Impressions of Bocas

Our last field trip was to the archipelago of Bocas del Toro on the Caribbean side. This trip was one of my favorites because Bocas will soon be my new research area, and the lectures and field activities were very rewarding.

For our first snorkeling immersion we visited, with Aaron O’dea, one reef where the main component was some patches of Acropora cerviconis. The population of this species, which once was relatively common from Florida to Venezuela, had been collapsing since the 80’s due to different threats like disease outbreaks, mainly of white band disease, algae overgrowth and human impact. This decreasing of this species happened to be around the same time of the mass mortality of the sea urchin Diadema antillarium which is an algae grazer in reefs, and usually is helpful to create space for coral recruits.

Picture via Flickr

From my perspective, the reef in that particular immersion didn’t seem very healthy. There were only a couple of patches where other fish could be seen swiming with the few damselfishes found throughout the reef.  This made me think a lot about the “shifting baseline,” a concept that usually crosses my mind due to the all the environmental changes that are happening now, and also about how fast these changes are happening, and what we can do to preserve or restore the coral reef ecosystem, so that we may share it with generations of humans, fishes, sponges, and sea urchins to come.

Picture via Flickr

Later during the same trip Nancy Knowlton mentioned something that I think is very true and meaningful. A lot of times we believe that the big players like climate change and acidification have already taken over, and do not place much importance on what can be done on the local scale. If we take a look, there is a big difference between ecosystems where human activity is taking place and areas that are more “pristine,” even though climate change is affecting both. I think this is beautiful, because there is an opportunity for the consciousness of the biggest player, which happens to be us, to effect a change.

Thanks for reading!



Eavesdropping on nature

One of the two core themes of the Integrative Tropical Biology course is that detailed and intimate understandings of the natural history of a given model system are essential to be able to ask meaningful questions and apply modern technologies to experiments in that system. In biology, there seems to be an increasing trend toward more and more complex and technical conclusions made about systems, based primarily on laboratory or bioinformatics studies alone. As our technological capabilities keep accelerating, I think that there will be an increasing need for scientists who understand the basics of natural history and ecology, in a broad sense. These types of people will be essential to keep our conclusions grounded in biological and ecological relevance.

Understanding natural history begins with keen observation of the natural world. Daily attentiveness and curiosity must be cultivated. An excellent example of a scientist who embodied these talents is the late Thomas Eisner, an entomologist and chemical ecologist extraordinaire. In his astonishingly illustrated reflections on a lifetime of discovery, For Love of Insects, he writes in the afterword that many of his discoveries were made by “eavesdropping on nature.” He would then follow his observations with slight manipulations of the system, to see how a perturbation might lead to ideas for controlled experiments.

Bullhorn acacia (Vachellia cornigera) spines and foliage

On 12 January 2015, on a course field trip to the Smithsonian canopy access crane at Ft. Sherman, our group had ample time and space for making observations as we walked on the gravel road and peered into the ruderal vegetation along the edges. One plant encountered on the walk was the bullhorn acacia, Vachellia cornigera. Known as cachito (“little horn”) in Panamá, this small leguminous tree is an oft-cited textbook example of a myrmecophyte. Wanting to get close enough to see if I could smell the alarm pheromone of the protective ant, Pseudomyrmex ferruginea, and watch the hordes emerge from their hollow stipular spine domatia, I approached with caution. After seeing the ants, one of the first things that I noticed on the acacia was a caterpillar resting on a spine, in a still posture with its body held erect from the spine (see photograph below). The ants would occasionally contact the caterpillar, but did not seem even to pause and sense its presence. Intrigued, I decided to remove the medium brown larva from its perch and place it on foliage to see if that would elicit an aggressive response from the ants. To my surprise, the geometrid (I now knew the family by the caterpillar’s “Earth-measuring” gait), inched along rapidly, immediately back to one of the nearest spines. The ants did seem to respond with increased activity, but when they encountered the caterpillar, they merely antennated the body of the larva and moved on. The caterpillar returned to a resting state. From this, I wondered what the caterpillar was doing in the acacia. Was it an herbivore? Was it providing any benefits to the ants? How did it avoid being attacked by the ants? Did it have chemical signatures that the ants might be recognizing as self semiochemicals?

Geometrid larva on acacia spine

In the few minutes that I spent at the tree, while enduring several ant stings, I happened to notice two other arthropods in the tree – a scarab beetle (I think likely a ruteline) and a salticid (jumping) spider. I was surprised to see the scarab feeding on the acacia leaflets, and apparently tolerating ants that were swarming on it. Could the ants not penetrate its smooth, tough exoskeleton? What about the spider? It was resting on the Beltian bodies at the leaflet tips. I had heard of a fairly recent report of a “vegetarian” jumping spider, but the one that I saw did not appear to be Bagheera kiplingi. Unfortunately, my hiking partner and I were already far behind the group and we could linger no longer. Our observations would remain only observations and extrafloral fodder for thought for the time being.


‘The Machandai’ chocolate has a taste that reminds me of the past’

In the community of Charagre in the district of Changuinola Bocas del Toro, exists a humble family that, has been devoted to the production of chocolate for three generations.

Mr. Lozada explained the production of chocolate from ‘Cacao” has been their livelihood that since the time of his grandparents. . However, even more than the preservation of tradition, what gives the family the most pride and distinction is that their cocoa plantations are based on an agroforestry-sustainable system. He explained that they had learned of this system of agriculture from their ancestors. The cocoa plantations are situated amongst other plants such as bananas, plantains, and trees used for wood, like cedro, caoba, etc. The use of agrochemicals products is avoided; therefore the chocolate is considered Organic. 

Mr. Orlando Lozada

Mr. Orlando Lozada Photo credit: Librada Atencio


As an alternative method to agrochemicals, monitoring is used for pest control on these plantations. For example, when small seedlings are monitored and a plague is suspected, the plant or just its leaves are eliminated. The fruit is also monitored and is removed if either the Phytophora and Monilia diseases are present. The latter is classified as an algae, which is extremely aggressive for cocoa beans, as it completely destroys the fruit.

Monilia disease

Monilia disease Photo credit: Librada Atencio


The Lozada family also uses organic compost from other sites as a sustainable resource. This is one of the ways that they use all the resources at their disposal, reducing expenses and increasing sustainability.

Currently the chocolate is sold under the label ‘Machandai’ which is a very meaningful name for the entire Bocas del Toro town and will be marketed by the ASAP (Association Silvo-Agropecueria), in which many Bocatoreños, including small farmers, engineers and doctors (see

The Machandai name was selected because it refers to the railroad that existed for many years in that area and whose function was to transport dry goods (mainly bananas) and thousands of people. The railroad was key to the economy of the region of Bocas del Toro.

Demolition train of the banana transport railway, of the Bocas Fruit Company between Almirante and Changuinola with locomotive 817 (GE 32 tons). (Photo: Patrick Rudin)


The Machaindai, both in name and product, is a reminder of the rich history and agricultural traditions of the region.

By Anakena Castillo (Indicasat-aip)

Reflecting on a nest

Let us step out onto the front porch of the schoolhouse, it’s another beautiful day in Gamboa!

Front porch, Gamboa Schoolhouse, picture by Elise

Front porch, Gamboa Schoolhouse, picture by Elise

Say, what’s that?  Look up there!


See that clay colored robin up there, sitting on a nest?  Gosh, how cool!  This brown bird is the national bird of Costa Rica, chosen in part because it is common and familiar to the majority of the population.

It does seem unusually early for this species to start nesting, as previous studies in the area (over at Summit Gardens) found the species breeding from about late February to mid-June (Morton 1971, Dyrcz 1983). Still, let’s check the nest!

Eggs in the clay colored robin nest on Gamboa School House, picture by Elise

Eggs in the clay colored robin nest on Gamboa School House, picture by Elise

Why, it’s incubating!

(My feet never left the ground, this was all a matter of attaching things together to give me enough reach, safety was a top priority here)

Four eggs, which is in the range for the species although on the high end and a good deal higher than the modal clutch size in the tropics (2 eggs).  One egg looks a little small, if it survives to hatching, it may still wind up starving as smallest nestlings sometimes do…  Perhaps the fruiting trees provided sufficient resources for the parents or, perhaps, because we’re in a human-dominated area, there may be other food sources that these birds can count on (but IF food for adults sufficient for growing nestlings is another matter altogether).

It makes one wonder.

We live in a rapidly changing world. Even if temperatures don’t change rapidly in the tropics, rainfall patterns are expected to shift.  Morton (1971) suggested that high rates of nest predation during the rainy season drives these thrushes to breed in the dry season. Will those predators track changes in the rainfall regime?  Depending on the direction of change, it could go either way for these common birds.  What might happen for rarer (and thus potentially more vulnerable to extirpation) species if nest predation pressures change?

This nest is right here, on the Schoolhouse, right above the door where there’s frequent (but not necessarily predictable) human presence.  The human population on this is boiling, bubbling, burgeoning up past the 7 billion mark, predicted to race towards 8 billion by the next decade.  The tropics are predicted to experience dramatic growth in human population (with rapid and unplanned urban expansion occurring as a consequence). That’s going to make it (even more than it already is) very, very difficult to address big problems like climate change (and it really won’t be fixed JUST with individual action.  Do your best, do your part to help, but the commons are pretty tragic, huh?), urbanization, food security, etc.

Now, Gamboa sure isn’t a big city, but the habitat has been altered by and for human habitations (and, well, the giant canal with the gigantic boats going through right over there was a pretty major alteration to the area too…) and small towns can also alter wildlife populations. Avian populations in more urban habitats, where there are concentrated sources of food and potentially reduced rates of nest predation, may remain viable due to high rates of survival and higher numbers of offspring produced per female(Stracy and Robinson 2012). However urban areas may become ecological traps in which immigrants settle into lower quality habitat and face novel sources of mortality, such as from collisions with vehicles (Stracy and Robinson 2012).

The combination of climate change and urbanization may be just a bit too much instability for species to deal with, perhaps a breakdown of biotic interactions will occur when one species is less able to tolerate human-induced changes, perhaps populations persist in certain landscapes only because adults become sedentary once a territory is established even if they are unable to generate offspring, perhaps I’m thinking too much about one early-breeding pair of thrushes that are probably pretty tired of the fool with a camera on a stick pestering them for photos.



Dyrcz, A. 1983. Ibis 125: 287-304

Morton, ES. 1971. Science 171(3974):920-1

Stracey & Robinson. 2012. Journal of Avian Biology. 43:50-60.

A species by any other name (may be just as irrelevant)

When I was a bright-eyed, attentive freshman in my first biology survey course in college, I thought the definition of species was cut-and-dry with few exceptions. Species was the most basic unit of taxonomic structure, outlining individuals that, under natural conditions, could mate and rear viable offspring. Great, I thought, clapping metaphorical dust off my hands, let’s store this somewhere for an exam and not worry about it. Fast forward a bit: in the past few weeks, I’ve realized that I don’t understand the first thing about species or speciation, nor do I know if we’ll ever have an understanding that doesn’t involve a fair deal of hand-waving and/or philosophical reasoning. In this post, I’ll give an example of the species problem, and I promise nothing will be resolved.

Oscar Puebla’s lecture at Bocas del Toro considered reef-dwelling hamlet fish as models of adaptive radiation. Hamlet (Hypoplectrus spp) populations diverge in marine environments, where speciation within a local environment cannot be so easily attributed to geographical isolation. Though hamlets are similar in an ecological sense, they’ve radiated to give rise to a number of colorful phenotypes, somehow having reproductively isolated and branched off to form new species. Using RAD-seq, an inexpensive way of comparing genomes while skirting around the issue of not having a complete assembly, Puebla compared two species that rarely hybridized, but were able to produce viable offspring upon doing so. Perhaps to be expected, the divergence was ridiculously low, to a point that fancy statistics were required to pick out a lowly SNP that stood out as the only real difference between the two. And it was in a Hox gene. Not some master regulator transcription factor, just a developmental patterning gene that I probably learned about in that same class where they lied to me about what species meant. Could such outstanding phenotypic and behavioral divergence be attributed to a change in developmental patterning? No. I don’t think so. But these findings are by no means uninteresting; they point to much bigger questions we need to ask.

Okay, sure, the genomes aren’t complete, maybe the divergence is actually higher. Still, I am coming to terms with how poorly I understand the question of what makes two species distinct, at what point do two populations of organisms go from mating to hybridization to reproduction isolation? The non-mating rule, which I once held fast as unbreakable, is so commonly violated in natural settings, so scratch that one (even some ligers aren’t sterile, ya’ll). What level of divergence should we require before we say one species is not another, and when can we safely conclude that?


On the big connections

Since the IGERT – 2015 started, the big boss keep saying “it is important to make big connections, god dammit!”. Of course, he has not said it this way but he has always made clear the importance of making big connections, from ecology and evolution to social and environmental issues. However, the lectures that gringos and Latin American students attended to show that such connections are a big challenge to young and dinosaurs researchers. But why?

897a918834677201c3a4d7761a3ae5741d6780a9Well, we only have two eyes. In fact, our understanding and explanatory capacity decrease with each variable that is added in whatever system we want to elucidate. How salinity, temperature, and rainfall influence the life of estuarine organisms, for example? Only three variables in a system and I doubt anyone can easily give a reasonable explanation, even though we all might know they do have an influence. However, the issue here is exactly to understand how they interact to play a role in the life of these organisms; more importantly, we struggle to understand whether to which extent the influence of one of these factors change with variations in the two others. What about the niche of species? So many axes that potentially explain how species distribute and interact with others that one can get crazy! And if we integrate the niches of all species in a community to get to know what’s up over there? Dude, that is crazy.

continuum                    Another issue is that scientists who do not work in social or natural resource management are not interested in integrating their know-how in applied science. This is more an opinion than a fact. What I know is that many professors I had/have contact with in academia do not like applied science. The other way around is also true: “so, your research does not have any utility for people?” I have heard that a few times…Pure applied scientists also seem to not care or are really skeptical about basic, pure science. Anyways, things are connected not matter what.



Communication issues among scientists are another problem. They arise even between ecologists and evolutionary biologists so it is not a surprise it also occurs among basic and applied science researchers. One say “come around”, the other understands “camarón”. This one is to me the least of the problems, though:

2014-10-10-TGAG_491_Applied_Scienceit potentially can be fixed, while the others do not seem to be easily solved. If scientists are interested in answer the big questions that inevitably arise from THE big connections, they will be more likely to find an “oreo in the dark”, the big answers they are looking for if they are willing to fix such communication issues instead of giving up. It might be difficult though, with so many things to deal with…

I would like to end up this blog post with something cool or funny, but I do not have any. So I will just say that the more we try to make big connections the happier the big boss will be, the more beers we get, and the more we find the big answers we still do not have. In a world which is constantly changing, such answers are fundamental to change how we deal with our surroundings (environment and social interactions).


Connections are broader than expected

From the onset of this course it was made clear to us that its primary goal was to enable us to identify connections. The course topics spanned coexistence theory, life history theory, kin selection, natural selection, and sexual selection (to name a few) and our in-house and in-field lectures covered an equally diverse array of organisms. How are these theories united? How can we use concepts from one field to address questions in another? How can we integrate genomics with trait variation with species distributions? Essentially, how can our questions and methods replicate the same scaling up of complexity that we witness in nature? This course immersed us into highly complex systems, both physically and intellectually, and therefore provided the perfect environment to begin developing creative questions.

But as we now wrap up our studies, I can see that the connections we made in this course far exceeded those of an environmental nature (and I think this may have been an unspoken goal): We established connections within the scientific community.

Across biological disciplines, the scientific community is changing in the same direction: fields are getting too crowded, and competition is increasing at any accelerating rate. As many of my mentors have told me again and again, “we make too many PhDs”. We’re constantly confronted with the dogma that, through replacement, each PhD advisor will have only one PhD student that obtains a tenured faculty position. We have H-indices to quantify our scientific impact, an increasing quantity of articles that we’ll never have time to read, and the future of funding often appears grim. To put it bluntly, the competitive atmosphere of biology is scary.

In addition to generating novel questions and publishing elegant science, establishing connections within the community is critical. By connecting with members of the scientific community you increase your chances of success. One positive meeting may generate a collaboration, or give you an advocate on a search committee, or lead to a great postdoc opportunity.

This course has awarded us a tremendous opportunity to meet exceptional scientists in a low-stress environment. Most grad students meet researchers during the hustle and bustle of conferences, when everyone is struggling to combat psychological exhaustion with a never-ending drip of caffeine. We met researchers during non-chalant walks through the forest and followed up with casual conversations over dinner. Instead of the conference-style blitzkrieg of 30 talks in two days, we enjoyed 30 talks in three weeks, with time to digest and discuss the questions that really struck us. I feel fortunate to have met and connected with so many scientists on this trip, and to have been so warmly welcomed into the STRI community. I am sure this course will jump-start our careers in more ways than we could have expected.

-Tara E. Stewart-

A place we didn’t wind up going to…

Well, we didn’t actually get to Isla de Pajaros in Bocas del Toro.  It’s a pity, as it’s a pretty dang awesome place (I mean, birds!  Lots of birds!  It must be that system pride thing, but it’s acceptable because they’re also dinosaurs).  I’d planned a bit of a babble on the seabirds there, and it seemed an alright topic for a blog post.

So, check out this lovely rock!

Pictures taken by Elise

Pictures taken by Elise


At this site, we could’ve seen Red-billed tropicbirds, Magnificent Frigatebirds (up close!), and brown boobies with babies (oh, come on!  Sure, birds get common names that sound mildly inappropriate, but…).

We have seen Magnificent Frigatebirds- perhaps the only seabird that is strongly sexually dimorphic (and, interestingly, females tend to breed every other year due to long post-hatching care of the young while males breed more frequently, thus they don’t really have that long-term pair bond thing going (seabirds tend to have lowish EPC rates and high fidelity (at least to the site))- fairly regularly during this course (they’re the big ones that sort of look like the mental image of a pterodactyl in flight (apparently they can remain aloft for days while they forage)).  These birds are rather well known for their kleptoparasitic behavior, attacking other seabirds and stealing prey, although it may not make up a significant portion of their diet (Vickery and Brooke 1994).  When not stealing hard-won fish from boobies (okay, fine, you are allowed to laugh it out…), frigatebirds feed on fish and squid at the surface (apparently a soggy frigatebird is a drowning frigatebird, they rarely deign to touch the waves).

Seabirds tend to live long (37+ year old frigatebirds for example, and that 63 year old Laysan Albatross (the oldest known bird in the Northern Hemisphere) that was still raising chicks on Midway), reach sexual maturity late, usually have a single egg (or siblicide that will bring the number of chicks down to one in the end), and extended parental care.  At least in some more temperate zone breeding seabirds, if forage fish drop below a certain abundance threshold (one-third of maximum biomass recorded) then seabird productivity is consistently reduced (Cury et al. 2011).  As these birds tend to breed once a year (or once every other year in some cases), reduced productivity isn’t something to sneeze at.

When you all next head back to visit Bocas del Toro, please swing by to Isla de Pajaros and say hi to the seabirds!


Wind or lose?

Today, the use of electric energy is more than a need. That’s why the search of alternative electricity generation is increasing in our country (I am talking about Panama), but how much more we will lose?

For example, a few years ago the construction of a wind farm was planned in Fortuna Forest Reserve. This Project wanted to install 75 wind-turbines (in two stages) able to generate 150 megawatts. According to the environmental impact study reviewed by the National Authority of Panama the localization of the wind farm was selected based on the wind power in the zone (14 m/s). But the study did not show the number of trees that would be felled.

Photo by Librada Atencio

Fortuna Forest Reserve      Photo by Librada Atencio


The Fortuna Forest Reserve has 19500 hectares of montane wet forest and the average temperature is 16º C. It is located at north of the province of Chiriqui, corregimiento of Gualaca. It forms part of the Mesomerican Corridor; with a huge diversity of plants (170 species/ha) and a diverse community of animals- most of them threatened species, including jaguar, tapir and puma.


Fortuna Forest




Big Tree

Studies have been carried out in this area showing the relevance of the preservation of the forest, from surveys of trees and animals to monitoring of the effects of climate change on a tropical forest.

I am not against the use of alternative ways to generate electricity as wind farms (because the energy is clean and cheap to produce, if we compare with the conventional forms to get electricity), but we need to pay attention to the places selected for the construction of such huge structures. In the case of Fortuna Reserve, the wind-turbines would also have a severe impact on the capacity to generate hydropower.


¡Gracias por leer!/ Thanks for reading!

-Librada Atencio-



External links


System Pride

Most scientists will tell you that their study system is the best study system. If they use a model system, their system is the best because it’s easy to bring to the lab, it’s appropriate for a broad array of questions, and it already has decades of research built around it. If they use a non-model system, it’s perfect because it adds to our understanding of global diversity/processes, it represents an open niche for one to make their name, and it may be more likely to reveal novel discoveries. But the degree to which a study system is defended and justified varies greatly across systems, and it seems as though system pride often increases as a function of distance from humans.

System Pride

 The invertebrate biologists go bonkers for their barnacles.


 The plant ecologists take pride in their perennials.


 And the soil biologists smile at the stratification of the soil pit they’ll push you into if you dis their soil.


And there is an awful lot of system pride among the parasitologists, who are constantly defending their work because of the disgust that’s so attached to the term “parasite”. We study the “abusers of life”- the reviled alien creatures that live in guts, tissue, and feces. A cheetah may kill an antelope instantly (forever ridding its prey of true love, happiness, and reproductive success) while the lowliest tapeworm may only take a few bites. But – let’s face it – to most people that cheetah is way sexier.

parasite cheetah

Due in part to their system pride, parasitologists have recently begun to ask an important question: what role do parasites play in ecosystem function, and how are parasites important components of biodiversity? And recently the BBC did a piece on just this question, asking:

“What would happen if all the parasites disappeared?”

You should definitely read the article for yourself if you get the chance. The author, Lucy Jones, interviewed a number of eminent parasite ecologists, including Andres Gomez, Kevin Lafferty (who we met in Bocas), Jaap de Roode, Levi Morran, and Luis Zaman. And the piece quickly became an interesting thought experiment, covering everything from human health, to population regulation, to niche partitioning. One scientist even posited that, in the absence of host-parasite red queen dynamics, sex would disappear!!!

The moral of the BBC story was that, without the tremendous diversity of parasitic interactions, our world would change drastically and probably for the worst. And I certainly believe that to be true. But is that really unique to the disappearance of parasites? It seems the complete disappearance of any group of organisms would cause fundamental changes in the way our ecosystems work. Try to imagine a world without vertebrates, a world without invertebrates, a world without plants, or… a world without soil.


System pride may sometimes seem silly or even annoying, but it is integral to the progress of biology. It is developed through a deep and intimate knowledge of a system- and without it, we would not have the understanding of each system’s importance to our world. We need the bird lovers, the fossil hunters, and the fungiphiles. We need people who are passionate about different units of biodiversity, as well as the connections that link them.