Ask us anything: choosing functional traits

We should probably call this one “Ask Brian anything”, since this is in his wheelhouse…

When seeking specific ecosystem services or assessing functional diversity, is it worthwhile to consider traits that might slip under the radar of genomics? For instance, how important is it from the standpoint of theory that diatoms and nudibranches can turn toxic or green via kleptoplasty? (from Aabir Banerji)

Jeremy: I’m worried that I’ve misunderstood your question, because I’m not quite sure why you’re asking in the first place–the answer seems too obvious. Shouldn’t you  consider whatever traits seem worthwhile to consider, even if they’re traits that can’t be usefully studied via genomics? And isn’t that what ecologists mostly do? I mean, isn’t there lots of trait-based work in ecology that considers quantitative traits for which we don’t know, don’t care about, and don’t have any prospect of discovering, the underlying genes? (because they’re many genes of small effect) Doesn’t a lot of trait-based ecology consider traits that are highly plastic? Doesn’t a lot of trait-based ecology consider traits that have all sorts of mechanistic/developmental bases, whether kleptoplasty or maternal effects or whatever? Are you asking because you think that in the near future things are going to change, so that many people will no longer consider it worthwhile to study any trait for which the genetic basis is unknown or not readily discoverable via genomics?

I also don’t really follow the flip from asking about traits that might slip under the radar of genomics, to asking about the importance of certain traits from the standpoint of theory.

More broadly, I’m on record with the view that, for purposes of biodiversity-ecosystem function/services-related work, a “trait” is “a number attached to a species” (Fox and Harpole 2008). Note that that paper considers a terrible coinage of mine, “synecological” traits, by which I meant a trait of species X that can change depending on the context. Where “context” is interpreted very broadly and would include stuff like kleptoplasty. The examples in Fox and Harpole 2008 are to do with traits like “a species’ diet breadth relative to that of the average species in the community”, which can of course change if the average changes, even if the focal species’ diet doesn’t change. But my point of view on this is pretty idiosyncratic. I tend to think of species’ traits and their relationship to ecosystem function as an abstract conceptual problem (in case you couldn’t tell that from reading Fox & Harpole 2008…). I have no background in physiology or evolutionary ecology and so don’t tend to give physiological, morphological, or life history traits any special status in my own mind. So my stance on “what’s a trait” for purposes of BDEF work might look weird to someone who does trait-based work for a living.

Irrelevant aside: I’m not sure that “functional diversity” is even a thing, as opposed to a bunch of different measures of different things (see also this comment thread). But here again my stance is that of an idiosyncratic outsider to the whole functional trait bandwagon. So you should probably just ignore me and pay attention to Brian. 🙂

Brian: In my opinion (and I think a lot of others), functional traits are firmly about phenotype, and thus the genetic basis of the trait is not important. Note, I didn’t say completely irrelevant – at some point theory about traits is going to have to deal with whether traits are heritable or not (plasticity vs genetic vs instability components of phenotype). But heritability is a weaker condition than what I take you to mean by genomic – your examples are all heritable even if highly plastic. And even heritability is sort of a 2nd order question in traits. Functional traits is a license to ignore genetics* to see how far we can get by doing that.

In opposite of Jeremy, I am on record that traits are a property of individuals. As Jeremy hints it probably depends on the goal and context. And I don’t think this is central to your question, so we’ll have to discuss that another time!

*I’m sure I’ll get push back on this statement. And it is an exaggeration, but one with an emphatic point behind it.

7 thoughts on “Ask us anything: choosing functional traits

  1. Jeremy and Brian, thanks so much for your great response! As Jeremy suspected, I asked this question because I’m wondering how much ecology, in the near future, is going to be biased by the availability of new and improved molecular techniques (à la Maslow’s hammer). For instance, will we routinely fail to recognize a species capable of bioremediation on account of its not producing a particular enzyme? Will we overlook symbiosis and phenotypic plasticity as mechanisms of pesticide/antibiotic resistance because we’re too busy searching for mutations?

    • Jessica Green has an interesting paper arguing that for microbes (e.g. bacteria) *omics might be the closest thing we have for functional traits for microbes, and I am sympathetic. But in other cases, I think an obsession with tying everything to genetics is a mistake. Ecology is about phenotype and evolutionary outcomes (e.g optimisation subject to constraints).

      • Couldn’t agree more. Have to admit, in fairness, though, that a lot of the new stuff is enabling us to get better and better at tracking microbial activity in real time (at least, when we know what we’re looking for and have already isolated some of the metabolic pathways). I imagine it won’t be long before we can explore microbial ecology as much in depth as we have been exploring the ecology of larger organisms.

  2. I’m not if anyone is aware of this nice commentary type paper on plant functional traits. Here Dan Laughlin argues that we should increase the dimensionality of the traits we measure and not simply measure as much as we can: there appears to is a diminishing return on the the amount of predictability we gain from including more traits. Specifically he argues that collecting few traits from multiple organs improves our ability to predict, in this case he demonstrates using an example of plant species abundances. I am by no means a “trait person” but this makes intuitive sense to me.

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