Saturday, June 9, 2012
Darwin in the genome
(I am posting a press release from McGill related to a paper that has just officially come out.)
A current controversy raging in evolutionary biology is whether adaptation to new environments is the result of many genes, each of relatively small effect, or just a few genes of large effect. A new study published in Molecular Ecology strongly supports the first "many-small" hypothesis. McGill University professor Andrew Hendry, from the Department of Biology and the Redpath Museum, and evolutionary geneticists at Basel University in Switzerland, studied how threespine stickleback fish adapted to lake and stream environments in British Columbia, Canada.
The authors used cutting-edge genomic methods to test for genetic differences at thousands of positions ("loci") scattered across the stickleback genome. Very large genetic differences between lake and stream stickleback were discovered at more than a dozen of these loci, which is considerably more than expected under the alternative "few-large" hypothesis.
By examining four independently evolved lake-stream population pairs, the researchers were further able to show that increasing divergence between the populations involved genetic differences that were larger and present at more and more loci.
As these results were obtained using new high-resolution genetic methods, it is conceivable that previous perceptions of adaptation as being a genetically simple process are simply the result of a bias resulting from previous lower-resolution genomic methods.
"I suspect that as more and more studies use these methods, the tide of opinion will swerve strongly to the view that adaptation is a complex process that involves many genes spread across diverse places in the genome," says Prof. Hendry.
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Source:
Roesti, M., A.P. Hendry, W. Salzburger, and D. Berner. 2012. Genome divergence during evolutionary diversification revealed in replicate lake-stream stickleback population pairs. Molecular Ecology 21:2852-2862. [Cover Article]. Link: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2012.05509.x/abstract
A News and Views about the article:
Nosil, P., and J.L. Feder. 2012. Widespread yet heterogeneous genomic divergence. Molecular Ecology 21:2829-2832. [Perspective]. Link: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2012.05580.x/abstract
Another paper employing SNP genome scans in lake-stream stickleback:
Deagle, B.C., F.C. Jones, Y.F. Chan, D.M. Absher, D.M. Kingsley, and T.E. Reimchen. 2012. Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions. Proceedings of the Royal Society B. Biological Sciences 279 1732 1277-1286. Link: http://rspb.royalsocietypublishing.org/content/279/1732/1277.abstract?sid=cc0e3784-2fc0-41ea-ac1d-a5dd3919d5fd
Thursday, June 7, 2012
Carnival of Evolution #48
So, it's Carnival of Evolution time again, and Carnival #48 is up at Pharyngula! (For more information on the Carnival itself, check out the Carnival of Evolution blog.)
We've got two posts in this Carnival (since we missed the previous edition due to a software glitch). One piece is by Kiyoko Gotanda, writing about fish, oxygen, and local adaptation. The other is by Emily Drummond, writing on dandelions, intraspecific genetic diversity, and ecology. But of course you've read those already, so now you should go enjoy the other posts in the Carnival!
PZ has chosen an Icelandic theme for this month. I don't have any photos from Iceland, since I've never been there myself; but here's a photo I took in Yellowstone National Park, which is kind of a mini-Iceland in the middle of the U.S.:
Late-breaking news: my parents were recently in Iceland, so here's a photo they took of Arctic terns in a stiff wind, against a panoramic Icelandic backdrop near Snaefellsness. No doubt, it being Iceland, the whole scene is about to be engulfed by floods of molten lava.
We've got two posts in this Carnival (since we missed the previous edition due to a software glitch). One piece is by Kiyoko Gotanda, writing about fish, oxygen, and local adaptation. The other is by Emily Drummond, writing on dandelions, intraspecific genetic diversity, and ecology. But of course you've read those already, so now you should go enjoy the other posts in the Carnival!
PZ has chosen an Icelandic theme for this month. I don't have any photos from Iceland, since I've never been there myself; but here's a photo I took in Yellowstone National Park, which is kind of a mini-Iceland in the middle of the U.S.:
Photo credit: Ben Haller, 2009.
Late-breaking news: my parents were recently in Iceland, so here's a photo they took of Arctic terns in a stiff wind, against a panoramic Icelandic backdrop near Snaefellsness. No doubt, it being Iceland, the whole scene is about to be engulfed by floods of molten lava.
Photo credit: Helen Haller, 2010.
Tuesday, June 5, 2012
Team Pinzones IMAX 3D
If you are going to have your research filmed, you might as
well go the whole hog: high definition 3D shown in an IMAX theater with Sir
David Attenborough narrating. In theory, that is what will happen with Team
Pinzones, our hard working and long suffering research team studying the
evolution of Darwin’s finches (pinzones). This week I was back in Galapagos with team
member Jaime Chaves to recreate our fascinating and exciting procedure for the
cameras: setting nets, catching birds, putting on bands, measuring wings,
measuring legs, measuring beaks,
measuring heads, photographing, weighing, and releasing (no blood samples this
time). It was quite an adventure.
Indeed it did, just in time for filming on that last day. The next worry – for us at least – was that the 3D camera, the crane, and all the other equipment would be so heavy and cumbersome and finnicky that the whole procedure would be very slow. It takes a long time to move the stuff around and they wanted to film several locations along the El Garrapatero beach – itself a decent walk from the parking lot. The equipment was all ferried down the day before and then we all arrived at first light on the filming day. But would there be enough time to film all the bird sequences before it got too hot for the birds – normally about 10 am? The answer normally would be an emphatic no because it generally gets really sunny and baking around that time. But fortune smiled upon us beyond all expectation and it was cloudy and windy all day. The next concern was whether we could catch enough birds at the right times? Sometimes at El Garrapatero, we can go a long time without catching birds and that might be a problem since we didn’t want to hold any individual bird for too long. We started with one net and, within half an hour, we had a male and female fuliginosa (small ground finch), a male and female fortis (medium ground finch), and a female scandens (cactus finch) – each of the species we might reasonably expect to catch here. Let’s start filming.
Then it was time for even wider shots – and now the crane
would be called into action. We were to walk from the net with birds in their
bags to our banding station and the 3D camera would swoop around us presumably
giving everyone vertigo in the theater. So we did this a few times for
practice and then did the actual sequence. As we sat down on this first take and
started to process the birds, we noticed that there were 4 or 5 finches hopping around not 2 meters from where we were processing. “Hey you guys
should film those birds,” we said. Yeah right. What are the chances that they
could set this complicated camera up on a huge crane, have some birds hop down
at random at just the perfect distance, swoop the camera on the crane 180
degrees, and have it plop down in front of the finches without them leaving. Well,
not only did that happen but as soon as the camera came near to the birds a bunch more
arrived until nine of them were all hopping around right in front of the
camera. They filmed this for a minute and then swooped around to show us
processing finches right beside the free-flying finches in one continuous sequence. Dial a finch
indeed.
Next it was time to film us taking a bird from the net. As
we did this, the entire crane was moved about 40 meters to a rock promontory between
two patches of sandy beach and reconstituted on a wooden platform that had been
constructed just that day as the other filming was going on. This platform was quite
substantial because it also had a rail on it so that the entire crane could be
rolled along smoothly as it swooped around a cactus and could then be pulled
back to show us walking across the beach and then the lava toward our net. We
got to watch them practice their crane moves with one "grip" holding the
counterweight at one end and swooping it around and the other grip rolling the
entire apparatus along the rail. Then we had to go off and perform our walk for
the real filming. After that, with the light just petering out, it was time for
an interview at yet another location – sitting on some (reasonably comfortable)
lava beside the beach. Then 5 tons had to be carried back up to the parking
lot. It was a good thing 24 people were involved.
![]() |
| Team Pinzones goes before the (3D) camera. (Photo by Aspen Hendry.) |
First, the permits weren’t approved until the very last
minute – after the last minute actually. Not only did the film crew (Colossus
Productions filming for BBC) need permits to film our work but we also needed
permits to speak to them about our work. That achieved the day after we arrived,
filming was set to occur in a few days. The next problem, however, was that the
filming equipment was delayed – 5 tons of it! Customs in Guayaquil had taken
every single part of the equipment and removed it from the packaging and
photographed it. This delayed things for a few days but then the equipment was
finally shipped – except the batteries, which were deemed hazardous cargo. This
battery delay pushed us past the official filming date, and so we had to
change our flights by two more days. Having done so, the batteries arrived the
next day but one piece was still missing – the base for the crane. Yes, the
crane. They needed a crane to film our work. So it came down to one final day
for filming before we really needed to leave Galapagos. Would the crane base
come in time?
![]() |
| It's not your mother's camera. (Photo by Jaime Chaves.) |
Indeed it did, just in time for filming on that last day. The next worry – for us at least – was that the 3D camera, the crane, and all the other equipment would be so heavy and cumbersome and finnicky that the whole procedure would be very slow. It takes a long time to move the stuff around and they wanted to film several locations along the El Garrapatero beach – itself a decent walk from the parking lot. The equipment was all ferried down the day before and then we all arrived at first light on the filming day. But would there be enough time to film all the bird sequences before it got too hot for the birds – normally about 10 am? The answer normally would be an emphatic no because it generally gets really sunny and baking around that time. But fortune smiled upon us beyond all expectation and it was cloudy and windy all day. The next concern was whether we could catch enough birds at the right times? Sometimes at El Garrapatero, we can go a long time without catching birds and that might be a problem since we didn’t want to hold any individual bird for too long. We started with one net and, within half an hour, we had a male and female fuliginosa (small ground finch), a male and female fortis (medium ground finch), and a female scandens (cactus finch) – each of the species we might reasonably expect to catch here. Let’s start filming.
![]() |
| Getting a finch ready for its close-up. (Photo by Jaime Chaves.) |
First we did the close-ups with the huge camera nestled
right up next to our hands (I had to bend my neck around the camera to see what I was measuring).
At the end of this close-up period, we suggested it would be good to film the
large and small beaked morphs of the fortis – the phenomenon we study at this
site – but we didn’t have a small morph bird already captured. So we started
filming a medium bird alongside a very large one but, as I was holding the
birds for the camera, Jaime ran off to see if he could set the net again and
catch a smaller bird. Five minutes later he was back with the perfect bird. After
that minor miracle the crew needed wider angle shots of the same thing but most of the
birds had been held in their bags for an hour already and they should be set free. So we went back
to the net, set it again, and had 5 birds of all three species in half an hour.
It was almost like we could just “dial a finch” and place our order, having it
delivered at a pace that would shame pizza delivery.
![]() |
| Even the banding equipment gets a close-up. |
![]() |
| Moments before the finches arrived. |
![]() |
| The camera on the crane on the rails on the platform. |
This experience taught me several things. First, 3D is much
much much more complicated than 2D – the camera is huge and needs to be
calibrated before every shot. Second, those shots you see in BBC videos require
an immense amount of work – and now I know what a “grip” really does, although
I forgot to ask what made one of the grips the “best boy grip” that you often see acknowledged in film credits. Third, film makers may often be
unlucky with the elements or animals – as you so often see in the behind-the-scenes
stuff for BBC videos – but the opposite can also be true. The weather we had
was perfect – beyond perfect. It was literally the best possible weather for
working with birds ALL DAY LONG. And the birds were incredibly accommodating.
With a single net we could catch exactly what we wanted within 15 minutes at
any time of the day, which is definitely not typical. And then a whole gaggle
of finches shows up right in the perfect place for the camera already on a
crane. I am pretty sure the film makers don’t realize how incredibly lucky we
all were. And maybe those extra birds we captured and measured will be the ones
that make all our statistical tests significant.
Now we just have to wait a year or so to see how it looks in IMAX 3D with narration by you know who (of course, our stuff will be only a tiny fraction of the entire movie). In the meantime, we need to interest someone in Team Stickleback IMAX 3D and Team Guppy IMAX 3D.
Note: Special thanks to key recent Team Pinzones members Jeff Podos, Luis Fernando De Leon, and Joost Raeymaekers.
Now we just have to wait a year or so to see how it looks in IMAX 3D with narration by you know who (of course, our stuff will be only a tiny fraction of the entire movie). In the meantime, we need to interest someone in Team Stickleback IMAX 3D and Team Guppy IMAX 3D.
Monday, June 4, 2012
Black Out Speak Out
Today, our blog joins the Black Out Speak Out movement to protest the Canadian government's Bill C-38 which would severely cripple many of Canada's important environmental laws. For more information about what the bill will do, more information is here.
For more information, please visit Black Out Speak Out
Wednesday, May 23, 2012
Genetic diversity effects on population performance in dandelions
[ This post is by Emily Drummond, I'm just putting it up. — BCH ]
Individuals vary in their phenotypic traits. The importance of this truism has long been recognized in the field of evolutionary biology; without such heritable variation, there would be no evolution, as Darwin rightly pointed out. In contrast, the study of ecology seems to have often blipped along merrily, while quietly sweeping variation within species under the rug. Perhaps it wasn’t naively that ecologists regarded all individuals within a species as identical when constructing models of species competition, predation, etc. but simply from a need to reduce complexity. When I began my MSc degree, back in 2006, the potential importance of individual variation for ecological dynamics was finally receiving some long-deserved attention.
At that point in time, we had a collection of rigorous studies showing effects of genetic diversity on population, community and even ecosystem variables – everything from primary productivity, to nutrient cycling, to community resilience and species composition might be affected. However, this result was by no means universal – and studies that did find positive genetic diversity effects also varied in the magnitude of the effects identified. Clearly, we knew that genetic diversity could be important to ecology, but we had little predictive understanding of these effects.
What mechanisms generate diversity effects? How does environmental context matter? Why does genetic diversity produce effects in some studies but not others? These are the kinds of questions that my MSc supervisor, Dr. Mark Vellend, and I pondered. We were particularly intrigued by the circumstantial evidence from studies of marine eelgrass (i.e. Reusch et al. 2005. PNAS 102:2836-2831, Hughes & Stachowicz 2004. PNAS 101:8998-9002) that genetic diversity effects might only be revealed under poor conditions (e.g. stress or disturbance). Mark and I wondered if this might be a general result – did diversity matter more under unfavorable conditions, which might magnify genetic differences among individuals?
We designed an experiment using locally collected (on the British Columbia coast), asexual dandelions to investigate this possibility. In the spring of 2007, we created replicate dandelion populations of low (1-genotype), medium (2 genotypes) or high (4-5 genotypes) genotypic richness under field conditions. This diversity treatment was fully crossed with an environmental treatment: dandelions grew in either unfavorable “mowed lawns”, or in recently tilled, favorable “fallow fields”. As you can see from the pictures, these habitat types were completely randomized across the plots (we created the fallow plots as needed, by turning over the sod) and the initial growth environment varied hugely depending on habitat. In contrast to the fallow field, plants in the mowed lawn were surrounded by other species and regularly disturbed by clipping.
Planting the dandelions in a grid pattern in each plot, we were able to assess seed number and total leaf area (a measure of plant size/biomass) for each individual over the course of two years. We found that genotypic diversity enhanced population performance universally, but to a greater degree in the fallow field. For example, the gain in plot performance with diversity, from low- to high-richness plots, was 52% vs. 20% for leaf area and 31% vs. 23% for seed number. Large genotypes dominated in the fallow field leading to positive selection effects and significant overyielding. In the mowed lawn, where performance was limited, there was evidence for complementarity among genotypes, but no overyielding. Hence, our diversity effects, while clearly environment-dependent, were stronger in the more favorable environment - contrary to our prediction. While we don’t have a precise explanation for this result, our conjecture is that the larger size of and the stronger competition among genotypes in our fallow field enhanced genotypic differences. There is some evidence for this in the data.
Unfortunately the capacity of dandelions to form multiple rosettes, all attached to the same taproot, eventually led to difficulties identifying “individuals”. After about 2 years, despite our handy grid system, the plants had become so large that figuring out who was who in our experimental plots became next to impossible. While this meant that we could no longer determine the underlying mechanisms, which requires data on individuals, we could still examine the plot-level diversity effects. When we terminated the experiment in the summer of 2010, genotypic diversity effects were still strong and present. In fact, these effects increased in strength with time – just as has been found for species diversity effects on productivity!
A complementary field seed germination trial we carried out in 2008 revealed that differences in performance (i.e. seed production) among genotypes in different treatments should carry over into the next generation. Hence, genotypic diversity effects may be more than merely transient dynamics, and could have long-term ecological consequences in our system. As I’ve also discussed, these effects were sensitive to environmental-context, possibly relating to the frequency of disturbance and strength of intraspecific competition. While it remains possible (and likely) that genetic diversity may have strong population-level consequences only under stress or disturbance in some systems, our study suggests another set of circumstances that might reveal important diversity effects: dense, monospecific stands of a focal species, with intense competition among individuals.
Behold the humble dandelion!
—Emily Drummond
To learn more, you can read our paper in PLoS ONE: http://dx.plos.org/10.1371/journal.pone.0030314.
Individuals vary in their phenotypic traits. The importance of this truism has long been recognized in the field of evolutionary biology; without such heritable variation, there would be no evolution, as Darwin rightly pointed out. In contrast, the study of ecology seems to have often blipped along merrily, while quietly sweeping variation within species under the rug. Perhaps it wasn’t naively that ecologists regarded all individuals within a species as identical when constructing models of species competition, predation, etc. but simply from a need to reduce complexity. When I began my MSc degree, back in 2006, the potential importance of individual variation for ecological dynamics was finally receiving some long-deserved attention.
At that point in time, we had a collection of rigorous studies showing effects of genetic diversity on population, community and even ecosystem variables – everything from primary productivity, to nutrient cycling, to community resilience and species composition might be affected. However, this result was by no means universal – and studies that did find positive genetic diversity effects also varied in the magnitude of the effects identified. Clearly, we knew that genetic diversity could be important to ecology, but we had little predictive understanding of these effects.
What mechanisms generate diversity effects? How does environmental context matter? Why does genetic diversity produce effects in some studies but not others? These are the kinds of questions that my MSc supervisor, Dr. Mark Vellend, and I pondered. We were particularly intrigued by the circumstantial evidence from studies of marine eelgrass (i.e. Reusch et al. 2005. PNAS 102:2836-2831, Hughes & Stachowicz 2004. PNAS 101:8998-9002) that genetic diversity effects might only be revealed under poor conditions (e.g. stress or disturbance). Mark and I wondered if this might be a general result – did diversity matter more under unfavorable conditions, which might magnify genetic differences among individuals?
We designed an experiment using locally collected (on the British Columbia coast), asexual dandelions to investigate this possibility. In the spring of 2007, we created replicate dandelion populations of low (1-genotype), medium (2 genotypes) or high (4-5 genotypes) genotypic richness under field conditions. This diversity treatment was fully crossed with an environmental treatment: dandelions grew in either unfavorable “mowed lawns”, or in recently tilled, favorable “fallow fields”. As you can see from the pictures, these habitat types were completely randomized across the plots (we created the fallow plots as needed, by turning over the sod) and the initial growth environment varied hugely depending on habitat. In contrast to the fallow field, plants in the mowed lawn were surrounded by other species and regularly disturbed by clipping.
Planting the dandelions in a grid pattern in each plot, we were able to assess seed number and total leaf area (a measure of plant size/biomass) for each individual over the course of two years. We found that genotypic diversity enhanced population performance universally, but to a greater degree in the fallow field. For example, the gain in plot performance with diversity, from low- to high-richness plots, was 52% vs. 20% for leaf area and 31% vs. 23% for seed number. Large genotypes dominated in the fallow field leading to positive selection effects and significant overyielding. In the mowed lawn, where performance was limited, there was evidence for complementarity among genotypes, but no overyielding. Hence, our diversity effects, while clearly environment-dependent, were stronger in the more favorable environment - contrary to our prediction. While we don’t have a precise explanation for this result, our conjecture is that the larger size of and the stronger competition among genotypes in our fallow field enhanced genotypic differences. There is some evidence for this in the data.
Unfortunately the capacity of dandelions to form multiple rosettes, all attached to the same taproot, eventually led to difficulties identifying “individuals”. After about 2 years, despite our handy grid system, the plants had become so large that figuring out who was who in our experimental plots became next to impossible. While this meant that we could no longer determine the underlying mechanisms, which requires data on individuals, we could still examine the plot-level diversity effects. When we terminated the experiment in the summer of 2010, genotypic diversity effects were still strong and present. In fact, these effects increased in strength with time – just as has been found for species diversity effects on productivity!
A complementary field seed germination trial we carried out in 2008 revealed that differences in performance (i.e. seed production) among genotypes in different treatments should carry over into the next generation. Hence, genotypic diversity effects may be more than merely transient dynamics, and could have long-term ecological consequences in our system. As I’ve also discussed, these effects were sensitive to environmental-context, possibly relating to the frequency of disturbance and strength of intraspecific competition. While it remains possible (and likely) that genetic diversity may have strong population-level consequences only under stress or disturbance in some systems, our study suggests another set of circumstances that might reveal important diversity effects: dense, monospecific stands of a focal species, with intense competition among individuals.
Behold the humble dandelion!
—Emily Drummond
To learn more, you can read our paper in PLoS ONE: http://dx.plos.org/10.1371/journal.pone.0030314.
Friday, May 11, 2012
Fusing theory and data: a plea for help from Dan Bolnick
I have a question for the readers of this blog - something I need to "poll" you on.
First, a little bit of background. When I was a beginning graduate student at the University of California at Davis, a faculty member on my committee asked me whether I intended to be "a consumer, or a producer, of theory". His goal was to determine what kind of statistics or pure math classes he should direct me to take, which is a decision every student is faced with. My goal at the time was to do empirical tests of theory (a vague concept - see below), so I casually said "consumer" and went for the statistics options. Fourteen years later, I look back at that decision as both correct, and unfortunate. Correct, in that the solid grounding in statistics that I gained has served me well in the following years. Unfortunate, in that it perpetuates an either/or view of empirical and theoretical work that has come back to haunt me this spring.
Here's why: Eva Kisdi and U. Helsinki has invited me to give a series of lectures (6 hours) in August on the intersection of theory and empirical work on speciation. Naively agreeing, I now need to figure out how theory and empirical approaches actually intersect. Turns out to be harder than I expected for several reasons. I raise two questions here, and invite readers to respond:
1) What does it mean for theory and data to intersect? I see several options, but would welcome additional ideas here:
A) Theory can make predictions about what is possible, empiricists can test whether the predicted phenomenon actually exists. This is a weak test because it does not actually show that the theoretical justification is correct, only that the end product is correct. Many different models might generate the same pattern (c.f., ecological neutral theory's "predictions"). Another problem is that many models predict many possible outcomes, depending on exact parameter values. For instance in my graduate work I "tested" the theoretical prediction that intraspecific competition drives disruptive selection (Bolnick 2004 Evolution), but really the model predicts either disruptive OR stabilizing selection, depending on parameter values that I didn't (couldn't) measure. I can think of a number of examples in the speciation literature, but would welcome suggestions as to your favorites.
B) Theory can make quantitative predictions that can be exactly tested for quantitative fit (see Optimal Foraging Theory work in the 70's for example) - I can't think of examples in the speciation literature: suggestions welcome.
C) Empirical data can demonstrate that something occurs biologically (e.g., sympatric speciation), and the models can be developed to formalize our thoughts about how this works. Examples include Schliewen's Nature paper on Cameroon cichlids that made sympatric speciation respectable again (for some people) and the subsequent irrational exuberance about the topic among theoreticians.
D) Empirical data can be used to parameterize a model to make biologically informed predictions (see my new paper with Mark Kirkpatrick in Current Zoology.
E) a model can be built for strictly statistical purposes to estimate parameters using empirical data. For instance, coalescent theory has been used to build analysis programs (e.g., Migrate, IM) that are used to estimate parameters (timing of divergence, subsequent gene flow) relevant to speciation. Lots of examples, mostly in the area of molecular evolution and phylogenetics and population genetics, all of which sometimes spill over into the speciation literature.
F) The holy grail: All of the above. Make an empirical observation, build a model to explain it. Parameterize the model with independent data to make a specific novel prediction, test this empirically. Are there ANY examples?
2) What are BEST examples you can think of, of papers that actually fuse theory and empirical data to address questions in speciation?
Please submit comments (or email me privately at danbolnick@austin.utexas.edu).
First, a little bit of background. When I was a beginning graduate student at the University of California at Davis, a faculty member on my committee asked me whether I intended to be "a consumer, or a producer, of theory". His goal was to determine what kind of statistics or pure math classes he should direct me to take, which is a decision every student is faced with. My goal at the time was to do empirical tests of theory (a vague concept - see below), so I casually said "consumer" and went for the statistics options. Fourteen years later, I look back at that decision as both correct, and unfortunate. Correct, in that the solid grounding in statistics that I gained has served me well in the following years. Unfortunate, in that it perpetuates an either/or view of empirical and theoretical work that has come back to haunt me this spring.
Here's why: Eva Kisdi and U. Helsinki has invited me to give a series of lectures (6 hours) in August on the intersection of theory and empirical work on speciation. Naively agreeing, I now need to figure out how theory and empirical approaches actually intersect. Turns out to be harder than I expected for several reasons. I raise two questions here, and invite readers to respond:
1) What does it mean for theory and data to intersect? I see several options, but would welcome additional ideas here:
A) Theory can make predictions about what is possible, empiricists can test whether the predicted phenomenon actually exists. This is a weak test because it does not actually show that the theoretical justification is correct, only that the end product is correct. Many different models might generate the same pattern (c.f., ecological neutral theory's "predictions"). Another problem is that many models predict many possible outcomes, depending on exact parameter values. For instance in my graduate work I "tested" the theoretical prediction that intraspecific competition drives disruptive selection (Bolnick 2004 Evolution), but really the model predicts either disruptive OR stabilizing selection, depending on parameter values that I didn't (couldn't) measure. I can think of a number of examples in the speciation literature, but would welcome suggestions as to your favorites.
B) Theory can make quantitative predictions that can be exactly tested for quantitative fit (see Optimal Foraging Theory work in the 70's for example) - I can't think of examples in the speciation literature: suggestions welcome.
C) Empirical data can demonstrate that something occurs biologically (e.g., sympatric speciation), and the models can be developed to formalize our thoughts about how this works. Examples include Schliewen's Nature paper on Cameroon cichlids that made sympatric speciation respectable again (for some people) and the subsequent irrational exuberance about the topic among theoreticians.
D) Empirical data can be used to parameterize a model to make biologically informed predictions (see my new paper with Mark Kirkpatrick in Current Zoology.
E) a model can be built for strictly statistical purposes to estimate parameters using empirical data. For instance, coalescent theory has been used to build analysis programs (e.g., Migrate, IM) that are used to estimate parameters (timing of divergence, subsequent gene flow) relevant to speciation. Lots of examples, mostly in the area of molecular evolution and phylogenetics and population genetics, all of which sometimes spill over into the speciation literature.
F) The holy grail: All of the above. Make an empirical observation, build a model to explain it. Parameterize the model with independent data to make a specific novel prediction, test this empirically. Are there ANY examples?
2) What are BEST examples you can think of, of papers that actually fuse theory and empirical data to address questions in speciation?
Please submit comments (or email me privately at danbolnick@austin.utexas.edu).
Sunday, May 6, 2012
Trinidad on my mind: of guppies, snakes, dogs, and testicles.
I first started working in Trinidad in 2001 and, in 2002, I
started sampling guppies from large numbers of sites from two rivers (Marianne
and Paria) on the north slope of the northern mountain range. These samples
were used to characterize variation in traits and genetic makers so as to infer
how interactions between selection and gene flow influenced adaptation. This first
project ended in 2004 and it had been great fun exploring, climbing over
waterfalls, and trying to find viable guppy populations throughout the
spider-web network of these two nearly pristine rivers. I therefore figured it
would be a good idea to come up with an excuse to keep visiting. My students
have since done many projects but I also created a project of my own to make
sure that I came back every year and went to the coolest remote sites. I
therefore selected 10 sites to start a long-term sampling protocol– ten sites
that were not only biologically interesting but that required walking long
distances in beautiful streams and camping in remote areas. This year marked
the 11th year visiting these sites and I have now amassed 5327
guppies (about 50 per year) from these 10 sites alone (many more have been
sampled from other sites). The idea is to use these long-term samples to study eco-evolutionary
processes as they act through time and space. With more than 10 years of
working in Trinidad, it seems a good time to go back to my notes and dig up a
few interesting events that occurred.
2012: This afternoon, Gregor (Rolshausen) went off to catch fish. When he came back to our house (Indra’s) after dark, he had a 2 m long snake with him. Apparently it had been tangled up in his windshield wipers when he had gotten back to his car. He wasn’t sure if it was alive or dead – or what kind it was – and so he had gone and asked the guards (he had parked his car at a water authority – WASA – station) if they could shine a light on it for him. The guards were very excited and apprehensive and brought a heavy metal pipe with them to use as a weapon. When they saw the saw the snake, however, their braveness evaporated and none would go anywhere near it. When Gregor removed it from the wipers they said, accusingly, “what are you, some kind of snake man or something”?
2011: Stayed home (Indra’s) and processed fish. The crew
(Felipe Perez, Kiyoko Gotanda, and Maryse Boisjoly) drove off the Simla to
check their email. I was in the kitchen when they returned. “Andrew, come quick
right now” they shout at me. They seem all crazy, almost panicked.”Damn,” I
think “Who’s hurt.” But then it becomes clear they are excited rather than
scared. “You’ve gotta come here right now you’ve gotta see this.” “Do I need my
camera,” I ask. “Definitely!” Ah, so it is something cool. I approach the car
but rather than all of them piling back in to driver somewhere, they sort of
stand away, as though the cool thing is actually in the car. Sure enough, there
on the shelf below the back window is a tropic screech owl. It seems that they
were driving along the road and the owl actually flew in the window, hit
Felipe’s head, and then the back window. They had all yelled in surprise and
pulled the car over to figure out what happened. The owl had seemed rather
dazed – sort of sitting there but drooping, with its eyes closed – and so they
simply drove back to Indra’s. We spent the next half hour taking pictures (just
a few) and watching as the owl slowly seemed to recover. It eventually flew off
- quite a unique experience.
2008: I walked up the Petit Marianne twice this year. Each
time while walking through the village of Avocat, a healthy looking, smallish,
golden dog started walking with us. He didn’t seem needy, or begging, or
aggressive – it just seemed like he wanted to go for a walk. Dogs rarely follow
us in this manner in Trinidad, and those that do invariably give up soon - but
not this dog. He was right with us all the way to the falls, then up over the
hill, and then all along the length of the river with us for several hours. At
first I wasn’t favorably inclined to having a dog along, but it was such a consistent
and pleasant companion, that I warmed to it. When we stopped for lunch, I gave
it a PBJ sandwich – but it wasn’t interested. This piqued my interest even more
– the dog clearly wasn’t along just for the food. After sampling, the dog
accompanied us back to our other sampling sites on the main stem of the Marianne.
He would curl up and sleep beside our equipment while we were sampling. Then it
stayed with us again on the way out until we reached Avocat, where it
disappeared. Our second day on the Petit Marianne, he did the whole hike with
us again and then stayed by the car as we took our gear off. Amazing, he would
stand in the way of cars coming down the road and growl at them – as though he was
protecting us. Needless to say, we were beginning to think this dog wanted to
adopt us; so when we drove off, we did so quickly. It immediately ran after us
at top speed, really fast actually, barking plaintively. In other
circumstances, I might have kept it. A final note: when the dog was facing off
with cars on the road, another man was there waiting for a ride. He lived at
Avocat and knew the dog. I related to him how the dog had reacted to us on both
of our hikes and his simple answer was: “Oh that dog – he likes white folks.”
2006: Yesterday I took my annual camping trip into the Paria,
this time with Martin Turcotte, Ian Paterson, and Paul Bentzen. We saw lots of
cool stuff, particularly two fer-de-lances, both of which I walked within
inches of before someone behind me spotted them. I must look very carefully
only where I put my feet. This stops me from stepping on snakes but I miss many
that are VERY close. In fact, this is at least the fourth snake I have walked
right past (yes, I have seen others before walking past them). We saw one on
the way into the camping site and one on the way out (see photo). This second
time, it was becoming dark and watching for snakes given our new-found piety
made us go quite a bit slower. [As of 2006, I have now seen 8 fer-de-lances in
approximately 12 weeks of work in Trinidad.] Oh, and lest I forget: a major
breakthrough on the splinter! I was squeezing hard all day getting puss out.
Eventually I squeezed so hard that the pus was welling up like magma and all of
a sudden, pop, out comes the splinter – floating on the pus like the negative
of a marshmallow floating on hot chocolate.
2005: We found two small pools (1-2 m squared) right at the
silk cotton tree, each with vast numbers of guppies. We captured 41 females, 32
males, and hundreds of juveniles in one and 42 females and 31 males in the
other. These were probably less than half of the actual number of guppies in
each pool. These pools are isolated from the mainstem although they would be
flooded in moderately high water. The males were very colourful in relation to
mainstem guppies just a few yards away. They are probably the most colourful
guppies I have seen, although the amount of orange is low. Instead they have
large patches of yellow, pink, purple, etc. I suspect that conditions in these
pools are very different from the main stem of the river and that the evolution
of high colour owing to female choice proceeds within them during periods of
isolation only to be reversed owing to predation when they are washed out
during the next flood. It would be very interesting to examine the dynamics of
this interaction. I took a sample with this in mind. (Note: I still haven’t done
this examination as of 2012).
2003:
... At this point David Reznick had worked his way down the cliff and reached
the tree. With remarkably little hesitation he sacrificed his testicles to the
6 inch tree by leaping forward, straddling it, and sliding ungracefully
downward, taking the bark with him as he went. Mike Kinnison, who was just
above, heard and saw David’s farewell to future children and filed this away
for future reference – which turned out to be needed in the immediate future. I
climbed up the steep rocks to the base of the sacrificial tree, with Mike
immediately above. He lowered the pack and then his eyes lifted to survey the
tree, as though seeing it for the first time. “I’m supposed to jump to that?”
he asked, knowing the answer but somehow not accepting. All he could now see in
his mind’s eye was David spread-eagled on the tree loudly decrying the state of
his testicles. “Is there any other way?” “Well” I said “I suppose you could go
up and around but I don’t know if you will find a way that is any easier.” Mike
looked uncertain. He knew he didn’t want to go back up that horrible cliff but
he also knew he wanted to have children. His eyes moved up and down the tree as
I waited not-so-patiently below, as if I might catch him should his jump not go
so well. After some moments of hesitation and in a wondrous display of
counter-intuition, he leaned out and fell slowly forward until his hands were
on the tree and his feet, almost horizontal behind him, were on the ledge.
Perched there, with no way back, his eyes clinically scanned the cliff below
him. “Maybe I could just walk down the cliff” he asked in defiance of all
logic. “Damn it Mike, jump” And jump he did, ever so much more graciously than
had David, informed no doubt by David’s demonstration of how not to do it.
(Note: Both David and Mike have subsequently had children.)
Stoies abound – and these are
just a few of them. Here’s looking forward to having new ones in the years to
come.
![]() |
| I think I see a guppy. |
2012: This afternoon, Gregor (Rolshausen) went off to catch fish. When he came back to our house (Indra’s) after dark, he had a 2 m long snake with him. Apparently it had been tangled up in his windshield wipers when he had gotten back to his car. He wasn’t sure if it was alive or dead – or what kind it was – and so he had gone and asked the guards (he had parked his car at a water authority – WASA – station) if they could shine a light on it for him. The guards were very excited and apprehensive and brought a heavy metal pipe with them to use as a weapon. When they saw the saw the snake, however, their braveness evaporated and none would go anywhere near it. When Gregor removed it from the wipers they said, accusingly, “what are you, some kind of snake man or something”?
![]() |
| Snake man. |
![]() |
| The owl in the car. |
![]() |
| Our campsite on the Paria River. |
![]() |
| Just missed. |
![]() |
| Paul Bentzen catching guppies. |
![]() |
| The site of David's and Mikes' sacrifice. |
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