Tag Archives: Amy 2019

In the Corals and the Trees (Reflection Post) with species lists

The coral reef and the rainforest are the most diverse marine and terrestrial ecosystems, respectively. They both represent what seems on the surface a paradox—nutrient poor soils in the rainforest and nutrient poor waters in the reef, despite the incredible diversity of organisms in each place. Coral reefs actually rely on the low nutrient density of the water, because when there are more nutrients available, algae tends to outcompete corals. In the rainforest, the nutrient poor soils are due to the rapid nutrient cycling and wide diversity of decomposers facilitated by high temperatures and rainfall and necessary for the incredible growth present there. In addition, my taxon groups in the rainforest and on the reef were somewhat parallel: the trees in the forest and the corals on the reef. Each of these is the foundation of the ecosystem, photosynthesize (or have a symbiotic relationship with photosynthesizing organisms), and are incredibly abundant.

I took the wide diversity of each species as a challenge, and tried to identify as many as I could, although in each case some of the organisms looked incredibly similar to one another and occupied similar niches.

Unfortunately, when I set out to take this course, I saw the obstacle of my food allergies first and any academic challenges second. The result of this was that I was thoroughly prepared to avoid food allergens, and less prepared for the actual coursework. Despite this, I learned more in these two weeks than I think I ever have in two weeks before in my life: about the rainforest, the reef, and research in the field. Interestingly (maybe this is TMI) I have a skin condition and thought it would get worse on the trip. It did the opposite and flared up as soon as we returned to Houston. Allergies also turned out to be easy to deal with, as the cooks on the island and in the rainforest were very careful and had limited ingredients in the kitchen to begin with (fewer contaminants).

It’s hard to choose a favorite part of the course. We saw spider monkeys shaking trees at us to get us to go away (we just thought they were cute); a tapir on one of our camera traps (we all cheered!), scarlet macaws almost every day in the rainforest, the inside of a leafcutter ant nest. I think the most intriguing things I saw were zombie ants. Zombie ants are ants that are infected with a fungus that somehow compels the ant to climb up (in this case on a palm). The ant then clings to the inside of the palm and slowly dies as the fungus eats it from the inside out, then sends out a fruiting body (mushroom). We saw several of these, and some ants that were still moving but appeared lost on the bottom of palm leaves, possibly controlled by the fungus. The phenomenon is incredible and frightening, as when I’ve related it to friends and family one of the first questions they ask is “can that infect humans?!” The answer to that question is no. At least, no known fungus will do that to humans.

In addition to the course content, I think we all learned how to split up the work to get something done, and not obsess about the details (for those of us inclined to do so). For example, the first research project we did took all day to analyze. We spent the morning making sure each morphospecies (“species” identified as “species A” based on observable characteristics when the species name is unimportant) was carefully identified, and the entire afternoon making a poster. We had all of our graphs on a laptop instead of the poster itself, and had the one person with some of the best handwriting and drawing skills (Liz) draw the entire poster (no printing facilities in the jungle!). By the end of the two weeks, we could whip up a poster in a few hours, max. A few people would work on each section, and at least two people would write and draw on the poster. We were much more efficient, and still conveyed our work effectively.

Scott requested a species count for each taxon in the reflection post, so here those are:


Elephant Ear/ Guanacaste (Enterlobium cyclocarpum)

Trumpet tree (Cecropia peltata)

Caribbean Pine (Pinus caribaea)

Rosewood (Dalbergia stevensonii)

Billy Webb (Sweetia panamensis)

Nargusta (Terminalia amazonica)

Mahogany (Swietenia macrophylla)

Spanish Cedar (Cedrela odorata)

Bull Thorn Acacia / Bullhorn Acacia (Acacia/Vachellia cornigera)

Basket Tie-Tie (Desmonicus schippii)

Banana (Musa sapientum/paradisiaca)

Prickly Yellow (Zanthoxylum sp.)

White Poisonwood (Sebastiana tuerckheimiana)

Black Poisonwood (Metopium Browneii) (Tropical Education Center)

Fiddlewood (Vitex gaumeri)

Kapik/Ceiba (Ceiba pentandra)

Horse’s Balls Tree (Stemmadenia donnell-smithii)

Guava (Psidium guajava)

White oak sp. (Quercus insignis) (Tropical Education Center)

Sapodilla/Chicle (Manilhara zapota)

Give-and-Take Palm (Crysophila staurocantha)

Gumbolimbo/ Tourist Tree (Bursera simaruba)

Jobillo (Astronium graveolens)

Bay Cedar (Guazuma ulmifolia)



Elkhorn Coral (Acropora palmata)

Staghorn Coral (Acropora cervicornis)

Mustard Hill Coral (Porites astreoides)

Thin Finger Coral (Porites divaricata)

Grooved Brain Coral (Pseudodiploria labyrinthiformis)

Boulder Brain Coral (Colpophyllia natans)

Pillar Coral (Dendrogyra cylindrus)

Symmetrical Brain Coral (Pseudodiploria strigosa)

Golfball Coral (Favia fragum)

Lettuce Coral (Agaricia sp.)

Mountainous Star Coral (Orbicella faveolata)

Massive Starlet Coral (Siderastrea siderea)

Additional Siderastrea sp., maybe stellata, dead coral

Boulder Star Coral (Montastrea cavernosa)

Day 15: The city is too… city

We woke up before 5 to meet, with bags packed, at the dining building. Breakfast was a cinnamon roll for most, but since that contains milk and I have an allergy, mine was fresh papaya. The mood was subdued; in part, it was 5 in the morning. In addition, we were worn out and ready to be back home. We took a calmer three hour boat ride back to the coast, then took a van to the airport.

We had time at the airport to buy souvenirs. Some of the popular ones included Marie Sharp’s brand jam, of various tropical flavors, and Belizean hot sauce. A couple of the hot sauce names were No Wimps Allowed and BEWARE. They also sold Mayan carvings and weavings, some at pretty steep prices. The prices were a mix of Belizean dollars and US dollars; a US dollar is worth twice that of a Belize dollar.

Marie Sharp’s Jam from the airport

The plane was a bit delayed, but not so much I think that the three connecting flights were too much of a problem. Once we got to the Houston airport (IAH), we had to say goodbye to the three students who were catching connecting flights to go home. Since three of the students on the trip were from Vanderbilt and Baylor, respectively, there is a good chance we may never see each other again. After two weeks in close quarters, we got to know each other pretty well, and it was sad to see everyone depart. Although, I will say that by the end of two weeks in such close quarters, with everyone exhausted and itching, we were beginning to step on each other’s toes a bit.

The rest of us took a bus back to Rice. The city was a bit of a shock after the island and the forest—so noisy, rushed, and concrete! Despite a packed schedule, there were fewer worries in the jungle than in the city.

Day 14: We found a boat in the Mangroves of Death

This morning we combined a research project with an exercise in awareness, in addition to helping the island with a major problem. You see, an island that is in the middle of the ocean (not near shore) still, perhaps surprisingly, collects debris.

We split up into four groups and went to different sides of the island: The Dock, The Touch Tank (named such because we collected animals for a touch tank there on Day 11), The Coral Graveyard (where corals wash up on the shore; this is the windward side of the island), and an area we termed the Mangroves of Death. For some unknown reason—okay, because few people were willing to go—I went to pick up trash in the Mangroves of Death. For the uninitiated, Mangroves of Death are full of mosquitoes and also, in this case, sand flies. Our group of three students went out there to the jungle gym of mangroves and alternated picking up old rags, plastic bottles, plastic bags, and other trash and slapping ourselves to rid our skin of mosquitoes. Having anticipated this, I was covered except for my face. As it turns out, the sand flies didn’t care and bit me all over anyway, but the mosquitoes just clustered around my face. I tried to get them off with my arms, because I was using my hands to pick up trash and didn’t want to rub the dirt on my face.

The highest count of marine debris was at the Coral Graveyard, and we decided this could be caused by the fact that this was where trash would hit the island when the surface of the water was moving with the wind. However, the second highest count and the largest volume of trash was found in the Mangroves of Death. This was partly due to the large metal and foam boat pieces we found and dragged back with us. Another reason this could be the case is that the mangroves form a maze of roots that collects, in addition to water, trash. Trash becomes tangled in the roots, so we had larger pieces of trash in general, leading to a larger volume despite a slightly lower number of pieces. We also found mostly plastic. Despite 12 people spending half an hour collecting trash, we all felt like we hardly made a dent in the marine debris washed up on the island, despite the fact that the staff on the island regularly collect what washes up.

Kaela and me counting marine debris from the Mangroves of Death

After lunch we dissected lionfish. Lionfish are invasive in the Atlantic (native to the Indo-Pacific) and have few predators here, so they proliferate and are destructive to competing carnivorous fish populations and eat young commercially harvested fish species. That could potentially have an impact on the fishing industry. We measured them (ours was 21.5 cm, or about 9 in, long) and pulled out the stomach. Ours looked pretty full but the contents were not identifiable. Another group found a whole fish in the stomach of their lionfish.

Herbie with a lionfish

We then had a snack of lionfish ceviche, made with the same fish we dissected, and took a break to pack until dinner.

In the evening we had a brief social gathering on the dock, looking back on our experiences. But it wasn’t just socializing—Amanda tied her dive light to the dock and attracted lots of tiny shrimp. This attracts fish that feed on the shrimp, and fish that will eat those larger fish. Eventually we saw a few stingrays and a shark, all right under our feet on the dock!

Day 13: The Urchins

This morning we met in the classroom to devise yet another method for measuring reef health. We decided on counting sea urchins, because they play a key role in eating algae. In the absence of such herbivores, algae can begin to take over coral colonies, so we decided a healthy reef would have more urchins. Again, we assessed a reef inside and a reef outside of the MPA.

We found more urchins inside the MPA during the same amount of collection time with the same amount of people (same total effort). Fishing is restricted in the MPA and carnivorous fish are often a target of commercial fishing, so the decreased presence of carnivorous fish and thus greater quantity of herbivorous fish might exist outside of the MPA. Herbivorous fish compete with urchins for food, so a larger number of herbivorous fish could decrease the number of urchins outside of the MPA. In addition, the site we studied inside the MPA had greater coral cover, which provides places for urchins to hide and could increase their numbers by improved protection from predators. We identified 5 different species of urchins.

Pencil Sea Urchin

A few people are still feeling a bit seasick from the trip to the forereef, where the wave action was greater. By lunch, I was feeling a bit off as well, despite not diving down at the forereef. I surmised after it only took a few hours to recover that I had been too cold in the water while searching for sea urchins. By the end of the day I think most people felt better, but we are all exhausted. Despite that, we did lectures in the afternoon today so that after dinner we could snorkel at night.

The point of snorkeling at night is that we can see bioluminescence. Corals are interesting at night as well because they extend their polyps (many species retract them during the day). I had trouble taking acceptable photos in the dark, and I kept alternating between being right on top of my buddy (Keegan) and trying to locate him because I got too far away. He was wearing all black, and it was dark—I guess I was easier to spot at a distance with my white snorkel and mask. I ended up wishing everyone was wearing more distinctive gear, because though we were supposed to stick together with our buddies, it was hard to tell who was who. It was also hard to find the reef in the dark and we initially swam past it.

We did manage to see the coral polyps, and some large Spiny Lobsters! The rest of the experience was marred by accidentally kicking and being kicked by my fellow TFBers, and trying to stick my head up out of the water to see where everyone was. In total we didn’t see that much.

Day 12: Swimming in the depths

This morning we went out first thing to catch the calm weather for snorkeling and get off the island which was very buggy (because there was no wind). We went again to a patch inside and outside of the Marine Protected Area, and in each place counted live coral using a quadrat method, 10 samples over a distance of 100 m for 5 groups. We ran into more trouble this time: the first sample was thick with fire coral—we even had to put our quadrat on fire coral once. Some of the reef was also deeper and we had to dive down to count the coral.

Fire Coral

Then, we got in the water only to realize it was full of jellies, and we had to rush back onto the boat while one of the safety officers pushed the jellies away by pushing them by the heads. I didn’t see them, but we also saw comb jellies at that location. Amanda picked one up. It looked just like a handful of gelatin.

We went to another location outside the MPA without jellies to actually take data. I took pictures of corals when I wasn’t taking data, and I saw Golfball Coral (Flavia fragum) and another coral I still need to identify. There was still a lot of Mustard Coral (Porites astreoides) and I also saw some purple branching Porites, possibly divaricata again. Most of the Porites we have seen so far, excluding Mustard Hill Coral, have probably been P. divaricata due to branching near the tips, although a few times I have seen colonies that form thicker branches that might have been P. porites or P. fulcata. P. porites is generally greater than 1 cm wide, P. fulcata is is in between, and P. divaricata is less than 1 cm. I also saw some Grooved Brain Coral (Pseudodiploria labyrinthiformis), which has a groove on the ridge between valleys (the valley contains a row of mouths where polyps stick out (like most corals, these polyps extend primarily at night).

Amanda also saw one Montastrea cavernosa, which is the Great Star Coral. The surface is described in the ID book as “blister-like corallites”. They (the coralllites) are particularly large, size ¼ to ½ in. The colonies of corallites can get quite large, but the one Amanda saw was smaller. I saw only a picture. I also think I saw a lettuce coral (Agaricia). There are multiple species, but my picture is not good enough to tell the difference.

In the afternoon we took the boat over the reef crest (boundary of the ring-shaped atoll) to the forereef outside of the atoll. This is an area of greater wave action where corals form thicker, larger, and more robust forms such as massive or encrusting that don’t stick up into the water where branches could be broken off. This is also one reason the forereef has less algae than the patch reefs we have visited before, which were all inside the atoll in the lagoon, which is sheltered by the reef. We first swam along the wall, where we could not see the bottom over the ledge, then went to a patch reef closer to the crest.

We saw larger fish here too, including a reef shark and some larger Parrotfish. There were some very large Symmetrical Brain Coral (Pseudodiploria ———-). This species is actually very similar to Colpophyllia, but apparently Colpophyllia has deeper grooves, which is a common identifying characteristic in meandroid corals. However, it would be a much easier characteristic to use with more experience. From what I can tell in the ID book, Colpolhyllia also has wider valleys, so that may be used as an additional identifying feature. The most notable species of coral we saw on the reef was Dendrogyna, which is apparently rare (used to be more common). This is the pillar-shaped coral, and has a more bulky skeleton than other species. I think I also saw the Lobed Star Coral, which is Orbicella annularis. Its form is a group of lumps tightly packed and protruding from a hard substrate.

Day 11: We found an octopus!

Today we started out by measuring coral density inside and outside the Marine Protected Area (MPA). The island we are currently staying on, called Middle Caye, is on Glover’s Reef inside of an MPA. This area is patrolled by the Belize coast guard, especially at night. Commercial fishing is not allowed in the area, and part of the point is to prevent overfishing and coral damage in the protected area. We tentatively found that the MPA patch we surveyed had about 28% live coral over total area and the area outside of the MPA had about 18% live coral.  That would seem to suggest that the MPA is protecting the corals and allowing them to grow. However, we identified some improvements we could make to our methods and will repeat the assessment tomorrow.

When not measuring, I saw a few distinctive corals, including Acropora cervicornis (staghorn coral).

In the afternoon we walked out to the seagrass and mangroves and collected some small animals, plants, and other living things to look at in the wet lab. We kept them in buckets of water to preserve the creatures. We found a wide range of creatures in nearly everyone’s taxon ID groups, and Kaela even picked up a fireworm. It stung her and released stinging hairs, but she brought it back to the collection bucket anyway. Other creatures we saw included an Atlantic Pygmy Octopus, which could change color and tried to hide under the conch shells, live Queen Conchs, which have a beautiful sunset pattern inside their shells which unfortunately attract collectors (often overharvested and picked up by tourists), a West Indian Sea Egg, which is a kind of urchin that is dark with white spines and covers itself with sea grass, several other urchin species, three-finger leaf algae, other Halimeda algae, Pearl algae, and a ton of hermit crabs.

In terms of coral, we picked up a Porites species and a Siderastrea species. Porites is a branching coral with corallites that are generally flush with the surface of the coral (they don’t stick out like Acropora, which include Elkhorn and Staghorn corals). This one branches near the tip and is probably P. divaricata due to that characteristic and thin branch size. The species is also called Thin Finger Coral. The Siderastrea are called starlet corals, and the one we picked up I think was S. stellata.

Siderastrea stellata, finger for scale

Day 10: Getting our sea legs

This morning we met after breakfast at 7:45 to use a quadrat measurement method in a coral graveyard (a rocky shore composed mostly of coral fragments). We measured coral density at the crossections of the strings in our quadrats, then computed a density of around 30% (A rough measure of exclusively recognizable corals, as most fragments were originally corals). We then brought some dead corals back to the wet lab (area beneath a building on stilts) to identify. We were able to identify Siderastrea (possibly radians), Mountainous star coral (Orbicella faveolata), Symmetrical brain coral (Pseudodiploria strigosa), Golfball coral (Favia fragum), Pillar coral (Dendrogyra cylindrus), Lettuce coral (Agaricia sp.), and possibly Mustard hill coral (Porites atreoides), and Staghorn coral (Acropora cervicornis).

A note about identification of the corals above: Orbicella spp. have grooves between polyps, while Siderastrea spp. has a smooth surface.

We went after lunch to try quadrat measurement in the water. It’s difficult because you are trying to maneuver this square made of a square of pipes with a women net of string while the current moves you, the quadrat, and the seagrass we were trying to count to quantify the difference in seagrass coverage between a seagrass patch and one of mixed seagrass and algae. When we try a similar procedure on the coral, it may be easier because at least the coral won’t wave back and forth.

Seagrass, quadrat and transect method

After that practice, we swam out to the patch reef and saw corals! Some others saw a nurse shark, but I was unfortunately too busy struggling with my foggy mask. I did see the Spiny Lobster, though. You can recognize them because their antennae are long and poke out from under rocks.

Also sand flies. They are essentially little biting gnats. They invaded our dorm. And we (mostly Cassia and Anna) spent a good hour trying to kill them all by slapping them with a notebook while they were still around the ceiling light, knowing they would disperse and spend more time biting us when we turned the light off. Lesson learned: close the door quickly. The sand flies are everywhere.

Day 9: Not ideal conditions, but coral!

Today we left the Tropical Research Center and took a 3 hour boat ride to Middle Caye on Glover’s Reef. As soon as we got here, after an orientation and lunch, we got in the water (around 2pm). The problem: The water was a bit choppy. We could tell on the boat ride over. One of the crew said he’d seen worse, but it got pretty rough after we passed the barrier reefs (a good demonstration of the sheltering effect of reefs!). The boat ride was actually kind of fun in this weather, but snorkeling, not so much. I ended up breathing in some seawater in an area where I couldn’t stand because we just jumped right in.  Fortunately we dove from the dock, so we weren’t far and one of the safety officers helped me and a few others get back to shore. In case you were wondering, and without too many details, breathing seawater is a bad idea. I was fine after recovering on shore for at least an hour.

Instead, we went to the shallow wade-able reef at the other side of the caye. We finally saw coral! Mustard Hill Coral (Porites astreoides) was on several of the clumps of coral we tried to avoid stepping on. We also saw several brain coral, which I think were all symmetrical brain coral (Pseudodiploria strigosa). There were several sea fans, though I’m not sure yet what kind. The most likely options are Venus sea fan (Gorgonia flabellum) or purple sea fan (Gorgonia ventalina). Most of these corals looked healthy. We tried not to kick sediment on top of the reef formation.

Shallow side of the island (Middle Caye)

We started a scavenger hunt which will be ongoing. Here, we found Christmas Tree Worms, Scleractinian (stony) corals, Gorgonian (soft corals), endosymbionts (corals) and several other items on the list.

Day 2: Tour of the Caracol ruins

On the way from the Crystal Paradise Ecolodge to the Chiquibul forest and Las Cuevas Research Station, we stopped in two different places: Rio on Pools (in the Mountain Pine Ridge) and the ruins of Caracol, and ancient Mayan city.


At Rio on Pools I took several pictures of trees that I want to identify when I get a chance (during daylight hours, when I can read the field guide). Of course, we saw the Caribbean Pine, which characterizes the Mountain Pine Ridge. For anyone reading this who does not know the regions of Belize, a ‘ridge’ is a description of a general area/ecosystem and not an actual landform of high elevation. I spent most of the time taking pictures, alternating between the trees and my classmates.

Rio On Pools
Rio On Pools

The Caracol experience was more notable in terms of learning about the region. The first time Scott came on this trip, he did not go to the ruins, but local people told him that it was entirely unreasonable to be this close to the ruins and not see them. The palace at the ruins of the ancient Maya city is the tallest building in Belize, and from the top (of course we climbed it!) you can see Guatemala. We learned quite extensively about the Maya for a few hours (religion, culture, social structures).


Caracol, from the top of the tallest palace/pyramid

We also saw tons of trees. Our guide pointed out the Kapok or Ceiba tree (Ceiba pentandra) and the fluff that comes from the seed pods that I think he said was used as padding, for example in a mattress. The tree also has huge buttress roots extending from the sides that serve several purposes, including structural support and nutrient absorption. [insert picture here]

Kapok tree (Ceiba pentandra)

We also saw today:

A few more trees at the Maya site: Cohune palm (Attalea cohune), Fishtail palm (Chamaedorea sp.), more Trumpet tree (Cecropia peltata), relationship with guarding ant species, a Strangler fig (Ficus sp.), and some Montezuma Oropendolas (Psarocolius montezuma).

Fishtail Palm, Chamaedora sp.

At Las Cuevas: a Cedar (Cedrela odorata), A Scarlet Macaw (Ara macao) and a Social Flycatcher (Myiozetetes similis).

We don’t have internet today because of the weather. It appears that the rainy season has started early this year. We will get to see how that effects the visibility of our focus species.

Day 3: Monkeys and the Monkey Tail Trail

Today we set up the camera traps for our week-long research project. We are testing the impact of the human disturbance at the research station is significant on diversity of animal species, so we will count species and individuals caught on the traps over the week. Setting up the traps involved hiking multiple trails in the area, so we saw a lot of wildlife.

This morning we hiked to a 50 hectare plot, which is an area marked for research purposes, to set up three cameras in that direction at 15 minute walking intervals. Onn the way there, we saw a mahogany and a fiddlewood tree, which were marked by the research station. In terms of trees, we saw Give-and-Take palms, another spiny palm called a Basket Tie-Tie, several Gumbolimbo trees, and at least a few Sapodilla. We also saw a small tree that I thought might be a Poisonwood tree, but it was too small to tell for certain. I was using leaf characteristics for identification—none of us were willing volunteers to test out the burning properties of the caustic sap.

Chicle/Sapodilla (Manilhara zapota) with slash marks from harvesting sap for chewing gum

On the same walk, we also saw spider monkeys for the first time. They remained high up in the branches, but hung around to look at us. It seemed they were as curious about us as we were about them. “Observe how poorly acclimated to the forest are these humans,” their tour guide could say. And that would be true, although Scott said we would find the hiking easier at the end of our stay here. We did not measure distance, but we spent a few hours in the morning and another few in the afternoon hiking out to place the cameras.

In the afternoon we hiked the Monkey Tail Trail. It was threatening rain, but we only got a few drops and a few distant thunderclaps. It is possible that the rain was captured higher in the canopy by epiphytes (some of these are known as airplants) or other organisms and did not reach us on the rainforest floor. The trees we saw on this hike included more Gumbolimbo. I could see why this was called the tourist tree. It is given the name because it is red and peeling like the sunburn of a tourist unaccustomed to the intensity of the sun here. It is also used locally as a remedy for a range of ailments from colds to gastrointestinal problems to measles to sunstroke. We also saw the Bull Thorn Acacia, which has hollow pairs of thorns in the shape of a bull’s horns which are inhabited by ants. The tree produces food and provides shelter for the ants in a way that induces the ants to defend the tree as they would any other nest. As a result, if you disturb the tree (especially if you break a thorn), you may be attacked by ants. This protects the tree from predators and describes a symbiotic relationship because both species involved benefit.

In addition to some interesting beetles, we came back from the hike with quite a few ticks each. Apparently ticks here don’t carry any serious diseases, but are mostly a nuisance. Picking them up today was the result of travelling an overgrown trail, and especially affected those who were not wearing insect repellant and/or were not trying as much to avoid brushing against the brush.

Note: We still have very limited wifi and may not be able to post at regular intevals.