Covering the coverage of the fox genome paper

Ah, the beloved Tame Fox Project! I worked in a lab that focused on these foxes for four years, during my PhD in Kukekova Lab at the University of Illinois at Urbana-Champaign. We worked on analyzing the fox genome for publication throughout those four years, and now at last the fox genome paper is published. (You can see my name tucked neatly in the middle of the authors list.)

What does it mean to have the fox genome sequenced and published? There is a flurry of news reporting about it, and I have issues with a lot of that coverage. I'll be covering the coverage here, letting you know what is accurate and what is less so. I'll update this post as I cover more articles.

Feel free to comment with questions, or with news stories you think should be included here.

• Fox ‘tameness gene’ identified in 60-year study (Independent): the title of this story is irresponsible, implying that there is one gene controlling tameness in these foxes and that that gene was discovered. The story itself does a decent job of untangling the facts: that a large number of genes affect tameness, and that the gene that was discovered influences whether the fox wants to continue to interact with humans during a specific behavioral test. However, I wonder how many people just read the headline and took away a very different message.
• A Soviet-era experiment to tame foxes may help reveal genes behind social behavior (Washington Post, Animalia): Great title, intriguing and also accurate. However, the story itself over-emphasizes the morphological difference in the foxes, stating that the Tame Fox Project "spawned an ongoing area of research into how domestication, based purely on behavioral traits, can result in other changes — like curlier tails and changes to fur color." We still don't know if the morphological changes in the tame foxes (which are much less frequent than most journalists suggest) are related to their behavioral changes, or if they're just a result of founder effect. (The lab that produced the current study is betting on founder effect.) The rest of this article is good, with an excellent description of the study's design.
• Sequenced fox genome hints at genetic basis of behavior (ScienceDaily): "today, with the first-ever publication of the fox genome, scientists will begin to understand the genetic basis of tame and aggressive behaviors" - I think this is overstating. The fox genome is an important tool for working with the genetics of tame foxes, and they are an important model for understanding the genetics of tame behavior. But this isn't the beginning of understanding the genetic basis of tame behavior - either we started that a long time ago, or we haven't really started yet, depending on how you look at it. As with other stories, this story also calls out the finding that there were some changes in aggressive foxes in a region similar to the one associated with Williams syndrome (hyperfriendliness, among other traits) in humans. Which is cool - but don't forget they also found changes in regions associated with autism and schizophrenia, which is also cool! (And which gives more perspective to the fact that a lot of changes were found in a lot of regions, and we don't know what any of them mean yet.) This story has a nice description of the behavioral trait associated with the SorCS1 gene, the one gene that the paper focused on that has changes associated with behavioral differences in tame foxes.
• The first detailed map of red foxes’ DNA may reveal domestication secrets (ScienceNews): wow, I really like this one! Read this one! It does a great job summarizing the paper, it pulls out interesting stuff, and it doesn't ever go overboard in its interpretations.
• Friendly Foxes’ Genes Offer Hints to How Dogs Became Domesticated (New York Times): quite short, so other articles are better bets for you to learn more about the study. However, I want to give a shout-out to this one for 1) not saying anything misleading and 2) explaining that tame foxes aren't great pets - something that can be really valuable to include in stories like this one.

Puppies and Pointing

Why are some dogs better at paying attention to humans, particularly human gestures like pointing, than others? We know genetics has something to do with it, because some breeds (like border collies) are a lot better at responding to human signals than others like beagles. To better understand the biology driving differences in ability to respond to human signals, researchers at the Family Dog Project compared dogs and wolves as they grew up. They knew that wolves can respond to human signals, but that they are better at this when they have been extensively socialized, whereas dogs can understand human signals with much less socialization. But at what age do these differences manifest?

Image from the Family Dog Project

The researchers used a pointing test to measure ability to respond to human signals. This test has been used on dogs before: if a dog is given a choice of two bowls, only one of which contains food, and he can't see where the food is, will he follow a person's pointing gesture to pick the right bowl? (The bowl with no food in it is rubbed with food so the dogs can't use their noses to get the right answer.) This test has been done in the past with dogs versus human children (dogs do about the same as two year old kids on this task), dogs versus wolves (dogs generally outperform wolves, unless the wolves have a whole lot of experience with humans), and dogs versus chimpanzees, our closest primate relatives (dogs outperform chimps!).

For this study, the researchers compared hand-reared (i.e., well socialized) 8-week old dog and wolf puppies; 4 month old dog and wolf puppies; and adult dogs and wolves. They tested the animals' abilities both with "proximal" pointing (putting their finger right up to the bowl) and "distal" pointing (standing farther away and indicating the bowl) - except that, since very young puppies and wolves don't see well, they didn't test the distal pointing in the 8 week old babies. What they found:

• The 8 week old puppies (dogs and wolves) had similar ability to follow the proximal pointing gesture with the researcher's finger right next to the bowl. However, 6 of the 13 wolf puppies tested had to be removed from the trial because they couldn't be held on the start line or didn't go choose a bowl. Of the 9 puppies, only one was removed for similar reasons.
  
• 4 month old dogs did better at distal pointing (with the researcher standing away from the bowl and indicating it) than 4 month old wolves did. In fact, the 4 month old wolves seemed to do no better than chance.
  
• Adult dogs and wolves did equally well with both proximal and distal pointing.
  
• At all three ages, wolves needed more time to establish eye contact with the pointing human than dogs did.

So all the animals at all ages were able to understand a pointing gesture when the human put their hand right up to the bowl. But pointing from farther away was harder, as you'd expect. Very young puppies (dog and wolf) were not tested on that task. At four months, wolves hadn't figured it out yet, but dogs had. As adults, the wolves had caught up. These were highly socialized adult wolves with a great deal of experience with humans.

It's interesting that dogs seem to develop the ability to understand a more difficult human pointing gesture at a younger age than wolves - and particularly interesting that this may have to do with the fact that wolves are not as eager to look us in the eye as dogs are. (If you don't look at someone, it's hard to follow their pointing gesture!)

So what does this mean for differences in different dog breeds? Do different dog breeds have differences in the timing of their cognitive development? Does this affect how much attention they pay to us, and perhaps how easy they are to train? We don't know, but I think this is one direction dog research needs to go.

(By the way, check out the original paper - it's open access, and has some great videos of dog and wolf puppies at the end!)

Gácsi, Márta, et al. "Explaining dog wolf differences in utilizing human pointing gestures: selection for synergistic shifts in the development of some social skills." PLoS One 4.8 (2009): e6584.

This post was originally published with slight modifications at Darwin's Dogs.

Corrigendum on a recent tame fox article

I came across a new article on the Russian tame foxes today, Russian geneticist repeats dog domestication with foxes in just fifty years. It's a nice summary of the Farm Fox Experiment, although I’m not sure why I've seen two stories covering the tame foxes this week — there’s nothing new going on with them! Why two stories in such a short time period?
 

This article does have a few mistakes in it:

 

[Belyaev] and his intern, Lyudmila Trut, wandered around Russia searching for foxes to start their experiment. Foxes were chosen based on their behavior in the presence of humans. Those that showed slightly more tolerance of humans were brought back to their Novosibirsk lab to serve as the start group.

and his intern, Lyudmila Trut, wandered around Russia searching for foxes to start their experiment. Foxes were chosen based on their behavior in the presence of humans. Those that showed slightly more tolerance of humans were brought back to their Novosibirsk lab to serve as the start group.

Read more at: http://phys.org/news/2016-09-russian-geneticist-dog-domestication-foxes.html#jCp

and his intern, Lyudmila Trut, wandered around Russia searching for foxes to start their experiment. Foxes were chosen based on their behavior in the presence of humans. Those that showed slightly more tolerance of humans were brought back to their Novosibirsk lab to serve as the start group.

Read more at: http://phys.org/news/2016-09-russian-geneticist-dog-domestication-foxes.html#j

and his intern, Lyudmila Trut, wandered around Russia searching for foxes to start their experiment. Foxes were chosen based on their behavior in the presence of humans. Those that showed slightly more tolerance of humans were brought back to their Novosibirsk lab to serve as the start group.

Read more at: http://phys.org/news/2016-09-russian-geneticist-dog-domestication-foxes.html#jCp

 

 The original foxes were imported from Canadian fox farms, not chosen from around Russia as this article says. Also, the very first foxes selected for the founding population of the study were not chosen based on their behavior. A control group was kept, so the researchers (of which there are more than two) didn’t want that first set to be more friendly than the average farm fox.

 

[The changes were] not all on the outside—their adrenal glands became more active, resulting in higher levels of serotonin in their brains, which is known to mute aggressive behavior.

 

The tame foxes’ adrenal glands became less active, and secreted less cortisol, a hormone which is associated with stress. Additionally, they have been shown to have higher levels of serotonin in their brains (not secreted by their adrenals, however), which is associated with less aggressive behavior, though I think saying that serotonin “mutes” aggressive behavior might be going a bit far. We don’t fully understand the link between serotonin and aggression.

I do like seeing the Farm Fox Experiment covered in the popular press, though. It’s such a great way of explaining how selection works and such a fascinating demonstration of how quickly selection can have an effect!

And it was not all on the outside—their adrenal glands became more active, resulting in higher levels of serotonin in their brains, which is known to mute aggressive behavior.

Read more at: http://phys.org/news/2016-09-russian-geneticist-dog-domestication-foxes.html#jCpMore importantly, the adrenals don’t control serotonin levels in the brain. They release cortisol into the blood stream. Tame foxes show reduced levels of both cortisol and serotonin compared to control foxes, but those are two different things.

 

Where did dogs come from?

What we know and what we don’t know about dog domestication

Want to learn more about dog domestication? It's not too late to sign up for my online class, From Domestication to Inbreeding!

Dogs evolved from wolves. We’ve been certain of that for several decades by now. But there remain a lot of questions: exactly when did dogs first appear? Did they join their fate with humans when we were hunter-gatherers, or were they attracted to us after the Agricultural Revolution, because we had begun to farm? Which group of ancient wolves did they come from? Knowing more about where dogs began will help us understand modern dogs and their behavior better. Academics are currently conducting a very polite debate about these questions in journals, waged over the course of years.

Grey Wolf

Why is the problem such a hard one? Until recently, the tools that we were using to get information about ancient canids were very limited. Our first tool was archaeology: digging up the remains of ancient canids, trying to figure out if the animal was more dog-like or more wolf-like, and then estimating the age of the find. It’s not entirely straightforward to tell an ancient dog from an ancient wolf using only bones, especially when many archaeological finds are incomplete. The important parts of the skeleton for this work are the teeth and skull: dog muzzles are shorter than wolf muzzles, so that their teeth are more crowded into the available space, and the last premolar and first molar are smaller in dogs than in wolves. Some interesting finds have suggested that dog-like canids first appeared between 15,000-30,0000 years ago — that’s just before agriculture was first developed.

A well publicized 1997 paper from Vilà et al. popularized a new tool for dating dog domestication: analysis of mitochondrial DNA, or mtDNA. Mitochondrial DNA is the DNA inside the mitochochondria in our cells. Mitochondria used to be free-living organisms; they began to live symbiotically in the cells of multi-cellular organisms billions of years ago, but still have their own separate DNA. Mitochondrial DNA gains new mutations at a regular rate, and this can be used as a molecular clock: compare the mtDNA of two different species, and by counting the differences, you can estimate how many years ago the ancestral species split into the two new species.

The problem is that this molecular clock isn’t very reliable or very precise: we don’t really know exactly how fast mtDNA mutates, which makes the clock hard to calibrate. The 1997 findings suggested that dogs and wolves separated about 130,000 years ago — an order of magnitude more than the archaeological estimates suggested! Other mtDNA studies have been conducted since then, with a variety of results, none of them conclusive. It turns out that dog and wolf mtDNA divergence is particularly difficult to analyze because dogs and wolves can and do still interbreed. My golden retriever may not have a wolf in his immediate ancestry, but I suspect you don’t have to go back all that many thousands of years to find one — certainly not all the way back to the domestication split. And there are quite a few populations of dogs in the world with much more recent wolf ancestry than that. This interbreeding really screws up the molecular clock.

In the last few years, though, the revolution in genomic tools — cheap and efficient sequencing of complete genomes — has gotten to the point where it’s affordable to completely sequence the genomes of a number of dogs and wolves for a study. This is significantly changing the kinds of things we can learn about how dogs and wolves genetically differ. Instead of guessing at changes in mtDNA, we can look at the actual genes that differ between the two species. These new studies have set the date of dog domestication at 11,000-32,000 years ago, a date which is similar enough to the archaeological findings to make a lot of sense.

We’ve learned a lot of interesting things from these new sequencing studies beyond just a more precise date of domestication. A little more than a year ago, Axelsson et al. found that dogs make more of an enzyme for digesting starch than wolves do. The enzyme is called amylase, and dogs have multiple copies of the gene, whereas wolves have only one. These researchers wondered if this improved ability to digest starch meant that dogs were domesticated after the appearance of agriculture — if starch digestion was part of the domestication process. However, a study published in January 2014 by Freedman et al. dug deeper into the amylase question and discovered that in fact, not all dogs have extra amylase genes. Some ancient breeds, like the husky, do not. Neither does the dingo. These very recent findings suggest that dogs were in fact domesticated before the Agricultural Revolution, and that some breeds later developed an improved ability to eat what we eat, adapting to their new post-domestication diet. You might imagine that such a change would have been less important to the husky, living in the cold north as it did, where meat was on offer much more often than plants.

Freedman et al. also suggested that dogs didn’t actually evolve from wolves. Wait, what? It's possible that both dogs and wolves evolved from a different ancient canid which doesn’t exist any more. Freedman came to this conclusion using a somewhat complicated genomic analysis which doesn’t tell us anything about what such a canid would have been like, but it’s an idea which resonates with reservations I’ve always had about the “dogs came from wolves” theory. Wolves are so shy, so hesitant to come near humans, and so focused on making their living by hunting. The ancestors of dogs seem more likely to have been scavengers, willing to live close to humans. Maybe some ancient canid did give rise to both species — the one moving closer to human civilization and becoming dogs, the other farther away and becoming wolves. With several studies coming out every year about dog domestication, we may learn more very soon.

For more information, check out “How Much Is That in Dog Years? The Adventof Canine Population Genomics,”a recent open-access review article that provided much of the information in this story.

Note: this story was originally published in the summer 2014 issue of  The APDT Chronicle of the Dog.

Image by Isster17 (Own work) [CC BY-SA 4.0 (http://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

References

Axelsson, Erik, et al. “The genomic signature of dog domestication reveals adaptation to a starch-rich diet.” Nature 495.7441 (2013): 360-364.

Freedman, Adam H., et al. “Genome sequencing highlights the dynamic early history of dogs.” PLoS genetics 10.1 (2014): e1004016.

Larson, Greger, and Daniel G. Bradley. “How Much Is That in Dog Years? The Advent of Canine Population Genomics.” PLoS genetics 10.1 (2014): e1004093.

Vilà, Carles, et al. “Multiple and ancient origins of the domestic dog.” Science 276.5319 (1997): 1687-1689.

Domestication and human evolution, streaming!

Domesticated humans, domesticated canids, domesticated finches! The Center for Academic Training & Research in Anthropogeny held a conference on domestication and human evolution, and live streamed it. I watched live, refusing to speak to my husband or dogs during it, which didn’t go over well. You, however, can watch the archive on YouTube.

The conference was a series of short talks from researchers. These included:

Robert Wayne, “The transformation of wolf to dog: history, traits, and genetics”

Wayne’s lab published a recent genetics paper on exactly where the dog was domesticated, and in this talk he stepped us through their findings. Previous work (and there has been plenty of it) on the location of dog domestication has begun with the assumption that dogs evolved from a population of wolves which still exists basically unchanged, inhabiting the same range now as it did then. Previous work has suggested that this occurred in Asia or the Middle East. Wayne’s group argues that the population of wolves which gave rise to dogs no longer exists, but lived in Europe about 20,000 years ago. It’s a different perspective on a question which is very difficult to answer, because dogs continue to interbreed with wolves so freely that these genetic studies are awfully hard to interpret.

Anna Kukekova, “Fox domestication and the genetics of complex behaviors”

This talk came out of the lab where I work and I got to see my own name on the list of contributors at the end of the talk. Kukekova gave an overview of the history of the fox domestication project, in which lines of foxes were selectively bred for tame temperament or aggressive temperament, and recent research. Our lab digs in to the question of what it is in the genetics of the tame foxes that makes their personalities so different from those of conventional farm foxes. Since this conference was about domestication, and the tame foxes are the best known and longest running domestication study, speakers returned to the foxes throughout their talks. They are a tough nut to crack. Behavior is exceedingly complex mechanistically and we (by which I mean all behavioral geneticists, not just our lab) are still trying to figure out how to get a handle on the genetics that affect it.

Robert Franciscus, “Craniofacial feminization in canine and human evolution”

Craniofacial feminization means that your face is flat, basically. Look at the reconstruction of a Neanderthal face: the chin juts out. Look at a modern human face: flat. Look at a chimpanzee face: jutting chin. Look at a baby chimpanzee: flat. Do humans look like baby chimps? We kind of do. Is there a significance to this? Franciscus argued convincingly that there is, and discussed differences in dog versus wolf muzzle length (and got quite technical about how his group investigated them). We don’t know why this feminization or neotenization (childlike changes) happens in domestication, but it seems to be a recurrent theme. This was the first talk that really grappled with the idea that humans are domesticated, with changes compared to our recent ancestors that parallel changes between dogs and wolves, or between tame and conventional foxes.

Terrence W. Deacon, “The domesticated brain”

Do domesticated animals have smaller brains than their wild counterparts? This is certainly the case in dogs and wolves. Is it the case in humans and our ancestors? Deacon’s group has studied Neanderthal brain size based on their skulls, and they conclude that modern humans do not have clearly smaller brains. He noted that the tame foxes also do not appear to have smaller brains than their conventional counterparts. Why does the difference in brain size show up in only some, but not all, examples of domestication? Is it perhaps not a necessary part of the domestication process?

Phillipp Kaltovich, “Neotenous gene expression in the developing human brain”

It is pretty difficult to study gene expression in human brains, because you have to cut up brains to get your data. Kaltovich did get his data from somewhere, though, and it was really interesting to see his comparisons of gene expression in young versus older brains. The question was whether gene expression changes with age, which helps get at the bigger question, are there gene expression differences in domesticated species compared to their wild counterparts, and are these expression differences similar to the differences in young versus mature animals? In other words, are domesticated species basically enternally young (neotenized)? He did find differences, but his group will have a long way to go to put them together into findings that really illuminate the domestication question. I have a lot of sympathy for how hard this particular approach is, as my research is currently also focused on brain gene expression.

Tecumseh Fitch, “The domestication syndrome and neural crest cells: a unifying hypothesis”

In a recent paper, Fitch’s group put forth the concept of a domestication syndrome, a set of changes associated with domestication: flatter face, behavioral changes, white markings, etc. Subsets of these changes are seen in all domesticated species. Fitch’s group hypothesizes that a particular kind of cell involved in early development is involved in all of these changes. This cell, the neural crest cell, migrates through the growing embryo and develops into many different structures and cell types, including coloration cells (explaining white markings), teeth (explaining dentition changes), and the adrenal medulla (source of adrenaline, explaining behavioral changes). It’s an interesting hypothesis and I’ll be curious to see where this group goes with validating it.

Kazuo Okanoya, “Domestication and vocal behavior in finches”

Okanoya’s group studies a species of domesticated finch and its very closely related wild ancestor. The wild finch has a simple song, while the domesticated species has a quite complicated one. Okanoya’s group investigates the difference in these songs, as a model for the development of complex language in domesticated humans. He played both songs, wild and domesticated, and the difference was dramatic. He linked the changes in the song between species to sexual selection.

Richard Wrangham, “Did Homo sapiens self domesticate?”

The question of self domestication was one of the recurring themes of the conference, and for me this was the most transfixing session. Wrangham studies chimpanzees and bonobos, two closely related species with very different aggression levels, as models of the difference between humans and our more aggressive, non-domesticated ancestors. He defines domestication as the reduction of reactive aggression. Reactive aggression is different from proactive aggression: humans are quite good at controlling our reactive aggression, as we are able to tolerate strangers and live in large groups very well. But we do still show significant proactive aggression, which he described as aggression performed in cold blood, such as armed robbery. Wrangham suggests that a reduction in aggression is the trait evolutionarily selected for in self-domestication, and the other parts of the package (flatter faces, white markings) come along for the ride as associated traits. Self-domestication is often seen in island species, and he gave the example of the red colobus with a neotonous (childlike) island version compared to the mainland population.

The whole conference was really fascinating. It’s available on YouTube now, so go, check it out!

What has cheap genome sequencing done for dog science lately?

So you have the full sequence of a couple few dog genomes, and a wolf genome to boot. (Yes, these days sequencing is cheap enough that genomics researchers can do this. There are more errors in these less expensive, “shallowly sequenced” genomes than the one that we use for the standard canine reference, but even with errors, you can still get the whole genome to play with.) So you have these genomes. And you are curious about domestication. What makes a dog different from a wolf? These genomes each are made up of millions of nucelotides, so when you do a straightforward comparison between dog and wolf, you get hundreds of thousands of differences in nucleotides, ranging from single nucleotides that are different to long stretches where chunks of the genome are repeated in one species but not the other. And what to make of the differences between pairs of dogs — are those important too? It can seem an overwhelming problem.

Luckily, in addition to having fast and cheap access to full genome sequences, we also have powerful computers for analyzing these sequences (and one of my favorite parts of my PhD program is that I get to use my programming skills in addition to my biomedical skills). What people do is think of patterns that suggest that certain areas are the interesting ones, and tell computers to look for those areas. It turns out that if you have a couple of genomes of animals of the same species, you can compare them to find regions where there is very little variation between animals. This suggests that this area is important — everyone has to have exactly the same sequence here, because anyone who has any differences is less fit and less likely to survive to pass on their genes. This is called a selective sweep, because at some point in the past, this change swept through the genome and everyone eventually got the identical copy of this region.

For an added bonus, if you have the ancestral species — in this case I am obviously talking about wolves, which are ancestral to dogs — you can compare this region in that species. If you find that this region is the same in all the dogs but different in the wolves, you have an area which is highly suspicious for being involved in domestication. So you can ask a computer to go find some of these low variation regions for you,

There are a lot of statistical tests that you can do to convince yourself that this area has sufficiently low variation to be interesting, but that area doesn’t, and it has been my pleasure this week to be reading about those in great detail. (Being a grad student rocks, but then sometimes there is statistics.) But the most recent papers I have been reading have pretty much done away with statistical tests to convince themselves that certain areas are involved in domestication. What they have done is to use stats to find areas that are just potentially interesting, and then they actually go look at the areas and see what they see. What known genes are in that area? Anything that could have to do with domestication? Yes? So let’s see how that gene differs in a whole bunch of dogs and wolves. The same in all the dogs, and different from that in all the wolves? Awesome. So what does this gene actually do? Can we understand how the genomic change between dogs and wolves — the mutation — changed the protein? Did it change the protein’s function? Or maybe dogs make more, or less, of that protein. Labs have just been selecting specific genes from these areas and investigating them intensely and seeing what they find out.

The best example of this approach (and the one I find the most interesting, because it was done in dogs, not pigs or chickens like the other papers I have been reading) was published early this year. You have probably heard it if you are interested in dog domestication, because it made a big stir by declaring that dogs had evolved to be better at digesting starch than wolves.

Axelsson E., Ratnakumar A., Arendt M.L., Maqbool K., Webster M.T., Perloski M., Liberg O., Arnemo J.M., Hedhammar Å. & Lindblad-Toh K. (2013). The genomic signature of dog domestication reveals adaptation to a starch-rich diet, Nature, 495 (7441) 360-364. DOI: 10.1038/nature11837

But when you read about this paper, did you know how they figured out that dogs are better at digesting starch? They did one of these low-variation genomic scans. They found some interesting regions. They looked at what genes were in these regions. They found a lot of genes involved in digestion, so they decided to chase that first. (They also found some interesting genes that work in the brain, and hopefully we will see a followup paper on that soon.) They focused on a few genes and tried to figure out what they did and how they had changed between dog and wolf. In at least one case they found that dogs just expressed a lot more of a particular protein than wolves do, and that protein is involved in digesting starch.

There are a lot more regions to look at in dogs, and there are some interesting things to hunt down in tame foxes, too, of course. We are in a fascinating time for genomics. The technology is becoming so inexpensive that we can actually look at the code of genomes belonging to individual animals more more readily than we could just a few years ago, and this is a game-changer. There should be many more discoveries to come soon about the mechanics of canid domestication!

The star coat pattern in foxes: what does it have to do with tameness?

Despite my previous voracious reading about tame foxes, as I settle in to my new lab I’m realizing how much I don’t know about them. For example, one of the most interesting things about the tame foxes is that although they were selected just for behavior (not running away from a human approach), they have physical changes as well, and those changes mimic physical changes between wolves and dogs: the appearance of white patches of coat color, floppy ears, and curly tails. I have learned that this is not an example of white patches related to tameness:

Platinum fox

That is a platinum fox, a color morph unrelated to the white coat markings that seemed to appear with tameness. The white coat markings come from the star gene. So what do we know about the star gene? What do those markings look like?

I started my hunt for information about the star gene in my own reference manager, since I knew I had read about it before. The only paper I had saved about it was from 1981 (!) but it was written by the mastermind of the farm fox project, Dmitri Belyaev, so it seemed like a good enough place to start.

Belyaev D.K. (1981). Inherited activation-inactivation of the star gene in foxes: Its bearing on the problem of domestication., Journal of Heredity, 74 (4) 267-274. URL: http://jhered.oxfordjournals.org/content/72/4/267.short

So back in 1981, when rock music was just starting to get really good, Belyaev was pondering the trickiness of the star gene. At that point, the tame fox project was only 20 years old. In 1969, the first white-spotted fox was born on the tame fox farm, with spots on his head and paws. Other foxes followed. The images from the paper show them looking like this (apologies for the poor image quality — it’s all I have to work with):

Fox kits heterozygous for star allele

This star pattern was not completely new. It had appeared on other fox farms, in foxes that were not selected for tameness. However, it was appearing much more often in foxes on this farm that were selected for tameness. In fact, the three families of foxes that were the most friendly to humans were showing this color pattern the most often. Unselected (not tame) foxes showed this star pattern 1.1% of the time, on multiple farms. (This includes foxes on the experimental farm which were from lines that were not selected for tameness.) Foxes in tame lines showed the pattern 3.7% of the time, or more than three times as often.

By the way, the fox kits shown above have only one copy of the star allele. Animals with both copies of this allele look much more like border collies:

But you can see how the non-white parts of their coats are a dark silver, unlike the platinum fox pictured at the top of this post.

Anyways, the question was: why were the tame foxes showing this pattern more often than conventional foxes? The pattern is particularly intriguing because it looks so much like the patterns we see in coats in domestic dogs, as well as in domestic horses and other domesticated animals. Was it possible that whatever mechanism was making these foxes more friendly to humans was also affecting their coat? The other explanation is just as likely but a lot less interesting: that when foxes were selected for tameness, the ones that were chosen just happened to have more copies of the star allele in their gene pool than average. Inbreeding would then cause this allele to show up more often.

Belyaev looked at family trees of foxes showing this pattern, trying to figure out if the gene for star pattern was recessive or dominant. The genealogy he found was somewhat perplexing. It didn’t follow the structure you'd expect for either a dominant or a recessive trait. The trait appeared to have variable penetrance, meaning that some animals with the star allele showed the star coat pattern, but some didn’t have star patterns, despite having the allele for it. This, of course, begs the question: if you have a group of animals, all of whom have the star allele, why do only some of them actually have the star coat pattern?

There are some possibilities:

• There may be a hormonal difference in the tame foxes which changes the effect of the star allele. In other words, the hormonal soup of a tame fox (less cortisol, less adrenaline) may affect coat color during development, so that those foxes are more likely to express the star allele if they have it. Conversely, the hormonal soup of a conventional fox (more cortisol, more adrenaline) may somehow suppress expression of the white spotting.
• The star allele has been around for a while, but perhaps it appeared in lower numbers in conventional foxes because it was somehow inactivated. Something about breeding for tameness may have activated the gene so that it was not “turned off” as often in tame foxes.

In 1981, no one knew which of these stories was more likely. This was before epigenetics was a hot topic, for one thing. But the nice part about reading historical papers like this one is that sometimes the answers to their questions exist in more recent literature. Which I am going to go hunt down now.

Repost: Learning from Domesticated Foxes

[This was originally a guest post on The Thoughtful Animal.]

Everyone loves reading about the Siberian fox experiment because domesticated silver foxes are so damn cute. There’s something deeply appealing about the idea of a cuddly fox. And the experiment raised some interesting questions about domestication. Could domestication really happen in just eight generations? (Apparently.) Domestication must just affect the brain and not the rest of the body, right? (Apparently not – domesticated foxes can have characteristic coat color changes, floppy ears, and curly tails, similar to morphologic differences between dogs and wolves.) But a research population of domesticated foxes hasn’t been maintained since the sixties just because they are cute. We’re still learning things from them. Like what? Get ready for some well-aged papers; a lot of this work was done back in the eighties.

Hormone and neurotransmitter soup

We use the hormone cortisol as a marker of stress: if you have more cortisol in your blood, you’re probably more stressed. It turns out, perhaps not surprisingly, that domesticated foxes have lower basal levels of cortisol than their unselected counterparts (Oskina, 1992). Their cortisol levels also don’t go up as high during a stressful experience as do the cortisol levels of unselected foxes (Harri, 2003). Personally, I think cortisol is going to play a key role in the mechanism of why domesticated animals are less flighty than wild ones. Cortisol levels influence the production of adrenaline: if you have more cortisol in your system, you are liable to make more adrenaline (Kvetnansky, 2009). If you have more adrenaline in your system, you are going to react more strongly to scary stimuli – in other words, your flight distance is going to increase. (Quick review – domesticated foxes were bred by selection for decreased flight distance from humans.) My friends and I noticed during our highly stressful first year of veterinary school, when our cortisol levels were certainly high, that were were inexplicably jumpy. One friend reported that she was so startled by the noise of a dropped glass that she actually screamed.

As for the ever-popular serotonin, the “happy hormone,” domesticated foxes have more of it in their midbrains and hypothalamuses (Popova, 1991). Yes, the same hypothalamus that is the beginning of the hypothalamic-pituitary-adrenal axis, which ends in the release of cortisol. Oh, and which is inhibited by having more cortisol already in the system, in a negative feedback loop.

There is nothing cuter than a baby domesticated fox

Wolf cubs have a much shorter socialization window than dog puppies, and this might be part of why it is so difficult to socialize a wolf cub to humans. It turns out that unselected fox kits have a shorter socialization window than domesticated fox kits, too. Prime socialization time in both lines seems to start around 30-35 days, when the kits can see and hear and are mobile enough to explore their surroundings. Like most very young animals, fox kits of this age aren’t as fearful as their adult counterparts; they have a chance to learn what is dangerous and what is not in their particular environment. A longer socialization window gives you more chances to learn that a variety of beings are not dangerous to you, but in the wild it also gives you a greater chance of getting eaten by something that is dangerous to you when you wander up to say hello to it.

Domesticated fox kits start showing fear of new objects after age 60-65 days. Unselected kits, on the other hand, start fearing novel things at day 40-45 (Belyaev, 1985). We don’t know what exactly causes this difference in a preprogrammed socialization window, but it’s very helpful to have these populations as we look for the cause.

An even lower level of programming

In recent years, researchers have had new tools to use in exploring the mechanisms of domestication in foxes, especially since the canine genome was sequenced. Comparing gene expression in the wolf and the dog is problematic, because they necessarily live in such different environments. Comparing gene expression in two populations of foxes raised in identical conditions is potentially much more fruitful. This research is in the early days. But as we learn more about the canine genome I think we’ll start finding some really interesting differences between the lines of domesticated and unselected foxes. My personal belief is that we’ll find subtle differences – maybe, rather than differences in actual genes, we’ll see changes in promoter sequences, which cause significant genes to be up or down regulated.

We’ve learned a lot from the Russian domesticated foxes so far, but we have a long way yet to go. We still have no real idea exactly what is at the root of the difference between a domesticated and undomesticated animal. Does the change in development affect cortisol and serotonin levels, or vice versa? Does just a single genetic modification cause all the physiologic changes we see? Or are we looking for a set of modifications? Hopefully the new genomic tools we’re developing will allow us to get to the bottom of the mystery.

References

OSKINA, I., & TINNIKOV, A. (1992). Interaction between cortisol and cortisol-binding protein in silver foxes (Vulpes fulvus) Comparative Biochemistry and Physiology Part A: Physiology, 101 (4), 665-668 DOI: 10.1016/0300-9629(92)90341-M

Harri M., Mononen J., Ahola L., Plyusnina I., Rekila T. Behavioural and physiological differences between silver foxes selected and not selected for domestic behaviour. Animal Welfare. 2003:305-314.

Kvetnansky, R., Sabban, E., & Palkovits, M. (2009). Catecholaminergic Systems in Stress: Structural and Molecular Genetic Approaches Physiological Reviews, 89 (2), 535-606 DOI: 10.1152/physrev.00042.2006

POPOVA, N., VOITENKO, N., KULIKOV, A., & AVGUSTINOVICH, D. (1991). Evidence for the involvement of central serotonin in mechanism of domestication of silver foxes Pharmacology Biochemistry and Behavior, 40 (4), 751-756 DOI: 10.1016/0091-3057(91)90080-L

BELYAEV, D., PLYUSNINA, I., & TRUT, L. (1985). Domestication in the silver fox (Vulpes fulvus Desm): Changes in physiological boundaries of the sensitive period of primary socialization Applied Animal Behaviour Science, 13 (4), 359-370 DOI: 10.1016/0168-1591(85)90015-2

Links post

Animals

• Do Dogs Inherently Understand Pointing Gestures? (The Other End of the Leash): Patricia McConnell weighs in on the ongoing research and debate about the canine ability to follow human pointing gestures, and whether it is genetically mediated/innate.
• Chicken Slaughtering: a day at a mobile poultry processing unit
• Domesticating the Fennec: Dog Domestication 2.0? (Retrieverman)
• Evolution: The Curious Case of Dogs (Observations of a Nerd)
  
  

Meta

• “The current phenomenon of ‘bloggers’ should be of serious concern to scientists” (Terra Sigilata)
• Science Cafes: Nice idea for getting people interested in science. How well does it work?
• The Trouble with Scientists (Speakeasy Science): “Ask yourself... whether young scientists are reward[ed] for spending time on public communication?” It would be awfully nice if, instead of being afraid that my school will notice that I am blogging, I could expect my school to reward me for trying to improve my communication skills. Just saying.

Links post

• Are clicks better markers than words? (The Other End of the Leash): Patricia McConnell gets nerdy about the mechanics of operant conditioning (in this case, animal training).
• Massachusetts Animal Coalition’s Pit Bull Spay/Neuter Task Force: “The task force recognizes that Pit Bulls are the most common breed surrendered to adoption centers and found as strays and that spaying and neutering that is affordable is key to reducing the number of homeless pit bulls in our state.” A constructive approach to the pit bull problem.
•  “Animal connection” helps separate humans from other species (Nobel Intent): Nice post reviewing a journal article about our domestication of various species, with a particular emphasis on how we domesticated dogs. If you want to read more about how humans and dogs developed together, and what the process of canid domestication might have looked like, I recommend reading Dogs: a new understanding of canine origin, behavior, and evolution, by Coppinger and Coppinger.

Domesticating foxes for fun and profit

The Thoughtful Animal has been writing about domesticated foxes and has pointed out that they are commercially available.

Dude! I want one right now! For the low price of $5,950, why not?

Let’s assume the cost isn’t actually an issue. (I want one of these guys badly enough that I would probably find the money somewhere.)

It’s just like a dog, and we know all about taking care of them. It won’t be like owning an exotic animal. It will be like owning an extra cute dog.

Well, it isn’t exactly just like a dog; they aren’t closely related enough to interbreed, for example. One thing vet school has impressed upon me is that species differences jump out at you when you least expect them. We have lived with dogs for a long, long time. In fact, I will hazard a guess that veterinary medicine was practiced on them very early. We know a lot about what makes them tick. We don’t know all that much about foxes.

Well, I live just up the street from a wildlife clinic. They could provide veterinary care.

Actually, in my case, this is true. However, the approach to veterinary care at a wildlife clinic is different from the approach at a small animal veterinary clinic. Ask me again after I have done my wildlife rotation, but I imagine they are not as used in that clinic to the kind of care we expect to give to our pets. For example, I had cardiology specialists caring for my cat when she was in heart failure. They knew all about how cats respond to heart failure (differently from dogs). Cardiologists wouldn’t have the first idea about species differences in foxes, but the wildlife clinicians would be much less skilled at reading a cardiac echo. Neither would be quite able to provide complete care for a pet fox. And the number of foxes a wildlife veterinarian sees a year is much, much smaller than the number of dogs a small animal veterinarian sees a year. It would just not be the same as getting veterinary care for a dog.

My guess is that your local vet would refuse to see the fox at all, with good reason. If you know someone who owns a bird or bunny, ask them how hard it is to find a vet to see one of those animals! And if you can only find one vet who’s even willing, you will have no choice of where you get care.

This will be a young, healthy animal, so I’m not worried about veterinary care.

Are you worried about behavior?

It’s domesticated. That means it’s just like a dog.

In this case, the foxes were “domesticated” by being bred to not be afraid of humans. They weren’t bred to be good house pets, though. They have been maintained as laboratory animals since their strain was developed, living in runs. They won’t bite you. But they may chew up your house, kill your cat, pee inappropriately — actually, a dog will do any of those things. Who knows what else a fox might come up with? We don’t have all the experience with their quirks that we have with dogs.

I’ll take him to a good trainer and make sure none of those things happen.

I’m betting you will have trouble finding a dog obedience class which will allow him in. You will have to shell out for private lessons.

Well, I’ll get him lots of exercise. A tired fox is a good fox.

Who will play with him? Will you take him to the dog park? Will his unusual smell and unusual body language (I’m just guessing here that a different species speaks a slightly different language) make it harder for dogs to accept him? Is it OK with you that he will never see another member of his species for the rest of his life?

And what will you feed him?

Dog food, of course.

There’s a lot of debate over what’s healthy food even for a dog these days. Again, we don’t know as much about foxes. And remember, they are only maintained in the laboratory for a few years, so the researchers don’t have experience with what is healthy for them as they get old. How hard is it to feed an animal right? Well, before we discovered that taurine was a required nutrient for cats, cats which ate commercial cat food tended to go blind as they got older. What might we be missing in a fox’s diet?

We take a lot of things for granted with dogs, and even so, they can be a big commitment. I really, really want a domesticated silver fox. But it is not a good idea for me or anyone else to have one. We have plenty of species of domesticated animals already which make excellent pets about which we know a great deal. We have a much better chance of providing good husbandry for a dog or cat. The foxes make for fascinating research animals, and I am glad that they exist (though I am sad that they have to live in a laboratory in order to be studied). But turning them into pets is not a responsible thing to do.

Links post

• How not to greet a dog. This poster should put posted everywhere. Children should have to learn it with their multiplication tables.
• Blogging in Academia: What Can It Do For You? (The Thoughtful Animal.)
• Whales, Dolphins, and Human Rights
• Guinea Pig domestication (The Thoughtful Animal). It makes me a little sad when the Thoughtful Animal has another excellent post about domestication, because I always intended to blog more about that. But I guess if I’m not going to get off my ass and do it, someone has to. Also, it’s possible his audience is slightly larger than mine.
  

Rats, dogs, foxes, and the SHRP

Working on my Master’s degree has made me yen for more letters after my name, so I’ve been doing some spare-time reading on subjects that might yield PhD-type projects. My putative interest is in development of the stress system in young dogs. The idea is that if a dog’s stress system develops poorly, whether through bad genetics or a bad early environment, then that dog is more likely to bite people when it grows up. The more we know about how their stress system develops, the more we can know about how to grow healthy dogs with good bite inhibition.

For several months I thrashed around in the literature, reading about development of the stress system in rodents (about whom we know quite a bit, because we are more willing to do experiments on them than on dogs), and reading about socialization periods in dogs. It was hard to find good direction, and I wasn’t quite sure where to start. Recently I have had a breakthrough, however.

First, some orientation. You are walking through the woods. You see a shape on the ground. Your brain interprets the shape: long, thin. Your amygdala (part of the limbic system of your brain) yells SCARY SHAPE SCARY SHAPE and you get a blast of adrenaline in your system. Half a second later your cortex (the thinking, conscious part of your brain) catches up: hey, that looks like a snake. Your hypothalamus (which deals with a lot of hormone regulation) sends a message to your pituitary (which releases a lot of your hormones), and the pituitary releases a hormone which travels down to your adrenals, near your kidneys. Your adrenals release our old friend cortisol, which gets into your blood and tells your body that you are having a stressful experience. Cortisol, you of course remember, is what I like to extract from the saliva of dogs to tell if they are unhappy about being stuck in a noisy hospital run. This whole system is what I’ve been referring to as the “stress system,” more properly called the HPA (hypothalamic-pituitary-adrenal) axis.

If you were a rat or mouse, instead of releasing cortisol, your adrenals would release corticosterone. It is a very similar hormone with similar effects. Dogs actually release equal parts cortisol and corticosterone, but we just study their cortisol levels. I still haven’t figured out why we chose cortisol to focus on in them; there are a lot of tools available for studying cortisol, since humans make it primarily, but also a lot for studying corticosterone, since we study rodents quite a bit.

Now, to get back to my recent reading, very young animals don’t get as frightened by scary things as slightly more mature animals or adults. This phenomenon has been studied intensively in the rat: rats younger than two weeks of age don’t show this corticosterone spike when exposed to something upsetting. This is called the “stress hyporesponsive period,” or SHRP.[1] There has been work on what part of the HPA system is responsible for this blunted response: the amygdala? The hypothalamus? The pituitary? Or are the adrenals themselves not responsive yet?

A good way to stress out an infant rat is to expose it to the odor of an adult male rat. Left to their own devices, adult males will happily eat infants, so the young rats are quite right to fear them. An infant rat, upon smelling a strange adult male, will become immobile. However, a neonatal rat younger than 14 days (in other words, one still in the SHRP) will not become immobile: it hasn’t yet developed the machinery to feel, or possibly just to express, fear. If you remove the infant’s adrenals, so that it is unable to make corticosterone, then even when it matures to older than 14 days it will still not properly become immobile when exposed to the scary smell. Moreover, if you inject corticosterone into one of these pre-14 day rats, it will be able to develop the immobility behavior at age 14 days, just like a normal rat. [2] This suggests that corticosterone is responsible for the immobility behavior. However, if you remove the adrenals of a rat which has already developed the immobility behavior (one which is older than 14 days), it will continue to become immobile in the presence of the scary smell. [3] And if you inject extra corticosterone into a rat too young to have developed the immobility behavior, it will develop it early. [4] This suggests that corticosterone is responsible just for the development of the behavior, not for allowing it to actually happen at specific times once it has initially appeared.

What’s going on up in the brain while all this is happening? When infant rats are too young to express (or possibly feel) fear, are their amygdalas just failing to activate? When neurons in a particular brain region have been recently active, they contain a protein called c-fos. You can check a brain region for the prescence of extra c-fos to see if it has been doing anything in the recent past. This was done with young rats. Rats too young to have developed the fear response did not have amygdala activity (no extra amygdala c-fos) after exposure to the scary smell; if they were injected with corticosterone to cause them to develop the fear response early, then they did have amygdala activity; rats old enough to have developed the fear response did have amygdala activity; and rats whose adrenals were removed prior to developing the fear response did not have amygdala activity. [4] Unfortunately, this study does not appear to have looked at whether rats which were allowed to normally develop the fear response (intact adrenals), but then had their adrenals removed after initial development of the response, still showed amygdala activation. Perhaps that question has been answered elsewhere.

So what does all this mean for dogs? Do dogs have an SHRP? I found one unreferenced assertion that they do, but I have not yet found a study actually examining the canine SHRP. The SHRP does exist in various species, and it seems likely to me that it exists in the dog. Puppies start out fearless, and develop fear later. I suspect that a canine SHRP will prove to be an important part of socialization: the time that puppies don’t yet feel fear may be an important one for introducing them to lots of different kinds of people, so that they can learn that these people are a normal part of puppy life and are not to be feared later on.

The development of the HPA system has been studied in domesticated silver foxes — foxes selectively bred to not fear humans. (These foxes show surprising physical similarities to other domesticated animals in body shape and color, despite not having been bred for these features, leading to speculation that there is some general mechanism of domestication. That general mechanism of domestication is actually what I’d like to get at in a PhD project.) Researchers took two groups of foxes: domesticated foxes, and foxes bred for increased aggressiveness to humans. They tested them for behavioral reactions to humans and cortisol level increases after exposure to humans, at ages 30 days, 45 days, and 60 days. The aggressive foxes did not show aggressive behavior or cortisol spikes at 30 days, but they did show it at 45 and 60 days. The domesticated foxes, on the other hand, did not show aggressive behavior until 60 days, and their behavior at that time was described more as “defensive” than “aggressive.” They never showed the cortisol spike. [5]

Is this the same thing as a silver fox SHRP? I’m not sure that this study exactly gets at that, but it seems suggestive. Questions I’d like to ask about the SHRP in dogs are: Does the SHRP definitely exist in dogs? Is the SHRP length different in dogs and wolves? Does the length of the SHRP affect the socialization of the dog? Is the SHRP length different in different dog breeds? And, most important but most difficult to get at, does length of SHRP have anything to do with a dog’s fearfulness as an adult?


[1] Walker Claire-Dominique, Perrin Marilyn, Vale Wylie, Rivier Catherine. Ontogeny of the Stress Response in the Rat: Role of the Pituitary and the Hypothalamus. Endocrinology. 1986;118:1445-1451.

[2] Takahashi L. K., Rubin W. W. Corticosteroid induction of threat-induced behavioral inhibition in preweanling rats. Behavioral neuroscience. 1993;107:860-866.

[3] Takahashi L. Organizing action of corticosterone on the development of behavioral inhibition in the preweanling rat. Developmental Brain Research. 1994;81:121-127.

[4] Moriceau S. Corticosterone controls the developmental emergence of fear and amygdala function to predator odors in infant rat pups. International Journal of Developmental Neuroscience. 2004;22:415-422. [Free full text.]

[5] Plyusnina I., Oskina I., Trut L. An analysis of fear and aggression during early development of behaviour in silver foxes. Applied Animal Behaviour Science. 1991;32:253-268.