Portrait of a Portuguese man-of-war

One reason why I’m so drawn to the ocean is that it’s never boring. Every hike along the coast, every day sailing the sea and every plunge beneath the waves is full of surprises.

The ocean is peaceful: so calm that the vessel you’re aboard may as well be slicing through glass, as you gaze towards the horizon that in this moment doesn’t exist, for in this moment the sea and sky are one.

The ocean is angry: its turbulent waves dwarfing even the grandest of ships, breaking spirits, taking lives and destroying cities.

The ocean is generous, feeding millions of people daily; the ocean is cruel, merciless for countless adventurers at the limit of their abilities. The ocean is a metropolis, teeming with an unfathomable diversity of life; the ocean is a desert, immense and empty for miles on end.

The ocean is full of contradictions, as are its inhabitants.

When we first arrived in Punta Galeta, Colón for our two-day excursion, I must admit that I was disappointed. We were staying at one of STRI’s renowned marine field stations on Panama’s gorgeous Caribbean coast, where waters are warm, waves are gentle and marine life is abundant. Part of what makes Panama’s coastline so unique and the perfect space to study marine ecosystems is the diversity of habitats that are observed in a relatively small area.

The immediate surroundings of the Galeta research station feature dense mangrove forests, blurring the border between land and sea, lush beds of seagrass, perfect for grazers such as manatees and sea turtles, and vibrant coral reefs, home to a dizzying plethora of brightly-patterned tropical species.

While the first two weeks of the course were undoubtedly exciting and inspiring—from waking up to howler monkey calls on Barro Colorado Island to breathtaking views atop the forest canopy from a research crane, to the warmth and hospitality of the indigenous groups of Lake Bayano—I couldn’t help but impatiently anticipate the amazing time we were going to have snorkelling in Galeta.

Unfortunately, we were met with unusually windy weather and turbulent, turbid waters. Heavy undercurrents made it dangerous to swim out onto the reefs, and underwater visibility was so poor that it was pointless to attempt to do so anyways.

Nevertheless, we still had a great time carrying out a predation experiment in and around the mangroves. And any disappointment I felt from being unable to identify said predators due to the murky conditions quickly evaporated, as a lone alien creature slowly and almost ominously drifted past while we were in the water.

At first glance, you might mistake them for a plastic bag or a discarded inflatable—we certainly saw a fair share of rubbish washing onto the shores. But then, there’s something off that you can’t quite place—you might be taken by how smoothly it cruises the waves, uncharacteristic for inanimate marine debris. And when you stop what you’re doing and squint your eyes to make sense of what you’re seeing, you’re struck by its brilliant magentas and blues, and the ethereal folding patterns of its crest above the waves—like a delicately glass-blown sculpture. As it dawns on you exactly what you’re witnessing, you forget about the experiment you’ve been setting up and just gaze in awe as it drifts by, wondering if it has any agency in deciding its path. You suddenly tense up when you remember its long tentacles trailing beneath the surface, unsure of whether you’re within range of their paralysing venom.

We saw four or five of these perplexing creatures during our brief stay, and they never failed to enchant me. Even its name, the Portuguese man-of-war, is intriguing, mysterious and a little unsettling.

The Portuguese man-of-war is the common name for Physalia physalis. They are not jellyfish but a species of siphonophore, which are organisms comprised of a colony of clones (called zooids) working as one. These zooids are unable to survive alone, which is why they’re physiologically integrated, each specializing to perform a specific function.

The part of a Portuguese man-of-war one usually sees is its translucent gas-filled bladder, or pneumatophore, which rests at the surface of the water. This bladder can be up to six inches tall and acts as a sail, letting the wind (as well as currents and tides) propel its course. The float is said to look like the sails of an 18th century Portuguese warship, hence its name. Portuguese man-of-war are said to live in groups of up to 1 000 or more, though we only saw lone individuals.

Beneath the surface lurk the man-of-war’s tentacles, which can be up to ten metres long. Covered in venomous needle-like nematocysts, they permanently drag through the water like abandoned fishing lines, stunning the likes of small fish, shrimp and copepods. The man-of-war’s potent cocktail of venoms includes compounds that lyse cells and break down proteins and fats, beginning digestion almost immediately. Their prey is then drawn up towards zooids specialised in later-stage digestion.

One fish species has taken advantage of the Portuguese man-o-war’s menacing anatomy: the man-of-war fish lives within the Portuguese man-of-war’s deadly tentacles, presumably as a form of protection from would-be predators and is even known to feed on the siphonophore itself. The fish has limited immunity to the siphonophore’s venom, and gambles using incredible flexibility and agility to avoid being stung by its tentacles.

Besides these basic facts, not too much more is known about Portuguese man-of-war’s life histories or ecology. They are usually found in the open ocean, are impossible to tag, and do not live long in captivity.

They are a perfect example of the self-contradicting nature of the ocean: capturing the intrigue of naturalists, artists and beachgoers alike, daring its observers to take a closer look—only to punish them should they overstep their bounds. As beautiful as they are deadly.


More info:



The use of evolutionary principles in the study of viral outbreaks

Have you ever heard the term “viral”? Usually is referred to a piece of information that is shared by a high number of people in a short amount of time. The term comes from the same property of virus to spreads and multiply among hosts, but instead of a cat video, virus spread their genetic code with some serious consequences to their hosts.

Today there are ways to prevent virus to spread, the most common treatment is vaccination. Vaccines are used as an imput for our immune system to build an immune memory. So, next time and actual virus comes and tries to replicate on our bodies, the immune system is ready to take any potential threads. Controlling viral outbreaks had become an arm race between vaccines and the ever-changing virus, however it is possible to understand how viral infections work using ecological, evolutionary concepts and the use of phylogeny models to study viral outbreaks.

A phylogeny is simply a visual representation of the evolutionary history of a species or group of species. Each branch represents a species, each node a common ancestor and each branch, depending on the model, shows an estimate of time or generations. Most recent species are at the tip of the tree and the root is the most recent common ancestor (MRCA) of that group (Fig. 1). In epidemiology, a phylogeny  can be used to study the spread of diseases, their mechanisms of evolution and to try to know the what?” where? why? and how? of viral infections. (Grenfell et al., 2004; Moya, Holmes, & González-Candelas, 2004).

fig 1

Fig 1. A phylogeny tree

Virus are very effective on replicating themselves, they can make millions of copies on a single cell. They infiltrate into the cell while avoid being recognized by the immune system. To infect the cell, some virus can recombine their genetic material with the host DNA to multiply. Others rely on their own replicative mechanisms, producing their own replicative proteins to make copies of themselves. But, most of them depend on the randomness of mutations and the later process of natural selection to be able to replicate. Mutations are any alterations on the genome that arise over a replication events, they can be neutral, detrimental or can be favored by natural selection if they offer an advantage (Fig. 2). Some virus replicates faster than others, this would depend on their genetic structure and method of replication, for most viruses it is possible to estimate their evolutionary rate in real time.

fig 1

Fig. 2 Traits influencing mutation and substitution rates (µ) in viruses. Traits that can increase substitutions and mutations rate are shown in red. Traits that decrease substitutions and mutation rates are shown in blue. Many of these factors are not independent, for example smaller genomes tend to replicate faster. Figure from (Duffy, Shackelton, & Holmes, 2008)

When enough advantageous mutations accumulate, the virus strain has changed so much that the immune system is not able to recognize it and a new potential outbreak can occur. But if the mutation rate of a virus is known we can be ready it with new vaccines. That’s why you need a flu shot every year!

Also, by using phylogeny models, it is possible to track each time there is a new outbreak and check for specific mutations that may occur over time. Each outbreak is different and within an outbreak it is possible to find multiple strains (Fig. 3). In that sense a viral sample from five years ago would be the equivalent of a “fossil record” from a sample from a more recent year and with this information you can track the origin and evolution of the virus in a certain location.

fig 1

Fig. 3 Phylogeny of Influenza H3N3 sampled weekly over 10 years in NY, USA. Bottom line shows time in years. The purple arrow indicates the concept of divergence, which is the distance of a group compared to the common ancestor or how realted the groups are. Each outbreak in any given year is different from each other, they diverge from the common ancestor. The pink arrow indicates the concept of diversity, which is the number of viral strains in each generation or outbreak. Notice that each new outbreak comes from a single branch of the previous one and diversifies in any given year, that is the visual representation of natural selection acting on the virus and how specific branches mutate to create new outbreaks in the next generation. Figure by: Nuno Faria, Epidemiology course, Ecuador 2015.

Most viral infections are host specific, but some viruses are capable adapt to new hosts. These events are rare, but they can happen if the hosts involved are in constant interaction with each other. Most common cases are expansions of human populations to new areas, second most common are hunting activities and interactions of wild animals with domestic animals (Johnson et al., 2015). These “hosts-jumps” or zoonotic outbreaks occur when a virus that is often associated with an animal is transmitted into humans. There are multiple stages of a zoonotic infection and there could be multiple evolutionary processes involved on each stage (Fig 4). Some viruses can jump from animals to humans, but they cannot be transmitted within humans. In other cases, is possible that the viral strains, once transmitted, mutate to be completely adapted to humans. Other times and rarer event is when two viral strains combine, one adapted to humans and another adapted to a different host, this is known as a recombination event, usually this type of outbreak is the most difficult to handle and predict due to the specific circumstances which they arise.

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Fig. 4. Multiple stages of zoonotic infections of four viruses: rabies, ebola, dengue and HIV-1. Each of these viruses is on a different stage of zoonotic infection. There are 5 stages, each one characterized for its transmission up to being completely adapted to humans. Figure (Wolfe, Dunavan, & Diamond, 2007)

One common approach on this type of studies is to relate the virus with its host distribution (they are usually bigger and easier to handle than a virus) to create an estimated distribution of the virus itself (Streicker et al., 2010). In that way, is possible to identify potential locations where several hosts species may interact together, which can help to make better decisions on preventing measures to specific risk areas. Vaccination can be location specific to prevent spread.

The study of epidemiology is a multidisciplinary one, this is only a glimpse of what can be done; from model studies, to in vitro experiments, to ecology research on host and pathogen dynamics and to field experiments in nature; each one provides useful information to predict and manage diseases and assure the well-being of people. Epidemiology research complements studies on drug resistance and immunity to create new vaccines. All these combined with evolutionary concepts help to answer fundamental questions about the genetic diversity of pathogens, how they vary through time and space and the processes that could determine these changes.

The study of viral diseases is the collaborative effort of epidemiologists, biologists, ecologists. Research can only reach so far as the people interested in it. The decision makers need to understand these basic concepts of epidemiology to improve disease control and its policies. If we understand how virus spread and how they evolve, it will be possible to prevent them.


Duffy, S., Shackelton, L. A., & Holmes, E. C. (2008). Rates of evolutionary change in viruses: patterns and determinants. Nature Reviews Genetics, 9(4), 267-276.

Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L., Daly, J. M., Mumford, J. A., & Holmes, E. C. (2004). Unifying the epidemiological and evolutionary dynamics of pathogens. science, 303(5656), 327-332.

Johnson, C., Hitchens, P., Evans, T., Goldstein, T., Thomas, K., Clements, A., … Mazet, J. (2015). Spillover and pandemic properties of zoonotic viruses with high host plasticity (Vol. 5). https://doi.org/10.1038/srep14830

Moya, A., Holmes, E. C., & González-Candelas, F. (2004). The population genetics and evolutionary epidemiology of RNA viruses. Nature Reviews Microbiology, 2(4), 279-288.

Streicker, D. G., Turmelle, A. S., Vonhof, M. J., Kuzmin, I. V., McCracken, G. F., & Rupprecht, C. E. (2010). Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats. Science, 329(5992), 676. https://doi.org/10.1126/science.1188836

Wolfe, N. D., Dunavan, C. P., & Diamond, J. (2007). Origins of major human infectious diseases. Nature, 447(7142), 279.


The Most Valuable Thing I Learned at STRI

Arriving in Panama I wasn’t sure what to expect from STRI (the Smithsonian Tropical Research Institute) or the NEO (Neotropical Environment Option) program. Here in Gamboa, you step outside of your day-to-day life and become immersed in an environment with individuals from all over the world who are united in a passion for scientific exploration. When spending time with other students and researchers our differences are evident, but our ability to look past these differences and turn them into advantages in the face of a common goal is arguably the most valuable resource STRI has to offer. Just within our small class of eight people we had tree ecologists, ichthyologists, an ornithologist, a mammalogist, evolutionary ecologists, a philosopher, a barber, musicians, photographers and the list continues. Thus, the diversity within our group was constantly sparking engaging conversations about science and the issues surrounding it. I distinctly remember one conversation held on the bus ride back from the Bayano region where a discussion about Indigenous land rights transitioned into a heated philosophical debate regarding the definition of ‘ownership’. By accepting and listening to one other, we are always able to grow as scientists. I have learned many things during my time spent in Panama, but this is perhaps the most exceptional.

During the first few days in Panama our group ventured out to Barro Colorado Island (BCI), a world renowned research center owned by STRI. While on BCI we participated in small research projects under the supervision of Brian Sedio and Jordan Kueneman. Raina, Francis, Gabriel and myself worked to understand more about the composition and function of microbiomes on BCI. The topic of microbiomes was relatively new to us, but Jordan led us in understanding the complex field of microbiomes by having us participate in each step of an actual microbiome analysis. These individual experiences were undeniably cool, but for me the most interesting part of our project was not the night hike or the katydid dissection, it was seeing the different ways each of us understood and approached our topic. My background in environmental science has coached me to always focus on the bigger picture. However, within our group everyone asked very different questions and we were all drawn to different parts of our project. For example, Raina was very quick to understand specifics about the methodologies behind microbe sampling, characteristic of her background in more focused areas of biology (i.e. neuro-science). I found that Francis was very good at explaining concepts to the rest of us and constantly asked questions that helped clarify parts of the project that we were struggling with as a group. I suspect (though I have not asked him) that this may stem from his experiences teaching. During this project on BCI was when I originally decided I wanted to write this blog post. This was the first time I saw the degree to which our individual backgrounds and interests could play a role in shaping a scientific product.


Photo by: Francis Van Oordt 

For our last class trip we travelled to Galeta, STRI’s main marine research station in Panama. We had been excited to go snorkeling since our arrival in Panama, so we were extremely disappointed to be met in Galeta by strong winds and mud-brown waters. The feeling of disappointment only deepened when our group consisting of Francis, Marko, Raina, and myself went out to test the water visibility and determined that our original project idea would not be possible. However, we brainstormed and came up with an alternative project which was quickly set in motion. To test our hypothesis we needed to plant squid pops around and within the mangroves outside of the research station. Due to an unforeseen injury and an extremely rational fear of crocodiles (I’ll let you infer who each pertains to), Marko and I were not able to be much help in the water. Raina and Francis (with some help from Felipe and Matt), were able to plant most of our squid sticks. We had a tight deadline so in the morning we went out and quickly obtained all of our data. Marco’s interest in statistics and ability to use statistical tools meant that he was able to complete the analysis quickly while I worked on our presentation. At the end of the day we finished with plenty of time to practice. Without our different strengths we probably wouldn’t have completed any project let alone one as extensive as ours, however, because of them we were able to pull off what I believe was one of the best group projects/presentations of the course.


Photo by: Marc-Olivier Beausoleil

The individual differences we had within our small NEO group are a reflection of the multi-dimensional STRI community. Over the course of our studies we were able to meet with many STRI researchers who all have various talents and research goals. What stood out to me most when meeting these people was the opportunity for collaboration presented by STRI. We met with people like Brian Sedio and Jordan Kueneman who are interested in questions related to molecular biology. We heard about projects by Michael Logan and Martijn Slot that are focused on climate ecology. We even met with people like Catherine Potvin who, along with her biological research, works on social issues related to her field. While the specific topics studied by these researchers seem very different, here at STRI there is a continuous emphasis on the interconnectedness of science. Many researchers on BCI who conduct their own projects are collaborating with Jordan Kueneman to provide microbiome samples from their own study species for his project. People like Jose Loisa who work on the One Health Initiative collaborate with people from all facets of biology (e.g. medical, ecological, evolutionary) to tackle issues related to disease transmission. These collaborations bring together different fields but they also bring together different people. These people bring with them different knowledge and experiences that give them the ability approach issues from different angles. It is my opinion that no project can be completed effectively from a singular perspective. STRI facilitates conversation and collaboration among people that contributes to betterment of our individual fields.

So often in the world we see people being torn apart as a result of their differences. Governments collapse, religions clash and professional sectors attack one another because ultimately we all see the world in different ways. However, it is hard to imagine a successful society in which everyone shares the same affinities and the same world views. STRI provides an example of how monopolizing each other’s differences can be vastly more productive than allowing them to drive us apart. Doing this lets us see the bigger picture associated with a single issue and leads us to consider factors we may have otherwise overlooked. Above all else my time here in Panama has taught me the value of individual differences. As wisely stated to us by Gordon Hickey back in Montreal “the more you know, the more you know you don’t know”, making collaboration with people different from yourself a vital part of practicing sound science. So whether I am asking Marco for help running linear models or having Chris and Francis teach me Spanish vocabulary, as a scientist I will now always see others’ differences as an opportunity to better myself and my own scientific practice. In my opinion, this is greatest lesson one can learn here at STRI.

Featured photo by: Felipe Pérez Jvostov

Should drawings be (re)introduced to our scientific training?

By Marc-Olivier (Paul) Beausoleil and Chris (Paul) Madsen.

You’re sitting in a class and the professor explains a new concept, say about the electron transport chain in a cell membrane. While describing parts of the concept, the instructor turns and walks in the direction of the chalkboard to draw a diagram. And then the famous sentence follows: “You’ll have to excuse me, I’m bad at drawing”. If this sentence still resonates in your head, or if even you say it from time to time, this post may help to remove some of the barriers we impose on ourselves when we want to draw something. This discomfort can be surmounted by understanding what drawings are for and how to improve your drawing skills. We argue that revaluing drawings, by offering training and time in the teaching curriculum, will help students to learn to observe efficiently and have a deeper understanding of the concepts they learn. Here, we discuss how drawing is an effective way of learning and discuss tips on how to improve your drawing skills. But before, let’s explore how drawing is deeply rooted in our history and in shaping science as we know it today.

The veritable cognitive feat of representing extremely complex, heterogeneous and dynamic objects in a frozen snapshot in time and in two dimensions dates back to our earliest predecessors. Cave paintings found in France and Romania date back to perhaps more than 30,000 years before present. Yawning caverns, hidden in shadow under the Earth’s surface for millennia, still hold testament to the artistic endeavours that celebrate humankind’s hunting and culture (Zorich, 2012). If we leap forward in time to the late 15th century, we find Leonardo DaVinci creating beautiful works of art in various media; his ‘Vitruvian Man’ (Figure 1) remains an iconic study of the human form. His diligence to the pursuit of deeply understanding the form which he observed can be felt in this quote:

[…] To obtain a true and perfect knowledge of which I have dissected more than ten human bodies, destroying all the other members, and removing the very minutest particles of the flesh by which these veins are surrounded, without causing them to bleed, excepting the insensible bleeding of the capillary veins; and as one single body would not last so long, since it was necessary to proceed with several bodies by degrees, until I came to an end and had a complete knowledge; this I repeated twice, to learn the differences. […]”


vitruvian man

Figure 1.  The iconic representation and exploration of the human form (specifically, a smaller, Italian model), by Leonardo DaVinci. Photo taken by Doug Williams.


Western culture and science has been conspicuously male-dominated for centuries; perhaps the first significant female presence in the intellectual pursuit of Biological Science was felt through illustration. Women such as Maria Merian, who drew butterflies, represent the vanguard of woman in the “old-boy’s club” of Western Science (Nic Eoin, 2017). If drawings were a first portal for women to make an impact on science, it is important we are clear what we mean by such “drawings” : “a learner-generated external visual representation depicting any type of content, whether structure, relationship, or process, created in static two dimensions in any medium.”, according to Quillin & Thomas (2015) (we suggest you eat a small cookie after reading that definition so as to replenish the glucose in your brain – you deserve it!). These authors continue to describe how drawings can be powerful tools for communicating, thinking, and understanding in more detail that which you are observing. This, in turn, may lead to the genesis of hypotheses, novel experimental design or data visualization, and more effective communication of results. This act of deconstructing and synthesizing choose aspects of your subject also improves our selection, organization and integration of the internal knowledge we possess about the subject.

In addition, learning may be positively impacted by sketching processes and cycles as opposed to simply reading or hearing about them – though this may depend on the “learning style” of a given student. Personally, I (Chris) find that being able to reproduce concepts such as the nitrogen cycle by hand through the visual medium of drawing helps me greatly in solidifying my knowledge and identifying possible holes in my knowledge that otherwise may escape my notice.

The spiritual value of drawings is also of great importance. Carl Ray, an artist who was part of the Professional National Indian Artists Incorporation, is quoted saying “What you are looking at is ancient and sacred. In fact what you see could be described as a part of my soul.

What are some disadvantages of drawing as a learning technique, a communication tool, or a method for spiritual expression and exploration? It takes time, which in our productivist world is a dearly cherished resource. This time might otherwise be spent learning skills or abilities which could be useful in an unlimited fashion into the future (think of those optimists who claim that diving into the abyss that is learning R can be quite fruitful for your future self). In addition, the act of representing something by hand introduced by necessity a simplifying element, rendering the new diagram or sketch less accurate or represented at a lower resolution than the original subject (refer to Figure 2). Finally, because we are not able to represent every form of variation possible in life, or even in the morphological variation of the leaves on one tree, drawings are themselves very specific and don’t represent fully the variation in the environment.



Fig.  2. The iterative process of sketching a wolf; after a few rounds, what was an accurate and (relatively) life-like representation of Señor Wolf becomes what might be mistaken for a horse, before switching media altogether to become a concept codified in writing.



What are some tips for newly initiated drawers? Here are some tips to for meaningful sketches:

  1. Take the time you need. Choosing between a quick sketch (such as an abstract drawing) or a fully detailed and colored image is important, as they do not take the same time. This will vary depending on your drawing skills and the goal you wish to achieve.
  2. Proportions. Add a scale (a ruler could be helpful, but anything so that you can know the size of your drawing could do the job). Note the magnification if under a stereo microscopes or microscope
  3. Coarse. Don’t worry for details at the beginning. Just focus on the general geometry (circle for the head, square for the body, etc.) and the lighting.
  4. “Life-like drawings”. If doing a scientific illustration, focus on the few important contrasting elements.
  5. Don’t be fooled. Don’t try to reproduce the “idea” you have of the subject you’re trying to draw.
  6. Legend. Remember to write a descriptive legend about what is illustrated, your name, and the date.
  7. Labels. Write the parts that you know and research the ones you don’t, if necessary.

In conclusion, we hope that we have made the case for the inclusion of drawing, a “classic” technique in the representation of both scientific and artistic subjects, in an ideal modern repertoire of skills. We don’t think it should be mandatory, nor should it remove modern technology like cameras, but it may be a valuable contribution to science. Perhaps, as you gain experience drawing, you will not only lose your hesitancy but even come to appreciate the illustrations in guidebooks of birds, flowers, and uglier things like toads, even more.








Leonardo, da Vinci. (2005). The Da Vinci notebooks. London (UK). Profile Books.






Zorich, Zach (January–February 2012). “From the Trenches – Drawing Paleolithic Romania”. Archaeology. 65 (1). Retrieved 1 January 2018.

Our Adventures on Barro Colorado Island

By Gabriel Yahya Haage, Raina Fan, Francis Van Oordt, Maria Creighton

As part of the Field Course, students took a trip to the STRI institution on Barro Colorado Island (BCI). Here we met with scientists and participated in student projects. While one group, henceforth known as the “uncool” group, was involved in some weevil collection madness, our project led us on a night hike on the island, where we collected katydids, which, as we all know, are way cooler than weevils.  But katydids were not our only targets.  We also caught geckos and frogs so that we could swab the inside of their mouths and their bodies.  And why did we do this?  To get a hold of their sweet, sweet micro-biomes, of course.  We then used data (sadly not the samples we collected, due to time constraints), to try to understand differences in the micro-biomes of 7 amphibian species.  Below are the highlights by each member of our group.  They may be scientific or not, but all these events were a part of our Barro Colorado experience.

Gabriel’s Highlight

For me, visiting the Katydid Lab was the highpoint of the project.  Getting to hold different katydids, many bearing wild coloration and each with its own personality (to the extent that an insect can have a personality) was a great experience.  The way that the katydid researchers spoke to us clearly revealed their passion for their work that I left the lab seriously considering getting a katydid as a pet.  

Trapping katydids was also easier than the other organisms we went out to get during the night hike.  For one, they were more abundant.  For another, once the Ziplock bag was placed on them, they tended to jump up, giving us the opportunity to close the bag, making sure to leave some air for them.  Geckos and frogs were trickier.  Geckos had the unfair advantage of walking on walls, so catching them required lunging at the wall while jumping upwards in order to lay our hands on them.  Since we wanted to swab for their micro-biomes, everything had to be as sterile as possible, which meant wearing gloves and washing the skin of the specimen before we could swab them.  The gloves can also help when the geckos choose to bite.  If you’re lucky, it’ll sink its teeth into the glove and not your fingers (I was not so lucky…).  In the end, whether katydids or geckos or frogs, this night expedition in Barro Colorado Island will be hard to forget.

Raina’s Highlight

Our collections night was definitely a highlight for me. We waited until a few hours after sundown before strapping on our headlamps and heading out with an “anything goes” attitude.

I was at first skeptical about whether we would be able to actually catch anything that we found — I would describe myself as the opposite of agile — but turns out there are some secret techniques™ to catching and swabbing small animals. I’ve compiled a few things I learned about how to be a real-life Pokemon master:

1. Let there be light

Like most humans, I see worse at night. In fact, I barely notice cryptic small animals during the day. Unsurprisingly, this can be a problem when your study species are nocturnal. Luckily, we learned that many of our insect, reptilian and amphibian target species tend to congregate around light sources at night. I don’t think there’s consensus yet in the scientific community as to why this is the case, but some theories suggest that artificial lights interfere with insects’ ability to navigate through phototaxis (navigating by moving relative to a light source, such as the moon. Other theories include artificial light containing frequencies similar to that of female moth pheromones, so male moths are responding to what they perceive as a mating signal. Whatever the reason, light sources are a great place to look for moths, katydids, dragonflies and more during the night. And where you find insects, you might also find animals that enjoy snacking on them, such as geckos, frogs and lizards.

There exists a lot literature detailing the use of light traps to catch insect specimens. For our adventure, we were fortunate to be able to explore the multitude of well-lit STRI research buildings adjacent to the rich tropical forest of BCI. We got hits very early on and ended up seeing quite a few cool species, including various beetles, dragonflies, geckos, and even freshly-laid frog eggs. Turns out, finding bugs and reptiles can be easy —  catching them is another story

2. Yes you (garbage) can

There are two parts to this one: first, get creative with your resources. Second, confidence.

Sure, wall-scaling geckos are pretty fast. But you’re human; you have the largest encephalization quotient (brain-to-body mass ratio) of the animal kingdom. Humans needn’t be the fastest or the strongest when they have ingenuity. So when you see a gecko three feet above your head zipping around at the speed of light, don’t fret — use that unusually large prefrontal cortex and come up with a plan.

Our ingenious plan involved locating a nearby empty garbage bin, flipping it over, and getting a tall person (me) to stand precariously on top of it with an outstretched arm. To my utter amazement, it actually worked! It does help to keep a light shined on your target to freeze it in place while you slowly creep your hand towards it. Finish by snatching it in one swift motion. This is where confidence is key — commit to the capture and don’t waver.

I should note that you should take precautions to make sure you don’t hurt your specimen in the process. For reptiles, it’s best to grab them in a manner where they can’t struggle too much or eject their tail (see above). For insects, you’ll often have better luck trapping them with a bag rather than trying to grab them directly and accidentally squishing them.

3. No glove, no swab

Okay, so this one’s not very catchy but it’s very important if you’re catching organisms for the purpose of studying their microbial ecosystem. We had to wear a new set of sterile gloves every time we caught a new subject, to prevent contamination from other samples and our own micro-biomes.

After catching our specimen, the first step was to rinse it with ultrapure water to wash out environmental debris such as algae or leaves. Then, we took care to use a sterile swab to take a microorganismal sample of three main zones: the mouth, skin and cloaca. This was often a cooperative effort, with one person securing the animal in place while the other sample the organisms that we were truly interested in: the invisible microbes.

All in all, our team had a great time getting a taste of the life of a field microbiome researcher. It’s clear that for someone who’s interested in analysing micro-biomes across different taxa within an ecosystem, you often need to get creative with your methods of collecting samples. And the field component is only a small part of the work! Back in the lab we learned how to dissect insects to sample their gut fauna, as well as techniques on how to extract DNA from our swabbed samples, sequence them and use reference databases to identify the diversity of bacterial taxa that call a host organism home. It was a fascinating process!

Maria’s Highlight

Okay, so I’m a primatologist NOT a collector of night-dwelling slimy creepy crawlies. So to put it mildly I was less than enthused to trudge through the dark swabbing lizards and putting bugs into Ziplock bags. Unless I am out searching for night monkeys (Aotus zonalis) I take no part in research endeavours between the hours of 9:00 pm to 6:00 am. I especially do not go out in the dark just to lunge down a steep flight of stairs bruising every natural surface on my body. However, even I must admit that our group’s night hike and subsequent research project was not without excitement. At the beginning of our night hike we ran into some researchers from Dr. Meg Crofoot’s lab who were tracking a male kinkajou as a part of the “Food for Thought” project. We were lucky enough to follow along and see this relatively reclusive animal up close. For me, this was especially interesting because I will be interning in Dr. Crofoot’s lab beginning February 5th, working on the very same project. For part of this project I will be collecting microbiome samples for Jordan Kueneman’s research from mammals that have been previously tagged, including the kinkajou we saw on the night hike.   


The work currently being conducted on micro-biomes is opening the door for an entire frontier of science that has been relatively unexplored. The potential for new discoveries in this field is inevitable and extremely exciting. Micro-biomes play a role in the biological make-up of most species and studies are currently testing the ways in which they influence the behaviour and evolution of their hosts. Our study showed that micro-biomes varied between amphibian species on BCI, Panama. For example, we found that the toad species Atelopus certus was the most different in microbe composition when compared to the rest of our study species. Upon doing research we found that A. certus secretes a powerful toxin to protect itself from predators (Yotsu-Yamashita & Tateki, 2010). With this knowledge, future studies could be set up to explore the relationship between microbe composition and host biotoxins. The results of our research project showed that micro-biomes are species-specific and vary between species even when there is significant overlap in habitat. The questions we asked during our research project are questions that are broadly applicable to my future research in the field of primatology. Micro-biomes are unique in that they are influential in nearly all facets of biology. Whether you are interested in population genetics or ecology, there are likely research questions about micro-biomes that remain unanswered. For this reason, micro-biome research is pivotal to our understanding of biology and even I, a narrow-minded primatologist, have adopted an appreciation for microbes.

Francis’ Highlight


The opportunity to finally work with vertebrate’s micro-biomes was pretty exciting (after some very interesting talks on plant ecology I was itching for some animal stuff). So the night hike was pretty appealing to me. But I have to be honest, micro-biomes have been just a distant image in my scientific career. The first time I heard about the idea of micro-biomes in an ecological setting was during my masters program from a fellow grad student. He was studying how socialization in young green iguanas Iguana iguana (strict herbivores) could potentially change their gut micro-biomes, which are shown to be highly specialized in digesting plant material. He concluded that there was no significant exchange of gut micro-biomes among young iguanas. Our conversations brought us to talk about the Hoatzin Ophisthocomus hoazin, the only bird known to eat leaves (plant material) almost exclusively. This bird, unique in its kind, has incorporated a series of microbes into its gut that allows it to digest and process plant material that is otherwise very toxic to several species. After this few rare events “dealing” with micro-biomes my experience was limited to human digestive systems and other fads on what we should eat or what we shouldn’t.

The impact that micro-biomes could have on wild populations of a wide variety of species has never really occurred to me. Trying to understand and evaluate this potential effect was the main purpose of this module at BCI. Working with micro-biomes, as the name implies, means doing a lot of microbiology work and following protocols that are not common in other macro-ecology studies, such as the ones I have been used to. So the combination of hiking at night on a muddy river bank wearing  rubber-boots (“gum-boots” for some rare specimens) looking for frogs or lizards and at the same time trying to take sterile samples of skin micro-biomes of the guys you catch, was pretty challenging. After a few tries I was an expert, catching only big and clumsy frogs (everything else would pretty much escape from me). But I guess now that micro-biomes of many organisms are not something they can escape easily from. Changes in micro-biomes of host organisms that have adapted to many specializations such as tree-frogs or other semi-aquatic reptiles may play a very important role in their fitness and overall survival. And considering that microbes are pretty sensitive (at least the “good guys”, not the disease causing ones), I think now that we should pay pretty close attention to what is happening not only in the macro-ecology scale, but also (quoting my classmate Gabriel Yahya Haage) in the “sweet, sweet micro-biomes” of many endangered (and why not all) species


Wehrle BA. 2013. Intergenerational lizard lounges do not explain variation in the gut microbiomes of green iguanas. Master’s Thesis. California State University, Northridge.

M. A. García-Amado,  F. Michelangeli ,   P. Gueneau,   M. E. Perez,   M. G. Domínguez-Bello. 2007. Bacterial detoxification of saponins in the crop of the avian foregut fermenter Opisthocomus hoazin. J. Anim. Feed Sci. 16: 82–85

JG Kueneman, L Wegener Parfrey, DC Woodhams, HM Archer, RKnight and VJ. Mckenzie. 2014. The amphibian skin-associated microbiome across species, space and life history stages. Molecular Ecology 23, 1238–1250

Yotsu-Yamashita, M., & Tateki, E. 2010. First report on toxins in the Panamanian toads Atelopus limosus, A. glyphus and A. certus. Toxicon, 55(1), 153-156.

Map of the Trees on STRI Gamboa Campus

By Élise Bouchard and Chris Madsen

As two graduate students working with trees, we were full of enthusiasm about identifying the tropical species we would see in Panama. On the first day at the Gamboa Campus, we went on a walk, started to take pictures and collected samples of the trees from the area surrounding the school house. Then we got this cool idea, that not only we could identify them, but make a map of their distribution in the neighborhood as well, so that the students in the years to come would have a reference for local, tropical tree identification. This would be a great opportunity for them to observe live specimens.

Our first objective was to identify around 15 different species, but we soon realized that this was hard to achieve. Here is the thing: we had no previous knowledge of Neotropical species and didn’t bring any identification field guide. We naively thought that it would be easy to find identification keys on internet, such as the ones available for boreal species in Canada. It turns out that there’s no such tool on internet, at least from what we’ve seen, and this can be explained by two reasons:  1- The number of species in Panama is tremendous (way more than our few Canadian species, up to 2 orders of magnitude more!), which makes it hard to summarize in an online identification key. 2- The species might be less well documented than the ones in boreal biomes.

We finally managed to identify a couple of species with help from guest lecturers and teachers, along with a list of the 50 more common tree species found on BCI. We also had some lucky findings on the internet through the really un-scientific process of clicking on all the names of a family until one of the pictures looked familiar to us (don’t try this at home, kids!).

In the meantime, we finally got an identification book for a couple of hours. We gave it a quick look in search for the missing species, and still, we couldn’t identify most of them. This led us to another hypothesis: Some of the species planted around the school house might be ornamental species, instead of natural species commonly found in forests. This is often the case in cities and would explain why some abundant species in the neighborhood weren’t easy to find in the field guide, internet or through our conversations with locals and teachers.

Anyway, here is the result of this work, with the 7 identified species. Their locations are indicated on the map so that you can walk and observe them in real life. We want to emphasize that this work hasn’t be verified by any expert, so it might contain mistakes, but we did our best to make it accurate.

Map of the trees (3)-001

Note: The background of the map is from Google Maps.

Danse Macrabre of the Mangrove

A melodramatic reflection of mangroves by Chris Madsen.

A strong breeze ruffles the dark green leathery leaves of a small copse of red mangrove trees. Scuttling crabs traverse the lignified curves of bowing roots. The saline water, an obstacle to most plants, is excluded or exuded as crystals from leaf stomata (Bompy et al., 2014). Stiff branches are adorned with green fruits, each of which is struck with wanderlust and so grows its radical root even as it sits on the parent tree.

Red Mangrove

Figure 1. Photograph of an island of Red Mangrove, borrowed from https://i.pinimg.com/originals/c6/96/93/c69693bc228ae2e9e3c53dc28667ec36.jpg.

    As it reaches maturity, our red mangrove propagule breaks off from the mother tree and plunk, starts to bob in this new, salty medium. Current replaces wind, and now without the secure anchor to the mother plant, our tree-infant is tossed and tumbled through the water, above and below the interface of those old elements, Air and Water.

               The wind buffets and the currents pull at this propagule, horizontal and bobbing along. At some point, conditions are suitable and the propagule swings upwards to be vertical so that its pointed root can stick in the muddy substrate. A low tide yields the opportunity and splorch, it sticks in the mud (Stocken & Menemenlis, 2017).

Red Mangrove IslandFigure 2. This photo of a newly landed Red Mangrove taken by (soon to be Dr.) Heather Stewart, of the NEO-BESS programme!

      As the newly recruited sapling explores two worlds with its root and shoots, the boundless sky and the swirling marine depths, difficulties arise: herbivores and obstacles damage and impede its roots, forcing the roots to bifurcate. One becomes two, two become four, and four become countless roots as the accumulation of sediment around the roots creates a new island in the sapphire sea. Fish dart amongst the roots, hunting and hunted, as the moon’s pull on the ocean waxes and wanes.

             Other propagules are caught in the colonizing tree’s roots and skirt of sediment. As new generations of propagules set down roots, the island doubles and triples in size. The gap begins to close between the mother tree’s coastal forest and the newly forming island. Each tree stretches higher and higher to seek the light, and their roots delve deeper into the muddy sediment. Years pass and the canopy closes; light and wind and sky are cut out but the dark and stifling canopy: a change has come to pass.

               Decades later, great changes have overcome the forest. As sediment accumulated, the freshening wind of the sea has retreated to leave stagnant and cloying air. Water trickles lethargically from streams to fill darkling pools which grow more still with each passing year. The familiar red mangrove trees from the coast are replaced by black mangrove trees, and another great change takes place: pneumatophores produced by the black mangroves, and reminiscent of skeletal fingers, erupt from the dark, waterlogged soil to drink in the moist air. A humid fog is clutched by the branches that bow and bend to embrace you. Scaly creatures slink and slither through pools full of decomposing leaves (Guo et al., 2017).

               As you walk through the black mangrove swamp, pneumatophores crunch under your booted feet like grasping graveyard hands which pull you down into the opaque and mucky water. Chitras swarm your pants and shirt as they seek the warm current of blood they perceive pumping through your veins. Echoes of the birdsongs that could be hear on the coast have faded and now only occasional belches of gas break the silence. The trees are still as you look, but when they aren’t being observed these trees are reaching, groping and walking through the water.  Methane gas bubbles to the surface from soil so deprived of oxygen and so saturated with water that life’s vibrancy and abundance is dimmed.

Black Mangrove

Figure 3. This photo of a black mangrove borrowed from http://l7.alamy.com/zooms/03e54991b8064549b8c591437942fc0f/the-aerial-roots-pneumatophores-mangrove-forest-in-krabi-thailand-edjxym.jpg.



Bompy, F., Lequeue, G., Imbert, D., & Dulormne, M. (2014). Increasing fluctuations of soil salinity affect seedling growth performances and physiology in three Neotropical mangrove species. Plant and Soil, 380(1–2), 399–413. https://doi.org/10.1007/s11104-014-2100-2

Guo, H., Weaver, C., Charles, S. P., Whitt, A., Dastidar, S., D’Odorico, P., … Pennings, S. C. (2017). Coastal regime shifts: rapid responses of coastal wetlands to changes in mangrove cover. Ecology, 98(3), 762–772. https://doi.org/10.1002/ecy.1698

Van der Stocken, T., & Menemenlis, D. (2017). Modelling mangrove propagule dispersal trajectories using high-resolution estimates of ocean surface winds and currents. Biotropica, 49(4), 472–481. https://doi.org/10.1111/btp.12440

Photo sources included in figure titles; Figure 2 borrowed from Heather Stewart


Meeting with the Tropics

By Élise Bouchard

Studying Forests Sciences in Québec implies spending a lot of time in boreal forests, the realm of balsam fir, spruces and mosses. I grew up with that forest, I had my first lessons about nature there. Indeed, I came to learn the biology and the ecology of these peculiar ecosystems, but also many lessons that can’t be taught by science, such as learning the ʺpersonalityʺ of the forests, the emotions they inspire and how we can relate to them. The process involved in every new experience begins with an emotion, a sensation, and thereafter come the questions and the science. Here, I would like to share this first experience I had with the tropics, the storm of ideas it has created in my mind, and how I can relate this experience to my boreal one.

Boreal forests are a place for calm, introspection and humility. Calm, because you can walk for hours in this quiet environment, where the branches of the conifers move slightly in the wind, and where from time to time the song of a discreet bird arises. If you are lucky, you might come across a moose, a beaver, or a porcupine. You would then look in silence at each other, with this fascination of two lonely creatures that don’t cross the path of others often. Introspection, because it is a wonderful place for letting your thoughts flow. The soil is covered with mosses, in a mosaic of different green and texture. The thick canopy of the conifers filters the sunlight even during the winter, so you always feel sheltered, enveloped in the shadow of the understory and  the peaceful mood it creates. Humility, because boreal forest are harsh environments, and experiencing their intense seasonal changes makes you realize that you are only a human, powerless in front of these natural events. The only way to feel comfortable in these forests is to be well prepared, with the help of many artifices such as multiple layers of clothes and staying for a brief time. The cold weather, the rain that freezes you to the bone, the hot days during the summer that trigger an explosion of flies and mosquitoes, are all elements that force you to humility, by realizing your fragility in this environment. Finally, the apparition of huge colonies of tiny plants at the end of the winter, that within a month emerge, cover the understory with hundreds of flowers, and die, remind you how the time flies, and how every opportunity has to be seized when the time is right.

In contrast, tropical forests are an explosion of life, in all its forms. Life screams at you, with the echoes of the howler monkeys and the toucans’ songs, it surrounds you, with the presence of multiple layers of vegetation that makes your progression into the forest difficult, and it comes to you, as the tireless march of hundreds of ants. The use of space first caught my attention. In mature boreal forests, on both East and West coasts of Canada, the understory is often sparse. The plants that grow under the canopy are usually small and located in patches, which gives you a sensation of space and liberty. In tropical forests, there is no available place. Life is everywhere, often high enough to obstruct your view, and to touch your skin along your way. It overwhelms you; you feel part of a huge community. In boreal forests, you always feel a bit like an intruder, as you know that your survival depends on external objects, such as clothes. In other words, tropical forests remind you that the natural fitness of humans is higher in lower latitudes, which might be an old heritage from our ancestors in the savannahs of Africa.

If I had to choose one word to describe tropical forests, I would choose Community. This idea of being part of a community started to take an increasing hold on me, as the course was advancing. The diverse guest lectures about the microbiomes, the fungi, the host specificity of many organisms, the evolution of diversity and its maintenance through time, astonished me. How much this concept of ‘’I’’ versus ‘’nature’’ seems irrelevant, when you realize that your own body is composed of a number of bacteria of about the same order as the number of cells in the human body (Sender et al., 2016), and that it shares one third of its genome with most of life forms (McFall-Ngai et al., 2013). These common genes should incite us to revisit the very concepts of what constitutes a genome, a population, an environment, an organism (McFall-Ngai et al., 2013), and from my point of view, a family as well. Our species has been protecting its family for a very long time. At first, it must have been applied to direct descendants and relatives, then to tribes, to nations, to countries, and finally, to all human beings, by the recognition of human rights. There seems to be a trend in human evolution as we pass through an extended notion of family. In the past decades, there has been a growing awareness of the recognition of animals’ rights. What will be the next step? What will be included in this large definition of our family, our community?

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Source: Felipe Pérez Jvostov

As I was wondering about this relationship between humans and nature, how they can relate to one another, I recalled some readings of Alan Watt that I’ve done, about the eastern philosophies of Tao and Zen. I would like to quote some extracts of these readings, because I think the answers are not always in Science alone, and that it is important to make horizontal connections with other spheres of existence, such as philosophy, spirituality, arts, etc. Whoever might read this post, I hope this might trigger some further reflections:

ʺ We suffer from a hallucination, from a false and distorted sensation of our own existence as living organisms. Most of us have the sensation that “I myself” is a separate center of feeling and action, living inside and bounded by the physical body — a center which “confronts” an “external” world of people and things, making contact through the senses with a universe both alien and strange. Everyday figures of speech reflect this illusion. “I came into this world.” “You must face reality.” “The conquest of nature.”

This feeling of being lonely and very temporary visitors in the universe is in flat contradiction to everything known about man (and all other living organisms) in the sciences. We do not “come into” this world; we come out of it, as leaves from a tree. As the ocean “waves,” the universe “peoples.” Every individual is an expression of the whole realm of nature, a unique action of the total universe. This fact is rarely, if ever, experienced by most individuals. Even those who know it to be true in theory do not sense or feel it, but continue to be aware of themselves as isolated “egos” inside bags of skin ʺ

Finally, my stay in Panama will soon end, and I’ll have to come back to the winter of Québec. This first contact with tropical forests has definitely improved my understanding of nature, triggered many questions and made me want to develop a deeper relation with these ecosystems, such as the one I have with boreal forests. I will conclude this post with a quote of Albert Camus, because it is beautiful, and it embraces both the warmth and the cold. It also gives courage to those, like me, who have to come back to the northern latitudes.

‘’In the depth of winter, I finally learned that within me there lay an invincible summer.’’


McFall-Ngai, M., Hadfield, M. G., Bosch, T. C. G., Carey, H. V., Domazet-Lošo, T., Douglas, A. E., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S. F., Hentschel, U., King, N., Kjelleberg, S., Knoll, A. H., Kremer, N., Mazmanian, S. K., Metcalf, J. L., Nealson, K., Pierce, N. E., Rawls, J. F., Reid, A., Ruby, E. G., Rumpho, M., Sanders, J. G., Tautz, D. et Wernegreen, J. J. (2013). Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110(9), 3229‑3236. http://dx.doi.org/10.1073/pnas.1218525110

Sender, R., Fuchs, S. et Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. http://dx.doi.org/10.1371/journal.pbio.1002533