Evolution Basics: New Genes, A New Diet, and Implications for Dog Origins

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April 5, 2013 Tags: Genetics, History of Life

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Evolution Basics: New Genes, A New Diet, and Implications for Dog Origins

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we examine a case of natural selection acting during the early domestication process, and how artificial selection later shaped the dog genome during the creation of breeds.

Is artificial selection a useful analogy for natural selection?

You will recall that Darwin presented examples of artificial selection as evidence that natural selection could produce the same effect on a species: a shift in average characteristics within a population over time. Darwin, of course, had no idea about how heredity worked. Now that we have access to genome sequences, however, we have the opportunity to test the strength of Darwin’s analogy at the molecular level. To do that, however, we need to compare the molecular details of both types of selection events. Interestingly, the dog genome also shows signs of natural selection during the early domestication process, which we can compare to examples of artificial selection.

Meat or potatoes? Natural selection during early dog domestication

The very same study (which we discussed yesterday) that demonstrated significant selection for variation in nervous system genes in dogs during the early domestication process also identified selection on a class of genes involved in starch metabolism. Starch is a long chain of sugar (glucose) molecules strung together that plants use as an energy storage mechanism. Wolves do not eat a diet with high amounts of starch, but do ingest some in the wild fruit they sometimes consume (e.g. berries). In order to benefit from starch, mammals use a class of enzymes called amylases that break the starch chain down into separate glucose molecules. In wolves, amylase is produced in the pancreas. Like wolves, dogs also have a pancreatic amylase enzyme—but instead of having just one gene, all modern dogs have between 2 and 15 copies of this gene, whereas all wolves have only one. The dog copies sit side-by-side in the dog genome, right next to where the original amylase gene is found in wolves, indicating that the gene copies were duplicated during chromosome replication. These extra amylase gene copies greatly increase the amount of amylase enzyme that dogs make compared to wolves, and allow dogs to benefit from a high-starch diet in a way that wolves never could.

This diet, of course, is a distinctly human diet: large-scale use of starchy plants is a feature of human agriculture, which comes on the scene about 10,000 years ago, give or take. The association of dogs with humans at this time thus seems to have provided a selective advantage to dogs that could derive more benefit from the food they were receiving (or scavenging) from human sources. In other words, the environment the dogs were in (access to high starch foods associated with proximity to human settlements) provided the selection: dogs that could derive increased nutritional benefit from starch would be able to reproduce at a greater frequency than dogs that could not. Over time, the average ability of dogs to metabolize starch would improve in the population, as more and more dogs would have duplications. Since no conscious human choice was made to identify dogs with duplicated amylase genes and select them for breeding (since the characteristic would not be readily observable) this is an example of environmental, or natural selection. Even today humans do not have the ability to select dogs for increased starch metabolism, despite the fact that modern dogs remain variable for the number of amylase gene copies they have.

From dog to dachshund: artificial selection for a new gene

Having domesticated wolves into dogs, our selective efforts didn’t stop there, of course: humans used artificial selection to create 400-plus dog breeds, and we can see the effects of this selection on the dog genome when we compare different breeds to one another. One striking example of a difference between breeds is leg length. Some breeds are defined by an unusually short leg without a proportional reduction in body size, such as in basset hounds and dachshunds. This trait, known by the technical term “chondrodysplasia,” is one that was selected for based on its utility for certain hunting roles, such as the pursuit of burrowing animals. The genetic basis of this trait turns out to be another duplication event that happened once within domestic dogs: all short leg breeds share the same genetic innovation.

Note: the molecular details of this duplication event are somewhat more complex than for the simple side-by-side duplications of the amylase gene that we have just discussed. I’ve included the details below for those readers who are interested in digging into the finer points. The take-home message, however, is simple: in this case, a new trait (shortened legs) came into being when a gene was duplicated and the copy acquired new properties during the duplication event. The shortened leg trait was noticed and intentionally selected for by human breeders, making this an example of artificial selection leading to breeds with a specific characteristic. If the details of the duplication event itself are not of interest, feel free to skip down and pick up the story under the “Comparing artificial and natural selection in dogs” heading.

The molecular basis of how this new gene responsible for chondrodysplasia in dogs came to be is very similar to something we have discussed in detail before: the new gene is in effect a processed pseudogene that acquired a function at the time of its duplication. Since the new copy was functional from the beginning, it is not best described as a pseudogene, but rather as a retrogene: the mRNA copy of a gene that was (a) reverse transcribed from mRNA back into DNA, (b) inserted into the genome next to sequences that could direct its expression, and (c) came under selection to maintain it:

The new retrogene turns out to be a copy of the fgf4 gene, an important regulator of growth and development. For reasons that are not yet clear, the fgf4 retrogene interferes with normal bone growth and causes the short leg trait in chondrodysplastic dogs:

Another interesting feature of the new fgf4 retrogene is that its regulatory sequence (shown in yellow in the figure above) is derived from a transposon. As we have discussed before, transposons are autonomous, self-replicating DNA parasites that can, on occasion, become part of the genes of their hosts – and this is another example. The new fgf4 retrogene is “cobbled together” from transposon sequences and the original fgf4 coding sequence and has a new function (attenuating leg growth) not seen in either the original fgf4 gene or the transposon sequence. 

Comparing artificial and natural selection in dogs

While the mutation that led to shortened legs in some dog breeds is a particularly dramatic example of a new variation arising (since it involves the birth of what is effectively a new gene), there were many other genomic regions selected during the creation of dog breeds. Other, more mundane examples abound: the small body size common to the “toy dog” group is determined by selected variation in the Insulin-like growth factor 1 (IGF1) gene; variation in three key genes have been identified as responsible for coat color variation; and even variation in a gene that is responsible for the characteristic skin wrinkling seen in the Shar-Pei has been described. In these cases, it is not the production and selection of duplicated or new genes that is responsible for these traits, but rather small mutations in existing genes that alter the function of those genes compared to the ancestral state in wolves or early dogs. Again, the main theme is clear: small changes in DNA, combined with artificial selection, can add up to large changes in form within a population in a short amount of time.

So, how comparable are natural selection and artificial selection? Both forms of selection have the ability to shift average characteristics of a population over time. Additionally, the molecular underpinnings of the mutation events for both types of selection events are comparable: the trait must arise through a mutation that produces a new heritable variant in the population. Note well: in the case of artificial selection, human intelligence and agency cannot produce the variation needed, but only select for it once it arises. In both cases, we have examples of small sequence mutations, duplications, and even new genes arising. Indeed, the only difference is the selection step—the filter that allows some variants to reproduce preferentially over others.

Human agency might be an efficient form of selection, but so, too, is nature. As such, Darwin’s use of artificial selection as evidence for selection in nature remains a valid approach, even at the molecular level.

In the next post in this series, we’ll explore how natural selection has shaped amylase function in the human lineage as well as in dogs.

For further reading:

Akey, J.M., et al. (2010). Tracking the footprints of artificial selection in the dog genome. PNAS 107; 1160 – 1165. (link)

Axelsson, E., et al. (2013). The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495; 360 – 364. (link)

Parker, H.G., et al. (2009). An Expressed Fgf4 Retrogene Is Associated with Breed-Defining Chondrodysplasia in Domestic Dogs. Science 325: 995 – 998. (link)

 


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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PNG - #78350

April 9th 2013

In the second reference above, almost half of the 3.8 million SNPs were seen only in dogs. This was sort of surprising to me - I would expect that most variants in dogs would also be seen in wolves and would be part of the prior standing variation. Was this because they only sequenced 12 wolves, or is there some other explanation? Any opinion, Dennis, Lou or other knowledgable folks?


melanogaster - #78430

April 12th 2013

Wouldn’t you expect far more to be seen only in dogs, since there has been such strong artificial selection favoring dog variants, particularly after the populations had become largely reproductively isolated?


PNG - #78434

April 12th 2013

I’m no expert on this sort of thing, so I’m only guessing. I would expect that since dogs originated from a pretty sizable group of wolves (I’ve seen 500 quoted as a minimum) that quite a lot of SNPs that would be neutral in both dogs and wolves would be in the dog population. I wouldn’t expect any more than a very small fraction to have been selected for during domestication and breed formation, but, again, that’s the guess of a non-pop gen expert.


melanogaster - #78470

April 12th 2013

“I would expect that since dogs originated from a pretty sizable group of wolves (I’ve seen 500 quoted as a minimum) that quite a lot of SNPs that would be neutral in both dogs and wolves would be in the dog population.”

Absolutely, but most of those SNPs would be linked to traits that aren’t neutral in terms of artificial selection.


PNG - #78471

April 12th 2013

Still, I would think that the variants selected during domestication and breed formation (and the SNPs in their haplotypes) would mostly be variants that were present previously in wolves, albeit at much lower frequencies. (And maybe the latter point is why so many weren’t seen in the 12 wolves sequenced.) The time since domestication doesn’t seem like enough to have produced very many new mutations. I’m generalizing from arguments that I’ve seen about mutations in humans, but I wouldn’t expect dogs to be too much different.


melanogaster - #78500

April 13th 2013

“Still, I would think that the variants selected during domestication and breed formation (and the SNPs in their haplotypes) would mostly be variants that were present previously in wolves, albeit at much lower frequencies.”

Exactly. Lower frequencies or not at all.

“The time since domestication doesn’t seem like enough to have produced very many new mutations.”

Ah, there’s your problem—you’re assuming that those mutant alleles arise de novo. I think your terminology is interfering with understanding. The variation exists; there’s no reason to assume that mutations didn’t occur long before fixation.

“I’m generalizing from arguments that I’ve seen about mutations in humans, but I wouldn’t expect dogs to be too much different.”

Try separating the problem of generating variants, which we know exist, from the problem of selecting among them. The dog population is expanding while the wolf population is contracting and going through bottlenecks. Even if the former wasn’t subject to strong artificial selection, we’d expect it to be more polymorphic than the latter. Mike Behe doesn’t get this.

Semantically, that means thinking about multiple alleles at a given locus (maybe you can’t tell which are mutant and which are wild type), not “producing new mutations.”


beaglelady - #78442

April 12th 2013

I’m really enjoying this series of posts, particularly the ones about dogs. Every year I volunteer as a beagle rescue representative at Meet the Breeds at the Javits Center in NYC.  “Meet the Breeds” is an expo showcasing the hundreds of dog and cat breeds.  It’s astounding to see in one place the tremendous variation in the dog breeds.   It isn’t just about physical differences, as astounding as they are; there are also differences in temperament and instinct.  

Although there is some variation in the different cat breeds,  it doesn’t begin to compare with that in dog breeds, and I’ve always wondered why that is.  Could it be that we haven’t been selectively breeding them as long? Or perhaps because they are not so trainable?  Or maybe it’s a combo of factors.


PNG - #78444

April 12th 2013

You might like this article. It compares dog and cat domestication and argues that cats are in most ways less domesticated than dogs. It’s freely available.

From wild animals to domestic pets, an evolutionary view of domestication http://www.pnas.org/content/106/suppl.1/9971.full

“The domestication of cats took a different trajectory. Wildcats are improbable candidates for domestication (see Table 3). Like all felids, wildcats are obligate carnivores, meaning they have a limited metabolic ability to digest anything except proteins (33). Cats live a solitary existence and defend exclusive territories (making them more attached to places than to people). Furthermore, cats do not perform directed tasks and their actual utility is debatable, even as mousers (34). [In this latter role, terrier dogs and the ferret (a domesticated polecat) are more suitable.] Accordingly, there is little reason to believe an early agricultural community would have actively sought out and selected the wildcat as a house pet. Rather, the best inference is that wildcats exploiting human environments were simply tolerated by people and, over time and space, they gradually diverged from their “wild” relatives (3536). Thus, whereas adaptation in barnyard animals and dogs to human dominion was largely driven by artificial selection, the original domestic cat was a product of natural selection.”


PNG - #78445

April 12th 2013

Another quote from the article. Love the characterization of cats as “delightful profiteers.”

“However, the most noticeable adaptation is the cat’s overwhelming tolerance of people, a key attribute of any domesticated animal, but certainly the primary feature that has made cats the delightful and flourishing profiteers in our homes that they are.”


beaglelady - #78456

April 12th 2013

Thanks for that, PNG! 


beaglelady - #78542

April 15th 2013

Now, horses make an interesting case.  A hallmark of domestication is genetic change, but horses seem to have underdone little change after domestication, at least morphologically.    (I’m not talking about  mustangs, which are really feral horses)  I saw some skulls showing animals before and after domestication.  Boar compared to pig was dramatically different. Wolf to dog was dramatically different.  And horses? Not different at all, at least to my untrained eye.  I understand that it’s difficult even for scientists to tell whether specimens they unearth are domestic or wild—other clues are often needed.  Behaviorally, horses are often unpredictable and spook easily.


lancelot10 - #78623

April 17th 2013

Again confusing breeding with evolution.  Evolution is a hypothesis which says that a species can evolve over time into another species eg a pig become a whale or a mouse or flying monkey becomes a bird.   The evidence is that this has never happened or is happening now.   The dog family is still a dog family - they wont fly or take to the sea.

Artificial selection should lower the time scale if evolution was proven - so take the most expert dog breeders in the world and ask them to use intelligent selection to change a deer into a sea creature over the generations - then after 12 billion years we will still have deers - maybe funny looking ones - but with none of the apparatus that would enable them to survive in the sea as say a dolphin.

The evidence that evolutionists conjure up is pure fantasy and a priori evidence that assumes evolution to be fact.


lancelot10 - #78667

April 18th 2013

Dennis - just as an aside - I was an extra vit C fan having read linus pauling whose theories were based on evolution - ie we had lost a gene so could get scurvy and we needed far more than the 100mg a day to bring us up to the standard of animals that could generate weight for human weight about 10-15 grams a day to fight off an illness.

I would take enormous doses for colds etc and convinced myself it worked - even though I got many colds - now I dont take any extra above a reasonable diet and never get colds or illness.  I remember Jesus saying do not worry what you eat or drink but I could not let go in faith thinking that the creator of the universe maybe forgot about vit C.

These doses were acidifying my body -unlike other creatures which were PH neutral in making their own vit c internally - and it led to a short temper I now realise since PH is so important to mental wellbeing.  This is probably why fasting is so good for prayer - the PH will eventually stabilise and calm our spirit.

Why God did not give us the gene for Vit C is known only to Him but there will be a reason.     Loads of vitamins and (so called) health foods are making provision for the body - the flesh - and paul spoke “I make no provision for the body”   .

 


lancelot10 - #78670

April 18th 2013

Sorry the “missing”  vitamin C gene was for Michael’s post not Dennis’s post.


Michael Buratovich - #80132

May 15th 2013

Lance - here’s a point upon which we truly differ.  It seems to me that if our genome has the remnants of the GLO gene, then it stands to reason that our ancestors had a functional GLO gene at one time and were able to synthesize their own ascorbate.  Because our ancestors ate copious quantitied of ascorbate-rich fruit, the selection for a functional ascobate biosynthetic pathway was relaxed and inactivating mutations in the GLO gene were not selected against.  The fact that chimpanzees have exactly the same inactivating mutations in their GLO genes seems to me, at least, to strongly argue for shared ancestry between our two species.  

Why God did not give us the gene for Vit C is known only to Him but there will be a reason.”  Yes, I would like to have a functional GLO gene, but the fact is, I don’t.  God’s grace is suficient for me, without without a functional GLO gene.  

Yes, I’m with you on hyperloading vitamin C.  Too much vitamin C does you not good and produces a lot of its breakdown product, oxalate, which is highly insoluble and can cause nasty calcium oxalate kidney stones.  I take 500 mgs every other day and I’m sure that’s more than enough (I sweat a lot so I probably lose a lot of it that way).  


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