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

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?
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!

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,



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.

The Many Homes of Hermit Crabs

My boy Harry, a purple pincher (Coenobita clypeatus) inhabiting a tapestry turban snail (Turbo petholatus) shell. These seem to be his favorite kind, even though they do not come from his native Caribbean.

Hermit crabs (superfamily Paguroidea) are most famous for using snail shells as their home, having evolved a soft, spiral abdomen to be able to use them for protection. But they are more flexible about their choice of abode than you might expect.

This crab was likely preserved buried alive in sediment. Note how it uses its claw as a protective trap door sealing the opening of the ammonite shell. Source: Jagt et al, 2006

Different groups of shelled organisms have risen and fallen in abundance through geological time. During the time of the dinosaurs, ammonites (relatives of modern squid and octopus) were among the most common marine organisms, and hermit crabs were there to recycle their shells when they died.

Each tiny pore (zooid) in this bryozoan contained a tiny tentacled organism. Together they grew in a shape that made for a nice hermit crab house (image 5 shows a cross section where the crab’s abdomen would fit). Source: Taylor and Schindler 2004

Mollusks aren’t the only contractors for hermit crabs. Some hermits utilize the skeletons of colonial organisms like bryozoans as a home. Bryozoans are filter-feeding colonial animals made up of thousands of tiny tentacled organisms living in the pores of a shared skeleton. The extinct bryozoan Hippoporidra lived in symbiotic partnership with hermit crabs, growing around a gastropod shell to attract a hermit crab partner. This was an example of mutualism: by providing a home for a crab, the bryozoan would be transported to new environments with plentiful food particles to eat, and also would be protected from their arch-enemy, nudibranchs (sea slugs). Some modern day hermits, such as Manucomplanus varians of the Gulf of California, have evolved very similar partnerships with live staghorn corals.

Manucomplanus varians at Monterey Bay Aquarium

Not all hermit crabs live in hard houses. Some deep sea forms partner with anemones, with the stinging tentacles serving as an effective defense.

Source: Okeanos Explorer

The recently discovered green-eyed hermit crab, which also lives in deep water, lives in a glued-together mass of sand created by tiny anemones, which continue to grow the structure to fit the crab as it increases in size.

The green-eyed hermit crab was found over 200 m deep off of South Africa. Source: Lannes Landschoff via Eurekalert 

Unfortunately, hermits adapted for gastropod shells are unable to find adequate homes in some areas, due to overharvesting of shells for the tourist trade as well as an excess of plastic trash. These crabs make do with whatever items that they can find. Plastic is not an ideal home material for hermits. Bottlecaps and narrow tubes do not allow the crab to fully retract for protection and leach chemicals which may harm the crab. The crabs also nibble on their shells as a source of calcium, which is obviously not possible with plastic.

Coenobita purpureus, a land hermit crab on Okinawa. Source: Shawn Miller

But hermits continue to impress me with their flexibility and ingenuity in their search for homes. For a hermit crab, home is where the abdomen is.