Thursday, 27 January 2011

Sometimes, it does matter where you're from.
One of the major thrusts of the research I've involved with in the last few years is in the world of "domestic introgression." Some times, when we move animals around, there will be a pre-existing wild form of that species. For reindeer transplanted to Alaska, it's the endemic caribou. Some mink farms are in areas that already have a wild mink population. And a dog is nothing, if not a very funny looking, strangely behaving wolf. The concern is often that our tame species - the domestic species - will breed with the native wildlife, introducing genes that have more to do with living with humans than in the wild. That's what we call introgression - broadly speaking, it's when genes from a species or subspecies sneak into a new species. In many cases, natural selection can do its thing and purge these genes, but with the right conditions, even these very poorly-adapted traits do filter in to the wild population.

Red foxes have been extensively bred for farm fur, not unlike mink. The sort that have ended up in these farms are a total hodgepodge of various foxes bred together for the best fur characteristics, while still being tame. You might remember the tame, Russian foxes I talked about earlier, with their collie like appearance and their cheery disposition. Some foxes escaped in Californian fur farms in the mid-1900s, where they established a growing invasive population in the Sacramento Valley over the ensuing time. From here, they've come into contact with the native foxes - foxes that have long been there, and are well adapted to the local environment.

Enter Benjamin Sacks and colleagues, working out of the University of California, Davis. They took DNA from foxes throughout the Sacramento Valley, and looked at a variety of markers - some mitochondrial, some microsats, and some SNPs. In addition to the typical analyses (For HWE, Linkage, and so on), they assessed whether there were domestic introgression into the wild foxes using STRUCTURE (a package that assigns individuals to populations when you don't know the number or placement of the clusters) and BayesAss, which assigns individuals to populations based on prior knowledge of the populations. Finally, they used Migrate-N to assess how much the geneflow there was between the domestic foxes and the native foxes.

From the traditional stats, they had a microsat HE of 0.65 and 0.69 - something I would think is low given an average number of 6.1 and 6.6 alleles per locus. They didn't have any HWE issues. Additionally, it was clear that the wild and the introduced groups of foxes assorted with themselves spatially - that is, there was a region of native fox, and a region of introduced fox, and not the two intermixed in the same area. You can check out the figure to the right to get the general feel for the lay out - the caption has a lot of useful information in reading it.

When they looked at information about potential migrants, and admixture, they found a small number of individuals who didn't match either the 'native' or the 'introduced' groups that they resided within. When they looked at the mitochondrial DNA with the nuclear DNA, it was clear that all of them were of clear hybrid origin - not migrants, but the first generation cross between a migrant and the local group of fox. However, the authors also argue that there's a region of individuals who are primarily of hybrid origin. Finally, the analysis of Migrate-N showed a generally low level of introgression between the groups, of about 1.31 and 0.91 effective migrants per-generation.

Taken together, Benjamin Sacks and colleagues argue that there is some sort of selection preventing the groups from intermixing. Something about the inherent ecology of the wild or domestic foxes (or both) is preventing too much of the domestic genes from bleeding into the native foxes, and vice versa. They suggest that the hybrids they do find are due to a low density area, and but that the mating system of red foxes makes it difficult for introduced foxes to interbreed with the native foxes. I remain somewhat skeptical of this argument, and I'd like to see some experimental evidence to back the claim.

The study was generally well done, but I do have a few general critiques. The sample size from their "hybrid zone" is very low indeed. I would really prefer to see additional data from there, to actually elucidate the strength (or lack there of) of the hybridization. Getting samples isn't always easy, but drawing inferences about those regions on the basis of n=3 and n=3 seems perilous to me. I'd like to see a better treatment of hybridization using BayesAss. Ideally, there should be 'reference' populations to check against. I recognize this isn't available for one or both groups sometimes (oh, what I wouldn't give for reference populations in some of my own work), but results must then be interpreted in light of the lack of reference populations. There could be previous introgression that we don't see, because it's gone to fixation in one or both groups. It is unlikely that this has happened here, given the high Fst and that hybrids seem to be selected against, but it's something I keep in the back of my mind.

SACKS, B., MOORE, M., STATHAM, M., & WITTMER, H. (2011). A restricted hybrid zone between native and introduced red fox (Vulpes vulpes) populations suggests reproductive barriers and competitive exclusion Molecular Ecology, 20 (2), 326-341 DOI: 10.1111/j.1365-294X.2010.04943.x

Figure reproduced from the above cited publication under a fair-use rationale.

Wednesday, 26 January 2011

Spare change

I was checking out Craigslist, when I noticed an interesting property up for sale:
Arctic Circle Hot Springs is located in the heart of some of Alaska’s best gold county, access is by the Steese Hwy. 134 mile N. from Fairbanks, or from lighted and State maintained, 4,400ft airfield. This property is in need of much TLC however it is definitely one of a kind, and the potential to the right owner is virtually unlimited.
It looks like someone finally moved Circle Hotsprings back to the market. Rumour was that it was tied up off the market for various and sundry reasons, most of them stemming from personality issues. I wouldn't know anything about that specifically, beyond the hearsay, but it'll be exciting to see if that gets up and running again.


Monday, 24 January 2011

For the lazy Skiier

I love because it's full of random gadgets, and I like gadgets. I don't own many, but I really like knowing they exist. Gadgets are all futuristic. But in this case...

Here's a gadget for the lazy skier. The Skizee is a four stroke that you put behind you, which pushes you along like a snowmachine track. But the Skizee (that's the link to their company webpage) looks horribly awkward, and the stance for that looks just plain unnatural. And more importantly, why would you? I can't think of a use for the gadget that isn't better suited by something else.

Scenario 1: You're using it as a skiier. That means you need to haul around a 4 stroke engine and that contraption on your back, or on a polk. In the case of the former, you don't get to carry anything else. In the latter case, what are you going to do with the sled after the fact?

Scenario 2: You're using it fulltime, as a snowmachine. You're going to have shorter range, it's going to be harder to service it, and you don't have any cargo space. Standing's got to be a pain, vs sitting. And it doesn't really have a smaller footprint than something like an Elan, so you're not likely to get into anywhere that you can't get with a snowmachine. The weight savings can't really be enough to make up for the float of a real mountain snowgo. And I can imagine the first time you stumble and the machine goes up between your legs is going to be preeeetty dang uncomfortable.

So... what's the point? Who, exactly, are they trying to sell this too?

photos via

Saturday, 22 January 2011

Nothing but cold and ice

Sorry for being absent. When the blog gets quiet, it’s because something in my life has either gone fantastically well, or horribly awry. Lately, it’s been more of the latter than the former. But I was taught not to complain when things go bad, so I won’t say more about that. I have been spending an awful lot of time out on the snowgo, hunting for a couple of things here and there.

I’ve also been sewing, though I’m embarrassed to show the final product. My aana would be annoyed I didn’t pay more attention when she taught me to sew.

We’ve been gaining daylight.

That wasn't a picture of yours truly, but a buddy of mine. My parka is far prettier. ;)

And the trip to Manly Hotsprings is now especially pretty.

But honestly, you can say that about almost anywhere in the state right now.

I’ve got more science-foo planned; I’m in talks with a grad student in my department about potentially blogging a journal club. Hopefully that’ll pan out.

Anyone know where I can get such awesome facemasks as they're wearing here? I wear a helmet for just riding, but hunting with a helmet on is very stupid. However, I've decided I don't like freezing my face off each time I ride, and most people I know either tough it out by just piling on the scarves or whatever (the frostbite solution) or put up with wearing the helmet (the stupid solution). Kotzebue brand not-freezing-your-face-off sounds especially appealing to me!

Friday, 7 January 2011

Not a reccomended Mfg Method

The sign allegedly translates to "Dependable handling of chemical products" (Sadly, I don't speak Dutch). Hat tip to Derek Lowe at In the Pipeline and Keeees (comment #1) for the link to the picture and translation.

Thursday, 6 January 2011

Snowmachine HUD

One thing I've always disliked about riding my snowmachine is that I have no idea how fast I'm going. I have a general feel for things, sure, and I divide it into two speeds - safe, and not safe (but fun). But the problem is that my speed gauge frosts over, and I can't actually read it all winter long. My snowmachine never gets hot enough to thaw the frost off the watchglass.

That's got me dreaming about a snowmachine helmet that's like a fighter jet helmet, where important information is projected directly on the visor of the helmet. That way you can see speed, fuel, oil, and GPS location without having to look down from the trail at the dashboard. I've found that when I'm riding in the interior (where I do the bulk of my riding now), you can't really take your eyes off the trail for very long at all, because most of the time you're in some very closed forest. Your snowmachine won't blow up like in True Lies if you hit a tree, but it's generally very un-fun to hit one.

Well, via Gizmodo, it looks like a company called Recon is going to produce goggles with integrated LCD screens. They're looking to sell these to skiers, but I think some things, like an HUD GPS, would be a godsend to snowmachiners. Of course, like everything else, a GPS isn't a replacement for good old fashion knowledge of the trails around you, and a map and compass never have dead batteries, but it'd be a really cool toy to have for riding!