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

Tuesday, September 9, 2014

MYScience: A newer faster cheaper easier BETTER open access journal

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  • Wearied by having to select only a few relevant references?
  • Irritated at having to submit your data to an online database?
  • Chuffed to say what you want how you want as long and as often as you want?
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  • Hope to publish the same study twice – or more?
If the answer to any of these questions is yes (or no), then we would like to encourage you to submit your paper to our new open access journal: MYScience.

MYScience has a number of critical advantages:
  • We accept all papers regardless of importance, content, scientific accuracy, or statistical rigor.
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  • If you feel compelled to do so, send us your data, raw or otherwise, in a file of any format you like and we will post it as is alongside your paper.
  • We will accept your paper instantly. In fact, consider your paper accepted immediately after submission even if you don’t hear back from us. We are likely accepting other papers (or tweeting) at the moment and will get to yours soon.
  • We will publish your paper as soon as we see it. Format it exactly how you want it to look – we won’t make any changes of any sort and we will post it on our website (www.MYScience.com) instantly and in the exactly form in which it was submitted, including the original file format. In fact, we won’t even open the file before publishing. That would just slow us down.

As this is an open access journal, we expect the authors to contribute to the cost of publishing. Our fee is $10 per submitted (and thus published) page, which is considerably cheaper than any other open access journal. We know this matters to you.

We look forward to receiving your paper so you can get on with your life.


SOME RESOURCES:




Wednesday, September 3, 2014

The Ghost of Plasticity Past, or Why Plasticity Inferences are too Plastic

Several months ago, I attended a meeting of the American Genetics Association organized by Robin Waples in Seattle, Washington. The theme for the meeting was “Evolution and Plasticity: Adaptive Responses by Species to Human-Mediated Changes to their Ecosystems.” The meeting was a particularly clear example to the current excitement about the role of plasticity (including epigenetics) in the evolutionary process – an enthusiasm that really crystalized around Mary Jane West-Eberhard’s “Developmental Plasticity and Evolution”. Much of the excitement centers around the idea that plasticity (a single genotype has different phenotypes in different environments) can promote evolutionary change. For instance, plasticity can provide the raw material necessary for evolutionary change by revealing otherwise cryptic variation. In addition, plasticity might generate immediate adaptive phenotypic shifts that allow individuals and populations to persist in new environments, thus allowing and promoting subsequent adaptation (without the initial adaptive plastic shift, the population would have gone extinct). This idea is not new, having originated with James Baldwin in 1896, but it has certainly become vastly more popular of late.

These (and other) ideas for how plasticity might promote evolution are certainly interesting, but how does one go about testing them? One of the things I found simultaneously most interesting and frustrating about the Seattle meeting was that seemingly any pattern in the data was being interpreted as evidence that plasticity promotes evolution. Perhaps most commonly, a finding that plastic responses to a particular environmental difference were in the same direction as evolved differences between populations evolving under the same environmental difference was interpreted as evidence that plasticity promoted evolution. For instance, guppies might shoal more in the laboratory when exposed to predator cues and guppy populations evolving with predators might shoal more than those evolving without predators (independent of proximate predator cues in the laboratory). On the exact opposite hand, however, evidence that plastic responses to a particular environmental condition were in the opposite direction as evolved differences was also interpreted (by other presenters) as evidence that plasticity promoted evolution. In this case, the idea is that the plasticity is likely maladaptive and so requires evolutionary compensation.

The current inferential scheme for whether or not plasticity promotes evolution
If either of two opposite patterns is interpreted as evidence for the same thing (i.e., plasticity promotes evolution, albeit in different ways), how do we proceed with rigorous hypothesis testing. Surely we also need a set of results that would be interpreted as evidence that plasticity does NOT promote evolution. That is, the hypothesis must also be clearly falsifiable through some particular outcome in the data. The lack of such a criterion reminds me of the classic criticism by Joseph Connell that competition was invoked when species have similar diets (because they obviously then use the same resources) and also when species have different diets (because past competition had presumably reduced diet overlap – the ghost of competition past).

In the past, when I pointed out to some ecologists that competition seemed of little importance as a mechanism determining a particular species' distribution, they often gave the following answer. The reason, they said, for my inability to find evidence for competition was because it had already been eliminated by past coevolutionary divergence between those species. However, for the reasons discussed in this paper, and until some strong evidence is obtained from field experiments along the lines suggested above, I will no longer be persuaded by such invoking of "the Ghost of Competition Past". (Connell 1980 – Oikos)

Although the Seattle meeting ended several months ago, I was just prompted to write a post about the topic owing to the recent publication in Nature of another study about the role of plasticity in evolution: “Developmental Plasticity and the Origin of Tetrapods.” Em Standen, Trina Du, and Hans Larsson wanted to test whether plasticity would promote major evolutionary transitions, especially the transition from swimming in water to walking on land. To test this possibility, they invoked a classic hypothesis test: if an ancestral species shows adaptive plasticity in response to an environmental shift, and that plasticity mirrors the evolutionary changes that accompanied the environmental shift, then plasticity likely promoted the transition. Specifically, they reasoned that rearing an air-breathing fish out of the water (by misting them regularly) would cause developmental changes in morphology that would lead those fish to be better walkers out of water. If so, the same thing may have taken place in the water-to-land transition. This is a cool idea – although, of course, plasticity in the ancestor is merely consistent with the hypothesis rather than proof of it.

The difficulty in any such study is that the actual ancestor (here the ancestor of land-dwelling tetrapods) is not accessible for study – and so Standen and colleagues needed an analog species. Coecocanths obviously wouldn’t work and lungfish are just too pathetic on land. So the authors chose to use another basal tetrapod – the Polypterus or “bichir.” Performing the experiment, they found that Polypterus raised out of water were indeed better at walking out of water than those raised in the water (see the cool video below) and showed developmental morphological changes that were similar to those in the fossil record associated with the move out of water.


This result is fascinating and I was privileged to see its implementation as the work was done in the lab of my close colleague Hans Larsson. In fact, I was able to talk to him about it multiple times on the train on the way to work. In addition to simply be jealous that I hadn’t thought of it first, I came to crystallize a particular criticism of the work. Specifically, I contend (if only as Devil’s Advocate) that the results could just as easily be interpreted as showing that developmental plasticity does NOT promote evolution. The reason is that Polypertus has never made the transition to land despite millions of years of opportunity to do so. Thus, all this wonderful plasticity did NOT accomplish the task it is inferred to assist.

Given all these flexibility in ad hoc interpretation, it seems to me that the field needs a critique and a careful (a la Connell) outline of the various patterns that might be observed in an experiment and what inferences they would and would not allow. Until such an endeavor is undertaken and adopted, inferences about plasticity are simply too plastic.

I wrote the above on the train a few seats away from Hans and, while then walking to work, we discussed what the optimal experiments would look like. We think that the ideal approach would be experimental evolution: have replicate plastic and non-plastic genotypes/populations, expose them to new conditions, and track their subsequent evolutionary trajectories. If the most plastic genotypes show the fastest and most dramatic evolution, then plasticity promotes evolution. If the least plastic genotypes show the fastest and most dramatic evolution, plasticity constrains evolution. If plastic and non-plastic genotypes don’t differ, plasticity does not influence evolution. Until then, I will no longer be persuaded by such invoking of "the Ghost of Plasticity Past".

Thursday, August 28, 2014

Carnival of Evolution #74

Well, it’s a couple of weeks late, but Carnival of Evolution #74 is now out.  Our contribution was Craig Benkman’s fascinating post about “A small mammal with an outsized impact”.  With more than 500 views already, it’s one of our most popular posts ever, and deservedly so.  So if you haven’t read it, check it out!  There are lots of other goodies in the carnival; I was very interested in the discussion of ring species by Jerry Coyne, for example.  Enjoy!


A ring species.

Saturday, August 16, 2014

The Divide: a survey about interactions between theoretical and empirical researchers

What is the proper role of theoretical versus empirical work in biology?  I self-identify as a theorist, and I do pretty much all of my work sitting at my Mac Pro.  However, I did my Ph.D. in Andrew Hendry’s lab, surrounded by empirical biologists working on stickleback, guppies, salmon, and other slimy real-world critters.  This was somewhat of an accident; initially, I was interested in doing an empirical Ph.D., but my past as a software engineer meant that I soon shifted into modeling.  (An early attempt at doing fieldwork on stickleback in British Columbia also convinced me that perhaps that was not my strongest suit.)  My position as the “token theorist” in the Hendry Lab worked out really well; I got a lot of exposure to empirical concerns and perspectives that informed my modeling work, both in what I chose to study and how I wrote about it.  At the same time, I provided a theoretical perspective that I hope was interesting and useful to the others in the lab.

This situation meant that I was often thinking about the way that theoretical and empirical approaches interact in ecology and evolutionary biology.  Should theoretical ideas drive new empirical work to look for the patterns and outcomes predicted by theoretical models?  Or should pure “natural history” observations of the real world drive new theoretical work to explain the patterns and outcomes observed?  Or is the ideal perhaps for the two perspectives to mutually drive each other, in a sort of ongoing feedback?  Do empiricists and theorists interact too little, too much, or just the right amount, in today’s world?  Which aspects of the interactions between these groups work, and which aspects are perhaps dysfunctional?  How do institutions such as journals, funding agencies, conferences, and universities influence (and perhaps hinder) such interactions?

My interest in such questions was whetted by discussions with Dan Bolnick, Andrew Hendry, Kiyoko Gotanda, Maria Servedio, and others too numerous to name, and the further along I got in my Ph.D., the more important these questions came to seem.  Some fascinating (and disturbing) papers came out on related topics, such as Fawcett & Higginson’s paper on the negative citation impact of equations in a paper, and Scheiner’s paper on the dearth of theoretical grounding in ecological research.  Eventually, I decided to conduct a survey of ecologists and evolutionary biologists to see what others thought about such questions.

And so that’s what I did, and the results of that survey are now published in BioScience.  I think the paper is quite accessible (it doesn’t contain a single equation!), so I won’t go into detail here about what I found.  In short, though, my results underscore three themes.  To quote from my abstract:

One theme is a widespread and mutual lack of trust, understanding, and interaction between empiricists and theorists. Another is a general desire, among almost all of the respondents, for greater understanding, more collaboration, and closer interactions between empirical and theoretical work. The final theme is that institutions, such as journals, funding agencies, and universities, are often seen as hindering such interactions. These results provide a clear mandate for institutional changes to improve interactions between theorists and empiricists in ecology and evolutionary biology.

That mention of a “clear mandate for institutional changes” in the last sentence is intended as a sort of clarion call, and although I didn’t devote much space in the article to my own personal opinions, this here is a blog post, so I will write a bit more frankly.

In the present institutional structure of science, attempts to collaborate and interact strongly across the theoretical–empirical divide generally go unrewarded; indeed, respondents to my survey often felt that such efforts were effectively punished, since such research is both harder to fund and harder to publish.  For this reason, it would be both unfair and unrealistic to ask individual researchers in the present climate to increase their interactions across the divide.  Instead, I think what we need are institutional reforms that provide incentives for greater interaction: funding programs specifically devoted to cross-divide research, editorial policies that encourage cross-divide publications, hiring policies in university biology departments that encourage the hiring of people with cross-divide publication records, and so forth.  Once the institutional incentives are in place, individual researchers will adjust their behavior; until then, individuals will continue to respond to the incentives as they presently exist.

So rather than suggesting that you ask “what can I, as an individual researcher, do to interact more across the divide?”, I suggest that you ask instead “What can I, as a faculty member, a journal editor, a manuscript reviewer, a conference organizer, a grant evaluator, a professor, a member of a professional society – a participant in creating the institutional structure of science – do to encourage everyone to interact more across the divide?”  And then please discuss this with others, and take action!

Reference:

B.C. Haller.  (2014).  Theoretical and Empirical Perspectives in Ecology and Evolution: A survey.  BioScience (advance access).  DOI: 10.1093/biosci/biu131

Wednesday, August 13, 2014

Right beneath our feet: amazing nature in our backyards (Reign of Fire II?).

Our normal environs tend not to excite our scientific interest on a daily basis. They can instead become so familiar as to become boring and mundane – or just effectively invisible. We are instead more likely to be captivated and amazed when we go somewhere new – the Arctic, the Galapagos, the Amazon, the Negev Desert. On these trips, we tend to get excited about all sorts of critters, no matter how small or common. When visiting new countries, I find myself eagerly taking pictures of the most typical birds, birds that locals would never photograph, nor even notice, much as I treat a robin or starling or crow around my home.

Jumping spiders are awesome.
Yet our normal environs can become exciting and fresh again when we achieve a new perspective. Macro photography is a good example. Although I have long been interested in photography, I hadn’t spent much time on macro work until recently. Now, however, I often find myself at equestrian events and I need something to occupy myself and the kids in the hours between my wife’s performances. So the kids are tasked with running around in the bushes to find insects for me to photograph. Numerous times, I have been amazed by a cool new spider, mayfly, leaf hopper, lacewing, or any number of other spineless wonders. They were there all along, of course, right beneath my feet, but I simply hadn’t paid them much attention because I hadn’t previously been magnifying the world with a macro lens.

I only saw the parasites when I blew up this macro image of a lacewing.
A robber fly near my house
New perspectives can also be achieved by getting away from solid ground, such as going underwater or into the air. We recently bought my brother, Mike, a quadcopter on which he mounted his Go Pro to shot aerial footage of places we had seen countless times from the ground. We recently assembled a video aerial tour of the Wagner Natural Area, near Edmonton, Alberta, a site near our home that we had explored many times on foot or snowshoe or ski. Now, however, we were able to see patterns of diversity that were not apparent to us while walking on the ground – the trees no longer obscured the forest.


Mike and his quadcopter.
Or one can take a typical perspective and change its speed. Slow motion is a time shift we are used to from sports replays; but speeding things up, less so. I recently shot a time lapse video a sunset in Haida Gwaii, British Columbia. It shows the cool things a time lapse normally does, such as clouds zooming by – but then came a new insight: you can see very clearly the different layers of clouds going in different directions. I certainly already knew that winds go in different directions and different speeds at different altitudes, but here was the first time I could really SEE it so obviously. And, in my very first attempt to shoot a time lapse, I recorded of a wooly bear caterpillar building its cocoon. For the first time, I appreciated that they rip off their own hairs to form the basis for their cocoon.



New perspectives can also come just by chance through witnessing a rare event, like the time I watched an epic game of cat and mouse between a hawk and a squirrel in my backyard. The hawk would repeatedly swoop around the tree trying to get the squirrel on the opposite side only to fail when the squirrel dashed around again to the other side. The hawk eventually won the battle, but only when the squirrel tried to escape by dashing across a patch of lawn. As another example, barred owls are very conspicuous in many forests – to the point that they have become, if not common-place, at least not surprising. A few years ago, I was able to get very close to one in a tree by the side of a pond. I watched it for some time and eventually moved on, which was unfortunate because I was later told by someone else that it swooped down and caught a frog. (I went back and watched for hours but it didn’t happen again.)

Hawk 1. Squirrel 0.
The barred owl before he went fishing.
My brother, Mike, had a barred owl experience several times better. Seeing some owls low in the trees at a remote fishing camp in BC, he wondered if perhaps he could entice them to come down for proffered prey. The camp had a trap that produced five or so freshly-dead mice every day and so he started the process of training the owls to take them. It started with a rubber band attaching the mouse to the end of a fishing line, with the mouse then reeled in in a presumably tempting manner. After several attempts, the owls started swooping down upon the “fleeing” mice, grabbing them and flying off to feast on their perch. Eventually, they were able to get the owl to take mice right out of their hands. Mike made an awesome VIDEO of the experience.

Finally, a new perspective can result from a happenstance shift in the environment that exposes something previously hidden. Just imagine all of the fossils beneath our feet that we will never see unless a rockslide occurs, we dig a new septic tank, or a stream floods and cuts into the bank. The proof is in those numerous construction projects or mines that have uncovered cool new fossils or amazing archeological sites (or those dragons in the movie Reign of Fire). Closer to home, every time they disc the soil in our family vineyard in California, they turn up a slew of obsidian arrowheads that generates a family competition to find the best pieces.

Just last week, Mike, the kids, and I were visiting my mother in Edmonton, where we were helping her move from her home of 30 years into a condo. On the very last day we were all together (we won’t be back before Mom moves out), we were taking the quadcopter for some aerial shots when we crossed a creek we had crossed thousands of times before. Mike, looking down, noticed a bone and sent the kids after it. Upon retrieval, it was clearly a very old bone that had been buried in the ground and recently exposed by high creek flows. Old bones found in the forest are always fun but hardly novel, and so we set it aside and continued on our way.

The site of the find.
On the way back from filming, Mike hopped down into the creek and almost immediately found a piece of skull that seemed to be from the same animal as the leg bone. A bit further along, he found another skull fragment with the bony base of a horn attached – a bison. Now it was time to get excited: bison hadn’t populated this area for at least 140 years.

Bison and moose bones
Then the mad hunt began. Mike and the kids found another 15 or so bones right away – of all shapes and sizes and types. Then, the next day after Mike left, the kids went off to find more. They took a walkie talkie and had great fun reporting their finds back to me as I was working on the house. At one point they had so many bones that they had filled their pail and so called me to come and replace the bucket so they would have room for more bones. And, then, of course, I had to take my own turn through the creek, finding a few more bones in places kids wouldn’t normally look. By the end, we had quite a pile of bones, which were certainly from a number of bison (and a few moose).

Grandma and the kids show off their find.
Now we need to solve the puzzle. The previous day we visited a friend to look at mammoth bones that had been collected in the Arctic. Now we immediately began hoping we were looking Pleistocene bison, which were larger than modern bison. However, comparison to various skull images online suggested the latter; but why so many in this one place? Our neighbour, a taxidermist who had worked for the Royal Alberta Museum, came over to look and told us that he too had found bison bones when digging a new pond. He suggested they might be 300 to 600 years old and were from a boggy area in which plains bison not used to soggy conditions had become mired. It is a good hypothesis and now we aim to test it, starting by dating some teeth we brought back to Montreal. These discoveries and questions and projects have brought a completely new perspective on our childhood home that was revealed to us out of the blue on the very last day we were all there together.


Big bison bones
Many amazing things are just beneath our feet right in our own backyards, awaiting only a new perspective. Sometimes we need to actively engage that perspective with an underwater camera or a quadcopter or a microscope or a fishing rod and a mouse. Sometimes we merely need to wait for the right moment when new conditions expose previously invisible phenomena (those bones were there the whole time!). Other times (indeed, all times), we have to keep our eyes open for when rare events finally happen (when that owl dives for that frog). Natural history, ecology, evolution, and biodiversity are just as fascinating at home as they are in the Antarctic or the tropics, sometimes we just have to shift our perspective to see it.

Quite literally beneath our feet - under the flagging stones near the fire pit.

Wednesday, August 6, 2014

Standing and flowing


Our paper on "The genomic signature of parallel adaptation from shared genetic variation" is finally out in print. Check out the funky cover they used.

The paper is also subject of a News and Views by John Welch and Chris Jiggins: http://onlinelibrary.wiley.com/doi/10.1111/mec.12859/full

Here is the paper: http://onlinelibrary.wiley.com/doi/10.1111/mec.12720/full

Here is the original blog post: http://ecoevoevoeco.blogspot.ca/2014/04/peaks-and-valleys-in-genome.html

Tuesday, July 29, 2014

It’s all about the variance: science and life at N > 2

Variation is the grist for, and the flour from, the evolutionary mill. Without variation, no evolution occurs. With variation, evolution can generate even more variation by causing organisms in different environments to evolve different traits. We all know this, and we proceed accordingly in our research; but perhaps we too often take it for granted. Only sometimes are we smacked in the face by variation in such a way that it makes us pause and re-evaluate the way we view the world. Well, variation smacked me upside the head a few weeks ago during a trip into the field. In so doing, it made me reflect on how we estimate and interpret variance – and how this flavors the way we view our research and our daily experiences.

Threespine stickleback (Gasterosteus aculeatus)
Threespine stickleback could be the world’s most variable vertebrate. In some populations, average size at maturity is less than 30 mm – in others it is greater than 85 mm. In some populations, the pelvis is a huge structure – in others it is completely lacking. In some populations, the side of the fish is almost completely covered with bony plates – in others plates are entirely absent.  In some populations, mature males are almost entirely black – in others they have massive amounts of red – and in others black and red can be minimal. In some populations, the head is huge and the mouth massive – in others they are very small. In some populations, mean egg size (dry mass) is less than 0.047 mg – in others it is greater than 0.089 mg. This is just a small set of examples: stickleback, even just in freshwater, vary dramatically both within and among populations in almost any trait one cares to measure. This is why they are such a spectacular model system for studying adaptation.

A representation of stickleback diversity. The marine ancestor is surrounded by various freshwater forms.
Tom Reimchen, a professor at the University of Victoria, has long maintained that variation in stickleback on Haida Gwaii, a modest-sized archipelago off the coast of northern British Columbia, Canada, are as variable as are stickleback across the rest of their massive range in the northern hemisphere. Ever the skeptic, I have – when reviewing or editing Tom’s papers – pointed out that this assertion isn’t strictly true as (slightly) smaller stickleback are found in North Uist, Scotland. I am sure my nit was annoying to Tom as it was just a technicality and it required him inserting some rather pointless qualifiers into a few of his papers.


Several weeks ago, I had the opportunity to visit Tom in the field to see Haida Gwaii stickleback for myself. The first lake we visited was Drizzle, where Tom lived for 15 years and worked for 40. Drizzle is a modest-sized (112 ha) and heavily-stained (tannic, the color of very strong tea) lake with large and dark stickleback. A highlight here (besides camping and having a breakfast of bannock beside the lake) was walking the shoreline on Tom’s annual survey of loon-induced stickleback mortality. Several species of loon, particularly common and red-throated loons, congregate on Haida Gwaii lakes like Drizzle in numbers I had not thought possible, despite visiting countless lakes in my life. On Drizzle, dozens of loons would cruise nearby checking us out during our survey. And they would capture stickleback as if on cue – probably dozens were dispatched as we watched. Not surprisingly, many of the stickleback we found on the shore had been captured and killed, but not eaten, by loons. (Of course, many others are eaten - but we obviously can't find those on the shore.) Tom has an effective strategy for motivating search efforts. The person in front gets one point for every dead stickleback found. The following person gets two points. The third person gets three points. Tom was first, then Hannah, then me. Although it was like following two vacuum cleaners – I named one Hoover and the other Roomba – I held my own as tail-end Charlie (on points anyway).

Tom's cabin at Drizzle Lake (the lab is the wing at left).
A common loon with a Drizzle Lake stickleback.
The next lake we visited was Mayer, where Ric Moodie had – before I was born – discovered and described what is probably the world’s largest freshwater stickleback. This lake is larger (627 ha) than Drizzle, also quite stained, and even more overrun by loons. I had the good fortune, the day before meeting Tom, to happen by Mayer Lake just as it had stopped raining, in perfect time to cook my breakfast while watching 33 loons swim back and forth in front of me. Our next planned stop was Boulton Lake, in which more than half of the stickleback completely lack a pelvis, but this plan was derailed by happenstance. It seems that some delinquent and potentially dangerous kids had run off into the woods around Boulton Lake, and police parked along the highway nearby strongly discouraged us from going in.


So we instead hiked into Rouge Lake. This lake is a very shallow and small (1.5 ha) lake in the middle of a bog near the northern end of Graham Island (Drizzle and Mayer are on this same island). Rouge Lake stickleback are exceptional in several respects, especially their frequent lack of one of their dorsal spines, their (until recently) extreme red colour, their occasional possession of two dorsal fins, and the complete fixation of an otherwise locally-rare genetic variant (the Japanese clade of mitochondrial DNA). It was on the way back from this lake, tramping my way through bog behind Tom and three students, that variance smacked me upside the head. Just walking to these few lakes and hearing about (and seeing some of) their stickleback had finally brought home Tom’s assertions about the exceptional variation on Haida Gwaii and, more generally, the exceptional variation that organisms can achieve on very small spatial scales.

The Abbey Road of stickleback biology – the Rouge Lake trip. (Note: the picture is inverted for a reason that should be obvious.)
Along with this abrupt realization came a more fundamental epiphany: why had I been really impressed by the variance only after the third lake (not counting our aborted attempt to visit Boulton)? All of a sudden, I was struck by the parallel that, in statistics, we require a minimum sample size of three to get our first proper (albeit still weak) estimate of variance. The reason is that we need at least N = 2 to estimate a mean, and estimating a variance requires first estimating the mean and then needing at least one more data point. This makes sense statistically, of course, but – walking back from Rouge Lake – I began to wonder if our brains work the same way. That is, we really have to experience three things before we begin to get some mental perspective on how much they vary – because we need to consider the possibility of outliers. That is, with N = 3, we can see if any of the points stick out particularly far with respect to the mean – something that is impossible with N = 2 because in that case each point is equally distant from the mean. Stated another way, a sense of how variable things are first requires us to get a sense of the “average” or “typical” value and then a distribution of values around this average, which requires at least N = 3. Perhaps statistical principles match our mental processing machinery.

Now I can hear you saying: “Sheesh, N = 3 is way too low for a proper variance estimate.” You are, of course, correct. My point is simply that an assessment of variation, both statistically and mentally, can only begin at N = 3. Getting this third data point (visiting that third site) is the first moment when one has the potential to be impressed by that variation. Following that, much more data needs to be collected (many more sites experienced) to get a real estimate/understanding of the variance, but N = 3 is the first time you might be inspired by experience to try further. Hmmm, in writing this, I am reminded that I have only two kids. “Sweetheart, I’ve been thinking …”

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Some other cool Haida Gwaii experiences:



More Haida Gwaii photos: https://www.flickr.com/photos/andrew_hendry/sets/72157645239128218/

Eagles were everywhere.
Bleeding tooth fungus - how cool is that?
Sandhill crane in the rain.
Drizzle Lake
Native tree frog.
Masset, Haida Gwaii.
River otters in a tiny rainforest stream.
Sandpiper squadron.
Sundew