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.

Does conservation have an impact?

For good or for ill, humans massively modify the world around them. From the perspective of other species, the majority of our modifications are "for ill." Some individuals realized that humans might irrevocably alter their favourite places, and thus was born the conservation movement out of local concerns. It wasn't until the 20th century that conservation of entire species really took off as a movement, and not until much later that the concept of protecting ecosystems and ecosystem services emerged. Biodiversity has continued to decline, however, leading to a period of mass-extinction that is unseen since the K-Pg extinction event (extinction event formerly known as prince. Er, K-T). Conservation biologists have truly emerged in the last 60 years to attempt to preserve some of this threatened biodiversity, but their over-all impact has been generally unevaluated.

In the latest issue of Science, the International Union for Conservation of Nature has published a systematic review of the current conservation status of vertebrates (verts), and whether conservation has had an impact on the status of those species. Before I get much further, this paper does two things I hate. The first is it has an insanely long list of authors. There's no way that 100+ list of individuals all contributed written material to the paper, and the list of author affiliations literally takes up over a page. That's just ridiculous. Secondly, much of the paper is in the supplementary material - which is seriously abusing the definition of "supplementary."

Now that I've got that off of my chest, the consortium of authors compiled the conservation for 25,780 species of verts -  this comprises all described mammals, birds, cartilaginous fish and amphibians, and a sample of reptiles (herps) and bon fish. Why they didn't do a complete enumeration of herps is beyond me. They only used ~ 19% of modern species (by my off-the-cuff estimation), and adding about 6500 more species doesn't seem like it would have been a huge amount of work. Perhaps there's a good reason that I'm missing. Broadly, the IUCN uses three major categories, which are broken down into sub-categories. Threatened species can be either Critically Endangered (CR), Endangered (EN) or Vulnerable (VU). They found that around 1 in 5 vert is classified as threatened, with a gradually increasing trend in risk since the 1980s. Amphibians are far and away the most threatened taxa, with over 600 species of them moving a category closer to extinction (e.g., changing from VU to EN). Generally, this was all known though it's nice to see it reiterated.

Next, the consortium of authors evaluated the impact of conservation efforts on this decline. They argue that of all the 'status' changes, 7% were improvements in status (e.g., CR to EN), and only 4 of these were not due to conservation efforts. Taking a digression here, the consortium do not really define what they mean by conservation. Conservation can be everything from highly intensive captive breeding to mostly laissez-faire restrictions on hunting or killing. It can describe setting aside habitat, or re-introducing a species actively. In short, it covers an awful lot of ground from "doing nothing" to "doing a whole lot." So when they say 64 of 68 improvements is due to conservation, it doesn't say anything about conservation effort. Indeed, some of that improvement could be due to factors not related to the conservation effort at all.

This is not a trivial point. The very title of the paper is "The impact of conservation on the status of the world's vertebrates." This merely confuses correlation of conservation activities with a causal agent in species improvement. When they next compare species status to what they would be, they implicitly bias the equation by assuming that absent conservation, species status would remain unchanged. While it is true that in most instances, threatened species would deteriorate without some degree of conservation, the only way they couldn't find that conservation leads to species improvement is if every species showed a decline. It precludes a species improving due non-conservation related reasons.

There's good reason think that a species wouldn't continuously diminish if left to its own. As species become rare, it becomes difficult for predators to effectively target them. Disease doesn't have as many hosts, so absolute rates can often drop. And species with small home ranges are difficult to stamp out from habitat loss. In rare cases, there have been evidence that some threatened populations have evolved to resist threats posed by invasives. They would be vulnerable to extinction from purely stochastic events (such as the odd harsh winter), but the time frame we're talking about (30 years) is not long enough to really capture that in its entirety.

I would argue that the proof that our current conservation is not as effective as we'd hope it would be is in the universally worsening Red List Index. To the right, there's a map of the net-change, and it's almost universally bad. By congratulating conservation for the cases of conservation, it ignores the cases where conservation has been applied and no improvement has resulted. I wouldn't argue that conservation has no impact. However, if I stated that my method of healing a bleeding patient caused individuals to improve 7% of the time, no one in their right mind would let me treat so much as a papercut. Conservation effort needs to improve, and seriously, if we're going to stem the global declines in biodiversity. But talk and criticism is cheap; I offer no plausible way through which we can do better. I just hope it isn't status quo.

Hoffmann, M., Hilton-Taylor, C., Angulo, A., Bohm, M., Brooks, T., Butchart, S., Carpenter, K., Chanson, J., Collen, B., Cox, N., Darwall, W., Dulvy, N., Harrison, L., Katariya, V., Pollock, C., Quader, S., Richman, N., Rodrigues, A., Tognelli, M., Vie, J., Aguiar, J., Allen, D., Allen, G., Amori, G., Ananjeva, N., Andreone, F., Andrew, P., Ortiz, A., Baillie, J., Baldi, R., Bell, B., Biju, S., Bird, J., Black-Decima, P., Blanc, J., Bolanos, F., Bolivar-G., W., Burfield, I., Burton, J., Capper, D., Castro, F., Catullo, G., Cavanagh, R., Channing, A., Chao, N., Chenery, A., Chiozza, F., Clausnitzer, V., Collar, N., Collett, L., Collette, B., Fernandez, C., Craig, M., Crosby, M., Cumberlidge, N., Cuttelod, A., Derocher, A., Diesmos, A., Donaldson, J., Duckworth, J., Dutson, G., Dutta, S., Emslie, R., Farjon, A., Fowler, S., Freyhof, J., Garshelis, D., Gerlach, J., Gower, D., Grant, T., Hammerson, G., Harris, R., Heaney, L., Hedges, S., Hero, J., Hughes, B., Hussain, S., Icochea M., J., Inger, R., Ishii, N., Iskandar, D., Jenkins, R., Kaneko, Y., Kottelat, M., Kovacs, K., Kuzmin, S., La Marca, E., Lamoreux, J., Lau, M., Lavilla, E., Leus, K., Lewison, R., Lichtenstein, G., Livingstone, S., Lukoschek, V., Mallon, D., McGowan, P., McIvor, A., Moehlman, P., Molur, S., Alonso, A., Musick, J., Nowell, K., Nussbaum, R., Olech, W., Orlov, N., Papenfuss, T., Parra-Olea, G., Perrin, W., Polidoro, B., Pourkazemi, M., Racey, P., Ragle, J., Ram, M., Rathbun, G., Reynolds, R., Rhodin, A., Richards, S., Rodriguez, L., Ron, S., Rondinini, C., Rylands, A., Sadovy de Mitcheson, Y., Sanciangco, J., Sanders, K., Santos-Barrera, G., Schipper, J., Self-Sullivan, C., Shi, Y., Shoemaker, A., Short, F., Sillero-Zubiri, C., Silvano, D., Smith, K., Smith, A., Snoeks, J., Stattersfield, A., Symes, A., Taber, A., Talukdar, B., Temple, H., Timmins, R., Tobias, J., Tsytsulina, K., Tweddle, D., Ubeda, C., Valenti, S., Paul van Dijk, P., Veiga, L., Veloso, A., Wege, D., Wilkinson, M., Williamson, E., Xie, F., Young, B., Akcakaya, H., Bennun, L., Blackburn, T., Boitani, L., Dublin, H., da Fonseca, G., Gascon, C., Lacher, T., Mace, G., Mainka, S., McNeely, J., Mittermeier, R., Reid, G., Rodriguez, J., Rosenberg, A., Samways, M., Smart, J., Stein, B., & Stuart, S. (2010). The Impact of Conservation on the Status of the World's Vertebrates Science, 330 (6010), 1503-1509 DOI: 10.1126/science.1194442

Figure reproduced from the paper under fair use rationale.

From one mad-man to another

Mugabe is making a gesture to the rest of the world, gathering up animals two-by-two to send them to that paragon of sanity, Kim Jong-Il.

According to conservationists, the Zimbabwean president, Robert Mugabe, will send a modern-day ark – containing pairs of giraffes, zebras, baby elephants and other wild animals taken from a national park – to a zoo in North Korea.

The experts warned that not every creature would survive the journey to be greeted by Mugabe's ally Kim Jong-il, the North Korean leader.

There are particular fears that a pair of 18-month-old elephants could die during the long airlift.

But what other brilliance do we expect from the man who made all of Zimbabwe billionaires.

Huzzahs are in order

What could drag me back from vacation to blog about something? Two words: Jurassic Park.

Technically, it's Holocene Park. Here's the meat and potatoes of the story, as the cool kids say: Researchers have successfully cloned an extinct subspecies of Ibex, where they had tissue preserved from the last surviving individuals. The Daily Telegraph has the story. This is a long sought holy-grail of conservation Genetics - to revive extinct species means that the end is no longer the end. Right now, when we lose biodiversity, it's 100% gone forever; impossible to recreate. But if whole-organismal cloning can be used to recreate extinct species, then then suddenly it opens the prospects that maybe we could get a second chance at a few species.

Especially the big, fuzzy lovable ones. You know, like Pandas.

Of course, whole organismal cloning is very crude currently, and the technique... well... it has issues. Our success rate with it is still very low. I can't help but wonder if our lack of success in cloning has to do less with DNA damage, and more to do with inappropriate epigenetic enviroment. How I hate that word, epigenetic. It basically means `Anything inherited, but not from the DNA, and we're not sure where.` Or maybe it's my cynicism showing through.

Still, our first subspecies cloned. To quote a TV show, Huzzahs are in order. I hope we do better, and we can make this work. Of course, the underlying causes of the species' extinction must be addressed, otherwise we'll just bring them back to die off all over again. But with some species, who knows? Maybe we stand a chance.

Doing it wrong

Here's a sign that you might be doing it wrong:

Wanted: PR firm to fight species listings

The Alaska Legislature is paying for a conference and public relations campaign to persuade Congress to limit the Endangered Species Act.

The argument goes "Polar Bears cost us money as an endangered species. So, we should have them unlisted as endangered species." If you can't spot the numerous non-sequitors in there, give it another read.  Since apparently it needs said, Polar Bears are very probably endangered by habitat loss.

I'm disappointed by this - it's nothing more than politicization of Science - but I'm not surprised by it. There's a phrase we hear often that goes "We need more science." That means, "We need more people who agree with us." It's one of the things you realize early on in the critter management field. If you're unscrupulous, it also means you found a willing payer to revisit some topic.

"So we've rediscovered the Ivory Billed Woodpecker. So what?"

We welcome the recent announcement by the conservation partnership BirdLife International that they have launched a "global bid to try to confirm the continued existence of 47 species of bird that have not been seen for up to 184 years" (see http://go.nature.com/6Hc2Cn). But there are pitfalls, as the recent history of 'rediscoveries' has shown.

One of the species on BirdLife's target list is the ivory-billed woodpecker (Campephilus principalis), a bird that was prematurely alleged to have been rediscovered in 2005. This seemingly improbable reappearance provoked intense debate within the scientific community about the veracity of claimed sightings and, more generally, about what represents sufficient proof of continued existence (or extinction). Accusations of 'faith-based' ornithology resulted, increasing scepticism among politicians and policy-makers that conservation organizations are often too willing to put public relations before scientific rigour. [...]

Some people really know how to get my attention.

I've been kicking around this idea for a while, too, though not as eloquently. The authors of the opinion piece make their case that even if we re-discover species living in the wild, the discovery means very little unless there's a minimum viable population. I would have taken a different tact, saying the quest to re-discover these species burns through vast sums of critical conservation money; money that would be better spent on species who are a little more accessible.

I do see a small amount of scientific utility in this, though - extinction rate is sensitive to what we a) declare a species and b) an and can't find. It's hard to talk about, say, Giant Squid demographics without being able to look at them (or otherwise detect them). So how hard we try to look for relictant populations influences our measure of current extinction rate. To get an accurate measure of the current extinction rate, it makes sense to apply copious effort.

That said, these expeditions are expensive. They're multi-person, multi-year affairs frequently requiring access to remote areas by specialist personnel. If you can't hear the dollar signs ring up as you read that last sentence, you should get your hearing checked! The price on the knowledge that a species isn't totally extinct, but instead a hairs-breadth away from extinction, is very massive, and surely that money could be used to keep other species from getting that far-gone to begin with.

Citation:

Ladie et al. Caution with claims that a species has been rediscovered. (2009) Nature 461, 723

Conservation priorities

Here are some facts that conservation biologists don't like to hear:

1. Conservation money is limited. Conservation effort is also limited.
2. There are many species in need of conservation.
3. The number of species in need of conservation is likely to grow.

And I'll add on one fact that I don't think any conservation biologist would disagree with:

4. Some species are harder to conserve than others.
   

Given these four basic premises, one conclusion pops out: we need to be selective in what we attempt to conserve, so to maximize the number of species we can conserve. It also means we shouldn't be wasting money on things that don't contribute significantly to conservation, like banning Canadian Polar Bear rugs, or wasting enforcement money chasing down native subsistence users who hunt polar bears through a ban (luckily, that one would be politically untenable).

Some species are challenging to conserve for space issues - try keeping a Grey Whale in captivity for captive breeding! Others are difficult for husbandry issues, like the Shanghai soft-shell turtle where the only male in China once attacked a female instead of mating. And ask the Black Footed Ferrets what re-discovery did to their numbers - I once heard a colleague describe the worst thing that happened to the Black Footed Ferret as being "Scientists discovered they weren't extinct yet."

The idea that we should maximize our bang-for-our-buck in conservation is a very unpopular one, though one that more scientists are coming around to. Recently, this argument poked its head up in the main stream media when a prominent scientist advocated just letting the Giant Panda go extinct. MSNBC downplays his comments through a rebuttal from another scientist - and would have thought the WWF, an organization that uses a Giant Panda as their logo, would oppose it?

Mr Packham is probably more in the right, here. The problem is that the Giant Panda is too much of a specialist, and its habitat is disappearing, and likely can't be re-created. Even if we stabilized their numbers at their current levels, they're (and would always be) highly vulnerable to chance events - like the introduction of a new disease, or a dry year. But from a public relations point of view, it would be un-reasonable to let the Panda go quietly into the night. People like bears (so long as they don't have to live with the). They're willing to shell out millions of dollars to see even a small return on their investment. Practically speaking, not the best course of action. But the one we're apparently taking, none the less.

Quotes from Orwell and North American Mammals

I found this quote at the bottom of a daily news update, and I like it:

The aim of a joke is not to degrade the human being but to remind him that he is already degraded. -- George Orwell

I was never made to read George Orwell at school, or collage, and so I came to appreciate what a good author he was without the negative memories of time in Engrish class. Which is good, this way I like him!

---

Here's some more science from the Conference, this one being talk number 54, titled "What's killing North America's mammals? A meta-analysis of cause specific mortality." It was authored by Christopher Collins and Roland Kays, out of New York State Museum.

As they write in their Abstract, everything eventually dies. What we'd like to know is across all mammals, what are the major drivers of mortality? We can quantify this by `Collering and follering` - putting on GPS or radio collars to track animals until they die, and investigating the cause of death.

Any given study can only look at so many animals at one time. GPS and radio collars are expensive, and so are putting them on critters. It's also very time intensive. So any given study only gets so much information, and that information is generally most applicable to a given species, or a group of species in a similar area. However, people can go in after studies are published and collect lots of peoples' different studies and bring them together. This is called a Meta-analysis. Meta-analyses frequently need lots of boring mathematical treatment, because people invariably collect their data in different ways, but well done meta-analyses can be very informative about large scale patterns that no one study would reveal.

Collins and Kays gathered in all the studies they could find with mortality data, and after working with the data, they found that surprisingly, 43.8% of across-species mortality was caused by humans. Most of this was hunting, though not all; Road-kill accounted for 7.9% of all mammals' mortality reported. Now, natural causes accounted for 40.9%, and unknown causes accounted for 15.3%, which is very large indeed. Natural mortality is probably much larger, because that 15.3% of unknown is likely a lot of disease related death, and predation. However, in those cases, the researchers got to the bodies late, or just couldn't figure out how the animal died - it's harder to figure out what disease killed an animal than you'd think!

Still, even if all of the unknown mortality was caused natural causes, that still leaves 43.8% in the hands of humans. Where other factors used to dominate, now humans apply the "Natural Selection" in North America. This has very profound implications for the direction that evolution will take in the long-haul, as species slowly adapt to human presence. Well, either that or they'll go extinct. One of the two.

I once took a course in Urban Ecology, which is the study of natural systems in human areas - farms, villages, dockyards, and big cities. What really stuck in terms of animal resilience was that species that thrived around humans either had a long history around human cities (usually Europe or Asian weeds and vermin), or animals that are so behaviourally complex, and so plastic and amenable to changing conditions, that humans really couldn't disrupt them. Racoons in the lower 48 are the perfect example of this.

With this in mind, and knowing what Collins and Kays said about human-cuased mortality, what Alaskan Mammals do I see with the best chance at persistence in 200 -400 years?

• Arctic Fox
• Red Fox
• Coyote
• Feral Domestic dogs
• Racoon - invade and expand.
• Ermine
• White Tail Deer - invade and expand
• Snowshoe Hare

This isn't a comprehensive list, but species that are behaviourally plastic, and stick out in my mind as things that can dodge human-induced mortality to a sufficient degree. I don't include moose because they're highly susceptible to diseases carried by White Tailed Deer, who are slowly invading northward.

There's some hope for other species, though. According to Collins and Kays, when humans designate an area as protected, it seems to work by-and-large. There's still human caused mortality, but it becomes considerably less. There just needs to be the political will to do it, and the public support for the designation.

Easier said than done.

Cauga una?

Here's last week's critter:
It's a wolverine! Dragonfly got it right! Some time, I want to learn how to trap them well, since wolverine is nice.
But trapping wolverine is more art than science. Not many people get it right... when they closed the Chugach, they didn't actually "save" that many wolverines. Wolverines just don't exist at high densities.


I re-learned some German this last week, because there were three really nice Germans helping out.
Was ist das?
Submit your guesses!

Genetic Bottlenecks

I'm not mucking with wolf systematics this week, not even a peek, as I'm focusing on another data set. I pushed out a manuscript to its completed first draft, and I'm starting to work on a second manuscript that unexpectedly grew out of the first. Re-reading one of my lab's papers turned out to be a good idea, as it's refreshed my thinking on Bottlenecks. And Bottlenecks are exactly what I want to discuss. .
No, Dave, not that kind of bottleneck

A bottleneck is when a population goes through an event that greatly reduces its size. I typically think of a bottleneck as being reduced to 10% of the pre-bottleneck population or less, but there's no hard, fast rules on what constitutes a bottleneck. Bottlenecks can occur from a variety of factors, but most frequently it's climate change that forces animals through them. Often, we find bottlenecks in species that were forced into refuges where they can survive, like Tahrs into the high mountains in a warm period, or Dall Sheep into foothills during glacial periods. Because the amount of space in the refugium (that's the fancy pants term for `refuge`) is limiting, the population is greatly reduced.

It's worth saying that these bottlenecks through refugia (pl. of refugium... I hate biologist-speak) are really important, evolutionarily. Because competition for resources is so high, animals tend to be come very well adapted to what they do. Anyone who doesn't doesn't leave behind as many kids, and are quickly outbred by their more successful cousins. But if bottlenecks are too tight, they can leave a species floundering on the shoals, because they've lost too much of their diversity, and too much of their capacity to adapt.

Here's a hand drawn figure!
This is what happens normally through time. The squiggly lines represent lineages, and the width of the tube represents the total population number. Since we frequently trace these with mtDNA (see my glossary to the right!), it represents the unbroken chain of female descendants. If you go back to your mother's great grandmother's grandmother, perhaps her sister had some children, but those children didn't have any children. Those would be a terminated lineage, represented by the little spurs that go out, but don't make it to the end of the tube. They stop early.

That's normal `lineage sorting,` as we call it. It doesn't require someone to have no children. It could be no female children, or no male children, or it could be that they didn't pass on the trait we're following. In a easy, simple example, if a tall female has children with a short male, but doesn't give any of the genes that made her tall to her children, they'll all be short. The lineage of descendants with the `tall` gene is broken, at that point. In our example, we start with three lineages, two of which are represented at the end. But each of the two lineages that made it has branched out, forming new spikes that persist. Some of them will go away, some of them will make up the successful families of tomorrow.

Here's what it looks like in a bottleneck
You can see that a lot of the lineages went away through the bottleneck. Only 1 of the 3 founding lines made it to the end. Compare this to the normal situation, where many more lineages persist. Because of the fewer surviving lineages, less diversity is passed on to the offspring, and the population at modern day is more alike itself (more monotypic) than those who didn't go through the bottle neck. By measuring the variability, we can look back and see which groups went through bottlenecks, and which didn't.

Warning: Dumb joke coming up.
So when I say I'm dating a bottleneck, it doesn't mean I'm going to a bar.

Some species that have gone through bottlenecks include Moose, Cheetahs, Galapagos Finches, some populations of Koalas, Northern Elephant Seals, and humans. At some point, the ancestral human population was reduced to around 15,000 people (possibly due to a volcano, I read?) which is part of why almost every human is closer related to every other human on earth than two random mallards, or caribou would be.

Outbreeding Depression in Arabian Oryx

As a reminder, if you need any definitions for terms, check out the link to my glossary in the righthand bar!

I've previously mentioned Outbreeding Depression, and given you a bit of a mechanism for it, in a previous post. However, outside the ibex example, there's not many good illustrations of the power of outbreeding depression in animals. Most of the good examples exist in plants, which are considerably easier to study.

I'd like to discuss one of the other examples of outbreeding depression, which was stumbled upon when conservation managers tried to save the Arabian Oryx. The advent of repeating rifles, motorized transport, and access lead quite a few Arabian rural users to dramatically over-harvest the Arabian Oryx, in addition to several species of Gazelle, Ibex, and the Arabian Tahr. All of these species were rendered endangered, and the Oryx was made completely extinct in the wild. Phoenix Zoo in Arizona instituted rescue breeding of Arabian Oryx to great success, and reintroductions began in 1980s. This is where the study of Marshall and Spalton (2000) really kicks in.

There's invariably some level of juvenile mortality, especially in that are reintroduced to the wild, and as part of on-going research to fine tune the reintroduction of the Oryx, they collected tissue and horn material post-mortum; additionally, they collected blood from live animals whenever possible. They went through and extracted DNA from the materials, and genotyped them at 6 microsatellite loci. Remember that microsatellites are meaningless repeat units in DNA that drift in frequency `randomly.`

Marshall and Spalton computed a few correlates of inbreeding and outbreeding - Heterozygosity (which I've previously defined/explained) and d^2, which is a measure of outbreeding, and it's the difference in size of alleles within an animal (measured in repeat units), squared. So if one animal has a 200 long allele at a loci that can grow or shrink by 2 units at a time, and a second allele that is 204, it is 204-200=4/2 and then 2^2=4. Sorry about the math! They also looked at protein content, and a few other factors

I'll spare you the statistical model they applied to see the effect that inbreeding and outbreeding had on mortality, but they found that analysed alone, neither seemed to be a major factor. That is to say, they couldn't detect it. In a low sample of 57, this isn't terribly surprising. But when they considered both together, they found both were significant factors.

Wait, how can you be both inbred and outbred? Well, to answer that, we need to go back to the re-introductions. The Oryx reintroduced into the Oman refuge, you see that they came from very different populations, and 5 of them. The unrelated populations can lead to intragenomic issues, when one part of their DNA is telling them to do one thing, and another part of their DNA is telling them to do another - they're not co-adapted. Alternatively, they could have traits from animals that might be really good in Saudi Arabia, but are terrible for Oman.

To add inbreeding on top of that, all you need to do is take these already out-bred individuals and have them mate with close relatives. Broken bits of DNA will accumulate as they always do, while they continue to have problems with the rest of their working DNA complement.

There's a few lessons we can learn from the Arabian Oryx, relating to over-harvest, land management, and so forth. Those are probably the issues that are going to doom the Arabian Oryx (if they're ignored), but let's just ignore them for the moment and focus on conservation implications. First, we need to take greater care to maintain better lines of animals. This is difficult, as we simultaniously seek to keep fairly diverse, non-inbred animals. Finally, Introductions need to be large enough that inbreeding is statistically unlikely.

(Photo credit: Wikipedia)
Cite: Marshal T.C. & Spalton J.A. 2000. Simultaneous inbreeding and outbreeding depression in reintroduced Arabian oryx. Animal conservation, 3, 241-248

Oh, yeah, it's earth day...

Oh! It's earth day. I didn't really remember until I read someone's post on things they're doing to `green` up (and I don't mean what comes after breakup!), and maybe get her girl a scout badge at the same time... ;)

You'd think a guy like me would be big into enviro-whatevers. I like sustainability, I'm interested in wind power, and I work for critter conservation. A lot of my co-wokers are all gungho about all this stuff, and they're somewhat aghast when I say I've never read Aldo Leopold. But just because I'm not nutty about it doesn't mean I don't care...

When we think about pollution, we think about New Jersy. Definitely not Alaska. The first indication I got that even remote areas aren't as protected as we like to think was when I was studying the Northern Shoveler in Utah. They're goofy looking ducks, with unmistakable bills. There's frequently concerns about mercury in waterfowl in Utah, due to the Great Salt Lake being about as polluted as my boots are muddy. I took feather clippings and studied them for mercury content. Unsurprisingly, I found quite a bit - more than I'd ever want to eat. Ready to scold the Utahns for sullying perfectly fine birds, a minor fact wafted to my forebrain: the feathers grew in while the birds were up in the Arctic.

The environment isn't just a few people in the lower 48's concern. Folks in China are doing things to poison our birds here. Global warming - sorry crazy guys in DNM's comment section - is real, and it's from folks in California and New York who are pushing it along. For as much as we complain about the lower 48 coming up here and telling folks what to do, it's about time we start doing the reverse.

So here's my modest earthday proposal: We should invade the lower 48, and get involved in the discussion about how they're going to live their lives. Because what they chose greatly influences our own choices.

Steer Deer on Kodiak Island

I was all ready to write about some silly post about a story in the BBC claiming that the moon effects the flavour of wine (short version - it only effects the people who believe the moon has power), when someone passed me this story titled `malformations seen in Kodiak deer.` Hey!, I thought to my self. This looks familiar. Perhaps it's that stuff from CSU.

I should have been ready for horrible disappointment. The story is awful. The story is from AP, where they had a single writer stumble through the science, and proceed to mutilate it. Because it's from AP, and it's Alaska related, both the DNM and the ADN instantly picked it up, without even a whit of review. I don't know what's worse, the people who wrote the story, or the people who passed this on. There's a little hope for journalism, though, because the Kodiak Daily Mirror did a better job with the story. Unsurprisingly, they wrote their own version.

Here's my own version.

A little background is in order. First, Sitka Black Tailed Deer (SBTD) are small ungulates endemic to the Alexander Archipelago, mainland SE Alaska, and parts of British Columbia. In 1924, 14 animals were translocated from Baranof island to Long Island east of Kodiak Island. 2 more came from POW in 1930, and 9 more came Kupreanof Island, and were released to north of Kodiak Island. For those of you who need to whip out the calculator, that's 25 animals total. All SBTD in the Kodiak Archipelago come from these founders.

Fastforward to the early-mid 90s, when reports began to emerge about deer with abnormal antlers - antlers with extreme points on the end, frequently with poor symmetry. The body profile of these animals also seemed altered, and most interestingly (to a wildlife biologist!), they seemed to suffer from cryptorchidism, or the failure of one or both testes to develop or descend. The scientists called them `cryptorchid deer.` Locals call them `Steer Deer.` I like the latter.

To compound the issue, there appears to be a locational trend in the Steer deer. A survey of the area found that there was even higher rates of incidence on the Aliulik Peninsula animals (76%) when compared to the rest of the Archipelago (12%). When you look at the rest of the SBTD's range <<5% are steer deer. Clearly, there's something going on here.

Well, if you remembered my post on muskox, you're probably thinking `gosh, 25 animals? That's a small group!` And I would give you a cookie for remembering. 25 Animals is a really small group. It's even smaller when you consider the estimates for heterozygosity - a measure of diversity - are tiny numbers. The Tasmanian Devil, which is critically endangered, actually has the SBTD beat. Now that's just sad.

Well, some people from Colorado State University decided to take a swing at idea that the deer are really inbred, suffer from low diversity, and this is causing their problems. They came up here, did sampling across the Kodiak Archipelago, some in the Alexander, and managed to leave quite a few furious Alaskan scientists in their wake. I hadn't dealt with them directly, but rumour around the coffee pot is that they earned the animosity of a few people.

After their data collection, they looked for a few things -

• Was there population structure between island?
• Was there population structure between Kodiak proper, and the Aliulik peninsula?
• Was there different levels of inbreeding between areas?

These were easy questions to answer, "Yes, No, No." The first, is almost expected, because the deer don't disperse over water, or don't frequently. So they're isolated from eachother. There were no DNA differences between SBTD on the Kodiak Archipelago between areas harder effected and areas less effected. Finally, inbreeding doesn't seem likely an effect, because measures that get at inbreeding and diversity seemed pretty comparable between SE and Kodiak, and within Kodiak.

So where does that leave us? It leaves us without any new answers, just a list of things that aren't causing it. There are still a few remaining hypotheses that need tested, but are much harder to tackle -

• It could be environmental toxicity.
• It could be a disease.
• It could be an epigenetic trait.

There's currently almost no evidence for any of these. Not because they aren't necessarily true - one of them probably is - but because evidence is really, really hard to get. However, people have jumped all over environmental toxicity with vengeance. This seems the hypothesis du jour today (I say, hoping I used du jour right). The AP service story basically said the evidence points to this, when the evidence does no such thing.

DNM on Online Bear Baiting

I've been thinking about Bear Baiting a whole lot, recently. I'm curious about the process, and whether it is an effective tool for population management. I'm especially curious whether the genetic characteristics of bears caught through bear baiting are different from those harvested via a more "traditional" hunt. I'm considering showing up to ADF&G's clinic on the subject, to give me a utilitarian grounding in the subject.

For those of you outside the state, bear baiting is using a large scent lure (often putrid fish and ungulate offal) to attract bears, where the hunter evaluates the bear from a tree stand or ground blind, and selects one for harvest. It's slightly controversial, and it's generally only done for black bears. In Alaska, you can only legally bear bait blackies.

Tim Mowry isn't a fan of bear baiting - that much is clear from his editorial piece in the Daily Minor News - but he's even more `down` on using the internet for certification. I'm curious whether there will be a difference in

1. Overall rates of incidents between last year and this year.
   
2. Difference in incident rates between hunters who took the course online vs. clinic.
3. Whether other factors (land use, etc.) predicts compliance better.
   

These are all scientific questions, and not something based in opinion. Either something has an effect, or it doesn't. So, I guess I'm adding a whole bunch more things `to watch` to my list!

Morning disarray.

Well, I'm writing this post while being distracted by Dave's `find the birds` picture. I've found one of the two stealthy birds, which leaves just one between me and fabulous prizes. Also, I'm fending off the urge to cook up some spam and eggs, after another blog on my list got spammed. Here's some random thoughts:

• I will not touch this story with a 10 foot not touching pole, exactly as I predicted.
• Scientists in Russia have found some of the missing Romanov children. Of course, this won't stop any conspiracy nuts out there, who'll say the Real Tsar is still out there. :)
  
• I haven't had a chance to read the decision, but the Board of Game is allowing moose hunt on the lower Kuskokwim again. I'll read at how many, and exactly what areas when I'm at work. I understand the huge pressure to open this area up to hunting again, since it's a critical subsistence resource. But my wildlife management side of my brain hopes that it's sufficiently limited this year, so they can recover even more.
• I had a strange dream that I was getting an award for launching a young teen through the air and getting them through a hoop using a catapult and explosives. Like a free-throw contest but with people. Usvipaa. The stranger thing is that in my dream, there was a Red-Head I once knew a long time ago, named Charlie. Except I could only call him Kavirliq, which means `red stuff.` Pretty much every redhead has that as a name. Or all the ones I know - three that I personally know are Kavirliq, and two people who I have never met (one of which is sadly passed on).
  

Muskox in Alaska

I want to write a little bit about muskoxen in Alaska. Most of this comes from my infinitely fallible memory, and a paper called `Status of Muskoxen in Alaska` by T.E. Smith in 1984. We're getting ready to do some work on Muskox in the Seward Peninsula, so this is a great way to collect my thoughts on the subject.

Muskox are a large terrestrial grazing ungulate that are a) smaller than most people imagine and b) larger than most muskox handlers would like. It's interesting to note that muskox are actually closest related to a group of species called `Serows;` evolutionarily, muskox are a sort of goat-antelope. Don't see it? It's weird, but apparently true!

They're sort of like the blue-bloods of ungulates, having about as much diversity as a 1920s golf course (and the intelligence of one to boot) - for example, at the MHC DRB locus, a region of DNA responsible for disease resistance, the species has one allele. Even moose have 11, and Cattle? 68, which is more the norm in the rest of vertabrates. There's a dumb science joke that if you've tested one muskox, you've tested every muskox.

Muskox are endemic to alaska, but have had a checkered history, in the 1800s, due to a myriad of reasons, hunting being one of them. They are thought to have been totally expatriated (locally extinct) from Alaska by the late 1800s. In 1930s, spurred by concerns of global muskox numbers, the US feds funded the capture of 34 east greenland muskox, and they were transported to Fairbanks for a 5 year quarintine. In 1935, they relocated four animals (two m two f) to Nunivak Island, choosing the island on the basis that it was an enclosed space with apparently rich forage and no native predators. In 1936, they transplanted the remaining surviving animals, and some offspring that had been subsequently born, totaling 16 males 11 females.

After 32 years, mannagers selected Nelson Island as the next reintroduct for Alaska. Though Nelson Island isn't far from Nunivak, they're seperated by a patch of ocean, and Nelson Island varies considerably in its topography and browse - how, exactly, I'm not sure, but I'm told the veg is different, and I trust the folks who told me. The first introduction was 8 in 1967 (5m 3f), followed by six males and 9 females in 1968. Nelson Island is really just an island in name, and there isn't as much barrier to dispersal (beyond habitat) for the Mox.

Future introductions were ANWR (1969-1970; 65 animals), Cape Thompson (1970 and 1977; 70 animals) and Seward Peninsula (1970 and 1981; 72 animals). There's been a number of other events, where they took animals into captivity for either the LARS herd, the Unalakleet herd, or zoo animals, but those really don't factor into my world (well, except the LARS animals). Currently, I don't know if there's been any moving animals around since 84.

You can see my lovely pen-addations to the Mox-map off to the left. I-are-an-arteest, yes, but that should give you the idea what happened. Nunivak came from a small founder population, and all other populations in the state are serial dilutions of the Nunivak Island population. This is of special note, because of the effects it would have on the over-all diversity of the animals. As I mentioned before, diversity was extremely low to begin with, but every time you go throug a `bottleneck` (a period where a few animals are responsible for all the resulting offspring) you experiance a large loss in diversity. This, by the by, is why humans are roughly 28th cousins with every other human. We love talking about how different we are, but thanks to a pre-history bottleneck, we've got scant diversity to talk about. If dolphins were studying us, I bet they'd treat us like a bunch of inbred yokels. :)

If you'll forgive a bit of math, in a randomly breeding population with non-overlapping generations (two huge assumptions!), the probability of losing any given allele (or form of a gene) is

(1-p)^2N

Where p=the frequency of the allele before the bottleneck and N is the size of the bottleneck. Let's pretend we had an allele that made up 10% of all the copies of the gene. That gives us

(1-.1)^(2*31)=0.001455

in the case of the Nunivak introduction, or .145% chance of it being lost. That assumes all 31 animals who were introduced into Nunivak had reproductive success. For the cows, that seems fairly probable, but given males engage in Harem defence, it seems improbable that all 18 males had success. Assuming only a third of the males had any success in their lifetime, we get,

(1-.1)^(2*19)=0.01824

Or about 2%. This may not seem like much, but taken across the whole genome, these effects are steadily accumulative.

However! While some is lost, as they say,`all is not lost.` If you run the numbers, a founder size of 10 is still enough to preserve 95% of the heterozygosity (the number of individuals with two different copies of the same gene). Using Van Coeverden De Groot and Boag's 2004 estimate of heterozygosity for perfect alleles, 95% of 0.504, while low, is dangerously low. However, if you use the previous H estimate of 0.018, 95% of that is a very small number.

Where does that leave us? Alaskan muskox are a currently mixed story. While some populations have shown success, others appear to be floundering markedly. As the state would like to see the muskox fully restored to its entire endemic range (as would many sport and subsistence hunters), we need to sort out what's going on demographically, and tease apart the factors involved in the success of some populations, and the detriment of others. We need to know how much nutrition is a factor in the troubles some are facing, and how much the high degree of relatedness has impacted this nascent population.

Mox picture brazenly stolen from LARS.

Meant to repost this earlier. From the village telegraph:

Federal Subsistence Board bans lead shot for hunting wildlife in Unit 18

2-19-09

The Federal Subsistence Board has approved a special action to prohibit the possession or use of shot shells containing size “T” lead shot or smaller for the taking of wildlife in Unit 18 in Western Alaska.
The use of lead shot for waterfowl hunting has been banned since 1991, due to the high mortality of waterfowl related to ingestion of lead shot. However, it was not banned for the harvest of other wildlife under Federal subsistence regulations. Officials with the Yukon Delta National Wildlife Refuge believe this ban would benefit waterfowl by helping to decrease the amount of lead shot in the environment.
Two species of eider that inhabit Unit 18, the spectacled eider and the Steller’s eider, are listed as threatened under the Endangered Species Act. Concerns over the effects of lead shot on these species resulted in this action. For additional information contact Chuck Ardizzone at (907) 786-3871.

I understand the rational behind this, but I don't think its an especially good call. A more gradual shift to a total ban would be better, so it gives people a chance to use up their lead shot as they transition to steel shot. If this is a major issue at all - I'm a bit unsure how they they estimate the amount of lead shot used in larger game to be anything but negligible. Most folks use centrefire rifles for large game, and furbearers etc. tend to get .22.

Population and diversity.

A little while ago, I left you all with this graph, and I asked which had more diversity, and why.
The answer is `Caribou,` because for each loci, there's a wider range of possible values (or `alleles` as we call them in the biz). While diversity in µsats (these chunks of DNA) doesn't translate 1:1 into total diversity, they're often a good proxy for them. Take Muskox, for example: They're monomorphic (meaning they have no diversity) at many regions of neutral diversity. Additionally, they're monomorphic at regions that are important to the function of the animal - such as MHC, which is important for disease resistence in us critters with backbones.

Part of the reason why Caribou have so much more diversity than Moose is probably due to the sheer number of critters - there's so many more Caribou than there are reindeer. Why, taken together, The Western Arctic Herd and the Mulchatna Herd of caribou outnumber the humans in the state of Alaska! That's not a trivial number of animals, and that's before you add in other major herds. Moose, to contrast, probably number between 60 and 80,000 animals in the state, depending on who's doing the counting. They exist at a pretty low density overall.

Why does population matter? Well, there's two reasons why. And I'll use two anologies.
First, imagine you have ten marbels, each a different colour. You have them all on the ground, when you drop a hammer and smash one accidentally. One of your colours is now no longer represented in your pool of marbels. But if you have 100 marbels, with 10 of each colour, and you drop your hammer, you could smash many more marbels before you lose any colours. The same is true with animal diversity - the more animals you have, the less likely you are to accidentally kill off all the animals with one sort of `allele.`

Second, imagine you're running a poor-man's xerox place. Instead of machines, you've hired a bunch of teenagers to copy things by hand. Teenagers are flakey, and make mistakes while copying pages. Right now, you're xeroxing stuff for the national archives, so all their mistakes will be preserved as they're made. If 1 in 10 teens makes a mistake, then on average, your shop of 10 teens will make one mistake each job. But if you're running a larger shop of 100 smelly, moody teenagers a) you're to be pittied and b) you'll, on average, make 10 mistakes per job.
The same is true with animals. When DNA is replicated so it can be passed on to baby animals, we invariably make mistakes in copying it. Some of it is bad, most of it doesn't matter, and a little fraction of the mistakes are good - this leads to some of the variation we see in nature. Each human, for example, carry around about 400 new `copy mistakes` that most other humans don't have. The more animals you have, the more new forms of `alleles` will be formed through copy mistakes.

Gene Diversity

Diversity is how many different forms of a region of DNA exist within a group of critters. By way of example, in my building there's genes for red hair, black hair, blond hair, and brown hair. So for that region of DNA, there's quite a bit of diversity. But inside this room, there's only the genes for a one hair colour. Much less diversity. In some fish, you have life history strategies: some have genes for becoming huge, mature adults, while others have genes for spawning young. If all the members of a species who would spawn young die out before breeding, then there's less diversity - now there's only genes for becoming big mature adults left.

One way we test for diversity is to look at neutral areas of DNA - these are areas that don't do anything. Much of it is just repetitious garbage, copy errors, and viruses that snuck in and went dormant. Most of your DNA, as far as we can tell, is non-functional. Some of it is very patently useless.

Because it doesn't do anything, neutral areas of DNA (loci) are free to do pretty much whatever they want through mutation, and they're passed on in the population. We can look at this as a proxy for total diversity*, which is harder to look at.

So, I want to show you two groups of loci, one of the loci in Caribou, and one in Moose. The length of the bars shows how widely the locus of DNA can vary.The colours mean something, but nothing important for here. Which species more diverse? Why do you think that species is more diverse?*Kinda sorta. Lots of boring caveats go here.

Outbreeding Depression is just plain depressing.

Opposite of Hybrid Vigour (sometimes), when you have two individuals of different populations, subspecies, breeds or species mate, Outbreeding Depression might occur. Unlike Hybrid Vigour, there's much less to explain here, but unlike it, Outbreeding Depression is less common in nature.

As generations of animals roll on, and nature does it's thing with picking the winners to have more babies than the losers (or even the slightly less winners), animals start to become very good at what they do, and often very adapted to where they do it. Their DNA has been winnowed down to genes that make them outstanding whatevers1. Arabian Gazelles are great at being arabian gazelles, and Turkish Gazelles are fantastic at being gazelles in Turkey. But what makes a good Caribou over here in North America doesn't make a good wild-reindeer over in Eurasia...

Take this case from Templeton (1986):

"...when the Tatra Mountain ibex (Capra ibex ibex) in Czechoslovakia became extinct through overhunting, ibex were successfully transplanted from nearby Austria (Greig 1979). However, some years later, bezoars (C. i. aegagrus) from Turkey and the Nubian ibex (C. i. nubuana) from Sinai were added to the Tatra herd. The resulting fertile hybrids rutted in early fall instead of the Winter (as the native ibex did), and the kids of the hybrids were born in February - the coldest month of the year. As a consequence, the entire population went extinct (Greig 1979)."

There's a number of species we're worried about outbreeding depression. Scottish Wildcats interbred with domestic felines, heavily burdening its genes with domestic copies. The same is true for Sand Cat in Saudi Arabia, and the Ethopian Wolf. Closer to home, there's evidence that domestic reindeer from our reindeer herding past (and lesser reindeer herding present) have introgressed into caribou herds - that is, left reindeer genes where they ought not be. No one's sure how extensive it is, and what, if any, consequences it has for North American caribou.

1 Though sometimes, natural selection traps them in a nasty situation (such as the Irish Elk, whose antlers were simply too big).

Greig, J.C. 1979. Principles of genetic conservation in relation to wildlife management in southern Africa. S. African Journal of Wildlife 9:57-78.
Templeton, A.R. 1986. Coadaptation and outbreeding depression. 105-116 in M.E. Soulé (ed.) Conservation Biology: The Science of Scarcity and Diversity. Sinauer Assoc., Sunderland, MA.