Monday, 18 May 2015

The Adaptive Radiation of Darwin's Finches: old, new, and personal perspectives

This is repost from

[Al Uy asked to me to write a pseudo-popular piece about the adaptive radiation of Darwin's finches for a forthcoming "" website. I decided to use this blog to present a first (and as yet overlong and too technical) draft of my contribution.]

When I went home for Christmas in 1995, I was an aspiring salmon biologist doing my Master’s research at the University of Washington, Seattle. By the time I returned to Seattle two weeks later, I was an aspiring evolutionary biologist. Now, 20 years later, I suppose I am an established evolutionary biologist, although I am still aspiring! I have worked on stickleback in British Columbia, guppies in Trinidad, and – of most significance to the present story – Darwin’s finches in Galapagos. I doubt I would have worked in any of these systems had it not been for one gift that fateful Christmas – a book.

The book was The Beak of the Finch by Jonathan Weiner, something my mother had seen in a book store and thought I might like. For the next few days, I sat over the heater vent entombed in a blanket with only a pane of glass between me and snowy −25°C Edmonton, losing myself in the tale of two Princeton University evolutionary biologists, Peter and Rosemary Grant, and their quest to understand how evolution works through detailed long-term studies of Darwin’s finches. Most amazing to me was the description of how this work had demonstrated evolution occurring on very short time scales, sometimes only a single generation. I had never imagined that it might be possible to watch evolution take place in almost real time – yet they had done it. From that moment onward, I wanted to do the same thing and, within a few days of returning to Seattle, I went to the library and photocopied every paper by Peter and Rosemary. Slowly, the story emerged.

An image of the Galápagos Islands and their topography. Image from Wikimedia Commons. 

The Galapagos Islands were formed by magma welling up from a hotspot on the ocean floor to build underwater mountains, some of which broke the surface and became islands. When the first island formed, more than 8 million years ago, it had no terrestrial life given its 900+ km separation from the mainland. With time, however, various plants and animals either flew, drifted, or were carried to the islands. One of those colonists, arriving approximately 1.5 million years ago, was a bird – presumably a flock of them – that probably looked something like a modern-day grassquit.

The Darwin’s finch ancestor may have looked this Black-faced Grassquit (Tiaris bicolor). Photo by C.J. Sharp on Wikimedia Commons.
These colonizing proto-finches arrived in an ecosystem that had been assembled from the relatively few long-distance migrants that had reached the islands, some of which had then diversified into multiple species on the islands. This initial finchless ecosystem had a number of different potential food types (insects, fruits, seeds, and leaves of various sorts), but very few – if any – other birds to eat them. These first colonists were thus confronted with a land of “ecological opportunity” filled with a number of “empty niches” that might be filled by finches.

The colonizing finches increased in abundance and spread across the various Galapagos islands. As they did so, they encountered different conditions. Some islands were very low and dry. Some islands were high and wet. Some had many insects, some had few. Some had certain types of plants, some had other types. Each of these different sets of conditions meant that a different way of feeding would be optimal at different locations. These different ways of feeding had a classic evolutionary target – the beak of the finch.

The diversity of pliers. Images from 
Bird beaks have been likened to pliers and, like pliers, different shapes and sizes are best suited for different tasks. The thin, pointed beak of a warbler is well-suited for gleaning insects, the long beak of a honeycreeper for probing flowers for nectar, the chisel-like beak of a woodpecker for tearing apart wood, and the robust rounded beak of a finch for cracking seeds.

The diversity of bird beaks and their functions. Image from L. Shyamal on Wikimedia
Thus, as the proto-finches spread across Galapagos and encountered different conditions, the different populations began to experience natural selection for different beak morphologies. Over perhaps a relatively short period of time, adaptation drove those different populations toward those different beaks, yielding a small pointed beak for insect eating (eventually to be called “warbler finches”), a long bill for nectar feeding (eventually to be called the “cactus finch”), a chisel-like bill for tearing apart wood (eventually to be called the “woodpecker finch”), a robust beak for cracking seeds (eventually to be called the “ground finches”), and so on. Yet, if it is geographic variation in food types that drives this “adaptive radiation” of finches, how does one end up with multiple species at any given location – as is currently the case in Galapagos?

One representation of the Darwin's finch radiation (Grant 1986: Ecology and Evolution of Darwin's finches)
Given that the proto-finches spread to the diverse locations in Galapagos in the first place, it seems just as plausible that newly-evolving species could similarly spread to different locations, some of which would already host locally-evolved species. If the end result of this “secondary contact” is to be a multi-species finch community, two requirements must be met. First, the invading species has to have a different diet than the resident species – otherwise one species will simply out-compete and thereby exclude the other species (“competitive exclusion”). Second, the invading and resident species can’t interbreed too much – otherwise they will simply fuse together into a single species. Fortunately, these two requirements often seem to be met for Darwin’s finches in Galapagos.

Crude depiction of the distribution of different finch species on the different islands. From A Field Guide to the Birds of Galapagos by Michael Harris. Collins. 

First, the previously described situation in which populations in different places show adaptation to different food types means that species coming into secondary contact have already specialized on somewhat different food types, thus reducing competition. This initial divergence can increase following secondary contact due to selection against individuals that have traits/diets/behaviors most similar to the other species, and that therefore experience the highest competition. The resulting process of “character displacement” will then further reduce competition and promote species coexistence.

David Lack's classic demonstration of character displacement. Image from Ricklefs' (1996) Economy of Nature
Second, the traits (beak size and shape) that undergo adaptive divergence influence mate choice so as to reduce interbreeding. In particular, beak size is strongly correlated with the types of songs that males can sing: for instance, large-beaked individuals cannot sing rapid and complex songs. Thus, adaptation to different food types should cause divergence in songs as an incidental byproduct. Moreover, offspring tend to “imprint” on the songs of their fathers and, at maturity, male offspring sing those songs and female offspring prefer similar songs. As a result, birds that have evolved different beaks automatically show reduced inter-breeding – making beaks an outstanding candidate for the so-called “magic traits” of speciation. Moreover, any successful interbreeding between species (which does occur reasonably often) produces offspring with intermediate beak sizes that have low survival rates because they are not well-suited to the diets of either parental species.

Different finches sing songs with different vocal properties. From Podos (2001 - Nature).

This rough thumbnail sketch provides a crude summary of the process of adaptive radiation in Darwin’s finches as it was understood at the end of the 20th century.

Although I now, at the start of 1996, wanted to be an evolutionary biologist, it never occurred to me that I might actually work on Darwin’s finches – they were simply too far away in space and too much a place of my imagination rather than reality. Instead, I turned my attention to studying how evolution works in fishes, where I already had some experience; but serendipity intervened. In 1998, I started a postdoctoral position at the University of British Columbia (Vancouver, Canada) studying the evolutionary biology of threespine stickleback. A short time later, I saw an ad for the “Darwin Postdoctoral Fellowship” at the University of Massachusetts in Amherst, Massachusetts. “Wow, what a cool name for a fellowship,” I thought, “maybe I should apply.”

One of my stickleback experiment field sites on Vancouver Island.
Less than a year later, I was ensconced in the Department of Organismic and Evolutionary Biology at UMASS in Amherst. My project was a logical extension of my PhD work and focused on natural selection acting on introduced Atlantic salmon in a restoration project for the Connecticut River. While at UMASS, I became friends with a new faculty member across the hall, Jeff Podos, who had started working on Darwin’s finches and had just published a paper in Nature about the vocal constraints faced by birds with different beak sizes. Soon afterward, Jeff received an NSF “Early Career” fellowship that enabled him to – pretty much – do whatever he wanted for research. So Jeff started assembling a team for new Darwin’s finch work and asked if I wanted to come along. Twist my arm.

Some of the Darwin’s finches I first encountered. Clockwise from upper left: medium ground finch (Geospiza fuliginosa), medium ground finch (Geospiza fortis), large ground finch (Geospiza magnirostris), cactus finch (Geospiza scandens), small tree finch (Camarhynchus parvulus), vegetarian finch (Platyspiza crassirostris), and woodpecker finch (Camarhynchus pallida).
In 2002, after all those years of reading and thinking about Darwin’s finches, there I was actually in Galapagos looking at Darwin’s finches hopping about on the ground making, as David Lack had said, “dull unmusical noises.” My goal that first year was simply to learn as much as I could about the finches and to think broadly and creatively about various projects that I might do in collaboration with Jeff and his team. One of the highlights that first year – perhaps even a rite of passage – was the afternoon I spent walking around in the field with Peter and Rosemary. Now, 15 years later, a number of projects have come to fruition, some of which have modified the basic tale of the adaptive radiation of Darwin’s finches as described above.

1. Darwin’s finches are “imperfect generalists”

As described earlier, a critical mechanism by which two young Darwin’s finch species coexist when they come into secondary contact is through adaptation to different resources. The assembly of a community of finches thus depends critically on the extent to which different species partition their resources. One of our first goals was to understand how this partitioning took place, so – starting in 2003 – we began what would become a long program of simply walking around our field sites, finding birds, identifying them (through binoculars) to species, and determining on what they were feeding. This task has been greatly facilitated by the fact that Darwin’s finches are very tame. In the early stages of this work, we were quite surprised to see that, contrary to our initial naïve expectations, most of the species seemed to be feeding on pretty much the same things. Where was this niche partitioning that was supposedly so critical to the adaptive radiation?

Those first years were very wet, with lots of plant reproduction, lots of seeds, and lots of insects. But then a major drought occurred and, for several years, plant reproduction was minimal and so seed and insect abundances declined dramatically. Fortunately, we had continued to record what the finches were eating throughout this period. During these drought years, we found that the different species increasingly diverged to use different resources – and niche overlap decreased accordingly. Thus, with 5 years of feeding observation data spanning wet and dry years, we were able to conclude: These results together suggest that the ground finches are ‘imperfect generalists’ that use overlapping resources under benign conditions (in space or time), but then retreat to resources for which they are best adapted during periods of food limitation. These conditions likely promote local and regional coexistence (De Leon et al. 2014). This finding that niche overlap decreased in years when little rain fell fit well with earlier observations that niche overlap decreased during the dry (as opposed to wet) seasons within a year.

2. The adaptive radiation is ongoing

During that early walk in 2002 with Peter and Rosemary, I asked them what they thought would be one of the most interesting questions to investigate on Santa Cruz, where we were planning to work. They suggested trying to understand the causes and consequences of the hyper-variable population of medium ground finches, Geospiza fortis. It turns out that this species is more variable on Santa Cruz than anywhere else – indeed, they are so variable that a paper by Hugh Ford in 1973 argued they were undergoing sympatric speciation. Just the next year, team member Anthony Herrel came into our dorm room to show us some data from the birds we had captured that year. The histogram of beak sizes was bimodal – just like Hugh Ford had reported. This result was inspiring because it suggested that the population might be in the midst of splitting into separate species, a rare event that would enable us to formally test the mechanisms thought to promote the adaptive radiation of Darwin’s finches. (It is difficult to test such mechanisms when species are already well established.)

We first formally confirmed that the G. fortis population under study (at El Garrapatero on Santa Cruz) was indeed bimodal (Hendry et al. 2006). We then used this bimodality to test a series of predictions stemming from the theory of adaptive radiation – and the results confirmed expectations. (1) The two morphs had different diets, with the large morph generally eating larger/harder seeds (De Leon et al. 20112012). (2) The two morphs differed in their feeding performance, with the larger morph that fed on larger/harder seeds having higher bite forces (Herrel et al. 20052009). (3) Males of the two morphs sing different songs and respond differently to each other’s songs (Huber et al. 2006; Podos 2010). (4) The two morphs mate assortatively: small females with small males and large females with large males (Huber et al. 2007). (5) The two morphs experienced “disruptive selection” in that intermediate birds survived at lower rates (Hendry et al. 2009). (6) Gene flow was somewhat limited between the morphs in that they showed some (albeit minor) differences at neutral genetic markers (De Leon et al. 2010). All of these findings supported the general model for adaptive radiation in Darwin’s finches: different diets leads to song divergence leads to different traits leads to reproductive isolation.

Clockwise from top left: The large and small beak morphs, the demonstration of bimodality, assortative mating, and disruptive selection

3. Human influences on adaptive radiation

Given a population of finches seemingly in the midst of splitting into separate species, none of the above results were surprising – yet we did have a surprise coming. The bimodal population of finches described above was not the same population previously described by Hugh Ford. For the latter population, found at “Academy Bay” immediately adjacent to the main tourist town of Puerto Ayorra, we couldn’t find evidence for bimodality in any of our new samples. Even though the population was still quite variable, it just didn’t show the dip in the frequency distribution of beak size that Ford had reported and that we were finding at El Garrapatero, just 7 km away. It seemed that Ford’s population had lost its bimodality between then and now, and we became curious as to just when that collapse had occurred. At this point, we rounded up all of the previous data available for G. fortis from Santa Cruz. Peter and Rosemary and their collaborators provided much of it, including data from David Snow’s collections in 1963–1964. The most fun for me, however, was to find Hugh Ford’s contact information online and send him an email:

In 1973, you published a wonderful paper arguing for bimodality in beak size distributions in G. fortis at Academy Bay. I have recently compiled morphological data from Peter Grant and other investigators from a variety of sites on Santa Cruz island. I am now testing for spatial and temporal variation in the extent of bimodality. This work would be greatly aided if you happened to have the raw data from your 1973 paper. … I hope that you have these data and would be willing to send them to me. It would be much appreciated.

To which he replied:

Amazingly I have found the data in my room. It is in old notebooks - no Excel spreadsheets in those days! I can enter the data into a spreadsheet but not right away. … Do you want date of banding - all August to October 1968 I think?

And so, not much later, I had the original data in hand, which was particularly exciting given that it was collected in the year I was born!

Compiling all of these data made the picture clear – bimodality had decreased substantially in Academy Bay G. fortis some time soon after Hugh Ford’s study (Hendry et al. 2006). Noticing that these decreases coincided closely with an exponential increase in human population density, we argued that humans were altering the food resources that had been so fundamental to shaping finch diversity. By subsequently comparing contemporary G. fortis from Academy Bay and El Garrapatero, we provided support for this hypothesis by showing that associations between beak size, diet, bite force, and genetic variation were all now much weaker at Academy Bay than El Garrapatero. Humans, it seems, can alter the “adaptive landscape” for finches and thereby reverse the process of adaptive radiation (De Leon et al. 2011). Whether or not such effects can extend to the more discrete species of Darwin’s finches, which do still hybridize, remains to be seen.

Top left: Academy Bay. Bottom left: finches eating rice provided by humans. Right: bimodality at Academy Bay the year I was born and at El Garrapatero when we started our work, but not at Academy Bay in the same year (2004).

From the inspiration initially provided by that one book my mother gave me back in 1995, my career has followed quite an arc, to the point where I am now contributing knowledge to our understanding of the adaptive radiation of Darwin’s finches. Sometime in the mid-2000s, I received a phone call from Jonathan Weiner, the author of that fateful book. He wanted to talk about some related work I had done on fishes. What fun it was to be able to tell him how influential his book had been to my own career path. But where to now?

The next frontier for Darwin’s finches is genomic work. Just this year, an initial study was published exploring genomic variation among the various finch species – and we have begun our own work on the topic. Over the next decade or so it seems likely that we will have answers to many questions that research on adaptive radiation has long pondered: how many genomic regions are involved, how big are the effects of particular genes, which specific genes are involved, and are the genes involved now (at the tips of the ongoing radiation) different from those that were involved earlier (at the deeper splits of the radiation)?

Another critical frontier is to examine how finches influence the evolution of plant traits and assembly of plant communities – work we are now starting with Marc JohnsonNancy Emery, and Sofia Carvajal. Much work remains to be done, and I am curious to find out just how Darwin’s finches will continue reshaping my life and career.

Thursday, 7 May 2015

Why So Colourful?

*Pour lire cet article en français
*This blog post was originally published in the “Sous la loupe” section of the Spring 2015 edition of Antennae, the Bulletin of the Entomological Society of Québec.

Who hasn’t felt awestruck at the sight of a monarch butterfly (Danaus plexippus). That feeling is to be expected. As many other insects, the monarch is desperately trying to be seen: it relies on aposematism, a strategy meant to avoid being eaten. A bird will only make the mistake of eating a monarch once. This butterfly is filled with cardenolides, toxic compounds that are acquired during the larval stage as the caterpillar is feeding on milkweed (Asclepias sp.). After this disturbing experience, the disgusted bird will remember to avoid any butterfly sporting bright orange and black wings. Butterflies are not the only fans of this strategy. Aposematism can be found in other insects, such as ladybird beetles, but also among animals as different as poison dart frogs and opistobranchs (colourful marine slugs). Just like the monarch, many species acquire toxic compounds from their food. Other species produce these poisons themselves. And to advertise their toxicity to the world, colour is not the only medium! Many species advertise to predators that it is better to leave them alone through sounds or odours. Simply said, aposematism means telling predators, through a variety of signals, that an animal is well defended.
Danaus gilippus
Danaus gilippus is a close relative of the monarch that can be found in tropical areas. Darién Province, Republic of Panamá (Photo: Nicolas Chatel-Launay).
Aposematism is not a novel discovery. This strategy was first suggested as a mechanism born from evolution by Alfred Russel Wallace in 1866. Even if aposematism is easy to understand, many questions still arise among scientists about this strategy. For example, how did it evolve? Could a butterfly like the monarch have developed it gradually, becoming more orange with each generation? Alternatively, did it evolve through rapid mutation? A lot of research will be needed to answer these questions. Other researchers try to tease apart the role of sexual selection in aposematism. Does a colourful animal have more descendants because predators avoid it, or because sexual partners prefer colourful mates?
Eumaeus godartii
Less well-known than the monarch, Eumaeus godartii (Lycaenidae) is another good example of aposematic butterfly. Chagres National Park, Republic of Panamá (Photo: Nicolas Chatel-Launay).
Another interesting aspect of aposematism is the phenomenal amount of mimetic strategies that arise from it. In Québec, one can meet the viceroy (Limenitis archippus) that, just as the monarch, covers itself in orange and black. But the viceroy is not poisonous! Thanks to this deception, the colours of the monarch allow the viceroy to be avoided by birds. This type of mimetic behaviour is called “Batesian mimicry”. This form of mimicry is also common in many harmless snakes that copy the colourful patterns of extremely venomous coral snakes.
A different situation is possible. What if many toxic species all look alike? If they do, all these species increase their chance of survival if a predator has learned to avoid the shared color pattern. All that is needed is for a predator to have had one bad experience with only one of the mimetic species for all to be protected. This type of mimicry is called “Müllerian mimicry”. Butterflies of the Heliconius genus, found in Central and South America are among the best studied cases. These toxic butterflies have very variable wing patterns, even within a single species. Surprisingly, two different species captured in the same locality look more similar than they do specimens of their respective species collected from far away locations. This regional similarity creates an effective protection for all mimics in the area.
Butterflies of the Heliconius genus and other closely related genera are an excellent example of Müllerian mimicry. Metropolitan Natural Park, Republic of Panamá (Photo: Nicolas Chatel-Launay).
Many scientists are presently working on the mysteries still surrounding aposematism. Some use the latest genomic techniques, while others continue a long tradition of behavioural studies. After more than a century of research on this relatively simple strategy, there is still much to unravel and entomology remains a limitless field of study.

Monday, 23 February 2015

Can we overcome the “blues” in conservation and natural resource management?

Can we overcome the “blues” in conservation and natural resource management?

By: Javier Mateo-Vega (Ph.D. Candidate - Biology/NEO)

It is surreal to grapple with critical conservation challenges occurring in the Kingdom of Bhutan (yes, that exotic country that lies at the eastern flank of the Himalayas) while sitting near the confluence of the Chagres River and Panama Canal in the town of Gamboa, Panama! But this is what happens when you take part in the course, “Foundations of Environmental Policy” (ENVR610), one of the two required NEO courses.

Under the guidance of Prof. Gordon Hickey (a rare scholar with vast experience as a practitioner and policy-maker), we had spent all afternoon discussing the issue of human-wildlife conflicts in Bhutan and attempting to identify viable solutions to this “wicked” problem. At first, it was fun to be transported momentarily to this remote Kingdom through our readings and complementary videos. But as we were challenged to explore options for addressing human-wildlife conflicts in a manner that is sensitive to the environmental, socio-economic, cultural and political realities of the country, many of us began to feel overwhelmed and even a little “blue”. Are true win-win solutions possible; who decides when it’s a win-win; are win-wins able to endure over time?

Over the course of the following five days, we were confronted with many similar cases, from deforestation and cattle ranching in Brazil, to horseshoe crab harvesting practices in eastern US, to community based eco-tourism enterprises in China. We also had the opportunity to visit the mind-blowing expansion of the Panama Canal on the Caribbean coast, and visit STRI’s Punta Galeta research station to discuss with Dr. Stanley Heckadon (STRI Staff Scientist), and other staff, the potential environmental and social impacts of megaproject developments on mangroves, coral reefs, forests, and the “social fabric” of the region. We were challenged to wear multiple “hats” and approach these problems as scientists, community members, indigenous leaders, policy makers and concerned citizens.

All of these cases illustrate the enormous difficulties in linking science with environmental policy, and the trade-offs that are inherent to managing any natural resource. Clearly, there are no right or wrong answers or solutions to these issues. In most cases, any decision or action will result in either a net loss of biodiversity or a net loss of livelihoods. Finding how those net losses can be minimized is tricky, especially because natural resource management decisions take place in contexts of changing conditions (e.g. environmental, political, social, economic), incomplete information and uncertainty, conflicts due to varying interests from different stakeholders, and complex - and often poorly understood - interactions between environmental and social systems.

At the end of each day of the course, some would joke, “environmental policy could lead any person to drink heavily”; “this course should include a therapist to ensure we don’t fall into a deep depression”; or simply “my brain hurts.” For many, it was the first time they had been exposed to the world of environmental policy and gotten a glimpse of where their professional paths may lead them. We have witnessed past generations of NEO graduates take on jobs in academia, NGOs, government agencies, and the corporate sector. Almost all have and will invariably engage in environmental policy at some point in their careers. This course undoubtedly prepares all of us for this process.

As I listened to each one of our classmates introduce themselves and their research at the beginning of the course, it is clear that NEO attracts individuals from all walks of life and corners of the world who are passionate about nature, science, rural livelihoods, politics, and economics, among many other topics. Over meals, you could hear conversations about genomics, manatees, seaweed cultivation, phylogenetics, indigenous peoples rights, etc. This proved to be the way I got over my “blues” throughout the week. Seeing the passion of the group, their sophisticated and innovative approaches to problem solving, and commitment to action was both empowering and inspiring. I think all of us walked away feeling much more motivated and prepared to participate in the environmental policy arena.

Friday, 20 February 2015

Tropical Biology and Conservation Course: Interdisciplinary Groups… or People?

The following is a blog post I wrote for the McGill-STRI-University of Illinois "Tropical Biology and Conservation" course. Enjoy!
There’s a prevailing idea in academia that we need increasing interdisciplinary partnerships, and increasingly interdisciplinary people. This is an ideology that framed my entire undergraduate career, and something I’ve noticed in several lectures throughout this course; collaboration is critical to producing high quality and publishable work. This is clearly a no-brainer; however, all that being said, I feel there is still a long ways to go.
Anthony Coates gave an incredibly interesting talk on the geologic history on the isthmus of Panama. Once I’d looked up what an isthmus was, I was intrigued by the sheer volume of work done by geologists. (An isthmus, in case you were wondering, is a small strip of land that rests between two oceans or seas that connects two much larger land masses, thank you Wikipedia). Tony opened his talk by stating that geologists and palaeontologists often spend much more time learning about biology, than biologists take the time to learn about geology or palaeontology. This is often the case, though there are always exceptions; however, much of this can be said for every discipline when it comes to research outside their own field. Not that this is justification for ignorance, but it raises the question of the value of specialization versus generalization. If diversity within academia is so critical to addressing our world’s problems, are we better off with a diversity of researchers, or a diversity within each researcher?
This same idea came up in a much different context a few days later, when we attended the STRI Tupper seminar on the History of STRI. A question was asked at the end of the talk regarding the limited integration of Latin American scientists into STRI, and what efforts have been made to improve the diversity within the research community. One of the responses to this question referred to the historical context of Panama and its relations with the United States. There is a significant, and tumultuous, history between these states that really has been more conducive to friction and separation, as opposed to collaboration. These relations have improved in the past few decades, but the remains of the political tension still persist. You might wonder where this relates to interdisciplinary research, but my point comes from the fact that as academics we often become so focused on our particular disciplines that we forget to look at the broader context of where and what we’re researching. We can be so focused on the microcosm that we study, that the history framing our study site becomes lost in translation.
On a more practical note, this history, be it evolutionary, political, economic, social or otherwise, can also explain why collaborations can be so successful… or not. This is where I think one of the values of this course lies, in that we have such diversity of perspectives, research focuses, and people, and we have no choice but to interact with and learn from each other. We are forced to expand our conception of how the world works, or how it should work. Collaboration is not an obligation so much as an exciting prospect. Perhaps the future wave of academia will move in this direction, or it already is. Tis food for thought at any rate.

Saturday, 31 January 2015

Of the Smithsonian Tropical Research Institute (STRI)

*Pour lire cet article en français
*This blog post was also published on the IGERT-NEO blog and on my Research Notes blog
When I tell friends that I conduct research at the Smithsonian, most think immediately of Washington. Fellow students and I are currently enrolled in a tropical biology field course at the Smithsonian... in Panamá, not not on the Potomac shoreline! So let’s make things clear with a quick overview (i.e. publicity shpiel) of STRI, one of the world’s flagships of tropical research.
The Smithsonian Tropical Research Institute (STRI) is a community of researchers and scholars interested in the tropics. It is part of the Smithsonian Institution network and hosts 40 permanent scientists, 400 support staff and 1,400 visiting scientists and students. My colleagues and I, all graduate students of the University of Illinois at Urbana-Champaign, the Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT) and McGill University’s NEO program, are part of this community.
Together, we seek to understand the tropics, in all their complexity, and merge our diverse areas of expertise to do so. According to STRI’s Scientist Emeritus, Egbert Leigh Jr., most of STRI’s research can be grouped under 12 broad areas. First, we seek to contrast and compare two oceans, the Pacific and the Atlantic, and understand how they came to be so different. We try to accumulate as much data as possible on the recent past, to understand what is happening today in both the human and natural worlds. We seek to understand the distant past through archaeology, and learn how our world came to be. We try to uncover why and how individuals diverge within a species to give rise to more species. We try to unravel the mysteries of mutualism, or why some species collaborate with each other while others prefer to cheat. We study social behaviour in animals, but also in humans within the Central American context. We want to understand what natural selection favors and why some traits make it to the next generation while others do not. We study the factors regulating populations of living organisms and the inner workings of food webs. We look at how species (humans included) cope with extremes (light, shade, drought, floods, lousy soils, etc.). We try to understand how so many species can coexist in a single place (900 species of birds in Panamá and around 300 tree species in 50 hectares of forest). We are definitely interested by a lingering question... why so many tropical trees (and why is their identification such a hellish job)? Finally, we want to get a global picture of tropical systems by unravelling the interdependencies that make ecosystems go-round.
Enough about questions, we need answers! Good research is backed by good infrastructure. Luckily for us, you can’t really beat STRI. We have access to 13 research facilities across the Isthmus of Panamá and here’s a very brief description of each.
STRI Platform

A map of all STRI research facilities in Panamá (Credit: STRI,
1) Earl S. Tupper Research, Library and Conference Center
This set of buildings hosts most of the administrative units, a score of laboratories equipped for all kinds of research, a herbarium, an insect collection and a library comprising over 69,000 volumes centered on tropical sciences. The old and rare books section is to die for... if you like getting your hands on the drawings of 17th to 19th century explorers.

The Earl S. Tupper Library holds over 69,000 volumes related to tropical sciences (Photo: Nicolas Chatel-Launay).
2) Center for Tropical Paleoecology and Archaeology (CTPA)
If you dig fossils, that’s the place you want to be. Specialized in geology, geography and archaeology, scientists working here try to unravel the distant past, from giant (and thankfully extinct) snake species to the processes that explain why North and South America became one land mass three million years ago. Scientists from CTPA are currently using the Canal expansion project as a way to dig further into Panama’s past.
3) NAOS Island Laboratories
Located at the Pacific entrance of the Canal, this research facility has a state of the art molecular and genetics laboratory. It also has all you need to keep oceanic critters alive for research. People here specialise in Pacific oceanography and paleontology.
4) Galeta Point Marine Laboratory
NAOS’s counterpart, this research facility is located at the Caribbean entrance of the Canal. It is best known for research on the effects of oil spills and on mangrove systems.

A view of one of the numerous coral reefs neighboring the Bocas Del Toro Research Station (Photo: Nicolas Chatel-Launay).
5) Bocas Del Toro Research Station
Located in the Bocas Del Toro Archipelago, this station hosts scientists who work on coral reefs, lagoon systems and lowland tropical forests. As it is located on the Caribbean side, in the middle of a cultural melting pot between Asia, Africa and the Americas, it is also a research hub on human sociality.
6) Rancheria Island
Located on a Pacific Island, this research station is in the middle of the Eastern Pacific Ocean’s largest concentration of coral reefs. It is the Pacific counterpart of Bocas Del Toro.
7) Punta Culebra Nature Center
Located on a Pacific Island, this center focuses on public awareness and outreach. Scientists try to test education strategies in order to better transmit knowledge to the coming generations.

The Fortuna Forest Reserve lets scientists work in a unique ecosystem... cloud forest (Photo: Nicolas Chatel-Launay).
8) Fortuna Field Station
Fortuna Forest Reserve is 1,200 meters (4,000 feet) up in the mountains and lets scientists study a particularly interesting tropical ecosystem... a cloud forest. I can tell you that the sun is rare out there, and it’s constantly wet. Some areas of the reserve receive 12 meters of rain a year (and have less than 30 rain-free days yearly).

A clear night sky in Fortuna is a rare event, less than 30 days a year are rainless (Photo: Nicolas Chatel-Launay).
9) Agua Salud
This project, located within the Panamá Canal watershed covers 300,000 hectares. Scientists involved in this long-term study try to test the best reforestation strategies and how different techniques can be used to store carbon, control devastating floods, or improve soil fertility... all without banning agriculture. People here try to get to an optimal land-use strategy for the tropics.
10) Forest Canopy Access Systems
People at STRI are all smart. But some have exceptionally smart ideas. Two construction cranes were permanently installed in the rainforest on both the Pacific and Caribbean sides so that scientists could easily access the forest canopy. Wonder how we could get this close to a mommy sloth and its baby in the posts from Scott, Librada and Flor? Yup, we were in a crane.
11) Gamboa Campus
Here we are! this is the main base our group used for the Tropical Biology Field Course 2015. Gamboa Campus is located at the dead center of the Panamá Canal, and has a suite of laboratories. Also, a lot of specialized research happens here. There is a system of “pods” to grow plants in different temperature and atmospheric conditions to unravel the effects climate change might have in the tropics. There are flight cages that bats call home and where their behaviour is finely analyzed. And there is Pipeline road, a well-known spot for anyone interested in birds (See Elise’s post on the IGERT-NEO blog).

Among all our activities in Gamboa, bat trapping was certainly one of the most interesting (Photo: Nicolas Chatel-Launay).
12) Barro Colorado Nature Monument (BCI)
The Crown Jewel! Barro Colorado is an island, surrounded by three peninsulas, all protected by the Panamanian government and the Smithsonian Institution. Only research can go on here. With its 5,400 hectares, it is the oldest STRI facility, first occupied in 1924. The island itself is a no-touch zone. You can measure and observe, but you can’t change anything. The peninsulas are used for experiments, as in... what happens if you kill all lianas in a forest? Do the trees grow better? Or again, what happens if you change the nutrient regimes by dumping tons of fertilisers?

A view of the main buildings on BCI island (Photo: Nicolas Chatel-Launay).
13) Center for Tropical Forest Science (CTFS)
Located on BCI Island and founded in 1980, this 50 hectares forest plot gave us the most precious data set ever collected in tropical biology. Every single tree stem larger than 1 cm (there are roughly 200,000 of them), is identified to species, measured, and recensused every five years. The same goes for lianas, and many groups of shrubs. We also have precise soil composition data all over the plot. We have mammal, bird and insect inventories for the area. Many mammals and birds even have radio collars; we can track their every movement in the forest. Basically, we can have lots of fun with lots of data. Not only is the 50-hectare plot an awesome dataset, it had children. CTFS plots are now all over the Americas, Africa, Asia, Europe, and Oceania. People there collect data in the same manner, using the same protocol. This way, we can compare forests through space and through time, precisely, individual by individual, all over the world. Imagine what questions you can explore with that.
So here we are! This was a small overview of what we do, and where we do it. STRI is composed of biologists, archaeologists, anthropologists, geographers, and specialists of other fields trying to answer one question. What makes the tropics tick? And if you’re jealous, well don’t be. You are welcome to join in this adventure.
Nicolas Chatel-Launay

Friday, 7 November 2014

Behavioural adjustments that improve reproductive timing

Timing is everything, especially when it comes to reproduction. Well-timed reproduction improves reproductive success. For example, offspring that hatch when food is abundant or predators are scarce are more likely to survive. However, changing environmental conditions may cause organisms to miss the best time to reproduce. Since environmental variability is ubiquitous on a wide range of spatial and temporal scales, the ability to adjust to changing conditions can improve an organism’s chances of reproducing “on time”.

Ovigerous Uca deichmanni female. Photo by Arthur Anker
During my time as a NEO student, I focused on how fiddler crabs respond to temperature changes to maintain the timing of hatching of their larvae. Temperature is a major factor affecting the timing of reproduction in ectothermic organisms because it determines the rate at which embryos develop. As temperature increases, the period of time between mating and when the babies are ready to hatch decreases, and vice versa. Fiddler crab females precisely time the release of their larvae during the large amplitude nighttime high tides that occur approximately every two weeks. By timing the hatching of their offspring during these particular tides, the females minimize the risk of predation by fishes to themselves and to the newly hatched larvae. But in order to hit this targeted timing, the females must either account for the developmental period of the eggs (and temperature-induced changes in it), or they must control it.  

Most, though not all, of the ways that organisms can maintain reproductive timing in response to temperature changes are behavioural. For example, as changing climate is causing earlier springs, some bird species are laying eggs earlier in the year so that their offspring still hatch when their food is most abundant. Another possible response is to select the location where the eggs will be laid and incubated based on temperature, such as a relatively warmer location if temperature decreases before the eggs are laid, or a cooler location if temperature increases. Some lizards and spiders use this method of adjustment. For species that carry their eggs throughout incubation or that can control the temperature of the incubation site throughout development, there is the option of actively regulating the temperature that the embryos experience. Some bird species actively maintain the temperature of their nests. This is also probably a more common response in egg-carrying invertebrates than has been documented thus far.

Uca terpsichores courting male. Photo by Kecia Kerr
As part of my PhD project, I studied the timing of courtship and hatching of larvae of two species of fiddler crabs across seasonal and spatial differences in temperature. My research was conducted in Panama, based out of the Naos Marine Laboratories at the Smithsonian Tropical Research Institute (STRI). My colleagues and I found that Uca terpsichores respond to changes in temperature by changing when they court: when temperature decreased, males courted earlier. In addition, we found that these shifts in timing of courting and mating minimize errors in the timing of larval release… most of the time…. Since this method of adjustment does not allow the crabs to account for changes in temperature that occur after incubation begins, this species makes errors in timing when temperature is variable. In contrast, despite large changes in temperature in its habitat, Uca deichmanni does not adjust its courtship timing BUT, for the most part, they maintain timing of larval release in the field. This species only made errors in timing when temperature was low and constant. It appears that female U. deichmanni may, to some extent, regulate the temperature of their embryos during incubation by moving up and down in their burrows and exploiting the thermal gradient in the sediment, although this hypothesis has not yet been tested. This species is vulnerable to large prolonged changes in temperature that may exceed the limits of their thermoregulating abilities. Thus, these two closely related species that often inhabit the same beaches, both appear to adjust to temperature variations behaviourally, but in different ways.
Uca deichmanni courting male. Photo by Kecia Kerr

Surprisingly, behavioural adjustments to environmental variability, and the diversity of responses that species employ, remain underappreciated. However, over the last few years there have been calls for increased attention to the potential importance of plastic behavioural responses in mitigation of detrimental effects of environmental variation (Kearney et al. 2009, Sih et al. 2010). While many species are already being negatively affected by climate change, many others are likely able to diminish the impacts, at least to some extent, via behavioural responses. Much more research is needed to better understand how organisms respond to variable environmental conditions and what impacts these responses may have on their ecology.

Kearney M, Shine R, Porter WP (2009) The Potential for Behavioral Thermoregulation to Buffer “cold-Blooded” Animals Against Climate Warming. PNAS 106:3835–3840

Sih A, Stamps J, Yang LH, McElreath R, Ramenofsky M (2010) Behavior as a key component of integrative biology in a human-altered world. Integrative and Comparative Biology 50:934–944

Thursday, 9 October 2014

Fighting the war on science

There has been a long-standing dogma within the scientific community that scientists can not, and should not, be activists. “To be effective,” my undergraduate mentor told me, “scientists need to be impartial, they need to do science and let others worry about the advocacy. If you want to go into advocacy, that’s great, but you have to choose that route or choose science.” As 120 heads of state met at a critical United Nations Climate Summit in New York last month, this dogma has never been clearly more out-dated and indeed, in need of “major revision."

On September 21st, more than 2,500 independent mobilization events were held in cities (including Montreal) across 160 countries around the world in what was collectively called the Peoples’ Climate Mobilization. The mission was this: to demand that the heads of state representing governments around the world make tangible commitments to work together to solve the climate crisis. Given the increasingly dire predictions of the international scientific community, including the Inter-governmental Panel on Climate Change, there has never been a more urgent time for action to reduce greenhouse gas emissions, especially from the largest per capita carbon polluters in the world, which include the United States and Canada.

People's Climate Mobilization in Montreal!

In order to make these momentous changes, not only in global climate policy, but also in environmental conservation and natural resource management, an informed public needs to have access to and understand science. It does not take a scientifically literate populace to see that dramatic climate changes is already taking place, but it does take scientific literacy to understand the potential consequences of increasing levels of carbon in the atmosphere and to recognize that human activities are driving these changes. However, the science that is essential to inform the public, and the scientists that provide this information, are under attack. Indeed, in Canada as well as the United States, there is a war on science on several fronts.

Founding director of McGill's Neotropical Environment (NEO) Program, Dr. Catherine Potion. Professor Potvin is the Canada Research Chair in Climate Change Mitigation and Tropical Forests and a UN Framework Convention on Climate Change negotiator for Panama and special advisor to Indigenous communities. She spoke at the protest, and I had the pleasure to march beside her (a hip, hip lady).

Several well-documented examples have now been made public that demonstrate a directed political agenda to undermine research on climate change and other environmental issues in North America. The first example is of the control of scientific information through the muzzling of government scientists working for Environment Canada. Under a directive put in place in 2007, scientists are required to have permission from several government agencies to be interviewed by the media and in some cases, need written approval for answers to journalists’ questions regarding the findings of peer-reviewed research. The result, according to a leaked internal policy review at Environment Canada, was an 80% decline in media coverage on climate science (1,2) and perhaps more importantly, a mis-informed public on critically important environmental issues, such as depleting fish stocks (3), ozone-layer depletion (4) and other major environmental issues.

This war on science has not only made the science less available to the media and thus the general public, but has also made the access to the data much more difficult for scientists to obtain through systematic budget cuts to research. These budget cuts have sliced their way through scientific research through 1. termination of employment for thousands of scientists working for Environment Canada (5) and the Department of Fisheries and Oceans (6), 2. closure of the Polar Environment Atmosphere Research Laboratory (PEARL), a failure to renew funding for the Canadian Foundation for Climate and Atmospheric Studies in 2011, and massive budget cuts to the Experimental Lakes Area, a vital program for long-term research that has been instrumental for discovering processes such as acid rain and eutrophication that elucidate the impacts of industrial processes on freshwater resources and aquatic ecosystems around the world (7).

Furthermore, these cuts to research coincided with a crushing blow to the environment in 2012 through the Omnibus Budget Bill C-38, which effectively dismantled government agencies, including The Canadian Environmental Assessment Agency, and gutted decades worth of environmental legislation working to protect the environment and local communities (including the Canadian Environmental Protection Act, The Canadian Environmental Assessment Act, Energy Board Act,  Species at Risk Act,  Fisheries Act,  Navigable Waters Protection Act, Coastal Trade Act, Parks Canada Agency Act, Canadian Oil and Gas Operations Act, Nuclear Safety Control Act, and the Canada Seeds Act, to list a few (8). Last but not least, this single piece of legislation also dismantled the Kyoto Protocol Implementation Act, thereby revoking Canada’s ratification of the Kyoto Protocol (9). Alarmingly, these cutting attacks on science will continue, as the Toronto Star reported earlier this year that Environment Canada's plans and priorities report reveals massive budget cuts, from 1.01 billion in 2014-2015 to 698.8 million in 2016-2017 and a more immediate gutting to their climate change and clean air program, from 234.2 million in 2014-2015 to a mere 54.8 million in 2016 - 2017 (10)

Clearly, there is a war being waged on both science and scientists (so far I have focused on Canada because I live and study in Montreal, but this war on science has been widely documented in the United States as well… In fact, it took me two minutes to find important examples in the US on the war on science from the federal government on basic research and climate science (11-12), and examples of Congress’ own Science and Technology committee’s war on science policy, specifically the autonomy and impartiality of the peer-review grant approval processes of the National Science Foundation (13) and more recent news on the committee’s war on climate science (14). 

This is a very real war on science and it has gotten personal for scientists. Remember the bogus “Climategate controversy” concerning the Climatic Research Unit email on statistical transformations that were taken as tweaking the numbers? What you may not remember was that this hacking incident and subsequent media frenzy that made the scientists look like the criminals rather than the victims, was just weeks before the UN climate change negotiations in Copenhagen?), the question remains… What are we to do? How can we stand by, aloft in our “Ivory Tower,” when there is a war raging below to burry us, our science and with it, the truth?

The Sustainability Canada Dialogues, an initiative spear-headed by Dr. Catherine Potvin, is a powerful group of scientists, scholars, colleagues and friends who are leading efforts to influence climate policy in Canada. Check them out!

In my view, scientists need to speak out about our science, and we need to stick up for ourselves and for each other. In my opinion, the world is not a playground full of schoolyard bullies. The world is a place where very powerful people, with vested interests and enormous concentrations of wealth and power attained by the wanton pillaging of natural resources, will subvert any and all efforts that they perceive will destabilize their position. When these activities not only endanger local communities but also reach the point where they affect the Earth’s life-support systems, an informed public needs to act. In order to inform the public, scientists need to know the facts and sound the alarm. When the alarm is silenced, scientists need to put ourselves out there, to respond. Louder.

That is why I, and thousands of other scientists, marched, and will continue to mobilize in advocacy of the science and in defense of scientists (…yes… wearing my lab-coat!!!!)

"[The federal government] is making it very difficult for scientists that are publishing on climate data, on fisheries data, on all kinds of environmental data, they are making it very difficult for scientists to make public their conclusions and their recommendations on how to move forward in a sustainable and responsible way." - yours truly

On a personal level, I was thrilled at the chance to march in New York City and be a part of an historic event. However, I decided to organize locally and join the mobilization effort in Canada, which has a tragic recent record on environmental issues and an alarming agenda against science. To add insult to injury, the Prime Minister of Canada, Stephen Harper, did not attend the UN Climate Summit even though he was in New York City, rolling through photo opportunities in an attempt to save face. Nice try, Stephen. But in effect, this attempt to save face and launch a public relations blitz (that highlights commitment to science and leadership in addressing climate change (15)…. WHAT!?!?!?!?!?!) demonstrates that he knows that people were paying attention, that Canadian citizens are alarmed and embarrassed at his lack of leadership.

In an effort to help with the mobilization effort in Montreal, I felt it was most effective for me to mobilize the academic community in Montreal and help to ensure that students, as well as faculty, were involved in the mobilization effort. In any social movement, students have always played a central role, be it in the Independence Movement in India, the Civil Rights and Anti-War Movements in the United States and the Anti-Apartheid Movement in South Africa. In the mobilization effort on climate change, it is also imperative to involve scientists as these men and women can be, and should be, the most informed and thus most powerful advocates for the reality of climate change and the role of human society as the major driver for unprecedented rates of changes in climate.
Multi-tasking scientists: representing at march as they educate in NYC. They are so rad!

The Peoples’ Climate Mobilization can be deemed a success for several reasons. First and foremost, it was the single largest climate mobilization event in history, with the centerpiece being the march in New York City that gathered hundreds of thousands of people from many parts of the world. Second, the mobilization, not only in New York but around the world, highlighted the diversity of people that are part of the collective effort to build political momentum to pressure governments to address the climate crisis. Third, and perhaps most importantly, it put climate change and the environment back at the forefront of discussion and debate, not only at the local level, but at the international stage. This unprecedented level of attendance by heads of state gathered at this Climate Summit demonstrates that momentum is indeed building, and that maybe, just maybe, “a change is going to come.”

So, to make that change, will you continue to mobilize with us, and march again when we have to?

Don't forget to bring your lab coat!


(A special thanks to two amazing women, Dr. Catherine Potvin and Dr. Aerin Jacob for their leadership and inspiration!)

Works Cited:
10) environment_canada_braces_for_belttightening.html