Saturday, October 18, 2014

How to write/present science: BABY-WEREWOLF-SILVER BULLET

As an editor, reviewer, supervisor, committee member, and colleague, I have read countless papers and proposals and have seen similarly countless presentations. Some work well and some don’t. Beyond the picky details of slides that are too wordy, speaking that is too fast, sentences that are poorly constructed, and so on – the most critical problem is making clear why the work is interesting and important. Why should we read further rather than moving to the next paper on the pile? Why should we give you money as opposed to your competitor? Why should we listen to your talk instead of tweeting about the party last night? This simple and yet pervasive inability to engage the reader and have them buy into your work is likely the single greatest flaw in the writing of every student (and many postdocs and faculty members). In this post, I will explain a simple metaphor that can help you to solve this problem in each and every one of your papers/proposals/presentations.

The metaphor emerged from a comment by McGill’s Dean of Science, Martin Grant, about what makes a good proposal. He suggested that you need a werewolf and a silver bullet. With a werewolf, a funding agency and their reviewers can see the problem that needs solving. With a silver bullet, the agency and reviewers can see that you have a realistic chance of solving the problem. When translating this logic to my own students, I have modified it somewhat to better fit the ideal outline of a paper/proposal/talk. The basic idea is that the structure of your paper/proposal/talk should follow this sequence:
  • CUTE BABY: First explain to the reader/listener the general umbrella under which the work falls – some umbrella that will make the reader/listener sit up out of their sleep-deprived torpor and say to themselves “Oh, OK, this talk is about something that is interesting and important. I better pay attention to what new insight they might bring.” Cute babies can be things that are important, such as ecosystem health and human well-being. A common cute baby here is biodiversity and its contribution to ecosystem services. Cute babies can also be things that are interesting, such as theories, with examples from ecology and evolution being the equilibrium theory of island biogeography or the ecological theory of adaptive radiation. In developing this cute baby, it is critically important to not overtly state that the baby is cute. “One of the most important topics in ecology is the maintainance of biodiversity” – this is a “motherhood” statement (http://en.wiktionary.org/wiki/motherhood_statement) that just annoys the reader by making them feel manipulated. Instead the reader should make up their own mind when reading about the baby that it is indeed cute. Stated another way, if you have to say that your study area/work is important, then people will think you are trying too hard. Instead, the reader should think “oh, that is important” without you having to say it.
Cute babies.*
  • SCARY WEREWOLF: Next explain how that cute baby is somehow threatened, so the reader/listener shifts forward on their seat and begins to empathetically furrow their brow in shared concern, thinking “Yes, that’s true, that really is an unsolved problem that could hurt the baby.” Scary werewolves for biodiversity and ecosystem services might be climate change and habitat loss and, well, pretty much anything. Scary werewolves for theories are things like potentially inappropriate assumptions, or the lack of empirical tests, or the failure to include an important idea, or low explanatory power. Here (as opposed to the above) it is more often OK to state that the werewolf is scary but it is still more effective to avoid motherhood statements and let the fear emerge within the reader’s mind. (How often do stories say “the werewolf was scary”? Instead they say that “a hulking beast with dark, tangled mats of hair emerged from the darkness dripping blood from its fangs with its eyes glinting in the moonlight.”)
Scary werewolf.*
  • SILVER BULLET: Finally, explain how the work that you did/will conduct has the potential to slay – or at least severely wound – the werewolf. If you do this effectively, the reader/listener will begin to unfurrow their brow and nod: “Ah, yes, that would be a great way to solve the problem.” Silver bullets can be applied solutions to problems, such as a new design for corridors that reduces the negative effects of habitat loss. Or they can be new experiments that address outstanding gaps in knowledge, or particular study systems that are ideally suited to show how some theory needs to be modified. Once again, you ideally don’t say “I have the silver bullet”; instead, the reader has this emergent thought while reading about the study system. And, of course, NEVER say your system is “ideal,” which means “couldn’t possibly be better,” as everyone who works on a different system will immediately think “no it isn’t.” Instead your system is “excellent.”
Silver bullet.*
  • DEAD WEREWOLF: For work that has already been conducted, one would ideally show that the silver bullet (new method/theory/experiment/observation) has killed the werewolf and thereby saved the cute baby. In reality, however, it is just as likely – and effective – to show how you have wounded or exposed the werewolf or how you have shown that the werewolf is scarier than originally thought or how you have found a new werewolf. These alternative end points nicely establish the need for further work. For work that has not yet been conducted, such as in a proposal, the dead/injured/new werewolf is not actually shown, but the reader has to see what it might look like. That is, they can visualize the werewolf lying dead on the ground while the cries of the baby fade into giggles while the baby bounces up and down on the werewolf’s belly. (Or alternatively, the werewolf is just a hairy uncle bouncing the baby on its knee.)
Dead werewolf.*
In implementing this schema, I suggest working from the goal that your Introduction will follow the above structure. The first paragraph (or section) describes the cute baby (the general area of research, subtly making clear why it is important), the next section describes the scary werewolf (the problem/gap/limitation of current knowledge/work), the next section suggests a silver bullet (the study system/experiment/new theory), and the final section postulates what the werewolf might end up looking like (the predictions/questions/hypotheses). In the context of a presentation, the entire talk should follow this structure, with the methods falling into the silver bullet part and the results/discussion taking the form of the dead/injured werewolf. Note also that studies sometimes examine multiple questions, in which case the baby-werewolf-bullet approach can take on a fractal appearance: the whole study, the individual components, and sometimes even within individual sections.

At this point, I am sure you have some thoughts or criticisms of the above plan. Although I presumably can’t predict all of them, here are some likely ones.
  • But my work just isn’t that important – it won’t solve world hunger, it won’t halt the loss of biodiversity, and it won’t overthrow the ecological theory of adaptive radiation. Surely I shouldn’t try to pretend it will. Indeed you shouldn’t, but don’t throw the cute baby out with the scary werewolf. Instead, you simply need to scale your baby/werewolf/silver bullet accordingly. If you have a relatively small problem, give us a clearly defined but only modestly scary werewolf. If your silver bullet is unlikely to slay the werewolf, then give us some silver pepper spray. The key point is that the above logic and outline applies regardless of the size of the problem or the actual outcome of the study – yet, it is true that you can’t oversell your baby-werewolf-bullet.
  • But I don’t want to oversell my work – reviewers will see through my attempt to make it seem more important than it is. This concern is related to the one immediately above and, again, it is correct that you shouldn’t promise something you can’t deliver or outline a werewolf you can’t kill. However, you can outline nested werewolves – like Russian doll werewolves where you can slay some small ones thus getting closer to the big one. Conveniently, the solution is the same as above – scale the baby/werewolf/bullet to the scope of your study and what you can deliver.
  • But I didn’t actually kill the werewolf. No problem. Explain how your silver bullet was tarnished (polishing will fix it up) or was made of aluminum (I need a new experiment) or how it missed the werewolf altogether (the werewolf was in our imagination or was really just a hairy uncle seen in low light). This outcome is just as satisfying in most instances.
Maybe it wasn't that scary after all.*
Or maybe it is the baby that is scary.*
Well, there it is – a suggested plan for writing every paper/proposal/presentation for the rest of your career. I hope it helps. I have certainly found it immensely helpful for improving the logical flow and engaging narrative of my students’ work, as well as my own. Of course it doesn’t always work and of course it doesn’t guarantee acceptance (rejection can occur for many other reasons), but I think it solves the problem of how to structure the presentation of ideas and how to make clear the importance of your study. And, even within this framework, many other improvements can be made to the grammer/writing/presentation. Here are my own suggestions: http://redpath-staff.mcgill.ca/hendry/writingtips.pdf and I list some additional ones below.
The Science of Scientific Writing

On whimsy, jokes, and beauty: can scientific writing be enjoyed?

-----------------------------------

* I did not take these photos but found them on google - the original source (and copyright holder) is not clear.

Monday, October 13, 2014

Imperfect generalism in Darwin’s finches

[ This post is by Luis Fernando De León; I am just putting it up. –B. ]

How species coexist in nature is one of the long-standing questions in evolutionary ecology. This is particularly relevant for understanding the process of adaptive radiation, which is thought to explain a large portion of the Earth’s biodiversity.

Adaptive radiation often results in a large number of coexisting, closely-related species that share (or compete for) similar resources, environments, or habitats. In these circumstances, several outcomes are possible. For instance, species could be maintained in sympatry by specializing on different portions of the resource spectrum (niche divergence), which could lead to character displacement and reduced gene flow between competing species. A second possible consequence is exclusion, in which a species is extirpated by its similar but more efficient competitor species. Finally, a third possible consequence is fusion, in which coexisting species sharing similar resources show large niche overlap that increases interbreeding between the diverging species. This suggests that the evolution of niche differences (e.g., low diet overlap) is an important mechanism maintaining divergence in sympatric, closely related species. Interestingly, this assumption of niche divergence is not always met when quantifying niche overlap in nature.

If closely related species are to persist even in the face of large niche overlaps, additional mechanisms are needed to promote coexistence while reducing the likelihood of fusion or exclusion of competing species. Some of these mechanisms include the interaction between temporal and spatial variation in niche overlap in highly heterogeneous environments.

In our recent study, published in the Journal of Evolutionary Biology, we set out to understand the combined role of these two factors by looking at spatio-temporal variation in the dietary niches of four coexisting species of Darwin’s ground finches from Santa Cruz Island, Galápagos, Ecuador. Specifically, we analyzed over 7000 feeding observations collected over a 5-year period (2003–2005) at three different sites on Santa Cruz Island (El Garrapatero, Academy Bay, and Borrero Bay). We also quantified available food resources at the three sites during three years.

Darwin’s ground finches on Santa Cruz Island provide a nice system to study spatio-temporal variation in diet niches within a young adaptive radiation. There are four closely-related species persisting in sympatry on the island: the small ground finch (Geospiza fuliginosa), the medium ground finch (G. fortis), the large ground finch (G. magnirostris) and the cactus finch (G. scandens). These species also show high variation, both morphological (bill size and shape) and functional (bite force), often with overlap among the species (Fig.1). These species show evidence for niche conservatism, given that they all exploit basically the same set of food resources (seeds and insects), but their niches are thought to diverge along the axes of seed size and hardness (Fig. 1).


Fig. 1. Darwin’s ground finches and their favorite foods.

Santa Cruz Island also presents an ideal ecological setting to test for these factors. Santa Cruz is the second-largest island of the Galápagos and probably one of the most ecologically heterogeneous of the archipelago. This island is characterized by variable climatic conditions (wet and dry periods) influenced by the wind currents and the effects of El Niño. These climatic factors, together with the geographic position of this oceanic island, promote large spatial variation in vegetation, which is expressed in the form of vertical zonification of the plant community, as well as variation among sites in the lower part of the island (Fig. 2).


Fig. 2. A panoramic view of Santa Cruz Island, Galápagos, Ecuador.

Our results showed that ground finches largely overlap in their dietary niches, and this overlap is often larger than anticipated from random expectations, indicating that these birds are typically generalists or opportunists in their feeding habits (Fig. 3). However, we also found that each species frequently exploits a set of food items to which its morphology is best adapted (for some examples, see Fig. 1). We call those sets of food items “private resources”, and we argue that they could have important implications for niche partitioning in Darwin’s finches. For instance, we observed that the use of private resources increased in periods of resource scarcity (the dry season), leading to an overall decrease in niche overlap among species. We also observed that spatial variation in available resources could have a similar effect, given that species tend to exploit those private resources according to their availability in different sites on the island (Fig. 4).

Fig. 3. Mean niche overlap between different pairs of species of ground finches from Santa Cruz Island. The upper panel shows Pianka’s (1973) niche overlap index; statistical significance was tested by comparing observed niche overlaps with a pertinent null model (dashed line) after 1000 simulations. The lower panel shows the variation in mean niche overlap across a five-year period (2003–2007). Error bars represent standard error.

Fig. 4. Diet partitioning in Darwin’s ground finches. Symbol shades indicate different sites: Academy Bay (grey), Borrero Bay (white), and El Garrapatero (black). Symbol shape indicates different species: G. fortis (circles), G. magnirostris (squares), G. scandens (rhomboids), and G. fuliginosa (triangles). Numbers indicate different sampling years from 2003 to 2007.

We propose that Darwin’s ground finches correspond to a model of “imperfect generalists” in which species are able to converge on a wide range of easily accessible food items in times or places of high resource availability, but can also retreat to private resources in times or places of scarcity. We discuss the implications of imperfect generalism in determining regional coexistence of closely-related species sharing similar resources, and consider how a spatiotemporal approach to niche partitioning could further our understanding of species coexistence in nature.

Reference

De León, L.F., Podos, J., Tariq, G., Herrerl, A., and Hendry, A.P. 2014. Darwin’s finches and their diet niches: The sympatric co-existence of imperfect generalists. Journal of Evolutionary Biology 27:1093-1104. DOI: 10.1111/jeb.12383

Thursday, October 9, 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.

McGill Professor and Environment Research Chair in Climate Change Mitigation and Tropical Forests, Dr. Catherine Potvin, has been a UN Framework Convention for Climate Change (UNFCCC) negotiator for Panama and special adviser to Indigenous communities in many parts of the world. She spoke eloquently at the protest and I had the pleasure to march beside her. 

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 that 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
http://www.cbc.ca/player/News/Canada/Montreal/ID/2526956920/


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.


Scientists representing in NYC!!! With data!!!

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?




Remember to bring your lab coat!

V.F.



(A special thanks to two amazing women, Dr. Catherine Potvin and Dr. Aerin Jacob for their leadership and inspiration. Please check out their initiative called the Sustainability Canada Dialogues!!! getting some press in the Guardian and the Montreal Gazette (16 - 17)!




10) http://www.thestar.com/news/canada/2014/03/12 environment_canada_braces_for_belttightening.html


Thursday, October 2, 2014

Carnival of Evolution #76!

It’s the beginning of October, and although here in Canada it means that winter is very, very close, it also means that it’s time for the Carnival of Evolution! In this 76th edition we have some posts, which somehow managed to have very little in common (-.-), except that they are all awesome! I’ve organized the posts in no specific order, but under three broad topics. I hope you enjoy it!

Gene expression/ gene regulation

Marine Sticklebacks have colonized many rivers all over the world, and with each colonization they adapted to the new freshwater environment. These adaptations came in many shapes and colours, including the loss of body armour, and more and stronger teeth. Robert Sanders explains how differential regulation of the Bmp6 gene in freshwater sticklebacks allows them not only to have more teeth, but also teeth regeneration! You can read the full post here.



According to the WHO, in 2012, 8.2 million people died from cancer, and 90% of these were due to metastasis: the spread of cancerous cells to healthy organs. This devastating disease has taken away many friends and family, and is in the back of the head of anybody with a family-history with cancer. However, not all is lost! Justine Alford reports on a paper recently published in Nature Chemical Biology, where the authors engineered a protein that would interfere with the metastatic process in mice. The results are amazing! The protein reduced in 78% the metastases and stopped the progression of the disease! Definitely good news. You can read more here.

Vertebrate evolution

If you’ve ever been in the jungle in the middle of the night without a light you will know the uncomfortable feeling: noises from animals moving everywhere, smells that you’ve never smelled before, and just a very unpleasant time overall. Well, this is because we, humans, are not adapted for low light conditions, and because the jungle is full of nocturnal creatures. Contrary to us, most other mammals are nocturnal, which was the main argument for their amazing flourishing after the dinosaurs went extinct. Tom Giarla talks about how a little bone (the scleral ring) brought new light, quite literally, to this assumption: the night was scary even back then! You can read the post here.


It seems that mammals are actually older than what we thought! Charles Choi talks about three species of Haramiyids recently discovered in China that revealed previously unknown similarities with modern mammals. Their skull and middle ear are so similar to modern mammals that they might be included in this group. If this were true, the origin of mammals would be 50-60 million years earlier than previously thought! Awesome. You can read the blog post here.

Somehow related to Stephen Jay Gould

Once. Yes, only once has multicellularity evolved. Isn’t it amazing that thanks to this single event we have the astonishing diversity of eukaryotic life on Earth. Me, you, my dog, your cat, trees, whales, mushrooms, carrots, and everything else that exists on earth are distant relatives. In a beautifully written post, Ed Yong describes not only this lucky event, but also the evolution of the research around it. You can read Ed’s post here

I have been to many introductory courses in Evolution – not because I failed and had to take them again, but because I was either taking the course for the first time, or because I was helping the teacher – and in every single one of them they quoted Stephen Jay Gould and his “tape of life".  Emily Singer takes on a recently published paper in Science, by Michael Desai’s group, about the predictability of yeast adaptation. Yeast actually evolved to the same evolutionary endpoint, despite evolutionary contingencies (initial genotype)!  So, going back to Gould, if we replay the tape of life, would we end up with the same life forms as today? This was actually an exam question in one of those courses, and was intended to get a feeling of student’s understanding on the mechanisms by which evolution occurs. I guess most students should’ve had that question wrong… You can read more here, or the actual article here.

Like many sciences, evolutionary biology is full of concepts, models and theories that as the science matures become more and more complex. But sometimes it is easy to take one step back, take all these concepts, models and theories, and make them more palatable – at least for the general public or people who aren’t evolutionary biologists. Bradly Alicea talks about “toy models” in Macroevolution: a “simple and intuitive (but sometimes counterintuitive) way to summarize complex and subtle evolutionary dynamics”. This post really made me think about how we teach high school and lower levels of undergraduate biology courses. Should we switch to toy models? Think about it… You can read the post here.


Many people, like myself, are huge fans of sci-fi movies with aliens, battleships and mechs – a good plot also helps. But have you wondered why most aliens are represented in a humanoid form? If, and only if, there is intelligent life somewhere in the universe, would they look a little bit like us? Well, maybe they won’t be as good looking and charming, but they could actually have many similarities with us. Charly Jane Anders explores some of the “mechanisms” that could give rise to humanoid looking aliens! Now, I wonder if I have ever met one… You can find the blog post here.
* If you think this is not related to Stephan Jay Gould, you are wrong. There is a sci-fi writer called Steven Gould: http://en.wikipedia.org/wiki/Steven_Gould


So this is the end of the 76th edition of the Carnival of Evolution, we hope that you’ve enjoyed it and will come back for more amazing blogging about anything related to Evolution. Remember to submit your posts for the next edition of Carnival of Evolution in their Facebook or via e-mail!

Saturday, September 20, 2014

A Tale of Two Morphs

Back in the summer of 2010, I was working on what became a chapter of my Ph.D. in Austria, as part of the Young Scientists’ Summer Program (YSSP) at the International Institute for Applied Systems Analysis.  You can read more about that amazing experience, and the research project that it led to, in my post on Evolutionary branching in complex landscapes.  While I was there, Andrew Hendry, my Ph.D. advisor, sent me an email saying “Hey, there’s a researcher in Zurich who has an interesting modeling idea, perhaps you might want to talk with her.”  And thus was a collaboration born that ultimately led to another thesis chapter – serendipity!  At the end of the YSSP, I hopped on a train from Vienna to Zurich (a truly lovely journey of about 8 hours), spent a couple of days with Elena Conti, Barbara Keller, and Jurriaan de Vos at the Institute for Systematic Botany, and together we sketched out the idea for what became a paper we just got published in PLoS ONE.  And that’s what I want to write about today.


A view from the train from Vienna to Zurich.  Photo: Ben Haller.  (For lots more photos from my time in Austria, including side trips to Prague, Budapest, Munich, and Abisko, you can check out cloudphotographic.com, my photography website.)

It’s a difficult project to write about, because it is deeply intertwined with the precise workings of a floral syndrome called heterostyly that is itself not easy to explain.  Heterostyly attracted the attention of Darwin himself, who wrote at some length about it in his treatise The Different Forms of Flowers On Plants of the Same Species, and it has proved fascinating to evolutionary biologists ever since.  In essence, heterostyly typically has two components: a floral polymorphism, and an intra-morph sexual incompatibility system.  In the simplest form, called distyly, there are two floral morphs, and these two morphs can cross with each other but (mostly, to varying degrees in different species) cannot cross with themselves. The two morphs are called pins and thrums, and they are characterized by different heights of the reproductive organs within the corolla tube of the flower, as drawn by Darwin:


A pin, on the left, with a high style and low anthers, and a thrum, on the right, with a low style and high anthers.  Drawing: Charles Darwin.

The key point to notice is that the positions of the reproductive organs in the two morphs are reciprocal: the high style in the pin is at about the same height as the high anthers in the thrum, and the low style in the thrum is at about the same height as the low anthers in the pin.  Although the precise way in which heterostyly functions to increase the fitness of flowers is a bit subtle, having to do with reduction of sexual interference between the male and female functions of the flower (see Barrett 2002 and Barrett & Shore 2008), the important point here is that studies indicate that this reciprocal positioning tends to lead to reciprocal pollination: pollen tends to move from pins to thrums, and from thrums to pins, rather than between flowers of the same morphology, because pollinators tend to transport pollen positionally.  Pollinators do this because they approach flowers in a somewhat consistent manner, and the same parts of their bodies tend to contact the same parts of the flower in each flower they visit.  So if a particular part of a bee’s glossa (like a tongue) brushes against the anthers of a thrum, and picks up pollen, then if the bee next visits another thrum, that pollen is relatively unlikely to be delivered to the second flower’s stigma; instead, that particular part of the glossa will brush against the anthers again, and will just pick up more pollen from the second flower.  When the bee eventually does visit a pin, that particular part of the glossa will again brush against the same spot in the flower – but now, there is a stigma there, because this flower is a pin, and so the pollen stuck to the glossa will be delivered.

I don’t mean to make this sound too precise; no doubt it is a very messy business, and pollen ends up all over the place.  What I am describing is only a tendency: the probability that pollen will be transported between different morphs is somewhat higher than the probability that pollen will be transported between identical morphs.  Or to put it in a more particular way, for reasons that will become clear: if a pollen grain starts at a particular height h in the corolla tube of a flower (the height of the anthers), what in the probability distribution for the height h′ at which that pollen grain is likely to be offered to the next flower by the pollinator?  What is the precision of pollen transfer, for a given species of pollinator?  The short answer is that nobody really knows the answer to this; it is extremely difficult to measure this empirically.  However, heterostyly has independently evolved more than 20 times in the angiosperms, so it appears to be quite beneficial; that suggests that the precision of pollen transfer might be high enough to warrant some careful thought about its potential consequences.


Pollination: a messy business!  (This bee is on a sunflower, a non-heterostylous species.)  Photo: Ben Haller.

The key idea that we wanted to pursue in this project is that this precise pollen transfer might lead to reproductive isolation between different populations of a heterostylous species, reducing gene flow between the species and thus promoting speciation.  How would this work?  Consider the diagram below:


A: Morphs with reciprocally matching reproductive organ positions cross well when pollen transfer is precise, because the pollen picked up at the anthers of one morph is delivered to the correct height to be received by the stigma of the reciprocal morph.  B: Morphs with mismatched reproductive organ positions do not cross well when pollen transfer is precise, because the pollen gets delivered at the wrong height (i.e., it is stuck to a part of the pollinator’s body that does not contact the stigma in the destination flower).  Diagram is from our PLoS ONE paper, Figure 1.

So if two populations of heterostylous plants evolved different reproductive-organ heights, that would decrease the gene flow between them to some extent – an extent that would depend on the precision of pollen transfer.  That decreased gene flow would allow them to diverge in other respects as well, since they would be (somewhat) released from the homogenizing effects of gene flow.  In the end, the divergence afforded by precise pollen transfer in the context of heterostyly might be the first step down the road to ecological speciation.

This post has rambled on long enough, and I haven't even gotten to what we actually did!  So, to make a long story short: we designed an individual-based model that tracked the movement of every pollen grain between every pair of flowers, we ran the model using various types of simulated pollinators, and we observed the degree of ecological divergence that two populations of flowers could reach when subjected to divergent selective pressures in their respective environments.  The pollinators occasionally flew from one patch to the other, transporting pollen with them and thus producing gene flow that constrained that adaptive divergence; but if the flowers evolved mismatched reproductive-organ positions, they could decrease that gene flow, and thus be free to become better-adapted to their local environment.  We varied the frequency of inter-patch pollinator movement, the strength of divergent selection, and the precision of pollen transfer, and we observed the extent of adaptive divergence attained between the two populations (relative to a set of control runs without precise pollen transfer).

What did we observe?  For details on that, you will have to look at our paper!  Suffice to say that it was a complex tale: in one scenario we observed increased divergence due to decreased gene flow, but in a different scenario we observed decreased divergence due to increased, asymmetric gene flow – a result that quite surprised us!  Furthermore, in one scenario the reproductive-organ traits acted as magic traits, influencing both the ecological fitness and the reproductive isolation of the populations, while in the other scenario they did not.  There’s discussion of “magic environments” and “magic modifiers” and all sorts of wonderful magical things; the upshot of all of it is that, as I and coauthors have written about before, the term “magic trait” is perhaps a bit of a misnomer.  The “magic” really happens in the interaction between an ordinary trait that happens to have an effect on assortative mating, and an environment that happens to produce divergent selection on that trait.  The effect size of the magic trait on divergence and speciation, furthermore, is again not entirely a function of the trait itself, but is instead affected by other genetic and environmental factors that influence the strength of the effect of the trait on non-random mating and on local adaptation.  In this paper, we call these external factors “magic modifiers”.  The precision of pollen transfer proves, in our model, to be such a magic modifier.

What does that mean in empirical terms?  What would be the actual magic modifier?  One possibility that we point to is the shape of the corolla tube.  Flowers with wide-open corolla tubes place relatively little constraint on pollinators, and so the precision of pollen transfer might be quite low between such flowers.  Flowers with long, narrow corolla tubes tend to constrain how the pollinator interacts with the flower, increasing the precision of pollen transfer because the same parts of the pollinator will contact the same parts of the flower in each visit.  Evolving a longer, narrower corolla tube might therefore be a way of evolving a higher precision of pollen transfer, increasing the degree of “magicness” afforded by the reproductive-organ heights of the flower, and thus allowing greater divergence and speciation.  This ventures well into the realm of speculation, but it is interesting to note that the ancestrally heterostylous clade Primula (including nested genera), with ~550 species, typically possesses long, narrow corolla tubes with the sexual organs concealed inside, whereas its sister clade, the genus Soldanella, is non-heterostylous, is typified by open, dish-shaped corollas, and has only 25 species.  So perhaps heterostyly does not always provide a magic-trait mechanism that promotes diversification; but perhaps Primula is an example of a case where a magic modifier, the corolla shape, evolved to allow it to do so.

So if you ask “are the floral reproductive-organ heights in heterostyly magic traits?”, the answer appears, according to our model, to be “it depends on the environment”.  This suggests that if we want to understand why magic traits appear to be common in nature, and how they influence the process of speciation, we will need to broaden our perspective from thinking about the evolution of traits to thinking about the evolution of ecological interactions, and in particular, the evolution of magic environments and magic modifiers.  It’s an eco-evolutionary problem!

Reference:

B.C. Haller, J.M. de Vos, B. Keller, A.P. Hendry, E. Conti. (2014). A tale of two morphs: Modeling pollen transfer, magic traits, and reproductive isolation in parapatry. PLoS ONE 9(9), e106512. DOI: 10.1371/journal.pone.0106512

Carnival of Evolution #75

Whoops!  The delay in the August Carnival of Evolution (#74) got me confused, so I forgot to post about the September Carnival, which came out right on the heels of the August one.  Well, maybe this gave you all some breathing room, anyway.

So, the September Carnival, #75, has been out for a couple of weeks now.  Our contribution to it was my post about interactions between theoretical and empirical research in ecology and evolution.  I conducted a survey of scientists in ecology and evolution, and got more than 600 responses.  The survey results were interesting, and it’s a subject that ought to be relevant to everybody!

There’s lots of other cool stuff in this Carnival too, from a discussion of a new (possible) case of sympatric speciation, to a takedown of a new claim for intelligent design from Behe, to Carl Zimmer on new findings in the evolution of land-living tetrapods from fish!  Check it out!

ALSO: Our very own Felipe Pérez-Jvostov will be hosting the next Carnival, #76, here at eco-evo-evo-eco in just a little over a week!  So if you’ve got a blog post about something evolution-ish, and you want it in the Carnival (because why not?), submit it to Felipe!  His email: felipe [dot] perezjvostov {at} mail (dot) mcgill <dot> ca, with appropriate symbolic replacements.  :->

Monday, September 15, 2014

The ideal experiment...

[ This blog post is by Sinéad Collins; I am just putting it up.  –B. ]

In a previous blog post, Andrew outlined the “ideal approach” for investigating whether plasticity facilitates evolution, and to my delight, he proposed experimental evolution. Not only that, but he proposed the experiment my group got published this week in Proceedings B. I was pleased to be accused of doing anything ideal, much less an ideal experiment, even if Andrew doesn’t seem to remember me presenting this very data at the American Genetics Association Meeting.

When Elisa Schaum (the PhD student behind all this work) and I planned this experiment 3 years ago, our main concern was that it was, if anything, too obvious: in order to test whether plasticity facilitates evolution, take plastic and non-plastic populations, put them in new environments, and watch them evolve. Not so easy if you study elephants, but completely doable if you study microalgae (like we do).

To conduct our “ideal experiment” (do I like the sound of that too much?), we used plastic and non-plastic isolates of the small but mighty marine picoplankton Ostreococcus. Ostreococcus is exciting for many reasons, among them that it is the smallest known free-living eukaryote and yet manages to house a huge virus. However,  we chose it mostly because it is distributed over most of the world’s oceans, and we supposed that Ostreococcus from different locations would differ in how plastic they were in their response to CO2 enrichment (we were right, and we published this in Nature Climate Change). We used 16 different isolates of Ostreococcus from different locations.  We found that isolates from environments with more variable and less predictable CO2 levels showed the largest plastic response to changes in CO2, meaning that we had plastic and non-plastic (and intermediately plastic) genotypes of Ostreococcus.

 
Two TEM images of Ostreococcus. Photos: C.E. Schaum.

Then, we set up the evolution experiment. We let all of the genotypes evolve in 4 different environments. First, we used a control environment where CO2 levels were normal and stable. Second, we used a fluctuating environment, where mean CO2 levels were the same as the control, but they fluctuated around this mean every few generations – we hypothesized that this environment would select for plasticity, but not for adaptation to high CO2. Third, we used a stable high CO2 environment, where we could look at how the initial plasticity of the genotypes affected evolution in a new environment even if there was no further need for plasticity. Finally, we used a fluctuating high CO2 environment, where mean CO2 levels were high, but also fluctuated every few generations, to look at how plasticity affected evolution in a new environment when there was also selection for plasticity.  Then, we let everything evolve for a few hundred generations. We are now up to 1000 generations in the lab, but the paper was written before we reached this point of insanity.

Aaaannnnnd… plasticity facilitates evolution. Genotypes that were more plastic evolved more in high CO2 environments. Not only that, but populations in fluctuating high CO2 environments evolved more than populations in stable high CO2 environments. And to make matters even more exciting, populations evolved in fluctuating environments were more plastic than populations evolved in stable environments, no matter what the level of CO2. So, even when plasticity itself is selected for, populations evolving in response to an environmental change still evolve faster than populations dealing with that same environmental change who don’t have to bother with selection for plasticity. I may have done a happy dance when I saw that data.


Dr. Collins expressing her love for Osteococcus, post-results. Photo: Jane Charlesworth. [We tried to obtain a video of the good-data happy dance, but it was not available at press time. – The Management]

Of course, things are never that simple. The evolutionary response of Ostreoccocus to high CO2 can only be described as weird. I think this is because CO2 is food for many photosynthetic organisms, including Ostreococcus. So, when CO2 levels increase, Ostreococcus cells divide faster. This means that working with high CO2 here is at odds with the usual way of doing an evolution experiment with microbes, where researchers generally starve, poison, overheat, or do some other horrible thing to decrease microbial fitness substantially at the beginning of the experiment. However, we discovered that we were (eventually, and inadvertently) also guilty of torturing our microbes, as it turns out that a higher growth rate is all well and fine for a few generations for Ostreococcus, but after a while, dividing so quickly takes a toll, and the cells become less able to survive the slings and arrows of outrageous fortune (heat), have leaky mitochondria, and are bad at competing against other Ostreococcus. So, the evolutionary response to high CO2 in Ostreococcus – the response that results in cells that have normally-functioning mitochondria, can handle a bit of heat, and can overgrow other genotypes – is to grow more slowly. Basically, evolution reverses the plastic response to high CO2. Even though cells grow faster in the short term in high COenvironments, they slow back down again if given enough time to evolve. Most theory for evolutionary biology isn’t tested in enriched environments, so it took us a while (and quite a few cups of hot chocolate) to figure that out.

So yes, I would say that the experiment was ideal. It had everything: tiny protagonists (Ostreococcus), clear results (plasticity facilitates evolution!), weird and surprising twists in the clear data (evolving slower growth than your own ancestor!), and a happy dance (possibly two).


Sinéad Collins and Elisa Schaum
Institute of Evolutionary Biology, University of Edinburgh
web: http://www.smallbutmighty.bio.ed.ac.uk/

Proceedings B paper: http://rspb.royalsocietypublishing.org/content/281/1793/20141486.full
Nature Climate Change paper: http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1774.html