Showing posts with label Selection. Show all posts
Showing posts with label Selection. Show all posts

Saturday, November 22, 2014

Guest post by Andrew Hendry: "Pitchfork Science: Guppies, Stickleback, and Darwin’s Finches"


The following post is an invited personal guest post by Andrew Hendry at McGill University, who kindly invited me to write a guest post on "Eco-Evo-Evo-Eco"/Erik Svensson

By Andrew Hendry

I study Trinidadian guppies, threespine stickleback, and Darwin’s finches, surely 3 of the top 10 canonical vertebrate evolutionary biology “model” systems. I thus fall at one extreme (or is it three extremes?) on the “pick a model system and use it to answer my question” versus “develop a brand new system all my own” continuum. Many students and postdocs find themselves facing their own decisions about where to position themselves along this continuum. Should they take the shortcut of working with an established system so they don’t have to work out the simple details and can get right to addressing the big general questions? Or should they forge their own path and become an expert in something brand new? It might seem, based on the above listing, that I consciously took the first approach but the reality is something quite different. In truth, I used a “follow your nose” coincidence-and-serendipity approach to study system choice. I here trace my own personal history in these research areas before closing with some general thoughts on how to choose a study system.

Why I study salmon - a 16 year old me with a steelhead from our cabin (Kispiox River, BC, Canada).
I worked on salmon for my MSc and PhD, largely because I grew up with salmon fishing as my primary passion. Thus, I began studying salmon simply because I liked them and liked fishing for them. This led me to choose an institution (University of Washington - UW), department (School of Fisheries), and supervisor (Tom Quinn) who were ideally suited to immerse myself in salmon work. As my graduate work progressed, I very gradually became more and more interested in general questions in ecology, largely through exposure to the research of other people in the department. I even started subscribing to Ecology in addition to – of course – Fisheries. Yet my thinking remained salmon-centric: “what can ecology tell me about salmon”. Nothing wrong with that, of course. Then, when visiting home for Christmas in 1994, I received from my mother a book: “The Beak of the Finch” by Jonathan Weiner. When your Mom gives you a book for Christmas and you then spend the next week at home… well, you better read it.

The laboratory for my PhD - Lake Nerka, Wood River, Alaska.
The book was amazing. It described in wonderfully readable prose the research of Peter and Rosemary Grant on Darwin’s finches in the Galapagos Islands. What struck me the most, while reading beside the heater vent looking out at the blowing snow and -40 C weather (literally!), was Jonathan’s description of how the Grants had documented generation-by-generation rapid evolution of finch beaks in response to natural selection resulting from environmental change. Wow – you can actually study evolution in real time! It was my own eureka moment and, in short order, I became captivated by the idea. As soon as I got back to UW after Christmas, I went to the library and photocopied EVERY paper on Darwin’s finches (ah, libraries and photocopying – the good [and bad] old days). From then on, almost as though my brain had achieved an alternative stable state, my thinking was inverted to become “What can salmon tell me about evolution.” 

My MSc and PhD work focused on sockeye salmon - this one in Knutson Bay, Lake Iliamna, Alaska.
Salmon did tell me a lot about evolution. I even edited a book (Evolution Illuminated, with one of my evolutionary idols, Steve Stearns) about merging evolutionary theory and salmon research. However, when one starts focusing on a topic (evolution) rather than an organism (salmon), one starts to become irked by aspects of the organisms that are not optimal for addressing the topic. Most notably, it is very hard to do experiments with salmon unless you have lots of water, lots of space, and lots of time. So, when thinking about a postdoc, I started talking to folks about which systems might allow me to better address basic evolutionary questions. I ended up moving in two directions.

The laboratory for my first postdoc. For more than a month of glorious weather, I camped on a small island in a small lake (Mackie Lake) at the end of a 4-wheel drive road. Those are my mesocosms floating in the lake and projecting from the island.
The first was the University of British Columbia (UBC) – because I didn’t want to go too far from my girlfriend (now wife) who was still at UW. I visited UBC and went from prof to prof telling them of my interest in a basic evolutionary question – the balance between divergent selection and gene flow – and asking if they knew of a system that would be good for testing my ideas. Many great suggestions were made, but Rick Taylor insisted he had the perfect system: Misty lake-stream stickleback – and he was right. So I started working on stickleback not because they were a model system, but because someone suggested they would be well-suited for my question and because it let me stay reasonably near my sweetheart.

A threespine stickleback guarding his nest.
The second direction came about through a conversation with Ian Fleming, who suggested that I should work with David Reznick on guppies. I hadn’t even considered this possibility, but I knew a bit about the system (it is also described in The Beak of the Finch) and it seemed cool. So I went to UCR and met with David and talked about how we might use guppies to study the interaction between selection and gene flow. David said he would be happy to help me with this work but that he didn’t have any money for me – and so I offered to write a full NSF proposal. I was just gearing up to do so when I heard that I had received an NSERC (Canada) postdoctoral fellowship to work with Rick Taylor on the Misty system – so off I went to stickleback, leaving guppies behind.

My favorite wild guppies captured in my first year of sampling, 2002.
UBC was great, an outstanding place for nurturing interest and insight into general questions in evolutionary biology, but one must eventually move on. My next postdoc was the Darwin Fellowship (I applied because of the title) at the University of Massachusetts (UMASS) Amherst, working with BenLetcher on salmon again (hard to shake the habitat). While at UMASS, my guilt started building about telling David I would write an NSF grant and then not having done so, so I went ahead and wrote one, which got funded on the second shot (after bringing in my salmony lab-mate from Tom’s lab, Mike Kinnison). So my work on guppies eventually developed owing to guilt about not carrying through on something I said I would do.

The laboratory for our guppy work - here the Paria River, Trinidad
While at UMASS, my office happened to be near that of JeffPodos, who was working on Darwin’s finches. Near the end of my Darwin Fellowship, Jeff received an NSF Career grant and had money to burn – I mean invest. Jeff knew of my interests and asked if I wanted to come along to the Galapagos on the project (he recalls me asking – or perhaps begging – to come with him), and of course I immediately said yes. So my work on finches was simply a case of being in the right place at the right time. It was every bit as exciting as promised that cold winter back in 1994. Several years later, Jonathan Weiner called to talk about my salmon work and I was able to tell him how influential his book had been and how it actually brought me (without any plan) to work on finches.
In short, a large amount of coincidence and serendipity determined my choice of study systems. Once in each of the three systems, I became enamored with them and never left. I have now 25 papers on stickleback22 papers on guppies, and 11 papers on finches, and I have no intention of ever pulling back from any of these systems. I have also published 33 papers on salmon, and I continually look for new opportunities for additional work on them.

The laboratory for our finch work, presided over by a marine iguana.
Peter Grant once told me that, in conversation with Daniel Pauly at UBC, Dan told him that he (Peter) was a “point person” whereas he (Daniel) was a “line person”: a point person being someone who takes a single subject/system (finches) and looks at every aspect of their ecology and evolution, and a line person being some who takes a single subject (fisheries) and looks at it across many systems. I guess that makes me a pitch-fork person – trying to go into depth in three systems. Of course, this means that I can’t get too deep in any one system, much to my frustration. However, comparing and contrasting results from the three systems has proven fascinating. For instance, I study ecological speciation in all three systems with essentially the same methods (catching, banding/marking, measuring, recapturing, genotyping) focused on revealing the same processes (disruptive/divergent selection, adaptive divergence, assortative mating, gene flow). The similarities and differences in results obtained from the three systems has proved very instructive and motivational. In fact, my favorite research talk involves walking through a comparative story of ecological speciation in the three systems.

Perhaps my favorite finch photo.
Beyond how many systems one works in, I need to return to the question of working with model (developed) versus new (undeveloped) systems. As noted earlier, a benefit of working in a model system is that one doesn’t have to do as much background work (although every system is nowhere near as well-understood as the impression given by the literature), whereas a cost is that you are never known as the expert in that system (because the experts are the senior folks working on the same thing). The cost-benefit payoff is not easy to calculate and so the temptation for many students and postdocs is to spend a lot of time debating the pros and cons of the different approaches. I think all this angst is a mistake (or at least suboptimal) and that one should instead follow one’s nose (and Mom’s book recommendations). I think everyone should work on the systems and with the people that they find the most interesting and inspiring – not the systems that have the best-described genomes (as an example). These inspiring systems might be model systems or they might be new systems or both (I also have students work on non-model systems), but they are – most importantly – the systems that feel right at the time, not the systems that have been rationalized based on a logical calculation of optimal career advancement. It worked out fine for me (and many others) – although I am sure my colleagues would argue I could still use considerably more career advancement.

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Resources:

An interesting perspective by Joe Travis on question-based versus system-based science: Is it what we know or who we know? Choice of organism and robustness of inference in ecology and evolutionary biology

Monday, September 19, 2011

Beyond the Fst-Qst comparison: Insights from the EGRU-blog



You are probably aware of the fact that there are many problems of Fst-Qst-comparisons to infer selection, and this method is also known to have weak statistical power. Essentially, this means that even if selection acts on a phenotypic trait, this method might not be able to detect it, and a finding that Qst equals Fst does not mean that selection is not operating on the trait in question. This low statistical power is a problem, because if one finds a positive result, one can always say that selection has operated on the trait of interest, but not much can be said if one finds a negative result. The trait might then be "neutral" and not subject to selection - or it might be subject to selection, but we cannot detect it with the current method.

There might be solutions and alternatives to the Fst-Qst-comparisons, however. At Juha Merilä's research group blog "EGRU-blog", he refers to a recently published theory-paper in Genetics, which seems like an interesting read. Although I have not read this paper in detail, it is a paper worth keeping in mind, and worth returning to in the future. I took the liberty to borrow the picture from Juha's blog and some of the text where he explains the main implications of their study:

"The main point here to note is that this method allows detection of signatures of selection also in the case where Fst =Qst: the selection in these cases (c,d) is inferred from the fact that population centroids tend to cluster according to selective regime (color) rather than their ancestry (shape of the symbol). It is also worth pointing out that the new method accounts for many other technical problems that have plagued traditional Fst-Qst comparisons. Read the paper and become enlightened!"

To this, I would like to add that it is unlikely that we will ever find the molecular method that can replace the vastly superior method of directly measuring natural or selection in the wild, or quantify quantitative genetic patterns that reveal the action of past selection. Observing something directly, and trying to quantify it, will certainly always reveal more about agents of selection and mechanisms, than indirect inferences like the Fst-Qst comparison.

This does of course not mean that these indirect methods should never be used. Far from it, and we have used such methods in the past in thisthis and this study of ours, for example. But these methods can only be a first step, and if selection is inferred, it should only be considered as a preliminary working hypothesis, that needs to be experimentally corroborated. And moreover, some forms of selection, such as negative frequency-dependent selection, might seldom, or never be detectable when there is weak genetic differentiation between populations (precluding the prospects of finding a pattern where Qst < Fst), and in these cases, direct experimental field studies might be the only possible option. There is never an excuse to avoid going out the field or doing experiments in evolutionary biology, if it is possible.

Sunday, September 6, 2009

"Human" vs. "animal" evolution

I thought a recent study from PLoS ONE might be of interest to some of you. In this meta-amalysis, McKellar and Hendry have compared within- and among-population phenotypic levels of variation in humans and animals, for body height and body mass. This study is I think very nice because it is clearly conceptualized, and the results are really straight-forward and well discussed. They also used an estimate of variation called CV, the coefficient of variation that was introduced by Houle in 1992 in a paper published in Genetics and that has in my opinion been a bit neglected by quantitative geneticists. This estimate has the advantage of being scale-free, and therefore allows comparisons between populations or species without bias.

They used an impressive dataset of 99 human populations, 210 animal populations and 848 animal species. Their main conclusions are that within-population variation in body height (but not body mass) is relatively low in humans, whereas among-population variation is more or less similar to what one might measure in animal populations. They interpret it as a sign for strong natural selection on body height in human populations which have become locally adapted.

This paper is, I am sure, probably going to be cited in the media, if it has not already been done, and will probably contribute to the growing success of PLoS ONE. Andrew Hendry has also been working on human influence on evolutionary rates of animals and more in particular human influence on beak size bimodality in finches. He is particularly interested in studying cases of rapid evolution and in the way ecology and evolution interacts on contemporary time scales. I am honored to have him as an opponent for my thesis defense that will take place on the 20th of November, and I can already tell you that Andrew will give a talk on these subjects on Thursday the 19th of November, at 13.00 in Blå Hallen at the Ecology Building.

If you are interested in contemporary evolution, if you have no idea what the term "eco-evolutionary dynamics" really means or simply if this PloS ONE paper has intrigued you, I recommend already now that you mark this date in your calendars, because you will probably don’t want to miss this talk.

Thursday, April 9, 2009

Lab meeting in the Darwin room on Wednesday the 15th of April at 10:15am

Hello everybody,

We have picked two papers for the upcoming lab meeting next week. The first one is by Masafumi Nozawaa, Yoshiyuki Suzukia, and Masatoshi Nei and is entitled Reliabilities of identifying positive selection by the branch-site and the site-prediction methods’

Abstract
Natural selection operating in protein-coding genes is often studied by examining the ratio (ω) of the rates of nonsynonymous to synonymous nucleotide substitution. The branch-site method (BSM) based on a likelihood ratio test is one of such tests to detect positive selection for a predetermined branch of a phylogenetic tree. However, because the number of nucleotide substitutions involved is often very small, we conducted a computer simulation to examine the reliability of BSM in comparison with the small-sample method (SSM) based on Fisher's exact test. The results indicate that BSM often generates false positives compared with SSM when the number of nucleotide substitutions is ≈80 or smaller. Because the ω value is also used for predicting positively selected sites, we examined the reliabilities of the site-prediction methods, using nucleotide sequence data for the dim-light and color vision genes in vertebrates. The results showed that the site-prediction methods have a low probability of identifying functional changes of amino acids experimentally determined and often falsely identify other sites where amino acid substitutions are unlikely to be important. This low rate of predictability occurs because most of the current statistical methods are designed to identify codon sites with high ω values, which may not have anything to do with functional changes. The codon sites showing functional changes generally do not show a high ω value. To understand adaptive evolution, some form of experimental confirmation is necessary.

And the second paper is by Thomas Lenormand, Denis Roze and François Rousset and is entitled ’Stochasticity in evolution’

Abstract
The debate over the role of stochasticity is central in evolutionary biology, often summarised by whether or not evolution is predictable or repeatable. Here we distinguish three types of stochasticity: stochasticity of mutation and variation, of individual life histories and of environmental change. We then explain when stochasticity matters in evolution, distinguishing four broad situations: stochasticity contributes to maladaptation or limits adaptation; it drives evolution on flat fitness landscapes (evolutionary freedom); it might promote jumps from one fitness peak to another (evolutionary revolutions); and it might shape the selection pressures themselves. We show that stochasticity, by directly steering evolution, has become an essential ingredient of evolutionary theory beyond the classical WrightFisher or neutralistselectionist debates.

You can contact me (Maren.wellenreuther@zooekol.lu.se) if you have problems retrieving the pdf files -and I will send them to you.

All the best and happy reading, Maren

PS: Any Fika volunteers? Please send me an email if you are bringing something to the meeting.