A coral, a worm and some clams walk into a bar…

On May 31, 2022March 21, 2023 By Dan KillamIn Biology, clamsLeave a comment

The tree of life is often portrayed as a neatly branching structure, with each division point cleanly delineated and separated from its neighbors. The truth is that the various twigs of the tree of life often overlap and become tangled in a process we call symbiosis. I’ve talked about symbiosis before on this blog, which falls along a spectrum of wholesomeness. At one end we have mutualism, a partnership where both organisms benefit and achieve more than the sum of their parts. The other extreme is parasitism, when one organism benefits at the expense of the other. Between the two, there is a broad gray area including commensalism, when one organism’s presence doesn’t necessarily cost or benefit the other in any way. The tree of life is crowded and unpruned, and so sometimes the twigs might wrap around each other quietly and without much fuss. We live on a small planet, and have had to get used to living in uncomfortable intimacy with all sorts of creatures, such as the mites that are living on your eyelashes right now.

But things start to get really weird and tangled when the tree of life loops over on itself twice, or three times, or more. “Three-way” symbioses are surprisingly common, and the more you look for them, the more you realize that the tree of life is more of a knot than anything else.

A view of the *Heteropsammia* coral from the side

A recent paper from researchers in Bremen (Germany) and Saudi Arabia looked at such a three-way symbiosis between a coral, a worm and bivalves found off of Tanzania in East Africa. The relationship between solitary corals (Heteropsammia cochlea and Heterocyathus aequicostatus), a sipunculan worm (Aspidosiphon muelleri muelleri) and the clam Jousseaumiella, is a complex triangle of dependencies that had previously been noticed by other researchers, but never investigated at great depth. The worm lives with multiple tiny clams attached, all inside of a small solitary coral the size of a dime (1 cm long). Is the coral a willing host for this crowded boarding house, or has it been parasitized? Does the worm gain anything from the clams? The researchers sought to find out.

Part of the reason I enjoyed reading this study so much was that it had to take a narrative structure to describe the evolutionary ménage à trois of its focus. So much of modern science has moved away from anecdote to hard data, and while there is plenty of that to find in the study, it turns out that a lot of the study of symbiosis is storytelling. We need to know the setting and the characters.

In this case, the main characters are small solitary corals living in the tropical reefs of the Indo-Pacific. We denote them as solitary to distinguish them from their giant colony-forming compatriots that construct the coral reefs currently threatened by climate change and pollution. But like those giant reef-builders, these solitary corals get much of their food from sunlight through a mutualistic partnership with algae called Symbiodinium. The algae provide the host with sugars and other photosynthetic products, and the hosts give them nutrients and a safe cozy home in their tissue.

You might be thinking, “Wait! Dan just said this was a three-way partnership between a coral, a worm and some clams. So this is actually a four-way partnership between corals, worms, clams and algae?” You’d be exactly right. And I’m happy to say that the plot of this sordid story is about to thicken even further.

The side of the coral. See the little pores?

The Aspidosiphon worm is found in a spiral-shaped burrow inside of the skeleton of the coral. It is a pretty cozy home, with walls made of calcium carbonate by the coral, with breathing holes in the sides to allow the worm to breathe and release waste. The researchers wanted to know more about the structure of the burrow. Was it dug out by the worm using acid or an abrasive motion, like some clams use to dig into coral? So the researchers essentially gave the coral a CT scan to see its 3D internal structure. Inside they found growth features suggesting the coral grew around the worm, as if intentionally providing it a home.

Cross-sectional CT scans of the coral skeleton. In figure D, you can see the silhouette of the chambers of the snail shell where the worm made its first home!

Even more crazily, they found evidence that the worm had first settled inside an empty snail shell, like a hermit crab! The coral probably settled on a snail shell as a larva, and grew to engulf the whole snail shell, leaving growing space for the worm inside, with windows and all! So to review, this is now a five-way symbiosis between a dead snail, a worm that moved into its empty shell, the coral (powered by algae) that grew around it and encased the snail shell within its skeleton, and we haven’t even gotten to the clams. How many creatures are hiding stacked in this trench coat? Please bear with me as I explain!

An SEM image of Jousseaumiella. These are less than 1 mm long! Pinhead sized!

What are the clams doing in this picture? Jousseaumiella is part of a family of clams called Galeommatidae, which we previously mentioned on this blog in the context of some bivalves found growing in the gills of unfortunate sand crabs. Many members of the Galeommatidae family are parasitic or commensal with other marine organisms. In this case, Jousseaumiella are tiny flat-bodied clams less than 1 mm long, found attached to the body of the worm, squeezed inside the burrow in the coral’s skeleton. It feeds on the worm’s waste and potentially food particles coming through the pores in the sides of the burrow. Not the most dignified existence, but a more mobile home means more opportunities to eat a varied diet similar to that that the worm and coral are seeking out, and the clam also gets protection from predation tucked inside the coral. It is unclear if it benefits the worm directly to have clams attached to it.

A time lapse of the coral+worm moving from the paper’s supplement! It would be handy to navigate to greener pastures, if it became too muddy in a certain place!

It is, however, clear how living inside a coral would be a pretty good deal for the worm, which gets a stable, protective suit of carbonate armor to protect it from predators, and grows to fit it as it gets larger. They are normally found inside of rocks, shells and other hard inanimate objects, but having a living home is a cool upgrade. What is the coral getting out of the deal? The researchers note that the corals are often found in the crevices between other large reef-building corals, in areas of the reef that receive high supplies of nutrients and turbidity (dirt that blocks out light). These sorts of environments aren’t necessarily friendly places for a coral to be, since they reduce the light and therefore the food that the coral can receive from photosynthesis. These crevices also have a lot of variability in other conditions like temperature and water flow. But because the coral has hitched a ride on the back of a worm, it can actually move in the sediment to react to changing conditions and avoid being buried by piles of sediment floating by! The worm can also act as a sort of anchor preventing the worm from sinking in the sediment underneath, which would be a big hazard for the small, stubby coral on its own. The coral seems to go to great pains to make its partner comfortable, not growing its skeleton to cover the pore windows to the outside. The researchers note that as coral reefs worldwide are subject to increasing human-made pollution and climate change, it would be interesting to research whether this complex three-(five?) way symbiosis provides the various participants with an advantage compared to other corals.

So like any good story, this symbiosis features complex, growing characters, a dynamic setting, and still plenty of mystery demanding a sequel! To that end, there are lots of other great three-way symbioses to investigate. Snails which farm fungus that parasitizes plants. Bryozoans living on snail shells that have a hermit crab inside. Gobies serving as lookouts at the entrances of burrows built by shrimp, with a crab freeloader along for good measure. Algae and bacteria teaming up to attack mussels. The list keeps going! I could see this becoming quite a franchise!

Research Explainer: How I learned to stop worrying and trust the clams

On September 3, 2021 By Dan KillamIn clams, scicomm2 Comments

Two giant clams off the coast of Israel. Left: *Tridacna maxima*, the small giant clam. Right: *Tridacna squamosina*

Another year, another new paper is out, another clamsplainer to write! The fourth chapter from my PhD thesis was just published in Proceedings of the Royal Society B. This study represents five years of work, so it feels great to finally have it leave the nest. In this study, we investigated the comparative growth of fossil and modern giant clams in the Gulf of Aqaba, Northern Red Sea. Back in 2016 during my PhD, I knew I wanted to study giant clams because they are unique “hypercalcifying” bivalves that grow to huge sizes with the help of symbiotic algae living in their bodies. The clams are essentially solar-powered, and use the same type of algae that reef-building corals depend on! Unlike corals, which are the subject of a ton of research related to how they are threatened by climate change, habitat destruction and pollution, comparatively little is known of how giant clams will fare in the face of these environmental changes. Are they more resistant than corals, or more vulnerable?

T. squamosa on the reef off the coast of Eilat.

I had strong reason to suspect that the clams are struggling in the face of human changes to the environment. They can bleach like corals do when exposed to warm water, and have been observed to be harmed when waters are less clear since they are so reliant on bright sunlight to make their food. But I need a way to prove whether that was the case for the Red Sea. I needed to travel to a place where fossil and modern giant clams could be found side by side, so their growth could be compared using sclerochronology. We would count growth lines in their shells to figure out how fast the grandaddy clams grew before humans were around, and compare that ancient baseline to the growth rate of the clams in the present. Giant clams make growth lines every day in their shells, giving us the page numbers in their diary so we can figure out exactly how fast they grew! We can also measure the chemistry of their shells to figure out the temperatures they experienced from the oxygen isotopes, and even what they were eating from the nitrogen isotopes.

A map of the Gulf of Aqaba, where our study took place. My talented marine scientist partner Dana Shultz made this map!

It just so happened that UCSC’s Dr. Adina Paytan was leading an NSF-funded expedition to the Red Sea in summer 2016, which represented a perfect place to do this work. There are many age dated fossil reefs uplifted onto land around the Gulf of Aqaba on the coasts of Israel and Jordan, and there are three species of giant clam living in the Red Sea today: Tridacna maxima (the small giant clam), Tridacna squamosa (the fluted giant clam), and Tridacna squamosina. Tridacna squamosina is particularly special because it is only found in the Red Sea, making it an endemic species. It is extremely rare in the modern day, with likely only dozens of individuals left, making it potentially endangered.

So I set off with Adina and two other students to live for two months in in the blazing hot desert resort town of Eilat, Israel, working at the famous Interuniversity Institute. Getting a permit from the Israeli National Parks Authority, I collected dozens of empty giant clam shells (no clams were harmed in the course of this study!) from the surf zone and from ancient reefs ranging from a few thousand years to almost 180,000 years old. I also spent a week over the border in Aqaba, Jordan where I worked with Dr. Tariq Al-Najjar, my coauthor and director of the University of Jordan Marine Science Station. Tariq is a specialist in algal productivity in the Gulf and was an excellent resource in trying to understand how water quality has changed in the area through time. He pointed out that over the years, the Gulf of Aqaba has had an increased nutrient supply far above what it received in historic times. For nearly 20 years the Gulf was subjected to excess nutrients from Israeli fish farms, which caused tremendous damage to the reefs of the area with their releases of fish waste. The farms were finally forced to close after a long lobbying campaign from Israeli and Jordanian scientists and environmentalists. But even after the farm pollution stopped, there was still increased nutrient supply from runoff and even carried into the Red Sea by dust in the form of nitrate aerosols. These aerosols are produced when our cars and power plants release nitrogen oxide gases, which react in the atmosphere to form nitrate and fall during periodic dust storms that hit the Red Sea a few times per year.

All of these sources of nitrogen are fertilizer for plankton, causing what scientists call “eutrophication.” When plankton blooms, it literally causes the water to be less transparent, which could reduce the clams’ ability to gather light and lead to them growing more slowly. At least that was my hypothesis, but I had to prove if it was true or not. So during that summer and over the next few months, I cut dozens of clam shells into cross-sections, used a special blue dye called Mutvei solution to make their growth lines visible, and took pictures of those lines with a microscope. Then I counted those lines to figure out how many micrometers the clam was growing per day.

A picture showing some of the fine daily lines visible in a blue-stained shell

Here I hit my first challenge: it turned out some clams were putting down one line per day as expected, but some were putting down twice as many! But the way I was using to discern between the two was to measure the oxygen isotopes of the clams’ shells, which forms a record of temperature. By counting how many lines appear between each annual peak of temperature, we confirmed some were daily and some were twice daily. But the oxygen isotope approach is expensive would not be scalable across the dozens of shells I had collected.

Annual growth lines in the shell of a *Tridacna maxima* clam

Then I remembered that I could measure the lines in the inner part of the clams’ shells, which are formed annually. By counting those lines and then measuring the length of the clam, I could get an approximate measure of how much it grew per year on average. This would allow me to calibrate my band-counting and discern which records represented daily lines and which were twice daily! What a relief.

So I went through all of the shells, counting lines and gathering growth info for as many shells as I could muster. It meant many hours staring at a microscope, taking pictures and stitching the pictures together, then squinting at my computer screen highlighting and measuring the distance between each growth line. I had hoped to come up with an automated way to measure it, but the lines turned out to be faint and difficult for the computer to distinguish in a numerical way. So instead I just powered through manually. When I had the raw growth data, I then transformed them to a pair of growth constants commonly used in the fisheries literature to compare growth across populations. When I put the data together across all 55 shells, I was surprised to discover that my hypothesis was totally incorrect. The clams were growing faster!

Growth constants for all three species, comparing fossils and modern shells. We used two growth constants (phi prime and k) to help control for the fact that our clams were at different sizes from each other. You wouldn’t compare the growth rate of babies and teenagers and try to make any broader assumptions of their relative nutrition without some additional attempts to normalize the data!

Science rarely goes according to plan. The natural world is too complex for us to follow our hunches in understanding it, which is the main reason the scientific method came about! But at a human level, it can still be shocking to realize your data says you were totally wrong. So after a few days sitting and ruminating on these results and what they meant, I remembered what Tariq and other scientists had said about nitrates. The clams are essentially part plant. They use photosynthetic symbionts to gain most of their energy. And much as nitrate pollution can fertilize plankton algae growth, maybe it could do the same for the algae within the clams! It had previously been observed that captive giant clams grew faster when “fertilized” with nitrates or ammonia. But such an effect had never before been observed in the wild. We needed a way to demonstrate whether the Red Sea clams were experiencing this.

Fortunately, the clams also keep a chemical record of what they’re eating within the organic content of their shells. Shells are a biological mineral, made of crystals of a mineral called calcium carbonate. But within and between those crystals, there’s a network of proteins the clam uses like a scaffold to build its shell. Those proteins are made of amino acids that contain nitrogen. That nitrogen comes in different “flavors” called isotopes that can tell us a lot about what an animal eats and how it lives. The ratio of heavier nitrogen-13 and lighter nitrogen-12 increases as you go up the food chain. Plants and other autotrophs have the lowest nitrogen isotope values because they use nitrate directly from the environment. For every level of the animal food chain, nitrogen isotope values increase. Herbivores are lower than carnivores. If you live on only steak, your nitrogen isotope values will be higher than a vegetarian. The same will be true for clams. If the clams were taking in more nitrogen from sources like sewage or fish farms, they would show higher nitrogen isotope values in the modern day.

We found that nitrogen isotope values were lower in the modern day!

Taking bits of powder from several dozen of the shells, we worked with technician Colin Carney at the UCSC Stable Isotope Lab to measure the nitrogen isotopes of the shell material. A machine called an Elemental Analyzer literally burns the shell material to release it in a gas form. A carbon dioxide scrubber absorbs the CO2 and carbon monoxide gas, leaving only the nitrogen gas behind. That gas is measured by a mass spectrometer, which essentially separates out the different isotopes of nitrogen and tells us what fraction is nitrogen-13 or nitrogen-12. Plotting all the shell data together, I discovered that my hypothesis was…totally wrong. The nitrogen isotope values of the modern shells were lower than the fossils. The clams had moved down in the food chain, but how?

https://www.israelscienceinfo.com/wp-content/uploads/2017/09/timna-park.jpg — A dust storm rolling over the Israeli Negev Desert. Source

After ruling out a bunch of other explanations including the preservation of the shells, we propose that this represents a human-related change in the environment that the clams are recording. As I mentioned before, the Red Sea these days is regularly hit by huge dust storms which are conduits for nitrate aerosols. Our cars emit nitrogen-containing gases which, through a complex web of chemical reactions in the atmosphere, end up in the form of nitrate particles called aerosols. These nitrate aerosols bind to the dust delivered by strong windstorms called haboobs, which carry the dust long distances, with some of it being deposited several times of year. This deposition of nitrate has been found to form up to a third of the nitrate supply hitting the Red Sea, and was a source of nitrogen that wasn’t available to the clams in historic times. These nitrate aerosols are extremely low in nitrogen isotope value, and would be very likely to explain the lower nitrogen isotope value in our clams! If the clams ate the nitrate, their symbionts would grow more quickly, providing them with more sugars through photosynthesis and accelerating clam growth!

Some additional factors probably also have influenced giant clam growth in the region. The Red Sea historically had regular monsoon rains which likely slowed growth in fossil clams, as storms are known to do for giant clams in other areas, but such monsoons no longer reach the area. The Red Sea also had much higher seasonal range of temperatures in the past, with colder winters and warmer summers. Both factors (storms and extremes of temperature) have been previously shown to depress giant clam growth, and so the modern Red Sea may be a goldilocks environment for the clams: a consistent year-round not too cold or hot temperature.

However, as we discuss in the paper, these factors don’t necessarily mean that the clams are healthier. Faster giant clam growth has been found in other research to lead to more disordered microstructure in their shells, which would have uncertain effects on their survival against predators like fish, lobsters and humans. Additionally, a higher nutrient supply to reefs often causes the corals that build the reefs to lose out to competition from algae that block sunlight and crowd out coral colonies. If the reefs are harmed by the climatic changes that have potentially helped the clams, the clams will still lose. Giant clams are adapted to live only where coral reefs are found, and nowhere else. So more research will be needed in the Red Sea to determine if the health of clams and corals is hurt or harmed by these nitrate aerosols, and what that will mean for their long-term survival in the area.

Over the course of working on this research, the giant clams taught me a lot about life. They taught me that my hypotheses are often wrong, but that’s alright, because my hypotheses can still be wrong in a way that is interesting. I learned to go with the flow and trust the clams to tell me their story through the diaries they keep in their shells. I have followed their lessons wherever they led. Now I am doing follow-up work growing giant clams in a giant coral reef tank at Biosphere 2 in Arizona, to directly observe how the clams’ symbiosis develops and create new forms of chemical records of their symbiosis! The work described in my paper here has led to a suite of different ongoing projects. The clams have many more lessons to teach me. Thank you clams!

Research Explainer: The chemistry across a “forest” of giant clams

On July 19, 2020July 20, 2020 By Dan KillamIn clams1 Comment

Another one of my PhD chapters is published in the journal G-cubed, resulting from work I did in the summer of 2016 in Israel and Jordan around the Red Sea. This is my first geochemistry article in a journal, so it is a big deal to me! I thought I’d write up a clamsplainer about what I was looking for and how we went about achieving the paper.

A slice of giant clam shell. You can see the difference between the inner and outer layers. The inner layer has visible annual growth lines.

I study the chemistry of giant clam shells. You might already be familiar with the concept of tree rings, a field called dendrochronology. It’s like reading the diary of a tree, where every “ring” is a page in the record of its life. The related field of sclerochronology looks at rings in the hard parts of shelled organisms. We can count those rings to figure out the ages of clams, or their health, and we can measure the chemistry of those rings to understand the temperature the clam grew at, and even what it ate.

A giant clam growing on the reef flat in Eilat

Giant clams are bivalves of unusually large size which achieve a very rapid growth rate through the help of symbiotic algae in their flesh. The clams are farmers, and their crop is inside their tissue! They grow their shells very quickly (sometimes up to 5 cm a year, equivalent to if a six foot tall man grew a foot every year from birth), and live a very long time, up to 100 years (their growth slows later in life). A whole bunch of talented researchers have measured the chemistry of giant clams all around the world to reconstruct past climate and even measure historic storms!

If we want to understand the ecology of a forest, we can’t measure just one tree!

But if you come back to the analogy of tree rings, we essentially have measured the rings and chemistry of individual “trees” in a bunch of different places, but don’t have as good an idea of how the chemistry varies within a “forest” of giant clams in a particular place. In our new study, we set out to describe exactly that, focusing on the Northern Red Sea.

A map of the Northern Red Sea. The right “toe” is the Gulf of Aqaba

Sites where we sampled shells along the northernmost tip of the Gulf of Aqaba

The Gulf of Aqaba represents the northernmost toe of the Red Sea, bordered by Egypt, Israel, Jordan and Saudi Arabia. It hosts some of the northernmost coral reefs in the world, aided by tropical temperatures and clear waters due to the lack of rainfall in the surrounding deserts. Here, we can find three species of giant clams including the small giant clam Tridacna maxima, the fluted giant clam T. squamosa and the very rare T. squamosina, which is found only in the Red Sea and nowhere else (as far as we know). In summer 2016, I went all around the Gulf of Aqaba collecting shells of clams from the beaches, fossil deposits, and even were able to work with shells confiscated from smugglers at the Israel-Egypt border. We cut these shells into slices and used tiny drill bits to sample powder from the cross section of their shells, which we could then conduct geochemistry with! We sampled large areas in bulk from the inner and outer portions of the shell (more on why later) using a Dremel tool, and also sampled more finely in sequential rows with a tiny dental drill bit (same brand your dentist uses!) to see how the measured temperatures varied through seasons. By “we”, I mean my coauthor and friend Ryan Thomas, who spent every Friday morning for several weeks milling out most of the powder we needed for this study. This data became part of his senior thesis at UCSC!

Two giant clams thriving on the shallow reef near Eilat, Israel

What kind of chemistry did we measure? The shells of clams are made of calcium carbonate, the same stuff Tums is made of. Calcium carbonate contains one calcium atom, one carbon atom, and three oxygen atoms. It turns out that all of those atoms come in “flavors” that we call isotopes, relating to the weight of those atoms. When you take the shell powder and put it into a machine called a mass spectrometer, you can figure out the proportions of isotopes of different elements present in the samples

The first isotope “flavors” we were interested were carbon-12 and carbon-13. The ratio of the two is thought to relate back mostly to the action of the algae inside (its symbionts) and outside the clam’s body (the floating algae the clam filters out of the water as an additional meal). This happens because as algae take carbon from the environment and bind it into sugars through photosynthesis, they naturally weight the dice in favor of carbon-12 making it into the sugars. So carbon-13 is left out in the water, and potentially in the clam’s shell. When photosynthesis is more active, it would leave the shell with proportionally more carbon-13. At least that’s what other researchers have confirmed happens in corals, and suspect happens in clams. In the world of isotope chemistry, this phenomenon is called “fractionation,” when a process causes isotopes to form fractions separated by mass. We wanted to test if that was true for giant clams, and could do so by comparing T. squamosina and T. maxima, which have more active photosynthesis, to the less photosynthetic T. squamosa.

Comparing carbon isotopes across different species and shell layers. The results are fairly flat all the way across.

It turns out that the more symbiotic species don’t have more carbon-13 in their shells. We set out several reasons that might be the case, including that the symbionts of these clams are actually more carbon-limited than many researchers might expect. Essentially, the algae lack an excess of carbon atoms to choose from, so they can’t be picky with which isotopes they use to make sugars. Therefore, the fractionation effect weakens and becomes possibly too subtle to manifest in the shell, even in the best-case scenario of three closely related species living the same area. This represents what I’d term a “null result.” We had a hypothesis and we demonstrated that hypothesis was not the case in our data. It was important to publish this result, because other researchers will know not to try the same thing. This means that when we try to search for evidence of symbiotic algae in fossil clams, we will likely need to use other types of chemistry to figure it out. But don’t worry, as finding such a “smoking gun” for algal symbiosis in fossil bivalves is part of my life’s work! I have a few projects in the works looking for exactly that kind of evidence! 😉

A look at how temperatures measured via oxygen isotopes vary through the lives of the animals. This is how scientists can use very old shells to figure out how temperatures varied through a year in prehistoric times!

But we had additional data we collected in addition to the carbon isotopes which actually turned out to provide some interesting results. This other type of measurement regarded the oxygen isotope ratio of the shells. Previous research has shown that the ratio of oxygen-18 to oxygen-16 in carbonate skeletons directly relates to temperature, a principle that has birthed a field known as paleothermometry. There are thousands of papers which use shells of corals, clams, cephalopods, microbes and more to reconstruct temperatures in ancient times. Giant clams have proven to be effective weather stations going all the way back to the Miocene epoch, millions of years ago! Because they grow so quickly (putting down a new layer every day), live for a long time, and don’t stop growing, they form very complete, high-resolution, and long records of past climate.

But no past studies had ever compared different species of giant clams from the same place. There would be interesting new lessons to draw from such a comparison, including seeing if one species preferred to grow at warmer parts of the reef. As complex, three dimensional structures, there are many remarkably different micro-environments throughout a reef, from the hot, sun-exposed reef flat and crest to the cooler, current-swept, deeper fore-reef. Do any of the species of giant clams show a consistently higher temperature than the others, and what would that mean if they did?

*T. squamosina* records higher temperatures than the other species. Outer shell layers also record higher temperatures than inner shell layers. More on that later in the post 😀

It turns out that the rare T. squamosina, only found in the Red Sea, does record a higher average temperature, almost 3 degrees C higher than the other two species. This is of interest because this species had been proposed by prior researchers to only live on the sun-drenched reef crest, at the shallowest part of the reef. We believe these results corroborate that observation. The previous research on the habitat of T. squamosina was limited to a single study which only was able to find 13 live animals along the coast of the Red Sea. But by independently confirming this life habit, we can ask further questions that may be borne out by further research.

An example of *T. squamosina* showing signs of possible bleaching (light parts at the center of its body).

Being restricted to the shallowest waters, is T. squamosina at greater risk of harvesting by humans along the shores of the region than its counterparts? Illegal poaching of giant clams along the Red Sea is believed to be a major stressor on their population size in the area. Could this explain why T. squamosina is so rare today, despite being proposed to have been more common in the past? In addition, being restricted to the top few feet of depth in the water could leave the species more vulnerable than the others to atmospheric warming. As with corals, when giant clams overheat they will “bleach”, expelling their symbiotic algae as a stress response. While the clams can recover, it is sometimes a fatal form of stress that leads to their death.

An excellent cartoon of the different shell layers in giant clams. From a peer of mine who also studies them, Michelle Gannon!

More research is needed to answer those questions. But the last aspect of this study relates to what is happening inside of the bodies and shells of the clams themselves. Giant clam shells have two layers. The outer layer grows forward away from the hinge, increasing clam’s length. The clam also makes an internal layer, growing inward to thicken the shell and add weight. We can read the growth lines of the clam’s diary within either layer, and different studies have used one or the other to make records of climate change. But very few studies have compared the two layers of the same individual. Do they record the same temperatures? Figuring it out would be important to determine how studies with just the inner layer or outer layer can be compared to each other across time and space.

A vividly blue example of the small giant clam, *T. maxima*. From user arthur_chapman on iNaturalist

In our studied clams, it turns out that the outer layer records warmer temperatures on average than the inner one! After ruling out other possible explanations behind this difference (the details are complicated and hard for even shell nerds to wrap our heads around), we settled on the idea that the outside of the clam is indeed warmer on average than the inside! This means that the outer layer, recording temperatures of the outer mantle, is indeed forming at a higher temperature than inside! Why is this?

Unlike us, clams are ectothermic. They generally stay the same temperature as their surrounding environment and don’t use their metabolism to generate internal heat. But that doesn’t mean that the clam doesn’t have hotter and cooler spots in its body. It makes sense that it would be hotter at the outer part of its body, facing the sun, as the solar rays hitting its outer mantle would then radiate out again as heat. The outer mantle is also darker in color than the inner mantle, allowing it to absorb more solar energy, much as you might feel hotter wearing a darker t-shirt in the sun than a white one. Photosynthesis itself produces a warming effect, a phenomenon known as non-photochemical quenching, and so the outer mantle, which contains the vast majority of the symbiotic algae, may be partially warmed by the activity of the symbionts!

More research is needed to confirm if this is true. As of yet, no researcher has ever stuck a temperature probe in multiple parts of a clam to see if the outside of it is indeed warmer than the inside. But until that day, it is interesting to think of how this would influence comparisons of diaries from the inner and outer layers of different bivalves. The effect is on the small side, so it doesn’t really mean one layer or the other should be preferred for future shell-based studies of climate change. But it could be an additional aspect to consider in the future as a way to record temperature differences within the body of an animal, and look into how those differences influence its overall level of stress.

Examples of juvenile smooth giant clams, *T. derasa*, that we’re growing at Biosphere 2. Photo by Katie Morgan.

So I hope this long explanation of my paper helps you to have a better idea of the work I did during my PhD thesis. There were other aspects to the paper that are too wonkish to get into here, particularly concerning the correlation we found between carbon and oxygen isotope ratios, but if you have questions or want a copy of the PDF, please message me! I have more clam papers in the pipeline, and my new postdoc at Biosphere 2 involves growing three species of giant clams in a controlled environment, where I hope to answer some of the physiological questions I mentioned above! But until then, stay hinged and happy as a clam (as much is possible in this chaotic time), and take comfort knowing there are colorful bivalves out there all at this very moment, harvesting sunlight for food and growing huge shells.

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

On July 4, 2020July 5, 2020 By Dan KillamIn Biology, clamsLeave a comment

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.

Weird Clam Profile: Hammer Oysters

On July 1, 2018July 2, 2018 By Dan KillamIn Biology, clams1 Comment

naturalis_biodiversity_center_-_zma-moll-1264_-_malleus_malleus_28linnaeus2c_175829_-_malleidae_-_mollusc_shell — *Malleus malleus* from Indonesia. Source: Wikipedia

Oyster. Reading that word, you probably formed an image in your mind of a rough-shelled creature with a shiny mother-of-pearl (nacreous) inside that someone pulled out of some silt in an estuary. And yes, that’s what most oysters look like. Some oysters are of additional economic value through their creation of pearls. These pearl oysters have long, straight hinge lines and live in the tropics in and around coral reefs.

4880314958_03e3a2b85c_o — A pearl oyster. See the straight hinge? Source: Pearl Paradise on Flickr

The hammer oysters are another sort of oyster, not of the Ostreidae family that includes most of the bivalves we think of as oysters, but still closely related and in its own family, the Malleidae. Malleus is the latin word for hammer, and the most distinctive genus of hammer oysters indeed look just like a hammer sitting on the seafloor.

73494_orig — In a typical life position in a seagrass bed. Notice all the algae, anemones and other encrusting creatures freeloading off the hammer oyster’s hard work. Source: Ria Tan on EOL

What the…that thing’s alive? How does that even work? This is an oyster? That’s how I imagine the first scientist to discover the hammer oyster reacting. Because they are weird and rather incomprehensible-looking. But when you know the way they live, it makes more sense.

maleus_albus — There is a small area of nacre (mother of pearl) in the area near the rear of the interior. Source: Archerd Shell Collection

The hammerhead part of the oyster is just a super elongated hinge. The creature has a long, straight hinge like other oysters, but it has evolved to instead have a relatively narrow set of valves attached to that ridiculously overbuilt hinge. Like other oysters, they secrete byssal threads from their backside to attach themselves to the bottom. The narrow valves commonly poke up out of sandy bottoms in tropical waters nearby coral reefs. They do particularly well in seagrass beds, and often live in large colonies similar to other oysters.

hammer-oyster-with-natural-attachment-seashell — Shell collectors seek out hammer oyster shells which have other bivalves attached. Here is a thorny oyster living on top of *Malleus*. Two for one! Source

The absurd hinge helps these creatures to stay anchored into the sediment, but also serves as “wings” that help it avoid sinking into the sediment over time. One thing us humans don’t realize sitting on sand is that it actually acts like a liquid. Over time, if we sat on wet sand, we would likely begin to sink in unless we spread out our arms and legs to increase our surface area. In the ocean, all sand is quicksand. Different organisms have different strategies to avoid being engulfed by the sediment they live on, and the hammer oyster has had good success with its strategy. It doesn’t care that you think it looks weird. It just sits there, filtering water for passing food particles and plankton. It’s very good at it, has been perfecting the strategy for over 250 million years, and doesn’t need your smartass remarks, thank you very much.

original — Another shot of a happy hammer oyster doing what it does best, in a seagrass bed near Singapore. Source: Wild Singapore on iNaturalist

The boring giant clam is anything but.

On June 21, 2018June 24, 2018 By Dan KillamIn Biology, Chemistry, clams3 Comments

crocea2 — *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.

bivalve_pholas_dactylus_common_piddock_24-08-10_shells_1 — Piddocks in next to holes that they made in solid rock. Source: Aphotomarine

medium — 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.

dscn0083 — 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.

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.

Weird Clam Profile: The Heart Cockles

On June 13, 2018June 13, 2018 By Dan KillamIn Biology, clams2 Comments

corculum_cardissa_002 — Corculum cardissa (from Wikipedia)

The heart cockle (Corculum cardissa) is so named because of its heart shaped shell. It is native to warm equatorial waters of the Indo-Pacific. While many bivalves sit with the their ventral valve facing down, the heart cockle sits on its side, with one side of both valves facing downward. The valves have adapted to resemble wings and are flat on the bottom, providing surface area that allows the bivalve to “raft” on the surface of soft sandy sediment and not sink. They may also sit embedded in little heart-shaped holes on the tops of corals.

corculum-cardissa-heart-cockle-solomon-islands-1 — Two heart cockles embedded in the top of a *Porites* coral. Source: Reefbuilders

Heart cockles are a member of a small club of bivalves which partner with symbiotic algae for nutrition created by photosynthesis. Most of the modern photosymbiotic bivalves are in the family Cardiidae, the cockles. The giant clams (Tridacninae) are also in this family and have a similar partnership with the same genus of Symbiodinium algae. This algae is also found in many species of coral.

So when you find a live heart cockle, it is often green in color, because of the presence of this algae near the surface of its tissue. Its shell has adapted to be “windowed” (semi-transparent) to allow in light for the algae to harness to make sugars. The algae are housed in networks of tubes within the soft tissue of the cockle. They trade sugars with their host in exchange for nitrogen and carbon from the clam.

As I’ve mentioned before regarding the giant clams, this is a very productive partnership and has evolved separately several times in the history of bivalves. However, we don’t know why almost all examples of modern bivalve photosymbiosis occur in the cockles. Why aren’t the heart cockles giant like the giant clams? What features are necessary to allow this symbiosis to develop? These are the kind of questions I hope to help answer in my next few years of work.