Sunday, November 24, 2013

Finding God (and other memes) in Paris

I was recently in Paris for a meeting of the scientific committee of DIVERSITAS, where I am co-lead of the core project bioGENESIS. Owing to the annoying tendency of airlines to charge double if you do not stay in Europe over a Saturday night (so they can fleece business travelers who would not do so), I had the happy inconvenience of a couple of extra days to browse Paris. This included my second entrance into Notre Dame de Paris, which got me to reflecting ...

Notre Dame de Paris.

As one would expect of a scientist, I take an evidence-based approach to ideas. Thus, if God were ever to provide concrete evidence of His existence, how could I do anything other than accept it? The closest I ever came to such evidence was on Christmas Day, 2001. I was visiting Paris, seeing all the sights, and taking copious pictures on my Nikon F4 camera. The F4 was the best professional camera Nikon made in the 1990s, and it had served me faithfully and without incident for 10 years. On that Christmas Day, I found myself outside the grand cathedral Notre Dame de Paris. I had never seen it before and it certainly didn’t fail to impress with its grandeur and age (almost 840 years old). Even though it was Christmas Day, they were letting tourists in. How memorable it would be, I figured to enter Notre Dame on Christmas Day 2000 years after Christ’s birth – and so I did. It was spectacular indeed – all the more so because Christmas Mass was underway. The penitent were in the center of the cathedral singing various hymns while the tourists walked around the outside taking pictures. It seemed rather rude to me that folks would be taking pictures, including with flashes, while the faithful were speaking to God, but everyone was doing it and there I was. So I sheepishly brought the camera to my eye, composed the photo, and pushed the shutter button. Nothing happened. Absolutely nothing. Then, of course, I went through all of the problems that might seem obvious – dead batteries, some weird setting, and so on – but I couldn’t find anything obviously wrong, except for the fact that everything was seemingly wrong. The camera was just broken. And it never worked again until I got it back from a repair shop months later. 

Notre Dame de Paris

A pious interpretation of this event might be that God punished my impudence and sent me a message. Or perhaps it was just a coincidence. If, however, the same thing happened on my next visit to Notre Dame de Paris, then perhaps I would need to reconsider. Well, that chance came last week. There I was, standing outside the grand old dame – still just as impressive and now even older, precisely 850 years. Again I entered, again Mass was underway, and again I had a top-of-the-line Nikon camera in hand. I raised the camera to me eye, composed an image, pushed the shutter button, and click. Click, click, click, click … 

God is a meme – an idea that spreads from one mind to another – and it is a very effective one. In fact, a number of social scientists have argued that this meme has not only spread effectively but that it has increased the fitness of individuals carrying it. I suppose this isn’t too surprising given that a tenet of most religions is that reproduction is good (and contraception bad), which presumably increases the chances that the meme will pass effective to more people (the children) and thus spread farther and faster.

Eiffel's meme.

Paris is full of memes. The Eiffel tower is one. I had been to Paris many times but never to the top of the Eiffel Tower – it just seemed too kitschy and touristy. So I had instead spent my time wandering around the just-as-touristy, if considerably less kitschy, Louvre and Orsay museums. Plenty of memes there too, like Greek sculptures copied by Roman and then French sculptors, like Théodore Géricault’s Raft of the Medusa begetting Romanticism, like Titian forever the art of portrait painting – and so on. On this trip, however, I figured I had better also do the tower just to have done with it. So up up up I went, walking as far as possible and then by elevator the rest of the way to the top, which was buried in the clouds. I quickly realized that the Eiffel Tower wasn’t so much a kitschy tourist attraction as a spectacular engineering feat – and displays on the way down showed how the design was much copied immediately afterward – the tower as a meme.

A design much copied.

Religion and engineering marvels might seem admirable or important memes but other memes are just silly – and Paris has no shortage of those either. How about those bridges that are covered in thousands of locks – literally thousands and thousands of them? Who was the first person who put a lock there? Or, perhaps more importantly, who was the first person who put the lock there simply because someone else had put a lock there. And when did someone decide to call these “love locks,” with lovers writing their names on the lock and throwing the key into the Seine. Even governments can’t stop this meme – they keeping cutting them off the bridges in many cities and they just keep coming back.

A new meme and an old meme

As this is an eco-evo blog, I suppose I need to get somewhere with this meme theme. I could perhaps just do the easy “how would memes influence eco-evolutionary dynamics” - but that would lead to rather obvious ramblings about how memes, like any behavior, could dramatically alter ecological dynamics at the population, community, and ecosystem levels – and that this effect might be more dramatic because memes can spread more quickly than genetically based behaviors. But that would just be trying too hard. So instead, let’s just stop to marvel at memes, big and small, important and trivial, good and evil – and also to remember that scientific ideas are memes too: they come, they compete, they fade away. But some are here to stay, such as heliocentrism, relativity, natural selection, hopefully eco-evolutionary dynamics, and – dare I say it – the God Particle. Now that I believe.





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Wednesday, November 13, 2013

Ecological effects of camouflage evolution in the stick insect Timema cristinae


Shortly after joining Patrik Nosil’s newly formed lab at the University of Colorado, making it a busy research group of two, I was coming to grips with the reality that I needed to gear up for a serious transition from pure community ecology to hard-core evolutionary genomics. This all turned around on a dime, however, after Andrew Hendry’s epic visit to Boulder during the winter of 2009. Details are fuzzy, though I vaguely recall a near-boiling hot tub, and too few beds at the end of a long night. Anyway, despite scalded feet, Andrew’s visit ended with a changed direction for my PhD and a new line of research for the Nosil Lab: eco-evolutionary dynamics!

Independent of my reorientation towards the community ecology of eco-evolutionary dynamics, we were contacted by Ilkka Hanski who, knowing Patrik’s work, was keen to use the stick insect Timema cristinae to evaluate one of his recently developed mathematical models, which makes fine-scale predictions about spatial patterns of local adaptation (Hanski et al. 2011). Timema cristinae experiences strong divergent selection from birds for crypsis on its two dominant host-plant species, Adenostoma fasiculatum and Ceanothus spinosus, causing the evolution of striped and unstriped morphs, each better camouflaged on Adenostoma and Ceanothus, respectively (see figure below, Nosil and Crespi 2006). However, the homogenizing effects of gene flow create complex spatial patterns of local adaptation throughout the landscape (Bolnick and Nosil 2007), setting up an excellent scenario to test Ilkka et al's model. It seemed as though Ilkka’s proposed research would dovetail nicely with the ecological work we were planning to do in Timema come spring, so we began a collaboration with him and his postdoc Tommi Mononen. This collaboration culminated last month with a nice publication in Current Biology (Farkas et al. 2013).

 (A) striped and (B) unstriped T. cristinae, (C) Adenostoma fasciculatum, (D) Ceanothus spinosus
Black bar indicates approximate 1 cm scale 

Rewind to the spring of 2011, when Tommi, Patrik, my labmate Aaron Comeault, and I shared a one-bedroom apartment in Santa Barbara, in which Patrik insisted on sleeping directly in front of the only bathroom, apparently to prevent mid-night toilet visits by the rest of us. Led by Tommi, we trekked into the Santa Ynez National Forest and began to collect data. Using steel fence stakes, flagging tape, string, and a tape measure, we manually mapped (old-school) 186 host-plant patches of Adenostoma and Ceanothus inhabited by Timema, and sampled the bushes by whacking their branches with a stick, recording the abundance of the two morphs on each bush. We also performed two field experiments, one of them in 2012, manipulating the number of striped vs. unstriped Timema on bushes of Adenostoma. After the fieldwork was done, behind the scenes in Helsinki, Tommi and Ilkka scripted away the wee hours of every morning, evaluating their model with our data, and generating new predictions for us to test.

From these studies, we found a very strong influence of evolutionary dynamics in T. cristinae on ecological patterns, both for T. cristinae populations themselves, entire cohabitating arthropod communities, and interactions between herbivores and their host plants. In the mapped metapopulation network of T. cristinae, we found significantly lower local abundances in host-plant patches harbouring populations with high proportions of the poorly camouflaged morph (unstriped on Adenostoma and striped on Ceanothus). Also, as it turns out, the mathematical model performed quite well to predict the spatial patterns of local adaptation in Timema, and made some interesting predictions about patterns of patch occupancy and modified evolutionary trajectories for the Timema. These results were corroborated by our manipulative experiments, which showed lower abundances on Adenostoma bushes stocked with the unstriped morph. Furthermore, we found lower abundance and species richness of cohabitating arthropods on those bushes, as well as lower rates of herbivory from sap-feeders. These community-level results suggested that when birds are attracted to and forage on populations of poorly camouflaged Timema, they opportunistically eat or scare away other arthropods as well, reducing herbivory. Our second experiment involved a bird-exclusion treatment, and supported this hypothesis. 

 Graphical summary of the empirical results.

The various authors of our paper differ a bit in their opinions about what is most interesting about the study, but I will point to three main things. Firstly, eco-evolutionary research, and much ecological research in general I venture to claim, tends to use single types of evidence. I think one of the major strengths of our study is that it combines manipulative experiments with field observations and mathematical modelling: our experiments strongly support the notion that camouflage evolution in T. cristinae causes differences in ecological dynamics, and our observational data show that it correlates with naturally observable patterns. Second, evolutionary ecologists have little sense for how important evolution may be in driving ecological patterns relative to traditionally examined factors. In our observational study, we show that poor camouflage accounts for approximately 7% of variation in population size, comparable in magnitude to the effects of host-plant species (5%) and habitat patch size (14%). For T. cristinae populations, evolution is in this sense “important”. Lastly, our study is among few to empirically examine the ecological effects of evolutionary processes other than natural selection, since we also look at gene flow and founder effects. The consequence is that we have evidence in our system for ongoing effects of rapid evolutionary processes on ecology: year after year, natural selection rapidly increases local adaptation, and gene flow breaks it down, allowing eco-evolutionary effects to persist through time.

To bring it all full circle, Andrew was asked to write a news dispatch by Current Biology (Hendry 2013) to highlight the work he set in motion over three years ago. Thanks for everything Andrew!

Illustration credit: Rosa Marin Ribas


Bolnick DI, Nosil P (2007) Natural selection in population subject to migration load. Evolution 61:2229–2243.
Farkas TE, Mononen T, Comeault AA, Hanski I, & Nosil P. (2013) Evolution of camouflage drives rapid ecological change in an insect community. Curr Biol 23:1835–1843.
Hanski I, Mononen T, Ovaskainen O (2011) Eco‐evolutionary metapopulation dynamics and the spatial scale of adaptation. Am Nat 177:29–43.
Hendry A (2013) Eco-evolutionary dynamics: Community consequences of (mal)adaptation. Curr Biol 23:R869–R871.
Nosil P, Crespi BJ (2006) Experimental evidence that predation promotes divergence in adaptive radiation. Proc Natl Acad Sci USA 103:9090–9095.

Thursday, November 7, 2013

Carnivals #64 and #65, and some musings about continental drift and niches

The Carnival of Evolution had a hiccup that resulting in two monthly Carnivals coming out within a few days of each other, so I decided to wait and lump them into one post.  So now, for your delectation, double the usual number of cool blog posts about evolution!  Also, see below for some random musings about life and evolutionary biology.

Carnival #64 was hosted by Reconciliation Ecology, with a "cabinet of curiosities" theme; I guess sometimes it's pretty hard to find a theme that really unites everybody's posts!  Our contribution to that one was Njal Rollinson's very interesting post on non-adaptive explanations as null hypotheses in evolutionary ecology, which delves into questions regarding parsimony and the role of models.

Carnival #65 was hosted by Pharyngula, where PZ brings his usual flair to a Halloween horror theme.  We had two contributions that edition, due to some mysterious alignment of the stars.  One was Joost Raeymaeker's post Back to the future IV: Michael J. Fox encounters the Red Queen, an entertaining spin on host-parasite interaction evolution.  The other was Kiyoko Gotanda's post on the spatial patterns of directional phenotypic selection, introducing a cool new paper in Ecology Letters that pieces together what we know so far about spatial variation in directional selection, a key driver of adaptive divergence and ecological speciation.



And what else?  I was recently in Iceland, where I stood at a spot where the North American plate is separating from the Eurasian plate.


On the right side of the rift: Europe.  On the left: the abyss.  (The edge of the North American plate is a couple of miles away, on the far side of the rift valley.)

New land is being created here every day, a reminder of the constant environmental change that underlies everything, opening up new niches even as old niches are destroyed.  This was apropos for me, as my old niche of PhD student at McGill recently disappeared – being successful in that particular niche means, ironically, that the niche evaporates out from under you!  Perhaps I over-exploited that resource; maybe I should have found a way to sustainably harvest PhD funding for a couple more years.  Luckily, a new niche, postdoctoral researcher at CEFE/CNRS in Montpellier, France, opened up just in time for me to colonize it; indeed, I was in Iceland en route to join the lab of Luis-Miguel Chevin, where I am now starting on a project involving adaptation to multi-dimensional niches with mutational heterogeneity and all sorts of fun, complicated stuff.  May you all find a new niche just when you most need one!

Saturday, November 2, 2013

Evolutionary inferences from the analysis of exchangeability



In my classes that I teach at Pace University, the theme of parallel and convergent evolution is a recurrent topic. For example, we’ve discussed parallel evolution of lactase persistence in human populations from northern Europe and parts of Africa, and convergent evolution of the camera eye in vertebrates and cephalopods. Stickleback fish are a classic textbook case of parallel evolution, adapting repeatedly to freshwaters from marine ancestors, diverging into benthic and limnetic forms along similar lines in multiple lakes, and adapting along similar trajectories in lake and stream habitats throughout much of the northern hemisphere.

I first began thinking about parallel evolution as a master’s student at McGill when I was practicing analyzing microsatellite data. A question came to my naïve graduate student mind: Couldn’t we compare microsatellite and morphological data among populations to determine the proportion of within-population variation that is due to constraints versus adaptive evolution? I expected that a high level of “exchangeability” of neutral genetic markers would reveal a higher level of morphological “exchangeability” between lake and stream populations from the same watershed (due to gene flow or shared ancestry), whereas genetic (microsatellite) distinctiveness would result in morphological traits in lake habitats that are more similar to fish in other lake habitats than in the stream habitats (and vice versa) due to adaptation. I proposed that we could use classification techniques to directly compare genetic markers and morphological traits.

Years later, my ideas have culminated in a study on stickleback from parapatric lake and stream habitats from each of six watersheds on Vancouver Island. We used discriminant analysis to classify individuals to populations for each of several measures, including diet ecology (stomach contents and stable isotopes), trophic morphology (body shape, and gill raker number and length), armor traits (plates and spines), and microsatellites (6 neutral loci, and 6 loci linked to QTL). This approach differed from traditional analyses that compare means among populations in that “misclassified” individuals could inform us as to which populations were more “exchangeable”; that is, it could tell us whether a lake fish would be a better fit into another lake population than into any stream population, based on any of the traits or loci (and vice versa for the stream fish).

We found that populations within watersheds were most exchangeable with respect to genetic markers, which would make sense if gene flow occurred between lake and stream habitats. This was less likely to be the case with diet and body shape, however, for which fish were more likely to be classified into a similar habitat in a different watershed than into a different habitat. Why are these results important? In addition to shedding light on the deterministic nature of habitats in shaping parallel patterns of evolution, these results might provide insight to conservation managers planning to relocate individuals to new environments, for example when the native range is under threat or to enhance genetic variation in a bottlenecked population.

Reference:
Hendry AP, Kaeuffer R, Crispo E, Peichel CL, Bolnick DI. In press. Evolutionary inferences from the analysis of exchangeability. Evolution. DOI: 10.1111/evo.12160

Check your (taxonomic) biases at the door

Many of us like to believe that we are conceptually-oriented researchers; our particular study organism(s) are just means to an end, the en...