devastatingly effective. In fact, on the first outing when it was used, I questioned whether or not I'd continue helping. I eventually decided that I would, but I'm still not entirely comfortable with its effect.

Deployment on our first station.

Rotenone is a substance that occurs naturally in the roots of several plants (one of which is the commonly eaten jícama plant). It has actually been used for 1000s of years by indigenous tribes as a method of catching fish for food. It's a poison, but according to Wikipedia, it's only weakly absorbed through skin and the GI tract. So it's harmless to mammals. For fish, on the other hand, it's readily taken up through the gills and kills them quite quickly. What is being used here is rotenone in powder form. It gets mixed with water and a splash of dish soap (as an emulsifier) to make a sort of dough or thick batter (one of the researchers does this with his bare hands so it's some indication of how certain he is that it won't harm him). Then it gets double-bagged and is ready to be deployed.

The bags are taken down to a selected reef (usually on SCUBA), opened, and slowly shaken empty in the area. Since corals don't have gills, they are completely unaffected. The fish, however, die quickly. It has sort of a shotgun effect, killing everything with gills, whether a sample is needed or not. This is what made it so troubling for me. I don't like seeing things die for no reason. Fortunately, it quickly dilutes and is rendered inert by sunlight, so it doesn't have long lasting or widespread effects. It also mostly only kills small fishes. Anything larger than about 5 or 6 inches can withstand it long enough to swim to safety. Sadly, though, a large fish doesn't mean a large brain. Some big fish, mostly Yellowtail Snappers but also one large Yellowfin Grouper, were lured back into the toxic cloud by the prospect of an easy meal. They see the dead little fish and come swimming back in to gobble them up. If they do it enough times, they get a lethal dose themselves.

This big Yellowfin Grouper couldn't help but go after the easy meal. Not to waste, we took our genetic sample and then ate him for dinner.

This Coney was done in while attempting to down a Peppermint Bass. We also found 4 or 5 other small fish deeper in its throat. Apparently it entered and re-entered the rotenone cloud several times before it died.

After the cloud settles out enough for us to see, we swim in and scoop up the dead fish lying on the ground. Those that are easily identifiable and which have already been collected, are left behind and, eventually, eaten by scavengers (which is harmless even to fish because the toxin is only effective when absorbed through the gills). The affected area is eventually repopulated from neighboring reefs or from unaffected portions of the same reef (the size of rotenone stations being done here is only about 20 or 30 feet). Again, its a matter of viewing it from an ecosystem-wide level or on an individual level - the impact is minimal on the ecosystem, but the impact on individual fish is dramatic.

Its understandable, though, why rotenone is such an important tool for this project - many species just can't be captured in other ways. As you can see from the pictures of the lab, a great diversity is turned up:

Preliminary sorting by appearance before close examination under a microscope.

Waiting to be positively identified: Peppermint Bass, Fairy Basslet, and something with a yellow tail.

Three Tongue Fish

Blue Chromis, Redspotted Hawkfish, and a Juvenile Rock Beauty

Some sort of Brotula. Almost impossible to positively ID without genetic testing.

A Slender Filefish and two Blackfin Cardinalfish

Two of the new Soapfish (used to be confused with Rypticus subbifrenatus, but is genetically distinct). The spots on these ones cover the belly, but not so on the other.

A load of Brotula. Part of the reason I am troubled by the rotenone method - more specimens are taken than are needed.

A Happy Birthday

And a busy birthday. It started out in good fashion. First thing in the morning, I went out with the Smithsonian group on a dive to The Grotto to do some fish collection using quinaldine sulfate (the anesthetic) - there was a delay in the shipment of their preferred chemical, called rotenone. I found it a little difficult to use the stuff at depth (around 95 feet). It only really works on the smallest of fish. Anything larger than a coin only gets "sleepy" from it - I chased a groggy Longsnout Butterflyfish far too long trying to get it. Many of the small fish are quite difficult to get as well. Quinaldine works best when the fish stay in it for some time, so it's easiest to squirt it into holes where they can't escape. The problem then is that they're very difficult to get out. You can do so by swooshing water around, but it's only marginally effective.

After the dive the researchers got back to work in the lab, and I spent some time working on my PhD applications. And after lunch we geared up to go on a second collection outing. This time we were headed to Highland's Bay - an area on the Southeast side of the island. It's an interesting area for all of the odd coral formations, but the water is always very green and murky (probably because of the prevailing ocean current and extensive seagrass beds). Four of us were snorkeling with Hawaiian Slings (a type of spear), and three were diving with quinaldine again. I opted to dive. And, again, it was somewhat "under-productive.". I chased a sleepy damselfish for a while (it's just so hard to let them go when you get so close!) and didn't turn up more than a handful of anything else. It was alright for me - I just like being involved and getting to dive - but I think the researchers were disappointed in what we were able to get. They all kept worrying that the rotenone shipment wasn't going to turn up and that their visit might be a waste as a result. Finally though, we learned when we returned from the outing, it arrived.

There wasn't enough daylight left to use it then (and they had lots of work to do in the lab), so they didn't want to go back out. Ben (one of the SFS faculty) and I, however, decided to go out to Admiral's Aquarium (one of our usual snorkel sites) and fish with the spears for a little while. Admiral's is a shallow patch reef with very clear water and almost never any sharks, so I felt comfortable with the spear there. It can be quite fun to do, but sometimes pretty brutal. I hoped that my kills were swift, but sadly I know some were not. The inner turmoil and reservations I have over taking part in any of this project probably doesn't come across fully in these posts. I've never really killed things before and I can't help but have strong emotions about doing it. There are (at least) two ways of thinking about it. One is from an ecosystem-wide perspective, that we are doing very little harm to each of the species as a whole and essentially none to the environment. The other is on a individual level. Each fish that dies because of us, is a life that has ended, some of which (especially those that are speared) suffered considerably. I try to think of things in the first way, but I inevitably I come back to the suffering inflicted on individual fish.

Our catch from the evening outing to Admiral's was quite good for the short time we were there. I managed to get a Peacock Flounder, a Blue Chromis, a Yellowtail Snapper, a Schoolmaster, a Mahogany Snapper, a Sergeant Major, a Goatfish, and a Yellowhead Wrasse.

Peacock Flounder

Blue Chromis

Yellowtail Snapper

Schoolmaster

Mahogany Snapper

Sergeant Major

Goatfish (poor little guy suffered good bit)

Yellowhead Wrasse

And the rare Brettfish (suffering was minimal).

That evening, of course, I got my favorite carrot cake (and quickly hid the leftovers in the staff refrigerator). And finished the long (but very enjoyable) day off down at the dock watching bioluminescent sea-worms with Jessee and some of the other staff.

In the Lab

Not all the work of our visiting Smithsonian researchers is play. Each and every specimen that is collected needs to be processed in their mobile lab. They've brought a pared-down version of their lab here because they don't often bring their DNA sequence machinery on first visits to places. But there's still plenty to do (enough to keep them up until 1:00am the first night!).

Completed Samples

Holocentrus rufus - Longspine Squirrelfish

Taking a flesh sample of a juvenile Queen Angelfish.

Juvenile Goldentail Moray waiting to be measured.

I helped some, but I was worried about being in the way. They're cramped into our small conference room and they seem to have a well-functioning system in place already. The process includes measuring, identification (with the help of a microscope in many cases), photographing, flesh sampling, preservation, and recording of data. All of it is done with the precision and meticulousness you'd expect of a professional laboratory. I was particularly impressed with their photography station and the quality of the pictures they were getting.

Photo Station

The picture below is of a rare Soapfish. Until the Smithsonian's "Barcode of Life" project (of which our sampling is a part), there was believed to be 4 species - all of which are extremely similar in appearance. But their testing found 5 genetically distinct species.

Rypticus subbifrenatus - Spotted Soapfish

Fish Research

The Smithsonian researchers have arrived, and their fish sampling project is underway. I went out with them to a small patch reef at East Bay this morning to do some collecting. The method we used was primarily anesthetization using a chemical called quinaldine sulfate (I have no idea if that's spelled correctly). Apparently it has no effect on coral and, so long as no predator gobbles them up while they're dazed, the fish recover completely - except, of course, the ones we collect. We squirted the stuff from plastic bottles into the reef crevices and waited a few moments. The fish that got hit by it floated out and we scooped them up in our nets. This method works really well for all the small species that rarely come out of their holes. Today, since it was the first time they have ever sampled in this area, we were pretty indiscriminate. They're looking to take about 3 of each species they can find.

Several species of Grunt.

Among my catch were several Cardinal Fishes, a juvenile Four-eye Butterflyfish, a Blue Tang, a Blue-Stripped Grunt, and a Surgeonfish. I partially anesthetized many other fish that were still able to evade my net, including a few Sharpnose Puffers! One of them was probably dazed enough for me to get, but I couldn't bring myself to do it. (shh, don't tell the others, they'll think I'm soft). Sharpnose Puffers are pretty common, but they're one of my and Jessee's favorite fish. I was worried somebody was going to see me rooting for it to get away and be upset, but fortunately they didn't (now, of course, my secret is published on the internet). I also squeezed about half a bottle into one hole only to have a young Green Moray come darting out. It startled me at first, but it just found the nearest (uncontaminated) place to hide. They're not dangerous, just scary looking. It was small as far as Green Morays go (about 3 ft), but I asked before I collected it. They weren't sure whether or not to take it, but finally decided against it.

Nassau Grouper, Schoolmaster, Gray Snapper, Squirrelfish, Blue Tang, and two Surgeonfish.

When we ran out of quinaldine I decided (after all) to give one of the spears a try. The others had already been doing it and it felt like a fairly controlled setting. Spearing is much more selective. You target a single fish, so (in my opinion) it's less disruptive. I fired it off a couple times at the sandy bottom just to get the feel. Then I picked out a small Blue Tang and gave it a try. Bad shot, I missed. I watched the more experienced people get a couple fish, and as we were heading out, I lined up on a medium-sized brown fish that was camouflaged against the bottom, and released. It turns out that it was some sort of Puffer because as soon as I hit it, it started to inflate. I must have hit it just right so as not to puncture its belly because it grew to be the size of a softball. I quickly swam it over to our float and put it into the fish bag (we kept the speared fish in there rather than on us so any sharks in the area would take interest in the float and not us). When we got back to the shore, however, I learned that that particular fish bag had a hole in it! My first ever speared fish was lost. I felt bad that it was going to waste (at least with respect to the project - I'm sure some Barracuda was quite happy that it was left behind).

Fishing Licenses

Lately we've been a little lazy about updating this blog. It's not so much that nothing is going on, but more it really takes an effort to keep it up to date. And also, it would probably bore the audience if we wrote about every snorkel, every dive, every Eagle Ray, every shark, and every turtle. I have to say though, I quite like a life where those things are the mundane!

Over a week ago now, we finally got around to getting our fishing licenses (even though open season began on 1 August). We're now cleared to catch lobster, conch, turtles (!), and fish. So far we haven't caught anything (but we've only tried once). But after seeing one of the staff cleaning fresh fish last night for a meal today, I'm newly motivated. Catching lobster should be pretty easy and, of course, catching a conch is simple.

I didn't particularly want this photo circulating the internet, but oh well.

Our one fishing outing so far, however, wasn't for the purpose of food. We're both signed up to help one of the faculty in his fish research project. He's joined up with the Smithsonian and is collecting genetic samples for a broader, Caribbean-wide project. We went out one morning with him to test out a couple of seine nets. What we learned is that they're actually very difficult to use, especially when there's a strong current (which there happened to be). The flowing water pulled the net with such force that it made it almost impossible to walk with it. We didn't catch anything, but seagrass and some sargassum weed!

We'll be hosting a few people from the Smithsonian in October and they'll be bringing some other supplies for us, including Hawaiian Slings and a spear gun. Any sort of spearing of fish is (technically) banned in TCI, but we've gotten special approval from the DECR (Dept. of Environment and Coastal Resources) to use them for this project. This way we'll be able to target the specific fish that are needed for the project instead of pulling up ones that aren't necessary.