J.T., Chris and Francois head for a snorkel hunt

We’re back in the Big Apple.

Sadly, we left Moorea the day before the big performance by the “Tahitian Elvis” in one of the hotels. But we were happy to know that we collected a large amount of data for analysis.

For the last few days of our field expedition, we were extremely busy gathering species from more sites on the island so we could have sampling points across the entire coastline of the island. We combed the full range of manmade habitats, including sneakily snorkeling under expensive hotel bungalows that are suspended over the water. We took samples from piers, rock walls used to shelter small harbors and dock pilings used by boats.

But the manmade structures that harbored some of the highest degrees of biodiversity turned out to be tires. They were tied to docks and used as bumpers to prevent damage to boats. But to marine animals these tires provide the perfect place to call home. The tire acts as a substrate for a wide array of taxonomically diverse sessile animals (i.e. barnacles that stay attached to a surface) and on the tires of Moorea we found sponges, bryozoans, polycheates (segmented tube worms), colonial ascidians, bivalves (i.e. oysters and clams), and anemones. Why do tires provide such good habitat? Well, unlike other fixed structures, tires rise and fall with the tide and therefore are permanently available for sub-tidal species that normally live at much greater depths. From our observation these tires were heavily encrusted with various bivalve species, which provide an additional “base” habitat for other species to begin to inhabit.

Not only did we find a wide variety of sessile animals, on some of the tires we found several species of fish (damsel fish, butterfly fish and pipefish) as well as a small octopus. These were scooped up in the inside of the tire as we lifted it out of the water. We also found peanut worms, brittle stars, sea cucumbers, large flatworms, nudibranchs (sea slugs), numerous crabs, nemerteans and a pair of candy cane-patterned coral banded shrimp. All in all, each tire contained a dozen animal phyla (phyla are primarily the highest level category used for classifying animals into taxonomic groups).

But what about the invasive species? Detecting invading species can be a tricky business and this is especially the case for small marine invertebrates that might be hard to identify (and for many taxonomic groups there are only a few experts who can do the job properly). One of the motivations behind the DNA Biocode program is purely practical. Instead of having to rely on the taxonomic expertise of a few individuals scattered across the globe, we hope that the genetic data we generate will associate our collected specimens with previously collected individuals whose species membership is known. In a few weeks, the genetic data from all 390 individuals we collected should be ready for analysis and we will then finish writing up a paper describing the process behind detecting new species using this automated method, as well as reporting on what new species have been detected on the island.

Subsequently, our findings can be used to test ecological models that predict the stability of species interactions and how novel invasive species affect the structure of marine ecological communities.

For the last few days we have been snorkeling near docks, pilings and sea walls, collecting colonial animals and then processing these collections in the lab. Yesterday we collected in an area adjacent to an abandoned beachside hotel. There was an old broken dock over a sandy area, and the hotel itself gave us a nice scene out of a dystopian J.G. Ballard novel: a defunct concrete swimming pool with pate tiles broken up by tropical vegetation in full bloom and roots intermixing with the shards of broken glass. Check-in was free and nobody was around to ask us what we wanted from the poolside bar.

Later we collected at a very active marina in the town of Papetoai on the northwest coast of Moorea. This place was a treasure trove for finding creatures that like to literally hang out on tires and sea walls. We spent several hours underwater with our knives and bags in hand scraping off colonial ascidians, sponges, and bryozoans, as well as a giant oyster that we think had 20 or 30 species living on its shell (picture below; check out the scale size in the bottom right).

For every hour in the water we are spending two hours in the lab, so before lunch we headed back to the research station for an afternoon of work. Here we recorded locations, times, dates, identifier numbers. We took digital photographs of every  specimen we collected that day, followed by sub-sampling each animal for DNA extraction and sequencing. All told, we processed more than 80 different species of animals, and we suspect that several of them are non-native and not yet recorded in the Moorea DNA Biocode database. We will repeat this kind of sampling at different distances from the main port on eastern Moorea to quantify colonial animal biodiversity and their suspected conduits of invasion, ballast water from cargo boats.

Today we will head for collecting spots on the western portion of the island followed by another full afternoon of processing in the lab. We’ll get back to you in a few days, toward the end of our collecting expedition, hopefully with a full data set in hand.

Hitting the surf in search of invasive species.

The giant oyster overtaken by uninvited guests

Students Francois Desinor and Chris Ludvik collect samples from the dock of the research center on Moorea

MOOREA, Society Islands | We took the 30-minute ferry to Moorea and and were greeted by the friendly personnel from the Biocode Project field station. We settled into our bungalow, which included finding a gecko in the fridge (a real-life version of the ubiquitous Geico lizard), along with a semi-feral kitten friend who has been happy to take care of our food scraps and a multitude of roosters running around and making a racket. Then we were off to go snorkeling around some dock pilings to find … well we wouldn’t know until we looked.

Dock pilings are a likely home for invasive species because many of them are coming in from boats. On the next day and our first day of sampling, we found a number of potential invasive species, most notably a sponge that is not normally found in Polynesia (usually it’s found in the Indian Ocean and the West Pacific). We took our specimens back to the lab to be photographed, tagged for time and location and then sub-sampled for subsequent DNA analysis. It will be compared—and maybe added—to the biocode database.

Okay, so here we are in paradise snorkeling among beautiful coral habitat with multitudes of colorful marine species, but we have to be very cautious. This tropical paradise has many dangers. First on our caution radar is the deadly and sneaky stone fish, which likes to linger hidden on the sandy bottom. Bites are rare and can be avoided. Just don’t surprise them. Two scientists found that out the hard way only recently. We heard about this at the end of our first day of sampling, while hanging out with some of the other scientists at the research station, which of course entailed hearing about recent brushes with dangerous animals.

The first stone fish attack involved a researcher who was stepping out of a kayak and stepped on the stone fish. This is one way to surprise a stone fish. According to the story, they immediately applied some extract from a local plant, which prevented the onset of necrosis and decreased the pain. It was a less serious case than the second attack, which involved a researcher at the nearby French research station. This victim was sent to a hospital, given morphine and poison absorption, but his condition didn’t improve much. Finally they sent him back to France.

And since our arrival, a researcher was attacked by a grey shark. But he was all smiles when I asked him about it later on. Still, my graduate student, J.T., should be extra cautious when he nocturnally snorkels and collects tonight—in the same place and time as the shark attack. If all goes well, he should be returning with several samples to better understand this component of biodiversity.

Tahiti morning

PAPEETE, Tahiti | It is 7 am in Papeete, and the sunrise is beautiful, the smells are relaxing and for some reason I have a random Kinks song stuck in my head. Down here in the southern hemisphere, it is wintertime and the equatorial sun sets at 6 pm (all too early), with no angular lingering. After 14 hours on two planes and a six-hour time difference, my three students and I forced ourselves to stay up until 10 in order to get in synch with the local time zone. We sauntered through the grimy streets to the waterfront food carts and had ourselves some steak, frites, and tuna kabobs. Papeete is the largest city in French Polynesia—actually, it’s the only city in French Polynesia. We are really as far as you can get from all continental reach, which puts us roughly equidistant from Australia, the Americas and Antarctica.

We are here in the Society Islands to look for invasive species as part of an ongoing international project to examine the entire biological community at the DNA level, using a process known as DNA biocoding. This ecosystem-scale endeavor is manageable only on a relatively small, discrete and bounded system such as an island. The nearby island of Moorea is the project’s main site because it harbors a full range of complex tropical habitats—lowland forest, mid-elevation, mountain forest and marine coral. There are already two longstanding research stations here, providing us with an established infrastructure for our expedition. There really is no other place on the planet with all these characteristics. For more on the overall project, go to: http://mooreabiocode.org/

Though Moorea is the main event, it is here in Papeete, the central port of Polynesia, that has long served as the entry point for species coming in from all the world–carried here by the ballast water of cargo ships and various other conduits for hitchhiking species. I would not be surprised if most of the plants we see while walking around town came from other parts of the world in the last 50 years. But let us step back and note that the history of human expansion into Polynesia from Southeast Asia is one of humans and their invasive species sculpting newly colonized islands into “human ecosystems.” In fact, when looking for invasive species in Polynesia we have to partition and qualify what we mean by “natural” into “pre-human,” post-Polynesian, and … post-war.

Let us step back further and think about what’s actually meant by “natural” and unnatural manmade environments. They don’t form a dichotomy but a continuum. Modifying the natural environment so that it will yield more resources, be safer and more ascetically pleasing is as old as our species. Rather than being the “noble savage” in perfect harmony with our environment until some mythical fall from paradise, humans, in varying degrees, have always sculpted their surroundings to form human-centric ecosystems. One might appreciate the Mediterranean region’s citrus trees, olive groves, vineyards, wheat fields and nut trees as idealized natural beauty, but really none of these species are from this area. They are products of thousands of years of human interference with the natural environment and human-facilitated species invasions.

For volcanic Polynesian islands like Moorea and Tahiti, we can partition species “invasions” into a few vague categories. In the first scenario, after the volcanic island emerged from the ocean more than a million years ago, it got rained on by species from older islands—something predicted to continue until the island can accommodate no more species (a function of the island’s size). At this point the number of new species coming in is offset by a background species extinction, all of which is related to how geographically isolated the island is. This assumes, of course, that all species are equally suitable.

Another scenario is that a large burst of species settled on the island early on with later colonizations less likely because of interactions between competitive species. Although colonization and extinctions happen periodically, sometimes in bursts, a second way to introduce new species is by local in situ speciation—the formation of new species within an island. This seems to be quite common on islands, and it’s not very surprising given the isolation and the novel environments that can drive natural selection of traits that eventually result in reproductively isolated lineages and new forms (i.e. speciation).

After several waves of speciation and extinction, a third wave of species invasions occurred as humans expanded across the Pacific, bringing along their own “human ecosystem.” This bag of flora and fauna is a long list that includes pigs, fowl, crops, ceremonial plants, rats and parasites. This occurred only in the last couple of thousand years—maybe only hundreds—depending on where in Polynesia we are talking about, and in many ways falls within the normal spectrum of human environmental modification.

Finally, the forth major wave of invasions is what we are now experiencing and what we aim to characterize with modern genetic techniques. A huge genetic database has been accumulating as researchers from all over the world have come to Moorea to contribute to the DNA Biocode project. We can use this reference database as well as other global genetic databases to detect invasive species found here on the island. And that’s what we plan to do.

Tomorrow morning, we take the ferry to Moorea. I’ll talk to you from there.

Professor Hickerson with his students by Hudson river in Manhattan

With “barcodes” on every species, researchers can pioneer whole ecosystem approaches to investigating how food webs change in response to things like sea temperature changes and invasive species, as well as how these food webs were originally constructed when this volcanic island rose from the ocean.

The Moorea DNA Biocode project is a large-scale ongoing operation involving more than 100 ecologists and evolutionary biologists from many institutions, and it is hoped that the work can eventually be scaled up to much larger areas of our planet. The project is being orchestrated at the Gump Research Station run by the University of California, Berkeley, and we will be staying there for the duration of our expedition. My research team includes a CUNY graduate student, J.T. Boehm, and two Queens College undergraduates, Francois Desinor and Chris Ludvik.

Together we will be working on three different ongoing projects. First, we’ll be going all over the island to sample anthropogenic sites like docks and peers to look for invasive marine animals. Although many animals can be easily seen, there can be a multitude of very small animals and/or larvae in water or on structures that can be very difficult if not impossible to identify at the species level if one is not an expert at a wide range of taxonomic groups. However, we can use the “DNA Biocodes” to identify each marine animal and measure “exact” levels of biodiversity with respect to all the different species that are present and all of their relative abundances. Most importantly, we can use the DNA Biocodes to detect invasive species that may have otherwise gone undetected (until it was too late!). These data will be critical for investigating changing food webs dynamics in the context of ongoing drastic climate and oceanographic changes, as well as increases in the species pool due to invasions.

The second project will involve using DNA biocodes to figure out what a particular fish species eats. By collecting the DNA biocodes from materials found in the gut of a fish and comparing these with the DNA biocode database compiled from all species collected on the island, one can quickly  know all the different species a fish ate recently. The fish species we will be focusing on is the banded pipefish (corythoichthys flavofasciatus) which can be found swimming around the abundant coral reefs of Moorea.

Professor Hickerson with his student by Hudson river in Manhattan

While the Biocode project is providing the necessary data for answering such large-scale questions, the computational methods I am developing will be able to analyze data from such a large number of species while accounting for the complexity associated with species-specific differences and inherent randomness and messiness associated with using genetic data.

Talk to you in a couple of days…from the South Pacific.