Biosphere 2 Update!

A view from my parking spot at work

I am now several months into my postdoctoral fellowship at Biosphere 2 in Oracle, Arizona! I am working with Professor Diane Thompson on a project measuring the shell and body chemistry of giant clams in Biosphere 2’s huge reef tank. Our goal is to find better proxies (indirect ways of measuring) the symbiosis of these clams with the algae they farm within their bodies. The controlled, closely monitored conditions of the Biosphere 2 ocean tank represent the perfect balance between the real ocean and the more controlled environment of a lab. Using trace metals and isotopes in their shells and tissue, we can trace back the ways that clams record their own internal biology. Wild giant clams make chemical records via the growth lines in their shells, similar to tree rings. These have been the subject of many cool past studies, but there are aspects of the “language” they use to write their shell “diaries” that are poorly understood. Much like researchers used the Rosetta Stone to decode heiroglyphics, we are observing clams as they grow in order to better translate the shell diaries of their prehistoric ancestors. Doing so, we can better understand how their ancestors reacted during past periods of climate change, and identify similar bivalves in the fossil record which may have harbored symbionts.

A view of the ocean tank at Biosphere 2

I started my postdoc remotely in May. The following months were spent sheltering at home in Southern California with my mom, supervising the installation of a cohort of giant clams into the 700,000 gallon ocean tank over Zoom. It felt like a science fiction movie, watching technicians Katie Morgan and Franklin Lane from hundreds of miles away on my computer screen as they nurtured and installed the little clams in their new home. I felt like Mission Control back on earth, watching a group of space colonists work with strange alien creatures.

Some of the T. derasas in the Biosphere tank

But in August I was able to finally move to Tucson to meet these clams in person! We had three species in the first batch: Tridacna derasa, T. squamosa and T. maxima. Of the three, T. derasa (the smooth giant clam) has proven to be the most successful in the Biosphere 2 ocean tank. All of the derasa clams from May have survived and thrived, attaching themselves to the bottom with byssal threads and growing their shells, both very positive signs of clam health!

Some of our newer batch of T. derasa in the quarantine tank

So we have doubled down on T. derasa and installed 11 more individuals last week, sourced from Palauan clam farms via a reef supply company in Florida called ORA. They are currently in a shallow quarantine tank where we will monitor them for disease and unwanted hitchhikers before introducing them to the broader Biosphere tank.

The workers at Biosphere 2 are very creative problem solvers. Giant clams need intense amounts of light to sustain their symbiotic algae and create food for themselves, a quantity of light higher than is available in the current Biosphere tank. To provide a light supplement, the engineering team at Biosphere 2 constructed a floating lighting rig with hanging LED lighting, right over the lagoon where we have the clams!

The lighting rig glows with a blue light as the sun goes down outside the Biosphere

To make sure the clams have enough light, we installed a Li-Cor light sensor to measure the exact amount of photons (light particles) hitting the clams over the course of a day. The light is measured in units of micromoles of photons per meters squared per second. A mole is 6.02 * 1023 particles, and other clam experts like James Fatheree have suggested that the clams need light levels of at least 200 micromoles/m2s to make enough food for themselves. That’s 120,400,000,000,000,000,000,000 light particles we need to hit every square meter of their habitat every second. The clam channels as many of those photons as it can to its algae residing within tubes in its tissue. The symbionts use it in photosynthesis to make sugars, which they share with their host. A well lit giant clam is a happy, well-fed giant clam! But because the glass dome of Biosphere eats up some of the light, and plankton and floating particles in the seawater eat up another portion, we use the lights to make sure the clams have the boost they need to maintain their symbiosis like they would in the clear, shallow waters of a tropical coral reef.

The Li-Cor sensor floats above the clams, telling us how much light they’re getting

Much like a new dad might read parenting books to get ideas for baby care, I am always poring through the literature trying to figure out how to maximize the growth of these clams. Dr. Fatheree is kind of like Dr. Lipschitz from Rugrats, except unlike the suspect childcare advice in the show, this real-life giant clam advice is very valuable. Like human babies, these clams can be a challenge! The clams sometimes decide to move around and get themselves into trouble, requiring us to rescue them if they get trapped behind a rock or under a pile of sand. So I have had to do a fair amount of clam-herding during my time here.

We are growing the clams for science, and there will be data to collect. We will be monitoring data like the trace metal chemistry of the clams’ tissue and shells, the color of their mantles, and the pH, temperature and oxygen levels of their environment, all to relate together to make the best clam record of their environment possible. So far, I have been snorkeling in the tank every couple days maintaining their setup. Next week, I will dive in the Biosphere tank for the first time to collect data on their shell chemistry! I have other projects in the works to measure their valves opening and closing using magnetic sensors, and to measure their color changes through time through computational photography.

That brings me to what I’ve found to be the coolest part about Biosphere 2: the people. Something about this place attracts creative, brilliant, can-do people who solve problems on the fly and are always jumping into the next project. It has been a privilege to learn and pick up technical skills from them in the brief time I’ve been here. This place is really like a space colony out of The Expanse or Silent Running. There are endless valves, pipes, tanks, exchangers and other hardware needed to keep Biosphere 2 running. Getting to witness the technical competence behind the whimsical solutions the staff comes up with, like the floating light rig, has been the most exciting part of this job for me. Everyone has a deeply ingrained curiosity and passion for science that is inspiring to see; they are as interested in my clams as I am in their corals, tropical plants, and geochemical experiments. I would argue that the human team behind Biosphere 2 is a bigger treasure than the unique metal-and-glass structure they work under, and I look forward to seeing the results all of the collaborations we have in the works!

The Mystery of the Giant Clams of the Red Sea and Indian Ocean

I have always been fascinated by scientific discoveries that are hanging right in front of our noses. Cryptic species are one such surprise. Sometimes, researchers using genetic sequencing are surprised to discover that a group of animals that all look the same from the outside are actually reproductively isolated from each other; separate twigs on the tree of life. This surprise has happened over and over in the history of natural science.

It turns out such puzzles are frequent among the giant clams. These unusual bivalves are specialists in coral reef environments, growing to large size with the help of symbiotic algae that create sugars through photosynthesis. Within the genus Tridacna there are ~10 accepted species which vary in size, shape, color and mode of life.

Tridacna squamosina (right) sitting next to the small giant clam T. maxima (left) on the Israeli Red Sea coast

I specialize in the three species known (so far) from the Red Sea, including the small giant clam Tridacna maxima and the fluted giant clam T. squamosa, which are both found worldwide, all the way from the Red Sea to down past the equator along the Great Barrier Reef. The third local species, T. squamosina is more unusual, so far being only known from the Red Sea (an endemic species). T. squamosina is an example of a cryptic species, having previously been assumed to be a local variant of T. squamosa. It looks pretty similar, with long scutes (flap-like appendages) protruding from its shell, thought to help stabilize it on the flat bottom of loose coral rubble. But unlike T. squamosa, T. squamosina lives exclusively at the top of the reef in the shallowest waters closest to the sun. It has a very angular, zig-zag pattern in its plications (the wavy shapes at the edge of the shell) and a characteristic pair of green stripes where the soft tissue meets the edges of the shell. The soft tissue is covered with warty protuberances.

Pictures of details of T. squamosina from Richter et al. 2008

It was only first described in detail in the early 2000s, when an international team of researchers figured out using genetic sequencing that it was a distinct species and named it T. costata. They noted that in their surveys all around the shores of the Red Sea, they only found 13 live specimens, making it an extremely rare and possibly endangered species. Fossil specimens on local reefs appeared to be much more common, suggesting it had a much larger population in the past. Then in 2011, another team at the Natural History Museum in Vienna discovered a shell of one had been forgotten in its collection for over 100 years. Rudolf Sturany, the researcher on the 1895 research cruise who had originally collected the clam, had called it T. squamosina.

The T. squamosina shell in the collection of the Museum of Natural History in Vienna (from Huber and Eschner, 2011)

In taxonomy (the science of naming and classifying organisms), the first team to name the species wins, so the name T. costata was synonymized (retired) in favor of the earlier name T. squamosina, which became the name of record. It must be annoying to spend so much time working to name a species and then discover you had been scooped over a century before! But such is science.

A mystery clam thought to be T. squamosina, later identified as T. elongatissima found off of Mozambique by iNaturalist user bewambay

The strange part was that there were some murmurs over the last few years that T. squamosina was not only found in the Red Sea, but also had been seen along the coast of Africa as far south as Kenya, Mozambique and Madagascar. Divers and snorkelers had taken pictures of a giant clam that did indeed look strangely like T. squamosina, with a zigzag shell opening and green stripes at the edge of its tissue. But some aspects of these individuals seemed off. In the Red Sea, T. squamosina lives freely, not embedded in the coral as these pictures showed, and the geometry of the angles of the shell seemed a bit different. It also would be difficult for T. squamosina to be connected in population from the Red Sea all the way South to Mozambique, as there are natural barriers which would prevent its planktonic larvae from riding currents to intermix between the two regions. When populations are separated by a barrier, the flow of genes between them is cut off and evolution begins to separate the populations from each other until they are separate species, a process called allopatric speciation.

A large specimen of T. elongatissima observed by iNaturalist user dawngoebbels off of Kenya

I figured that someday, researchers would collect tissue samples from these mystery clams to settle whether they were actually T. squamosina or something else. And this year, a team did just that, traveling along the coast of Mozambique, Madagascar, Kenya and other places, collecting samples of tissue to compare how all the different clams they saw were related in a family tree. They genetically sequenced these “clamples” and in the process, found that the mystery clams were a new cryptic species, which they called T. elongatissima!

Shells of T. elongatissima from the Fauvelot et al. 2020 paper
For comparison, a shell of T. squamosina collected off of Sinai, Egypt. You can see why they’re easy to mix up!

T. elongatissima closely resembles T. squamosina, and they are sister species on the bivalve family tree. It’s hard to tell them apart without training. Even a professional would probably mix some of them up if they were all placed sitting next to each other. The major differences appear to relate to shell shape, with T. elongatissima having a less symmetrical shell than T. squamosina, and a bigger opening at the rear hinge for a foot to poke through. The symmetrical shell and closing of the foot opening may represent changes that T. squamosina took on to adapt to be able to sit freely on the bottom, rather than embedding in the coral like T. elongatissima seems to prefer. If you’ve read this far, you may be thinking “Who cares? A clam’s a clam and these look practically the same. Aren’t you just splitting clams at this point?” At the end of the day, a species is a man-made concept; an organizing tool for use by us humans. Species are the characters in our reconstruction of the history of the world. What can we learn about the world by having identified this species T. elongatissima?

A giant clam family tree! Notice T. squamosina and T. elongatissima right next to each other.

The researchers behind the new paper discuss that based on statistical analyses of the genetic differences between the species, the most recent common ancestor for T. elongatissima and T. squamosina probably lived more than 1.4 million years ago! Some researchers have previously suggested that T. squamosina probably began its development as a separate species due to geographic isolation by low sea level, caused by repeated glaciations. With so much water trapped as ice on land during this period, the narrow Strait of Bab al Mandab, currently the gateway to the Red Sea, became a land barrier as sea level fell (kind of like opposite of the Bering Sea land bridge that formed allowing humans to migrate to the Americas). Ancestral clams trapped on the Northern end of this barrier were proposed to have evolved to become the rare T. squamosina.

This has occurred with a variety of species that became Red Sea endemics (meaning they are unique species that evolved in the Red Sea and are found nowhere else), including a unique crown of thorns starfish. The issue is that during this time of low sea level, the Red Sea went through periods where it was a rather unfriendly place for clams to live. All sorts of creatures went extinct in the period when the sea was repeatedly cut off, because the water became extremely salty, along with other unfriendly changes. So it’s unlikely T. squamosina would be present for us to see today if it only lived in the Red Sea throughout the entire length of time.

A map from Fauvelot et al. 2020 showing the distributions of different giant clams the researchers identified along the coasts of Africa and the Red Sea. Notice the bright red dots representing T. squamosina, only found in the Red Sea, while green dots represent T. elongatissima. Notice how the currents (arrows) seem to meet and then go offshore from Kenya. More on that in the next paragraph.

The researchers of this new paper propose that T. squamosina was more likely to have initially branched off due to the barrier of the Horn of Africa. The seas off of Kenya and Somalia harbor a meeting of southward and northward currents which then group and head offshore, away from the reefs that giant clam larvae are trying to get to. So any tiny floating planktonic clam larvae would experience a strong “headwind” preventing them from crossing that point. It would also mean that during times that the Red Sea was not a happy place to be a clam, T. squamosina may have found refuge on the coasts of places like Eritrea, Oman and possibly even as far as Pakistan. During times when sea levels rose and Red Sea conditions became friendlier, it recolonized the area.

As far as we know, the Red Sea is the only place T. squamosina is now found, but it may well be present elsewhere like Yemen or Oman. If T. squamosina was found in other regions, it would be tremendously important for its conservation. Right now, the species is thought to be extremely rare, with a very small native range. If it inhabited a broader area, that would mean more reservoirs of genetic diversity. This would reduce the odds that it will go extinct as reefs are put under stress from climate change, pollution and overharvesting. To survive as a species, it helps to not put all your eggs in one basket. If you’re only found in one small place, it increases the chances that a disaster (like climate change) will wipe you out.

The only way we will know for sure is to visit reefs in understudied places like Yemen, Oman, Pakistan, Eritrea and Somalia, to understand the richness of the giant clams present. These areas are understudied for various reasons: lack of research funding for non-Western researchers, lack of interest from the scientific community too focused on familiar places, and geopolitical situations that make it difficult to conduct research. But I hope someday to collaborate with people in these countries to better understand the giant clams present in such understudied regions of the globe. It is virtually certain that there are more species of giant clams, both alive and as fossils, waiting to be discovered.

A Make-Up Presentation!

Hi colleagues! Several weeks ago, I was supposed to present a talk at GSA’s annual meeting in Phoenix at the session “Advances in Ocean and Climate Reconstructions from Environmental Proxies”, but I shattered my wrist in a scooter accident the night before and was in emergency surgery during my talk time. So instead I’ve uploaded my talk with voice-over to Youtube! The whole video is about 15 minutes. You can view it above. Feel free to comment on this post or email me if you have questions!

This work is currently in the last stretch of drafting before submission, but I also discuss some ongoing research and am always open if you have your own ideas for collaborations!

Correction: we are working with geophysicists to understand the shell transport mechanism.

These are the references mentioned at the end:

Crnčević, Marija, Melita Peharda, Daria Ezgeta-Balić, and Marijana Pećarević. “Reproductive cycle of Glycymeris nummaria (Linnaeus, 1758)(Mollusca: Bivalvia) from Mali Ston Bay, Adriatic Sea, Croatia.” Scientia Marina 77, no. 2 (2013): 293.

Glycymeris nummaria (Linnaeus, 1758).” 2019. World Register of Marine Species. 2019.

Grossman, Ethan L., and Teh-Lung Ku. 1986. “Oxygen and Carbon Isotope Fractionation in Biogenic Aragonite: Temperature Effects.” Chemical Geology: Isotope Geoscience Section 59: 59–74.

Gutierrez-Mas, J. M. 2011. “Glycymeris Shell Accumulations as Indicators of Recent Sea-Level Changes and High-Energy Events in Cadiz Bay (SW Spain).” Estuarine, Coastal and Shelf Science 92 (4): 546–54.

Jones, Douglas S., and Irvy R. Quitmyer. 1996. “Marking Time with Bivalve Shells: Oxygen Isotopes and Season of Annual Increment Formation.” PALAIOS 11 (4): 340–46.

Mienis, Henk, R. Zaslow, and D.E. Mayer. 2006. “Glycymeris in the Levant Sea. 1. Finds of Recent Glycymeris insubrica in the South East Corner of the Mediterranean.” Triton 13 (March): 5–9.

Najdek, Mirjana, Daria Ezgeta-Balić, Maria Blažina, Marija Crnčević, and Melita Peharda. 2016. “Potential Food Sources of Glycymeris nummaria (Mollusca: Bivalvia) during the Annual Cycle Indicated by Fatty Acid Analysis.” Scientia Marina 80 (1): 123–29.

Peharda, Melita, Marija Crnčević, Ivana Bušelić, Chris A. Richardson, and Daria Ezgeta-Balić. 2012. “Growth and Longevity of Glycymeris nummaria (Linnaeus, 1758) from the Eastern Adriatic, Croatia.” Journal of Shellfish Research 31 (4): 947–51.

Reinhardt, Eduard G, Beverly N Goodman, Joe I Boyce, Gloria Lopez, Peter van Hengstum, W Jack Rink, Yossi Mart, and Avner Raban. 2006. “The Tsunami of 13 December AD 115 and the Destruction of Herod the Great’s Harbor at Caesarea Maritima, Israel.” Geology 34 (12): 1061–64.

Royer, Clémence, Julien Thébault, Laurent Chauvaud, and Frédéric Olivier. 2013. “Structural Analysis and Paleoenvironmental Potential of Dog Cockle Shells (Glycymeris glycymeris) in Brittany, Northwest France.” Palaeogeography, Palaeoclimatology, Palaeoecology 373: 123–32.

Sivan, D., M. Potasman, A. Almogi-Labin, D. E. Bar-Yosef Mayer, E. Spanier, and E. Boaretto. 2006. “The Glycymeris Query along the Coast and Shallow Shelf of Israel, Southeast Mediterranean.” Palaeogeography, Palaeoclimatology, Palaeoecology 233 (1): 134–48.

How does a scallop swim?

Scallops spooked by divers’ lights and fleeing en masse to filter somewhere else

The ocean is a place of constant dynamic movement. Fish use their fins to push water away from themselves, and because every action has an equal and opposite reaction, they therefore move forward. Some cephalopods use jet propulsion, constricting their mantle cavity to push water out through siphons, allowing them to jet forward like a deflating balloon. And other life forms sail the seas on constantly moving currents , indirectly harnessing the power of the sun and earth.

Bivalves are a fairly sedentary bunch by comparison. While most bivalves have a planktonic larval form, when they settle they are constrained to a fairly small area within which they can burrow or scramble around with their muscular feet.


But some bivalves have evolved to move at a quicker rate. The most famous swimming bivalves are the scallops, which have evolved to use jet propulsion, similar to their very distantly related cephalopod relatives. But unlike the cephalopods, scallops evolved to use their hinged shells to aid this process!

Notice the expelled water disturbing the sediment below the scallop as it “claps” its way forward!

Many filter-feeding bivalves use their shell valves as a biological bellows to pull in water for the purposes of sucking in food, or even to aid in digging, but scallops have developed another use for this activity, to enable propulsion. Scallops draw in water by opening their valves to create a vacuum which draws in water to their sealed mantle cavity. They then rapidly close their valves using their strong adductor muscles to pull them together, which pushes the water back through vents in the rear hinge area, propelling the scallop forward.

Don’t panic if a scallop swims toward you. They can see, but not super well. This one is just confused.

Using this strategy, scallops can evade predators and distribute themselves to new feeding sites. It’s a surprisingly effective swimming technique, with the queen scallop able to move 37 cm/second, or over five body lengths per second! Michael Phelps would have to swim at nearly 35 km/h to match that relative speed (his actual highest speed is around 1/3 of that). I’m sure sustaining that speed would be tiring for Mr. Phelps, though, and it’s the same for scallops, only using their swimming for short-distance swims.

(video from Supplemental Materials of Robertson et al. 2019)

A recent paper from a team in Switzerland just came out describing an effort to engineer a robot which imitates the scallop’s elegant and simple swimming method. The resulting totally adorable “RoboScallop” closely imitates the design of a scallop, using a pair of hinged valves with rear openings to allow the movement of water backward. The internal cavity is sealed by a rubber membrane draped across the front so that all water is forced through these rear vents when the Roboscallop snaps shut.

Diagram from the Roboscallop paper (from Robertson et al. 2019)

As seen in the diagram above, the rhythm and relative velocity of opening vs closing is important to make sure the RoboScallop actually moves forward. If the scallop opened as quickly as it closed, it would just rock back in forth. It instead opens slowly so that it does not draw itself backward at the same rate that it can push itself forward. The researchers had to do quite a bit of calibration to get these rates right (equating to about 1.4 “claps” per second), but once they did, they ended up with a RoboScallop that can generate about the same force of forward movement (1 Newton) as a real scallop (1.15 Newtons), and similar rates of speed.

This paper really fascinated me because it is merely the latest in a long line of successful engineering projects imitating the ingenuity of evolution. Other marine robots have been made which emulate the locomotion of fish, manta rays, sea snakes and other forms of swimming. And now we have a clam! Let me know when I can buy one to play with in my pool.

The clams that sail the seas on rafts of kelp


The streamlined shells of Gaimardia trapesina. Source: New Zealand Mollusca
Bivalves are not known as champion migrators. While scallops can swim and many types of bivalves can burrow, most bivalves are primarily sessile (non-moving on the ocean bottom). So for many bivalves, the primary method they use to colonize new territories is to release planktotrophic (“plankton-eating”) larvae, which can be carried to new places by currents and feed on other plankton surrounding them. Many bivalves have broad distributions because of their ability to hitchhike on ocean currents when they are microscopic. They don’t even pack a lunch, instead eating whatever other plankton is around them. But once they settle to grow, they are typically fixed in place.

Not all bivalves have a planktotrophic larval stage, though. Larvae of lecithotrophic bivalve species (“yolk-eaters”) have yolk-filled eggs which provide them with a package of nutrition to help them along to adulthood. Others are brooders, meaning that rather than releasing eggs and sperm into the water column to fertilize externally, they instead internally develop the embryos of their young to release to the local area when they are more fully developed. This strategy has some benefits. Brooders invest more energy into the success of their offspring and therefore may exhibit a higher survival rate than other bivalves that release their young as plankton to be carried by the sea-winds. This is analogous to the benefits that K-strategist vertebrate animals like elephants have compared to r-strategist mice: each baby is more work, and more risky, but is more likely to survive to carry your genes to the next generation.

Brooding is particularly useful at high latitudes, where the supply of phytoplankton that is the staple food of most planktrophic bivalve larvae is seasonal and may limit their ability to survive in large numbers. But most of these brooding bivalves stay comparatively local compared to their planktonic brethren. Their gene flow is lower on average as a result, with greater diversity in genetic makeup between populations of different regions. And generally, their species ranges are more constricted as a result of their limited ability to distribute themselves.

A bunch of G. trapesina attached to kelp. Notice the hitchhiking clams have in turn had hitchhiking barnacles attach to them. Freeloaders on freeloaders! Source: Eleonora Puccinelli

But some brooding bivalves have developed a tool to have it all: they nurture their young and colonize new territories by sailing the seas using kelp rafts. The clam Gaimardia trapesina has evolved to attach itself to giant kelp using long, stringy, elastic byssal threads and a sticky foot which helps it hold on for dear life. The kelp floats with the help of gas-filled pneumatocysts, and grows in the surge zone where it often is ripped apart or dislodged by the waves to be carried away by the tides and currents. This means that if the clam can persist through that wave-tossed interval to make it into the current, it can be carried far away. Though they are brooders, they are distributed across a broad circumpolar swathe of the Southern Ocean through the help of their their rafting ability. They nurture their embryos on specialized filaments in their bodies and release them to coat the surfaces of their small floating kelp worlds. The Southern Ocean is continuously swirling around the pole due to the dominance of the Antarctic Circumpolar Current, which serves as a constant conveyor belt transporting G. trapesina across the southern seas. So while G. trapesina live packed in on small rafts, they can travel to faraway coastlines using this skill.

The broad circumpolar distribution of G. trapesina. Source: Sealifebase

The biology of G. trapesina was described in greater detail in a recent paper from a team of South African researchers led by Dr. Eleonora Puccinelli, who found that the clams have evolved to not bite the hands (kelp blades?) that feed them. Tests of the isotopic composition of the clams’ tissue shows that most of their diet is made up of detritus (loose suspended particles of organic matter) rather than kelp. If the clams ate the kelp, they would be destroying their rafts, but they are gifted with a continuous supply of new food floating by as they sail from coast to coast across the Antarctic and South American shores. But they can’t be picky when they’re floating in the open sea, and instead eat whatever decaying matter they encounter.

Falkland Islands stamp featuring G. trapesina. Source.

The clams are small, around 1 cm in size, to reduce drag and allow for greater populations to share the same limited space of kelp. Their long, thin byssal threads regrow quickly if they are torn, which is a useful skill when their home is constantly being torn by waves and scavengers. Unlike other bivalves, their shells are thin and fragile and they do not really “clam up” their shells when handled. They prioritize most of their energy into reproduction and staying stuck to their rafts, and surrender to the predators that may eat them. There are many species that rely on G. trapesina as a food source at sea, particularly traveling seabirds, which descend to pick them off of kelp floating far from land. In that way, these sailing clams serve as an important piece of the food chain in the southernmost seas of our planet, providing an energy source for birds during their migrations to and from the shores of the Southern continents.


The boring giant clam is anything but.

Tridacna crocea, bored into a coral head on a reef in Palau

There are many types of giant clam. Not all of them are giant; the boring giant clam, Tridacna crocea, only grows to 10 cm long or so. The boring giant clam is not so named because it’s dull; its main skill is its ability to bore into the coral of its coral reef home and live with its entire shell and body embedded in the living coral. They sit there with their colorful mantle edge exposed from a thin opening in the coral, harvesting energy from sunlight like the other giant clams. When disturbed by the shadow of a human or other such predator, they retract their mantle and close their shell, encased by an additional wall of coral skeleton. It’s a clever defensive strategy, and they are some of the most numerous giant clams in many reefs in the Eastern and Southern Equatorial Pacific.

But it’s always been a mystery of how they bore away at the coral so efficiently, and how they continue to enlarge their home as they grow their shell. There are other bivalves that are efficient borers, including the pholad clams (“piddocks”) which use sharp teeth on their hinge to carve their way into solid rock, and the shipworms, which have abandoned their protective shell and instead use their two valves as teeth to burrow into wood. Both of these methods of boring are pretty straightforward.


Piddocks in next to holes that they made in solid rock. Source: Aphotomarine


Shipworm embedded in wood. Source: Michigan Science Art via Animal Diversity Web

But the boring giant clam has no such adaptation. It does not have large teeth on its hinge to carve at the coral. Such abrasion of the coral would also not explain how they widen the opening of their cubby-holes to allow their shell to grow wider. This mystery has long confounded giant clam researchers. I myself have wondered about it, and was surprised to find there was no good answer in the literature about it. But now, a team of scientists may have cracked the problem once and for all.

At the back of T. crocea‘s shell at the hinge, there is a large “byssal opening” with a fleshy foot which they can extend out of the opening to attach themselves to surfaces. Giant clams that don’t embed in coral (“epifaunal,” resting on the surface of the coral rather than “infaunal,” buried in the coral) lack this opening. The researchers suspected that the foot was the drilling instrument the clam used to create its home.


Byssal opening of T. crocea with the foot retracted. Source: NickB on Southwest Florida Marine Aquarium Society

How could a soft fleshy foot drill into the solid calcium carbonate (CaCO3) skeleton of corals? I can confirm from experience that my own foot makes for a very ineffective drilling instrument in such a setting. But T. crocea has a secret weapon: the power of acid-base chemistry. CaCO3 can be dissolved by acids. You may well have taken advantage of this chemistry to settle your acid stomach by taking a Tums, which is made of CaCO3 and reacts with the excessive hydrochloric acid in your stomach, leaving your tummy with a more neutral pH. pH is a scale used to measure acidity, with low numbers indicating very acidic solutions like lemon juice, and high pH indicating a basic solution like bleach.

Scientists are well aware of the hazards corals face from decreasing pH (increasing acidity) in the oceans. All the CO2 we are emitting, in addition to being a greenhouse gas, dissolves in the ocean as carbonic acid and gets to work reacting and dissolving away the skeletons of corals and any other “calcifying” organisms that make shells. It makes it harder for corals to form their skeletons and is already worsening die-offs of corals in some areas. The researchers suspected that the clams use this phenomena to their advantage at a small scale, lowering the pH with their foot somehow to dissolve away the coral to make their borehole.

Using a wedge to keep open a Tridacna shell in my Red Sea work. We took a small blood sample with permission of local authorities. This caused no lasting effects to the clams.

But they needed to prove it, and that was a challenge. Giant clams can be unwilling research participants. I myself have observed this in trying to take samples of their body fluid for my own research. When they sense the presence of a predator, they immediately clam up in their protective shell. I used a small wedge to keep their shells open to allow me to take a sample of their body fluid, but the researchers working on T. crocea needed to convince the clam to place its foot on a piece of pH-sensitive foil, keep it there and do whatever acid-secreting magic allows it to burrow into coral. They would then be able to measure whether it indeed is making the water around its foot more acidic, and by how much.

Diagram from Hill et al., 2018 showing their experimental design.

In what I can only assume was an extended process of trial and error and negotiation with a somewhat unwilling research subject, the researchers found exactly the right angle needed to convince the clam that it was safe enough to try making a coral home. But it was not in coral, instead sitting in an aquarium, on top of a special type of foil that changes color when exposed to changing pH, like a piece of high-tech litmus paper. The researchers discovered that their suspicions were correct: the clams do make the area around their feet significantly more acidic than the surrounding seawater, as much as two to four pH units lower. Where seawater is around a pH of around 8, the clams were regularly reducing pH to as low as 6 (about the level of milk) and sometimes as low as 4.6 (about the pH of acid rain). Small differences in pH can make a big difference in the power of an acid because each pH unit corresponds to 10x more protons (hydrogen ions, H+) in the water. The protons are the agent that dissolves CaCO3. Each proton can take out one molecule of coral skeleton. The clams are dissolving away coral skeleton to make holes with only their feet!

Footage of the pH- sensitive foil, with darker areas corresponding to lower pH. The areas of low pH (high acidity) correspond exactly to the “footprint” of the clam!

But what in T. crocea‘s foot allows them to make acid? I know that my foot does not do this, though that would be a very entertaining and obscure superpower. The researchers found the enzymes called vacuolar-type H+-ATPase (VHA) present in great quantities in the outermost cells of the clam’s feet. These enzymes are found throughout the tree of life and are proton pumps that can quickly reduce pH through active effort. Other prior researchers like the influential Sir Maurice Yonge, a legendary British marine biologist who worked extensively with giant clams, had suspected that the clams had used acid but had never been able to detect a change in pH in the seawater around the clams’ feet through more conventional methods. It was only because of new technologies like the pH paper that this research team was able to finally solve this issue. And now, I suspect other groups will want to re-investigate the importance of VHA in their study organisms. Many branches of the tree of life may be utilizing acid-base chemistry to their advantage in ways we never had previously imagined.

Oh, the seasons they grow! [research blog]

My latest clamuscript is published in Palaios, coauthored with my advisor Matthew Clapham! It’s the first chapter of my PhD thesis, and it’s titled “Identifying the Ticks of Bivalve Shell Clocks: Seasonal Growth in Relation to Temperature and Food Supply.” I thought I’d write a quick post describing why I tackled this project, what I did, what I found out, and what I think it means! Raw unformatted PDF of it here on my publication page.

Why I did this project:

I study the growth bands of bivalve (“clam”) shells. Bivalves create light and dark shell growth bands as they grow their shells, much like the rings of a tree. The light bands form during happy times for the clam, when it is growing quickly and putting down lots of carbonate. The dark bands appear during times of cessation, when the bivalve ceases growth during a hibernation-like period. This can happen in the cold months, or the hot months, or both, or neither, depending on the clam and where it lives. It turns out that there are a lot of potential explanations for why these annual cessations of growth happen. Different researchers have suggested through the years that temperature (high or low) is the biggest control on the seasons that bivalves grow, but others have suggested that food supply is more important. Others say it’s mostly a function of the season they reproduce, when they’re putting most of their energy into making sperm/eggs and not growing their bodies. I wanted to try to see if I could find trends across all of bivalves which would shed light on which factors are important in determining their season of growth.

Annual growth lines in the shell of a giant clam. The transparent spots are the times that it was growing more slowly and not happy. Was this because of temperatures? Or was it getting less to eat? I wanted to know.

What I did:

I read a ton of papers in the historical literature about bivalves. These were written by people in many fields: aquaculture, marine ecology, paleoclimate researchers (using the clams shells as a chemical record of temperature), and more. All of the papers were united by describing the seasons that the bivalves grew, and the seasons that they stopped growing. I ended up with nearly 300 observations of marine (saltwater) bivalve growth for dozens of species from all around the world. I had papers as old as the earliest 1910s, and some as new as last year.

A map of all the places the observation of bivalve growth came from. Blue means they shut down in the winter, while red means they do not.

We have mussels, oysters, scallops, clams, cockles, geoducks, giant clams, razor clams, quahogs, and more in the database. Bivalves that burrow. Bivalves that sit on the surface of the sediment. Bivalves that stick onto rocks. Bivalves that can swim. With each, I noted data that the researchers recorded. If they grew during a season, I coded it as a 1. If they didn’t, I coded it as a 0. So a bivalve growing in summer but not winter would be recorded as 1,0. I also recorded environmental data including temperature of the location in winter and summer in the location, as well as seasonal supply of chlorophyll (a measure of phytoplankton, which is the main source of food for most clams). It turned out that not enough of the studies recorded temperature or chlorophyll for their sites, so I wanted to back these up with an additional data source. I downloaded satellite-based temperature and chlorophyll data for each location, as well as additional studies which directly measured chlorophyll at each site. I wanted lots of redundant environmental data to ensure that any trend or lack of trend I observed in my analysis was not due to a weakness of the data.

I then compared the occurrence of shutdown by season with these environmental variables using a statistical technique called regression. Regression basically involves trying to relate a predictor variable (in this case, latitude, temperature and chlorophyll during a certain season) to the response variable (did the clam grow in that season or not?). We wanted to see which environmental variable relates most closely to whether or not the clam grows or not. Because our dependent variable was binary (0 or 1), we used a technique called logistic regression, which tries to model the “log odds” of an event occurring in response to the predictor variable. That log odds can then be back-calculated to probability of the event occurring.

What we found:


In a clamshell, we found that latitude (distance from the equator) is a very good predictor of whether or not a bivalve shuts down for the winter. As you’d expect, bivalves in the far north and far south of our planet are more likely to take a winter nap. However, bivalves at the equator mostly grow year round and are not likely to take a summer nap. In relation to temperature, the lower the winter temperature, the more likely the bivalve is to stop shell growth. High summer temperature is not as good a predictor for the occurrence of a summer shutdown, but the majority of summer shutdowns seem to occur at the low temperate latitudes, where the difference between the annual range of temperature is largest. Unlike at the equator, where bivalves likely can adapt to the hottest temperatures and be happy clams, they have to adapt to a huge range of temperatures in places like the American Gulf and Atlantic coasts, the Adriatic and Gulf of California. And if they are restricted at the northward end of their range, they may have no choice but to shut down in summer as there is nowhere cooler to migrate to.

GIF of the satellite data showing white as hotspots of phytoplankton ability. Notice that the food is more available in summer months for each hemisphere. We were trying to see if this relates back to when the bivalves grow in every place we had data for.

Food supply, on the other hand, is not a good predictor of when bivalves shut down. When we went into this project, we expected food to be a powerful control on seasonal growth because it is intuitive and well understood that the better fed a bivalve is, the larger it will grow overall. But the seasonal low amount of chlorophyll (and therefore the amount of photosynthesizing plankton) in the bivalves’ areas had no relationship to whether or not the bivalve shut down in a certain season. To double check that this wasn’t a weakness in my satellite data, I downloaded additional direct observations from the same places as many bivalve studies in the dataset, but I still couldn’t find the relationship. We propose that the seasonal supply of phytoplankton is not well related to seasonal growth of bivalves because: 1) phytoplankton supply isn’t very seasonal in nature in most of the sites we studied. There are peaks in multiple seasons rather than a clean up and down wave shape like temperature. 2) Bivalves are pretty flexible in what they eat. They also eat other types of plankton and suspended particles that are even less seasonal. It may be pretty difficult to find bivalves that are seasonally starving. One of the most probable places to find such starvation shutdowns might be the poles, where seasonal ranges of temperature are quite small but plankton does really have a seasonal pattern of availability. More research will be needed to describe the nature of polar bivalves and why they shut down growth.

What’s next?
This is the first chapter of my PhD. I have two more chapters I’m working on, both related to the geochemistry of bivalve shells. I am writing those manuscripts this summer and looking for postdoctoral fellowships in the fall related to geochemistry of marine organisms in the fossil record. I hope to pursue more projects looking at the season of growth in bivalves, switching to understanding the role that changing seasonal cycles in their environment and biology play in their evolution. Do bivalves that live closer together tend to reproduce at different times? Can we track season of reproduction in relation to temperature and food supply? There are a lot more clam stories to be told and I look forward to sharing them all with you. Until the next research blog,



The Snails that Farm

File:Marsh periwinkle 001.jpg
Littoraria grazing on Spartina marsh grass. (source)

Us humans really like to talk up our skills at farming. And while it’s true that we have domesticated animals and plants to a degree not seen in other life forms, the act of nurturing and harvesting food is actually not really that special, and is broadly observed throughout the animal kingdom. Perhaps the most iconic invertebrate farmers are insects. Leaf-cutter ants, termites, and some beetles have been observed to actively cultivate fungus by gathering plant material to feed it, growing the fungus, protecting the fungus from competition, and then harvesting the fungus to feed themselves and their young. Ants are also known to keep livestock in the form of aphids, which they lovingly protect and cultivate for the sweet nectar they excrete. Such practices are called “high-level food production” because, like human farmers with their seeds and fertilizer, insects have evolved a highly complex symbiosis with their fungus. The fungus has shaped their behavior as much as the ants cultivate the fungus.
The marsh periwinkle Littoraria irrorata (source)

Less well understood is the “low-level food production” that may occur more broadly throughout the tree of life. There is less direct evidence of such behavior because it is more indirect and less specialized than high-level food production, but it may be equally advantageous for the cultivator and the cultivated. One study published in 2003 uncovered a simple but powerful relationship between marsh periwinkles of the genus Littoraria and fungus which they cultivate and harvest.
Close-up of a snail’s radula (source)

Marsh periwinkles are small and not particularly charismatic creatures. Like many snails, they are grazers with a shell, a fleshy foot and a rough, abrasive organ called a radula which they use like sandpaper to graze on pretty much whatever they can get into. Snails are not known as picky eaters. But researcher Brian Silliman of Brown University and Steven Newell of University of Georgia noticed that these innocuous snails regularly undertake the risky, low reward activity of grazing above the water on the blades of swamp grass, stripping off the surfaces of the blades of grass. The researchers were confused why the snails would expose themselves to predation and the harmful open air for such a low-nutrition food.


A typical snail farm, complete with liberally applied fertilizer. Yum.

They discovered that the snails were investing in the future. By stripping away the protective surface of the swamp grass blades and liberally fertilizing the surface of the grass with their droppings, the periwinkles are ensuring that the swamp grass will be infected with an active and very prolific fungal infection. The fungus, unlike the plant it lives on, is of high nutritional value. The researchers demonstrated the active partnership between the snails and fungus by conducting caged experiments where they showed that snails which grazed on grass but not the resulting fungus did not grow as large as snails which were allowed to return and chow down on the fungus. The fungus loves this deal as well. They grow much more vigorously on grass that is “radulated” (rubbed with the snail’s sandpapery radula) than uninjured grass. The fungus grows even faster if the snails are allowed to deposit their poop next to the wounds. The researchers found that this same relationship applies at 16 salt marshes along 2,000 km of the Eastern Seaboard.

The periwinkles don’t really know what they’re doing. They aren’t actively planting fungus and watching proudly like a human farmer as their crop matures. But over millions of years, the snails have been hard-wired to practice this behavior because it works. Snails that abrade a leaf of swamp grass, poop on the wound and come back later to eat the yummy fungus do a lot better than snails which just stick to the safe way of life below the surface of the water. The fungus loves this relationship too. The only loser is the swamp grass, which the researchers unsurprisingly found grows much more slowly when infected with fungus. But marsh grass is the largest source of biomass in swamp environments, and the snails that partner with fungus are able to more efficiently use this plentiful but low-nutrient food source, to the extent that it is now the dominant way of eating for swamp periwinkles on the East Coast of the US, and probably in a lot more places too. The researchers noted that there are likely far more examples of low-level food production that we simply haven’t noticed.

Since this work was published, other teams have discovered that some damselfish like to farm algae, fiddler crabs encourage the growth of mangrove trees, and even fungus get in on the action of farming bacteria. We love to talk up our “sophisticated” high-level food production techniques, but such relationships probably got started at a similarly low level. Our activities as hunter-gatherers encouraged the growth of certain organisms, we stumbled upon them, ate them, kept doing what we were doing and eventually our behavior developed into something more complex. Next time you see a snail munching its way up a blade of grass, consider to yourself whether it knows exactly what it’s doing. Come back later to see the fruits of its labor.

What is Conservation Paleobiology?

In undergrad, I felt like my school and internship were training me to be two different types of researcher. At USC, I was majoring in Environmental Studies with an emphasis in Biology. It was essentially two majors in one, with a year of biology, a year of chemistry, a year of organic chem, a year of physics, molecular biology, biochemistry, etc. On top of that, I took courses on international environmental policy and went to Belize to study Mayan environmental history. Meanwhile, I was working at Jet Propulsion Laboratory in Pasadena researching trends in historical rainfall data. I loved both sides of my studies, but felt like neither was exactly hitting the spot of what I would want to spend my career researching. I love marine biology but am not particularly interested in working constantly in the lab, looking for expression of heat shock protein related genes or pouring stuff from one tube into another. On the other hand, I was fascinated by the process of untangling the complex history of rainfall in California, but I yearned to relate this environmental history to the reaction of ecological communities, which was outside the scope of the project.

During my gap year post-USC, I thought long and hard about how I could reconcile these disparate interests. I read a lot, and researched a bunch of competing specialized sub-fields. I realized that paleobiology fit the bill for my interests extremely well. Paleobiologists are considered earth scientists because they take a macro view of the earth as a system through both time and space. They have to understand environmental history to be able to explain the occurrences of organisms over geologic time. I really liked the idea of being able to place modern-day changes in their geologic context. What changes are humans making that are truly unprecedented in the history of life on earth?

But it doesn’t have to be all zoomed out to million-year processes. A growing sub-field known as Conservation Paleobiology (CPB) is focused on quantifying and providing context of how communities operated before humans were around and before the agricultural and industrial revolutions, in order to understand the feasibility of restoration for these communities in this Anthropocene world. Sometimes, this means creating a baseline of environmental health: how did oysters grow and build their reefs before they were harvested and human pollution altered the chemistry of their habitats? I’m personally researching whether giant clams grow faster in the past , or are they reacting in unexpected ways to human pollution? It appears that at least in the Gulf of Aqaba, they may be growing faster in the present day. Such difficult and counterintuitive answers are common in this field.

Sometimes, CPB requires thinking beyond the idea of baselines entirely. We are realizing that ecosystems sometimes have no “delicate balance” as described by some in the environmental community. While ecosystems can be fragile and vulnerable to human influence, their “natural” state is one of change. The question is whether human influence paves over that prior ecological variability and leads to a state change in the normal succession of ecosystems, particularly if those natural ecosystems provide services that are important to human well-being. In a way, the application of paleobiology to conservation requires a system of values. It always sounds great to call for restoring an ecosystem to its prior state before humans. But if that restoration would require even more human intervention than the environmental harms which caused the original damage, is it worth it? These are the kinds of tricky questions I think are necessary to ask, and which conservation paleobiology is uniquely suited to answer.

At the Annual Geological Society of America meeting in Seattle this year, the Paleo Society held the first-ever Conservation Paleobiology session. The room was standing room only the whole time, investigating fossil and modern ecosystems from many possible angles. This field is brand new, and the principles behind it are still being set down, which is very exciting. It’s great to be involved with a field that is fresh, interdisciplinary, and growing rapidly. I look forward to sharing what my research and others find in the future.