Tuesday, 25 November 2014

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 NiƱo. Poaching doesn't help the matter.


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


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.

Monday, 10 November 2014

Local Flavour

As the lone SS&S member still living in Edmonton, I feel a certain responsibility to keep the dream alive in the blog’s ancestral motherland. Unless the dream is a buck, of course.

Dustin turned me on to a ½ section about an hour outside of town, right along the river, with the tip that the deer tended to stay on the river-side of the property, moving through the many draws in and out of the valley. On opening weekend, I brought Josh and Jess out for a day in the field, hoping to connect on a deer and, in the process, continue the tradition of bringing more department people into the hunting fold. Unfortunately for them, I don’t really know what the hell I’m doing. Despite getting a deer in each of the last 3 years, my entire strategy consisted of driving to Pincher and walking around with Jesse until we saw something to shoot, often flushing several deer in the process. Ah, high ungulate density. As ecologically sketchy as it is freezer-fillingly satisfying.

In any event, I had the first part of our process nailed down – 3 separate deer groups, all flushed. Rats. The last of which was about an hour before sunset, when we set up facing downslope near a draw that had some sign nearby, expecting to catch a deer coming up out of the valley to feed in the fields behind us. Comfortably leaning back on trees, we had a good 180 degree view, with decent sight lines through relatively open conifers. After a few minutes of sitting, I detected footsteps, in a distinctive deer-y cadence. “Excellent – it’s all falling into place” is what I would have said, except the deer were right. Fucking. Behind us. By the time I heard the doe-fawn pair, they were maybe 15 yards away, directly upslope from us, but there was no way to turn around without getting busted. On top of that, out of the corner of my eye, I could see they were facing us head-on, not giving much chance for a good shot, especially given that any opportunity would have to be extremely quick. So I just sat there like an idiot, hoping they’d somehow walk right between the 3 of us without detecting us, which of course worked out about as well as you’d expect. Oh well - at least now I knew which damn way to face. Better luck next time.

Next time being yesterday, when I headed back to the same spot with a different crew (Todd & his buddy Miles), both of whom also had tags. We spent time in the same general area where we’d seen critters the previous weekend, but despite a layer of fresh snow, we saw almost exclusively coyote tracks.

Aside – if you ever want to shoot a coyote, apparently fawn distress calls are your friend. About 2 minutes after blowing the call, a coyote burst out of the trees 20 yards away and stopped along the trail I was looking down. We had a nice staring contest. I waved. He ran off and barked. Good times were had by all.

At the same time as my coyote encounter, Todd happened across some fresh buck tracks nearby, plus a scrape and a rub. Nice. Unfortunately, they led into the thick stuff, so following stealthily was not in the cards. We spent the rest of the afternoon wandering around aimlessly in search of (as it turned out) very few tracks, but upon our return to the area of the coyote encounter and nearby buck tracks we found 3 sets of tracks on top of our boot prints – it looked like the buck was chasing 2 separate does. We set up in the area for the last hour of light, each a few hundred metres apart, each facing a likely place to intercept the buck or one of the does moving downslope. This also happened to be within spitting distance of our almost-opportunity the previous week.

Crunch, crunch, crunch. The sound was coming from my 4 o’clock. I slowly turned my head and spotted a snout, then a couple of legs, then a full body and set of antlers emerge from the trees. By the time he was completely in view, he was no more than 25 yards away, fully broadside. Undetected, I turned to level my rifle, and even in the half-second between the click of the safety and the shot, he was still unaware that anything was amiss. One through the heart, and he rather determinedly trotted forward, clearly worse for wear. He stopped another 30 yards on, and I could just barely make out his rump between the trees in the rapidly dwindling light. I watched him for several minutes, neither of us moving an inch, until he slowly collapsed on his side.

The elation at my first buck quickly faded with the realization of how big he was, and how far (and uphill) the road was. We dragged in shifts, two of us on the deer, with the odd man out holding the rifles. After several hundred metres of slow and exhausting progress, Todd ran back to the truck to fetch his secret, high-tech friction-reducing device: a crazy carpet. Glorious. I was never a fan as a kid – always being partial to flying saucers  but damn if I don’t appreciate them now. Finish the drag, get him into the back of the car, zip back home to hang him in my garage, and sit back for a quick bowl of Hank Shaw’s chili I’d made the day before with the last of my 2013 deer. Just in time.

Saturday, 1 November 2014

Moose Bulgogi

It has been a while since I put up a food post, but it has also been a while since I had a bunch of wild meat in the freezer.

I've been on a bit of a kimchi binge, so am pretty much constantly looking for things to eat with it. I remember some pretty lavish bulgogi meals in Edmonton, so thought I would give that a shot. I found this recipe, and followed it. I used a few bottom round steaks which I sliced thinly while they were still a bit frozen. Asian pears were hard to find, so I substituted another nameless variety. It seemed to work. I also added toasted sesame seeds because they are delicious. 

The meat marinated for a couple of hours in the fridge, then was seared hot and fast. Those of us with opposable thumbs made lettuce wraps with kimchi, enoki mushrooms, pickled vegetables and cucumber. They were very good. I think next time I would make some kind of Korean spicy mayo too, if that is a thing. I am not yet at the point where I am making my own kimchi, but will get there soon. Anyone got a good kimchi recipe to let me in on?