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.