Genomics: more questions than answers

I have been meaning to do a post for a while. Dustin - in a front-runner for post of the year - wrote about our Lapland trip, which meant my SS&S material was restricted to a few grainy shots of mushrooms already used on instagram. But I can't resist, it was a great year for mushrooms in Sweden:

I thought I would tell all you a bit about my research, or rather what I think of my field of research.

Generally I use genetic information to learn something about the ecology or evolutionary history of a species. To publish my research it gets framed as hypothesis-driven but it is just as much curiosity-based. My career goal is to provide tools or methods or information [or anything really] that can be used to conserve biodiversity. I had some success with this at the U of A, and by success meaning I got the attention of mountain goat managers (in Alaska). My research and outreach in part resulted in this delay and likely ACEC designation for an area in southeast Alaska, something I am quite proud of.

Fast-forward to Uppsala and my genomics era. Again, I am doing the same thing, but instead of using genETic information it is now genOMic. The difference made by these two letters is huge.

Practically speaking it means my desktop is all but useless (everything gets done on a massive computer cluster), most lab-work is outsourced, I rely heavily on government-funded bioinformaticians (it is Sweden after all), R turns out to be too slow for my needs, and I uncover patterns for which there are no clear (but often opposing) interpretations on what it means.

Academically, this is great - I am in the middle of a real transition and I can contribute to the development and maturation of the field. For example, I just ran simulations for half a year to figure out what demographic parameters can and cannot be estimated with a new type genomic data. Turns out we can't estimate effective population size worth shit. In the hypothetical two-population scenarios below, A and B are easy to resolve, C and D are not:

Who cares right? Well, C and D focus on changes in effective population size over time, and this can be an extremely valuable parameter for conservation and management. Did a population just crash or has it always been small kind of stuff. Yet with one of the most touted types of genomic data, it is essentially impossible to estimate - and this hits me where it hurts (remember my career goal).

For a while now there have been essays and reviews written about genomics and conservation, largely discussing how genomics will revolutionize the conservation sciences - I have counted almost 20 of these articles (bizarrely, there are few case-studies). The pervasive opinion of a panacea didn't seem to gel with my above work, nor the understanding of such data here at Uppsala (a world leader in non-model organism genomics - my boss just published this in Science).

This frustration lead me to organize a workshop titled: Conservation Genomics: Academic exercise or transition with real-world applications where I hoped we would discuss these issues among others. The workshop started off with this image (higher quality of course):

The Galapagos sea lion - one of my main study species at the moment - is endangered. The culprit(s): dogs and El Niño. Poaching doesn't help the matter.

Translation:

i) Genomics will have little to do with species conservation in this case.

Opinion:

ii) This is probably the norm for species conservation.

Resulting question:

iii) How and when can genomics inform conservation?

I am still developing my views on the matter, but I think genomic data can play a role in conservation planning, the extent of that role has yet to be determined. Monitoring and inbreeding estimates are clear beneficiaries of genomics - but getting that info into conservation action is another matter. And at the very least there are some chinks in the armour (see simulations above) that researchers need to be aware of. The field is incredibly young and we are still figuring things out.

I definitely found some like-minded folk at the workshop. Others clearly had different views - the best analogy being that if they caught a glimpse of an off-colored black bear they would argue it is locally adapted and should be preserved at all costs. Of course, egos played a big role at the meeting, and many simply refused to acknowledge their research isn't as important [for applied conservation] as they think it is. Time will tell as to how it all plays out, but I managed to put together an article on the subject that will be published soon in TREE - keep an eye out for it.