Many of us like coffee. Love coffee. And consume so much coffee. So maybe I should not be that surprised to learn that coffee is the second most important commodity in the world (petroleum being first) exported by developing countries. When coffee comes to our minds we may wonder how it is that coffee can taste so great and be so popular, or how it is prepared and served in so many different ways. The sad thing is that often we may not really think about where does coffee exactly come from, as well as who was involved in all the many steps until it finally arrived to our cups. The second course that we took (Foundations in Environmental Policy, given by Prof. Gordon Hickey) forced us to think deeply in some of these issues, such as the challenges any supply chain poses (specially as our daily lives become dependent on more and more globalised products). Thinking about these issues can make you feel uncomfortable, frustrated and confused (as it really did), but also despite the initial powerless feeling when dealing with such complex issues we realised that we as consumers have not only a significant power but also the minimum responsibility to be informed consumers (which ideally should lead to responsible consumers).

Documentary  “Black Coffee” (in small letters “A glimpse into the dark side of the brew”) directed by Irene Angelico. A great film about the history of the coffee, the beginning  of the coffee industry and the current state.

During our field trip to Fortuna we visited two very different farms (and not so much for what they cultivated but for their approach): a coffee plantation in Boquete and a cacao farm in Changuinola. The coffee plantation owner seemed particularly  focused on the quality of the coffee (rather than on sustainable practices, for example he did not believe in shade-grown coffee because he thought its lower yields would not improve poverty conditions). I found this a bit shocking (probably due to my biologist bias) because he did not seem to consider that shade-grown coffee could be the a sustainable practice benefiting both the environment and the farmers. On the other hand, the cocoa plantation  farmer came from a family tradition where more environmentally-friendly practices were encouraged: the cacao trees were grown with other tree species, and the cattle ranching was based on a silvopastoral system. During our visit I thought  about these initiatives we hear more and more about: fair trade products, organic products and shade-grown coffee, and wondered how they would apply (or could be) to the farms we visited. Although the issue of whether these initiatives actually work and are making a difference has been debated (for example see “The Problem with Fair Trade Coffee”), for now I just wanted to review some of them by focusing on their philosophy.

Coffee can be fair-trade, organic and/or shade-grown certified (some of the most common certifications). And a particular coffee may have one, two or all of these three. Although the goals of these initiatives overlap in some areas, their conditions and standards differ relative to their priorities. Fair-trade certified coffee (certified by third-parties such as the FAIRTRADE Foundation, or Fair for Life) aims at ensuring a fair price for the farmers in developing nations who grow the coffee, while at the same time promoting fair labour conditions, community development and sustainable practices. This is achieved in part by establishing direct, long-term contracts with the farmers and by agreeing on a minimum price for their coffee (for protection from the market fluctuations). On the other hand, organic certified coffee focuses on the production of coffee without chemical pesticides and fertilisers, as well as using environmentally-friendly practices such as multilayered crops and multi-species plantations. And finally, shade-grown certified coffee (the opposite of full-sun plantations) aims at returning to the way in which coffee grows naturally (hybrid coffee was created to grow under full sun conditions, which gave rise to the creation of massive coffee plantations due to the higher yields obtained, but at environmental expenses). Shade-grown coffee ensures the protection of the soil, bird populations, carbon sequestration and benefits farmers with the resources they are able to obtain from the non-coffee trees.

 

Interesting, the Smithsonian Migratory Bird Center created the “Bird Friendly” certification label, which requires the coffee to be both organic and shade-grown. One of their main claims is that their certification is based on solid science and rigorous controls. They analysed several studies in order to compare shade-grown coffee vs. full-sun plantations and concluded  that “shade-grown coffee is the next best thing to a natural forest “, as it is able to provide all the following benefits: improved soil conditions, carbon sequestration, natural pest control and pollination and protection for migratory birds. Shade-grown coffee systems not only benefit the farmers through ecotourism and natural resources (medicinal plants, firewood, fruits), but also consumers because it is a better tasting coffee as it matures slowly under the shade accumulating the flavour.

References:

• http://www.groundsforchange.com/learn/index.php?
• http://www.fairtrade.org.uk/en/what-is-fairtrade/what-fairtrade-does
• http://ssir.org/articles/entry/the_problem_with_fair_trade_coffee
• https://nationalzoo.si.edu/scbi/migratorybirds/coffee/
• http://nationalzoo.si.edu/scbi/migratorybirds/coffee/bird_friendly/ecological-benefits-of-shade-grown-coffee.cfm

 

 

To be honest, I lost most of my interest in molecular biology and genetics couple years ago (in the middle of my undergrad), mainly because I did not like the way they were taught: it involved lots of memorisation of details I could not retain for more than couple days after the final exam, as well as it seemed too abstract to me sometimes!. So I decided to focus my heart and brain solely on ecology, evolutionary and behavioural biology and avoid the molecular component as much as I could. I recognise that this is not a logical, smart or useful behaviour at all, and that it has been one of the criticisms towards ecologists  and behavioural biologists who decide to completely forget about the molecular basis (however the opposite is also true when scientists merely focus on the molecular and genetic level and lose perspective of how this matters to the organism and its environment). One of the main goals of this course is to (as Owen puts it) “keep making connections” between the different topics and fields, and this can ve very valuable as you can approach the same issue from a different perspective to gain new insights.

During our field trip to Fortuna I was surprised (due to my molecular-genetic resignation) of how much I enjoyed Greg Wray’s talk “Genomic approaches to ecological and evolutionary questions” because it made me re-think of genomics as a powerful  tool to try answer the questions in the areas that interested me the most. For example, genomics can be used at  the different levels of biological organisation, from the individual (to study movement, hybridisation, trait-inference) to the population level (to study population size and sub-structure, amount of genetic variation), as well as at the level of communities (to investigate species interactions such as parasitism and prey-predator relationships).  This made me wonder how genomics could be applied to my masters research: biological invasions.

The invasion process by an exotic species can be broken down into five different stages: transport, introduction, establishment, spread and impact. One of the current challenges of invasion ecology is to understand how the transitions between the different stages actually take place, as well as the quantification and prediction of invasive species’ impacts. Without this knowledge, it will be difficult for management practices and interventions to succeed. Fortunately, genomic approaches (to the rescue!) are being recognized as very useful tools to understand the invasion stages and to design the according management practices.

Taken from aquaticfieldcourse2013.wordpress.com

For example, genomics can be used during the initial stages of an invasion (transport and introduction) to detect the presence of invasive species throughout DNA barcoding, DNA metabarcoding (multiple species) and environmental metabarcoding (eDNA, where DNA is extracted from a sample of water or soil). The later one can be particularly useful when applied to the ballast water of ships (ballast water is responsible for a great deal of worldwide introductions), but also to have a better understanding of the ecology of microbial invasions, which can be extremely hard to detect using traditional survey methods. Additionally, genetic markers can be used to identify the source populations of introduced species, which can accelerate the management process. On the other hand, genomics can be used to study the levels of genetic variation present in introduced populations, which can help in predicting the probability that such populations become established and/or spread. This is important because it has been suggested that greater genetic and phenotypic variation increase the probabilities of a successful colonisation.  Genomic tools can also be used to detect hybridisation (either among invasive species or among introduced and native species).  Hybridisation has been shown to facilitate the invasion process (as it increases genetic and phenotypic variation) but also can have a direct impact on native species through “genetic pollution”. Finally, using genomic approaches one can identify the functional genes that underlie exotic species adaptation to their non-native ranges, such as environmental tolerance.

                   A very nice image representation of environmental DNA (eDNA)! Taken from geogenetics.ku.dk

In the context of invasive species prevention is the most cost-effective solution, therefore investing in tools able to detect invasive species early on should be prioritised. Genomic approaches seem to be a very promising tool in this regard, with future improvements aimed at providing  information in a faster yet reliable way, as well as making the tools accessible to non-specialists to widen their range use.

References:

• Chown, S. L., Hodgins, K. A., Griffin, P. C., Oakeshott, J. G., Byrne, M., & Hoffmann, A. A. (2015). Biological invasions, climate change and genomics. Evolutionary Applications, 8(1), 23-46.
• Rees, H. C., Maddison, B. C., Middleditch, D. J., Patmore, J. R., & Gough, K. C. (2014). REVIEW: The detection of aquatic animal species using environmental DNA–a review of eDNA as a survey tool in ecology. Journal of Applied Ecology, 51(5), 1450-1459.

 

 

 

 

 

 

Sound is essential in the communication between species, but not all the species have the same range of hearing (see table 1) and do not produce the same kind of sounds. The human ear is sensitive to sounds with frequencies from about 20 Hz to 20,000 Hz, the frequencies under the 20Hz are called infrasound and the frequencies over the 20,000 Hz are called ultrasound.

African elephants and the blue whales use the infrasound for intraspecific communication. These sounds are low frequency and can travel long distances (several kilometers) through the ground or in the water and dissipate less fast in the air. The disadvantage of the infrasound is that they give less information of the ambient to the animal. In the other hand we have the bats (20–60 kHz), and dolphins that communicate using ultrasounds, this are characterized by waves of high frequencies, travel short distances but have the advantage that can give more information of the ambient to the animal. Bats use the echolocation sounds to found and catch preys at night, but nocturnal insects have also evolved ears sensitive to ultrasonic bat calls to avoid being predated.

One of the facts that surprise me during the bat nigh was that many species of frugivorous bat loss the hability of echolocate; instead they developed bigger eyes to be able to see better the fruits and the “tongue clics”. The echolocation sounds are more important for bats that need to follow and catch a prey through the forest.

The study of the sound, especially the echolocation sound (ultrasound) was the base for the construction of the sonar system ans the ultrasonic used in the medical care.

Literature

McComb, K., Moss, C., Sayialel, S. & Baker, L 2000. Unusually extensive networks of vocal recognition in African elephants. Animal Behaviour, 59, 1103-1109.

Nakano, R., T. Takanashi and A. Surlykke. 2015. Moth hearing and sound communication. Journal of Comparative Physiology A. 201: 1 (111-121).

 

Being now in Trinidad for my fieldwork, I can take some time to think about this last month in Panama. These past few days have been extremely rich in discoveries, great discussions, and science in general. We talked about various subjects as forest diversity and composition, primate movements and feeding behavior, but also vampire bats and social behavior, or cacao farms and sustainable development. I have to say that no topic was directly related to my field of study – that is freshwater fish and their ectoparasites – but I probably learned even more from such different perspectives.

The last week, we had an environmental policy course that raised a ton of interesting questions about biology and research in general. So even if this blog is about the biology course, I thought it was interesting to highlight some of the debates we had. They almost all come from the fact that for most of us, our work is coming from public funds. So because we have a certain responsibility to the public, we discussed on whether, and to what extent, scientists should communicate their research. Every one seemed to agree that we have to do it, but that we don’t take the time to really think about outreach at our level. Should we do everything by ourselves? Should we hire communication professionals? Should we try to be less competitive, i.e. spend less time on publication, but allocate more time to outreach? This last idea seduced a lot of us, but don’t seem realistic in a world where you have to publish or perish.

Another great question that was raised by Dr. Gordon Hickey, our professor during that course, was: “If the government has the choice between giving money to a hospital to save children from horrible diseases, and fund your research, what will be your argument? Why is it important to fund scientific research?” An easy answer would be: “Because it’s interesting and exciting!” but I’m not sure that it would convince the government. I am still searching what is the contribution to science of my thesis and what could be the applications of my work, and I don’t have a simple answer to that question, but this course definitively helped me to think about research in a more global perspective.

 

I would like to end that post, and my contribution to this blog, by a quote of William Beebee, a great explorer and researcher that gave his name to the research station I am staying right now:

 

“If one looks the jungle straight in the face and transcribed what is seen, there is evolved technical science, and until this can be done with accuracy and discretion, one can never feel worthy now and then, of stealing quietly up a side aisle of the great green wonderland […]. It is possible to enter a jungle and become acutely aware of poison fang and rending claw […] but it is infinitely more wonderful and altogether satisfying to slip quietly and receptively into the life of the jungle […], to sense the beauty, the joy, the majestic serenity of this age-old fraternity of nature into who’s sanctuary man’s entrance is unnoticed, his absence unregretted. The peace of the jungle is beyond all telling.”

 

And of course I’d like to thank many people that allowed us to benefit from the peace of the jungle: Owen, Carlos, Luis, Paola, and all the professors/postdoc/graduate students that gave incredible talks and tours about their research.

There is no ecosystem in which the organism lives independently, biological interaction occur at all levels and in different ways. They can be beneficial or prejudicial for the organism involved. During the second week of the course we had the opportunity to learn more about these interactions by the hand of Allen Herre, a specialist in the relationship between a tiny wasp and the figs and Hermógenes Fernández, who study the mutualistic symbiosis between leaf-cutter ants and their fungal.

If you ask me, who invented the agriculture, I have to answer that the leaf-cutter ants (genus Atta) do it! These ants live in an obligated symbiosis with a fungus that they grow to eat. The ants collect pieces of leaves from the forest, take it to the nest underground and use them as a substrate to grow the fungus; and, just as we do with our crops, they take care of the fungus, they use their own feces to fertilize it and produce their own antibiotic to protect them from other pathogens fungus. This is a beautiful example of mutualism and coevolution, where the surveillance of one species depends of the other one.

But not everything is perfect in the world of the mutualism, there are cheaters, and some host learned how to sanction the cheaters. This is the case of the the fig tree – fig wasp species. Both species are dependents for the reproduction success; the fig wasp can only oviposit and reproduce in the flowers of the fig, in reward the wasp have to pollinate the flowers of the fig. But, when the wasps do not pollinate the flowers the fig sanction the wasp aborting the fruit.

Bibliography

Jandér, K.Ch. and E. A. Herre. 2010. Host sanctio ns and pollinator cheating in the fig tree – fig wasp mutualism. Proc. R. Soc. B . 277, 1481–1488

How many of you have been surprised with some wildlife pictures of the Nat Geo magazine or videos from the BBC? How many of you know how much time scientist and photographers spend in the wild to get those Incredibles images? Well, the story that I will describe in the next lines is one of the many stories behind science that scientist and photographers have to spend to show you the amazing world where we live.
At the beginning of 2015, I was walking in one of the trails of Barro Colorado Island (BCI) and I found a group of video-photographer of the BBC. I asked them what they were doing on BCI, they explained to me that they were staying a month on the island just with one goal, get a video of an ocelot hunting a prey. I was very surprised, and told them: well, I have five years working everyday on the island and I had seen the ocelot just twice and at night. They respond, no worry we are 10 different teams spread in different countries in the tropic trying to get the same video. At the same time, they were advised by one of the expert on ocelot behavior on BCI, Jackie Giacalone. Any video or photographs do not have sense without a good story based on scientific data. Jackie have been monitoring the ocelot population of BCI for the last 28 years, her knowledge deserve to be shared.

Being a scientist is not only be smart, have to be athletic to be able to walk long distances in the forest and even to catch a butterfly; be strong to carry all the equipment that you need in the field or dig deep in the ground looking for leaf-cutter ants; patient, to spend long hours watching the behavior of your target organism or identifying specimens; carefully to keep yourself save in the field, persistent to continue working despite everything and the most important, love your work and have fun. As a PhD student, we will spend five years of our life studying an organism, and at the end, after many months of hard work in the field, long hours in the computers and many days of stress we will present our results in a 20min talk, Yes! In 20 min we have to summarize our five years of work. Now, you can imagine how much effort and dedication is needs it to produce one hour of a documentary film.

The first three days of our course we visited the Nature Monument of Barro Colorado Island (BCI), one of the most important Field Research Station in the Neotropic and administrated by the Smithsonian Tropical Research Institute (STRI). Barro Colorado was established in 1923 as a Biological Reserve by James Zetek, and entomologist who came for the first time to Panama to study the yellow fever and the malaria diseases during the construction of the Canal. During the next years of the establishment, the station becomes very famous between scientists from the US interested in the flora and fauna of the tropics. Nowadays, the Island receive annually an average of 350 students from Universities all over the world and more than 5,000 visitors for a day-trip whose learn about the different projects related to the ecology and behavior of the flora and fauna of the Island.

 The new visitor center, is a replica of the first laboratory of the island, this place was the scenery of many scientific discussion and collaboration between scientists. One of the big ideas that were discussed, in 1980 by Stephen Hubbell and Robin Foster, was the establishment of a 50 hectare plot to study the dynamic of the forest. The plot is located in the plateau of the island, 145m over the sea level. Every tree and vine in this plot has been identified, mapped and tagged and every 5 years there is a census that quantifies and answer question like: How many trees died? How is the distribution of the different species? How fast the gaps are recovered? Most recently, with the climate change, and international collaboration with more than 10 countries, 46 plot have been stablished in different parts of the tropic following the same methodology developed in Barro Colorado.
We also had the opportunity to walk through different trails which names honor the pioneer’s scientist of the Island, like: the entomologist William M. Willer, the herpetologist Thomas Barbour and the first keepers and research assistants Fausto and Donato. During these walks we were accompanied by a new generation of researchers that have been working on the Island for several years. Lissy Colie and Tom Kursar, using the Iga genus as an example, explained us the ecology and evolution of the plants chemical defense and how different species of plants can coexist in a small area as Barro Colorado. Meg Croofot and Chritine Rhiel talked about the behavioral ecology in White-face capuchin monkey and the Greater Ani respectively.
STRI and Barro Colorado had served to the scientific community for almost one hundred years, offering them all the facilities and the tools to develop the most Incredibles ideas and experiments. Hopefully, this collaboration continues for another hundred years for the good of knowledge and humanity.

Some days reading the news on the internet is hard. Seeing articles like “Court halts Obama’s key climate plan” (BBC News) and “Emaciated polar bear pictures raise global warming concern” (The Telegraph) is heartbreaking. But over the past few months a few things have happened which has made me refocus when I see articles like this.

It started with the 2015 Paris climate talks in Paris. Although my advisor, Catherine Potvin, wasn’t directly participating in the conference, she was contacted by many people involved to get her advice about the negotiations. Watching the concluding remarks of the talks, Catherine told us (her group at a Christmas dinner) that she thought the French delegation should be awarded a Nobel Prize for how they organized and coordinated the event by giving each country something to be responsible for. She said it was like their “baby” and they were responsible for bringing it up as proud parents. Writing about it doesn’t really do what she said justice, but just listening to how she spoke about the conference really made me feel like there was hope for the future (and the polar bears!). You can follow some of Dr. Potvin’s work on her twitter site, Sustainable Dialogues.

Again, this idea of fostering hope and optimism came up again in Nancy Knowlton’s talk on conservation of coral reefs. She gave many examples of how coral reefs all over the world were being lost from outbreaks to acidification. But she ended on such a positive note, talking about her work on Citizens of the Sea whose stated objective is to spread #oceanoptimism. I think what Nancy said is so important that I wanted to devote my last blog post to it. I think this tropical biology course has done a lot for me in helping me to fully appreciate the diversity of organisms, their habitats, and their behaviours. Thank you Carlos and Owen!

While in Gamboa, we had the opportunity to spend time in the tropical forest mist-netting birds during the day and bats at night. Because I really enjoyed the field work and lectures on bth birds and bats, I wanted to find a topic common to both which I could write about for the blog. So I’ve decided to focus on social learning which we talked about a little in the field for bird song and which was the focus of a lecture about frog-eating bats by Rachel Page. Social learning, which is information acquired from other individuals, is used with self-acquired information as a strategy to avoid the costs incurred by each.

In Marler’s (1970) work on white-crowned sparrows, the tape-tutor paradigm was used to study song learning. Under this paradigm, a young bird is placed in a soundproof room while song is played to him using speakers. By design, this paradigm explicitly excludes social factors by not using an actual songbird as a tutor. Researchers, such as Baptista & Petrinovich (1984), discovered the importance of social cues in learning bird song because individuals of some species failed to learn song from tapes. There was also evidence from field studies (e.g. Beecher, Campbell, & Stoddard 1994) such that a young sparrow establishing its territory will learn the song of its neighbours. There are two general ways birds use social cues to determine which songs they learn: 1) they learn and memorize the songs of higher-status birds, and 2) the songs a young bird learns is dependent upon the relationship between student and tutor.

As night follows day, I’ll now move onto bats from birds. We learned about how frog-eating bats in the tropics prefer the calls of palatable over poisonous and small over large species of frogs. But how do they learn which call is which? The specific question put forth by Dr. Page is: “Can foraging be transferred via social learning?” She and her fellow researchers put a test bat together with an experienced tutor and then used that test bat as the tutor in the next trial. They found no evidence of degradation of the foraging information acquired and passed on between trials. Work was then then to establish under what circumstances bats use social learning. They found that the reliability of self-acquired prey cues affects learning of novel prey cues via a tutor in these bats.

Image: Experimental protocol used by Jones et al. 2013 to test social learning in frog-eating bats.

REFERENCES

Beecher & Burt 2004, The role of social interaction in bird song learning, American Psychological Society 13:6.

Jones et al. 2013, When to approach novel prey cues? Social learning strategies in frog-eating bats, Proc R Soc B 280:20132330.

As we were taking the course all of, or most of the researchers mentioned el NIÑO and its effects. I hope I can just give you a basic description on it. The idea is to make you feel curious about it .

The first thing is, What is it?

It is a climatic event that causes changes in precipitation, causing higher temperatures and longer and more severe dry seasons. And the strength of this phenomenon is the highest recorded in the last 150,000 years.

And then what are some of the documented effects on biodiversity?

It can affect distribution and composition of communities; can also lead to local extinctions.

Increased Bleaching and mortality in coral reef assemblages in the pacific coast has been reported during el Niño years.

On seabird populations in the Galapagos, mortality increases and breeding just does not happen.

Primate’s reproduction changes have been reported, the shortage on available food caused by high temperatures reflects negatively on female condition and fecundity.

Lizard’s populations suffer population decrease after each el Niño event. A population decline over the last 30 years has been reported for Anolis populations in Barro Colorado Island, Panama.

If you are studying any organism in Panama this year, consider looking for the effects of el Niño in your research.

Literature

Nott, M. P., Desante, D. F., Siegel, R. B., & Pyle, P. (July 01, 2002). Influences of the El Niño/Southern Oscillation and the North Atlantic Oscillation on avian productivity in forests of the Pacific Northwest of North America. Global Ecology and Biogeography, 11, 4, 333-342.

Tudhope, A. W., Chilcott, C. P., McCulloch, M. T., Cook, E. R., Chappell, J., Ellam, R. M., Lea, D. W., … Shimmield, G. B. (January 01, 2001). Variability in the El Niño-Southern Oscillation through a glacial-interglacial cycle. Science (new York, N.y.), 291, 5508, 1511-7.

Valle, C. A., Cruz, F., Cruz, J. B., Merlen, G., & Coulter, M. C. (December 15, 1987). The impact of the 1982-1983 El Niño-Southern Oscillation on seabirds in the Galapagos Islands, Ecuador. Journal of Geophysical Research: Oceans, 92, 14437-14444.

Stapley, J., Garcia, M., & Andrews, R. M. (January 01, 2015). Long-term data reveal a population decline of the tropical lizard Anolis apletophallus, and a negative affect of el nino years on population growth rate. Plos One, 10, 2.)

WIEDERHOLT, R. U. S. C. E. N. A., & POST, E. R. I. C. (October 01, 2011). Birth seasonality and offspring production in threatened neotropical primates related to climate. Global Change Biology, 17, 10, 3035-3045.

Yocom, L. L., Fulé, P. Z., Brown, P. M., Cerano, J., Villanueva-Díaz, J., Falk, D. A., & Cornejo-Oviedo, E. (January 01, 2010). El Niño-southern oscillation effect on a fire regime in northeastern Mexico has changed over time. Ecology, 91, 6, 1660-71.