Friday, September 27, 2013

The emerging synthesis of evolution with ecology in fisheries science


[ This post is by Dylan Fraser of Concordia University, MontrĂ©al; I am just posting it for him.  –B. ]


It is both a harrowing and hopeful time to be a conservation biologist: harrowing in the sense that our species is, of course, rapidly altering and diminishing the Earth’s biodiversity and ecosystems. But there is hope: the present and next generation of conservation biologists really do have the opportunity to help stem the incoming tide of rapid species loss and habitat change, and to contribute substantially towards more effective conservation strategies for retaining the services that species provide to humanity. Why am I optimistic that we can accomplish this? In part, our science is getting better. It is becoming more integrative and closer to biological reality. In particular, as many of the postings on this blog indicate, we are currently witnessing the emergence and crystallization of a true (and long-awaited) synthesis of evolutionary with ecological perspectives in the scientific literature.



The implications of this ecological-evolutionary synthesis for how we manage our own activities are profound. Perhaps this is nowhere more apparent than in fisheries and its associated activities. No other vertebrates are tinkered with more by us than fishes, save for lab mice and farm animals. Intentionally or unintentionally, we harvest vast numbers of fish in marine and freshwater, we rear and release them in enormous numbers in nature for aquaculture or to bolster natural populations, we block fish migrations when we build our dams, we routinely pollute their environments, and we regularly introduce fishes to new environments. As I summarize in a recent perspective paper in the Canadian Journal of Fisheries and Aquatic Sciences, such activities regularly generate rapid changes to population abundance, density, and (or) mortality. Under such conditions, evolutionary dynamics might strongly influence ecological dynamics and vice versa within fish populations, and within the communities and ecosystems they inhabit. Indeed, the evidence is accumulating that human-induced evolutionary changes in fisheries-related activities can elicit a rich array of ecological changes on short time scales, in some cases equal to or exceeding the changes brought on by classical ecological effects.

These changes are not merely of academic interest. They matter to everyone because they can and do affect the persistence, recovery and productivity (and profitability) of exploited fishes, and hence the services that fishes provide to us for our own survival and health. Once again, there are profound implications of applying ecological-evolutionary science to manage our own activities, as exemplified by a growing number of studies in fisheries science.


I am certainly not the first person to plead for more consideration of evolutionary perspectives with ecological ones in fisheries management (or any other natural resource management sector). I have found other such pleas in the literature going back at least two decades. The reality, though, is that despite such pleas, and although I firmly sense that conservation/applied biology has become more oriented toward the ecological-evolutionary perspective in many instances, management decision-making often has not (as was raised by the one of the reviewers of my paper). Why is this? Is it that evolution is still often viewed as happening too slowly to be of relevance to many management timescales? Perhaps increased recognition of evolutionary change may reveal that the current way of doing things needs tweaking, but isn’t that consistent with adaptive management? I am optimistic that the growing arsenal of studies demonstrating the significance of evolutionary change to managed species’ demography and productivity will eventually lead to more, and more positive, management decision-making change. So for those of you with a genuine interest in conducting and applying combined ecological-evolutionary science for conservation and natural resource management: keep at it! And get the message out!

References

Fraser, D. J.  (2013).  The emerging synthesis of evolution with ecology in fisheries science.  Canadian Journal of Fisheries and Aquatic Sciences 70(9), 1417-1428.  DOI: 10.1139/cjfas-2013-0171

Photos provided by D. Fraser.

Wednesday, September 18, 2013

A brand new bandwagon: a lifetime of ASN (and SSE and CSEE)

Scientific societies are cool things to be part of. You get free access to their journals, you have low (or no) page charges when publishing in their journals, you get cheap registration at their conferences, you get to have all sorts of wonderful interactions with colleagues, and - perhaps most important - you get to be a part of something bigger. Ever since I started as a graduate student, I have been enamored with all of these benefits and have been a member of a number of societies, with examples including the American Fisheries Society (AFS), the Ecological Society of America (ESA), the Society of the Study of Evolution (SSE), the American Society of Naturalists (ASN), the European Society of Evolution Biology (ESEB), and the Canadian Society of Ecology and Evolution (CSEE). Great fun.

Twenty years on and in the midst of all those crazy little administrative things that faculty members have to do, it has gotten annoying to have to renew these memberships each year. I frequently forget to re-up even when I want to keep dating a journal and then journals I stop dating keep pestering me. What a pain.

The solution came to me a few years ago - become a lifetime member. You get all of the above benefits and none of the above annoyances. And it is cheaper in the long run . For CSEE, annual membership is $50 per year and a lifetime membership is $800 per year - 16 years and I start saving money! Given my anticipated long life span (see this analysis), I will save tons of money. At SSE, it will take only 17.5 years. The hitch, of course, is that even if one saves money in the long run, it might be too expensive in the short run. Fortunately, McGill has a "Professional Development Fund" that gives $500 per year for professional development, which includes society memberships.

So, a few years ago, I started chipping away at the societies. I first bought a life time membership in CSEE - how could I not, given that I was on their council? Then I waited two years for the fund to build up again and bought one to SSE - I was an editor at Evolution after all. Then I waited two more years and bought one for ASN. Oops, no I didn't. They didn't have a lifetime option. Damn. Well, what to do? At this point, I was so used to not buying yearly society memberships anymore that I decided to protest. I emailed ASN and said that I wanted to be a lifetime member but because that wasn't an option, I was not going to be a member until it was. I suspect that my personal protest didn't have much effect but I was told this was already under consideration.

I just checked today and - yes - you can now become a lifetime member of ASN!!!!!!!! Within half an hour I had registered and paid - $700 (plus tax) for life versus $40 (plus tax) per year. Twenty years from now and I will be golden. In fact, I will start saving money at about the "normal retirement date" of 65. Too bad I couldn't have started with ASN first.

Although it only took half an hour, as just noted, it really should take only 5 minutes - so why the difference? Well, the problem was that the lifetime option was on the ASN website but wasn't available when I tried to pay. A few emails later (thanks Dan and Trish) and the problem was fixed - which got me to thinking - was I the first? So I emailed Trish and Dan and they confirmed it. I am the first ever (non-honorary) lifetime member of ASN. Yeeha - something to put in my obituary, which is hopefully far enough away that I start saving money on my membership.

The take home message of this post is to join the lifetime bandwagon. Get that lifetime membership and never have to worry about those renewals (and renewal notices) ever again! Do it now so that you can start saving money before you go out to pasture. And - if you do it now - you can be the second-ever (non-honorary) lifetime member of ASN!!!

Some membership links:
ASN
SSE
CSEE
ESEB - doesn't seem to have a lifetime membership - I guess I will protest there now
ESA - the link wasn't working


Wednesday, September 11, 2013

Darwin jumped on a bandwagon


I was surfing the web and noticed something interesting on Jonathan Davies' home page - rare, I know. I repeat it here with Jonathan's permission.

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Darwin jumped on a bandwagon, Mendelian genetics retarded the expansion of evolutionary theory, and the recent resurgence of interest in fruit.

Google’s Ngram viewer (http://books.google.com/ngrams/) provides a fascinating insight into the changing frequency of occurrence of keywords through time, mining the vast information database that is Google Books.

As someone with an interest in ecology and evolution, I thought it might be fun to map their trends. Because I was not sure what biases might exist in the database, I also included what I thought would be a neutral keyword ‘fruit’.



Here is my very non-scientific interpretation of what I found. Evolution is much more popular than ecology, and even overtook fruit in the 1960’s. The rise of evolution predates publication of the Origin of Species, suggesting Darwin jumped on the evolution bandwagon. Mendelian genetics and a better understanding of inheritance temporarily stalled evolution’s growth, which only recovered after Watson & Crick’s publication on the structure of DNA. Evolution continued to gain in popularity up until around 2000, at which point both ecology and evolution decline but there is a resurgence of interest in fruit – just a coincidence?

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For more details and erudition, see Jonathan's website.

To see Jonathan dating a fish phylogeny look here.

Tuesday, September 3, 2013

Non-adaptive explanations as null hypotheses in Evolutionary Ecology


Non-adaptive explanations as null hypotheses in Evolutionary Ecology

 A response to "Dulling Occam's Razor - or the Perilous Principle of Parsimony"

As a general rule, the Graduate Student tries with great conviction to avoid public humiliation. The Graduate Student will spend long hours in the isolation of his laboratory, reading his Advisor's doctoral thesis with furrowed brows, diligently applying the appropriate statistical tests to partially-failed experiments, and avoiding the departmental seminar coordinator as if she had Zaire ebolavirus. Most of all, though, the Graduate Student is motivated to plod along by the terror and anticipation of the Week of Reckoning: the annual (and sometimes mandatory) sojourn to a scientific conference.

As far as the Graduate Student is concerned, all kinds of disastrous things could happen at a conference. A good example of such an eventuality is when the Graduate Student is invited to a conservation with a Well-Respected Member of his Field, usually by his well-meaning Advisor. Typically, the Graduate Student is caught off-guard by this invitation, such that the invitation results in an over-stimulation of the Graduate Student’s adrenal glands. (This is maladaptive).

During subsequent conversation, the Graduate Student is expected to accomplish two things. The first is to make one small - but nonetheless meaningful - contribution to the discussion. The second expectation is that the Graduate Student will not make an Ass of himself. Both expectations are exceedingly difficult to meet.


When is a non-adaptive explanation reasonable as null hypothesis?

I am well-versed in this area, as I have first-hand experience. I was at a conference a number of years ago, as a Graduate Student (I suppose I am still a Graduate Student, as I haven’t actually received my sheepskin in the mail yet). There I found myself in discussion with a Well-Respected Member of my Field. The discussion was going well, at first, but I eventually found myself in an error-catastrophe loop. I was trying, with great desperation, to explain the predicted relationship between temperature and body size, and I eventually asserted that the negative relationship that I expected to observe was based on a physiological constraint that maps body size to rearing temperature… at this point the Well-Respected Member of my Field cut me off, furrowed his brow, and replied:

But everything is adaptive, if you go deep enough”.

A silence fell between us. I stared at him the way a duck might stare at a mirror. Around us, the drone of scientific murmur persisted, coffee cups clinked, and off in a corner, a fellow Graduate Student rifled stale muffins into his conference handbag. The Well-Respected Member of my Field looked at me expectantly. I became increasingly apprehensive. Then, not knowing how to dabble my next quack, my inexorable devolution from Graduate Student, to Duck, to Donkey occurred near instantaneously, as I blurted out,

“Yeah, you should publish that one in Nature”.

This reply was of course ludicrous, and it was made in an adrenaline-induced explosion of anxiety. At worst, it was unfair, because an association between a penchant for adaptive explanations and publication prowess was implied.

But I think we all have at least some idea of what “Everything is adaptive if you go deep enough” was meant to get at. In retrospect, I think my colleague just wanted to underline the fundamental role that natural selection has played in shaping the biology of all organisms, from the physiological factors governing cellular processes to realization of these processes at higher phenotypic levels. I have no problem accepting this general argument, nor do I think would most biologists question selection as an important evolutionary force in this sense.

But this ill-fated conversation got me thinking: how “deep” can we go before invoking adaptation as an explanation for phenotypic variation is probably ill-conceived? Or, said slightly differently, is there a level at which it is reasonable to believe that the variation we observe is generally the result of constraint? In my view, parsimony helps inform this end, such that there does come a point at which non-adaptive explanations can become a null hypothesis to explain phenotypic variation. Specifically, I argue that for functional traits, null hypotheses for variation among species should be adaptive ones (such that the non-adaptive hypothesis bears the onus of proof), whereas null hypotheses for variation within populations should be non-adaptive ones (such that the adaptive hypothesis bears the onus of proof); interestingly, for phenotypic variation among populations of the same species, parsimony is of much less value.

I was reminded of my ill-fated conversation with the Well-Respected Member of my Field shortly after my PhD defence, in which I was examined by a different Well-Respected Member of my Field: Andrew Hendry. I was thrilled that Andrew agreed to be my PhD examiner. I have the utmost respect for Andrew, as his research on investment per offspring ("egg size") and reproductive allocation paved the way for my PhD research. His work has been tremendously influential, both in the field of life-history tradeoffs and in terms of how I’ve come to think about evolution of investment per offspring. Andrew gave a terrific examination, but he certainly didn’t like the conclusion of my thesis. Motivated partly by this (increasingly infamous) chapter, Andrew has since started a discussion on the extent to which parsimony is a useful tool for evolutionary ecologists, and whether adaptive explanations are generally any more or less parsimonious than explanations that invoke constraint. So, I’m digging in my heels herein, as I attempt to give a reasonable response.

Electrofishing for juvenile Atlantic salmon during my thesis research

Before I recapitulate the conclusions I drew after being told “Everything is adaptive, if you go deep enough”, I should defend the use of parsimony in evolutionary ecology. My view is that parsimony is one of many useful tools that the evolutionary ecologist should keep in his toolbox. Certainly, a blanket application of parsimony in evolutionary ecology is unwise, as parsimony will be more useful in some cases, and less so in others. For instance, the use of “maximum parsimony” to generate phylogenies is reasonable because it assumes, rightly I think, that it is statistically less probable for characters to revert back to their ancestral state after undergoing a change (at least, this is my understanding).

But phylogenies are perhaps a special case in which parsimony is extremely useful. When evaluating the adaptive significance of phenotypic variation, on the other hand, to “express greatest confidence in the simplest hypothesis” is not always a wise approach. This is because parsimony, at least as I see it, is rooted both in probability statistics and scientific reasoning. That is, the plausibility of an adaptive hypothesis (or a non-adaptive one) is a product of both the number of assumptions and the viability or nature of those assumptions. I realize that this is almost like saying that “parsimony” in this context is the same thing as “what I think is reasonable”, which is an objection already raised by Andrew. Notwithstanding, I think the argument I develop below still has merit even if we adopt a more objective definition of parsimony (i.e., relating strictly to the number of assumptions in a model).

I do not dismiss the value of developing a complex explanation or a complicated model as an a priori hypothesis in evolutionary ecology. Many models, no matter how complex, will ultimately prove to be useful even if they are strictly incorrect. However, I think it’s important to acknowledge the assumptions in complex models are often complimentary and difficult to test in isolation, such that this approach, while potentially useful, can also muddy the waters without much empirical justification for doing so. This is a particular frustration of mine, because I believe that this is precisely what has occurred in my field of expertise: a wide range of rather complicated theoretical models (based on largely untested assumptions) have generated all kinds of generalized adaptive hypotheses that are extremely difficult to test. Parsimony will not be an exclusive means of eliminating these complex adaptive hypotheses, but parsimony can and should be used in conjunction with whatever empirical evidence is available to help choose among competing models.

Atlantic salmon eggs vary greatly in size, and there's all kinds of  adaptive and non-adaptive explanations as to why this is...

I also believe that there is some value in developing and testing simple explanations before moving on to more complex ones. In a reductionist framework, testing ideas that incorporate the fewest assumptions will, I think, lead more frequently to an unambiguous result. A clear result can then inform a linear and logical development of an idea, such that knowledge is acquired by the systematic elimination of the unlikely and the impossible. In this framework, the foundation upon which an idea is based is sound, such that any extension of the idea is well founded. Admittedly, some might want to label this notion as something like “misguided idealism”, but my point is that we should think very, very carefully about the number and nature of our assumptions as we develop hypotheses. This is the motivation behind Burnham and Anderson’s information theoretic approach for model selection in hypothesis testing, and I see no good reason why parsimony should not also be a consideration while evaluating the merits of adaptive and non-adaptive hypotheses.

So let us assume that parsimony is one of many useful tools that may help us discriminate among competing hypotheses. Even if this is the case, as Andrew points out, inferring the validity of adaptive and non-adaptive explanations based on parsimony is difficult, because explanations can be difficult to categorize as “parsimonious” or “less parsimonious”. The issue, as I see it, is that parsimony is strongly tied to the degree to which we understand adaptive and non-adaptive processes in the first place. The number (and nature) of assumptions that need to be made, and hence the degree to which an explanation is parsimonious, is directly linked to our understanding of the mechanism we’re invoking. It’s a quagmire, to be sure.

Notwithstanding, I believe that the argument can be refined. To recapitulate what I concluded after being told that “Everything is adaptive, if you go deep enough”, my view is that the extent to which non-adaptive explanations are parsimonious is related to the scale at which variation is identified, or how “deep” we delve into the levels of variation. My argument is a qualitative one, and I don’t think that it will resolve the differences in opinion that Andrew and I have. I do, however, believe that the issue of scale is important, and it might at least provide some insight into the issue of adaptation, constraint and parsimony.

If we consider the mean value of a trait in two different but related species, I think that the majority of biologists might agree that, in most cases, adaptation provides the simplest explanation for the difference (e.g., competition that results in niche partitioning). I think most biologists would agree that non-adaptive processes, such as drift, are in most cases not a simple or logical explanation for interspecific differences in, say, age-at-maturity or fecundity.

Does the extent to which parsimony informs a null hypothesis depend on the scale at which the comparison is made?

However, as Andrew alludes to, there might be far less consensus on what type of explanation is most parsimonious when variation in a mean phenotype is observed among populations of the same species. I think Andrew is quite correct here. Personally, I might venture, as Andrew does, that adaptive explanations are often most parsimonious in these cases, especially for life-history traits. But I think it ultimately depends on our understanding of the adaptive and non-adaptive mechanisms invoked, in conjunction with the demographic history of the population, etc. Thus, even if we accept parsimony as a useful tool in evolutionary ecology, I agree that it is not clear that non-adaptive explanations are generally more or less parsimonious at this scale.

But how much “deeper” can we go before invoking adaptive explanations for phenotypic variation becomes markedly less parsimonious? What about phenotypic variation among individuals within a population? If we’re discussing adaptation in a meaningful way, then I think the argument is that the focal trait is optimal or near optimal, such that variation among individuals represents different individuals converging on different phenotypic optima that exist within a population. This is, in fact, an argument that has been made time and time again in my field. Specifically, there are a number of rather complicated theoretical models which demonstrate that individuals can achieve the highest absolute fitness if they produce a particular egg size in conjunction with the expression of a particular set of other phenotypes, and that (therefore) variation in egg size among individuals may represent adaptive variation. Yet, in the vast majority of cases (especially those in which frequency-dependent selection and adaptive plasticity are unlikely), viewing phenotypic variation at this level as adaptive is mind-numbingly complicated, as the number of assumptions needed to make the model realistic is stupendous. The nature of the underlying assumptions can also be questionable; for instance, none of the theoretical models in my field incorporate the evolutionary genetics of investment per offspring, nor do they consider whether the model is valid under any given population-genetic scenario. Is it not both biologically plausible and simple to expect that variation at this scale represents, say, genetic covariances among traits that limit the extent to which any given functional trait can achieve its univariate fitness peak? Isn’t life-history theory rooted in the idea of trade-offs, such that there is an expectation that not all traits can be simultaneously optimized in an individual? Again, without drawing on specific examples, this argument is necessarily qualitative, but I nonetheless believe it to be a compelling one.

So, if you think that parsimony is at least useful in evolutionary ecology, as I do, then perhaps you also agree null hypotheses for variation among species should be adaptive ones (such that the non-adaptive hypothesis bears the onus of proof), whereas null hypotheses for variation within populations should be non-adaptive ones (such that the adaptive hypothesis bears the onus of proof).

I’m glad that Andrew has blogged about this, and I realize that my own response was a bit tangential and that I did not address all of the issues that Andrew brought up. I think it’s well worth discussing this subject in general, and I hope I am not the last to give my thoughts here on the blog.

Njal

 

Monday, September 2, 2013

Carnival of Evolution #63

Up now, Carnival of Evolution #63!  Step right up!

Our contribution this time around is by yours truly, entitled Evolutionary branching in complex landscapes, on the first first-author research paper from my PhD to get published.  It also has information on a great program for graduate students, the Young Scientists Summer Program at the International Institute for Applied Systems Analysis in Laxenburg, Austria, so check it out for info on that!

This month it is hosted by EvoAnth, so in honor of that, here's a little cartoon about our brothers and sisters in Georgia (It isn't new news, but see http://www.nytimes.com/2006/06/28/education/28education.html for a sordid tale):


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...