Starch gave canine evolution something to chew on

A dog’s dinner can be scraps from the table, a juicy bone or an incredibly unlucky piece of homework.  This omnivory has been present since their domestication around 15,000 years ago, just before humans developed agriculture.  Indeed, it appears that evolving the ability to break down starch (a large, complex molecule) into glucose (much simpler and easier to digest) was a key step in the speciation of dogs from wolves.  So what is the genetic basis of this varied appetite?  And was the evolution of broader gastronomic horizons the cause of domestication, or a consequence of it?

Dogs diverged from wolves roughly 15,000 years ago
(Creative Commons – Author: Dennis Matheson)

These are the questions that Axelsson and colleagues set out to answer.  They sequenced the genomes of 60 dogs from 14 different breeds, as well as 12 wolves to use as a measure of the ancestral state of dogs before their domestication.  Once the sequencing was complete, they pooled all of the dog genomes to make one genome representative of canine diversity (this was done to counter the effects that selective breeding may have had on particular dog breeds).  They then looked for regions in the dog genome that had low diversity (indicative of the action of selection at these sites), and high divergence from wolves (suggestive of a role in dog speciation).

They found 36 regions that had both low diversity and high divergence.  In these 36 regions were a total of 122 genes, 10 of which were involved in digestion.  This gave the authors 10 candidate genes, some or all of which could have driven the adaptation to starch digestion in early dogs.  They found evidence for selection on three: AMY2B, MGAM and SGLT1.

AMY2B is an amylase that breaks down starch into maltose.  Intriguingly, the number of sequencing reads mapping to this gene in dogs was far higher than in wolves, suggestive of a duplication of this gene in dogs (two copies would be expected to double the number of reads, four copies would quadruple it, and so on).  Investigating this further using qPCR (which quantifies the level of expression of a gene in RNA, or the number of copies of a gene in genomic DNA), the authors found between 2 and 15 copies of AMY2B in different dog breeds.  And when they measured AMY2B expression and the ratio of starch to maltose in the blood (a proxy for AMY2B activity), both were 5-20 times higher in dogs than wolves.  AMY2B duplicates have clearly been retained by selection, and this increase in AMY2B copy number is correlated with increased starch digestion.  However, what is not clear is how many of these different copies are contributing to starch digestion in each breed.  There could be slightly elevated expression of each copy, or one or two copies could have massively increased expression; both situations would lead to the increase in overall amylase levels seen by the authors.

Starch was an abundant food source, making the ability to digest it selectively advantageous in early dogs (Creative Commons – Author: Antony Stanley)

Intriguingly, duplication has also been documented in human amylase.  At some point after humans diverged from mice, amylase (which is usually expressed only in the pancreas) duplicated to produce two copies.  One of these copies remained pancreas-specific, while the other specialized to be expressed only in the saliva (Meisler & Ting, 1993).  It would be fascinating to know whether a similar situation of duplication and specialization has occurred in these dog amylases.

The next gene showing evidence of selection was maltase-glucoamylase (MGAM), which breaks down maltose into glucose.  The authors sequenced MGAM in an additional 71 dogs from 38 breeds, and found that 68 of these dogs carried the same allele (gene form).  They also found that expression of MGAM was 12 times higher in dogs than wolves.  That this allele has been preserved in such a large proportion of dog breeds is powerful evidence for its importance in starch digestion.

The final gene implicated in the evolution of starch digestion was SGLT1, which helps transport glucose across the gut wall into the blood.  Again, the authors looked at the sequence of SGLT1 in 71 dogs, and found a high level of divergence from wolves.  However, the evidence for selection on this gene is weaker than the other two for a couple of reasons: firstly, their sequencing covered only one end of the gene, not its entire length; and secondly, they found no difference in expression of SGLT1 in dogs and wolves.

There is one caveat to the expression studies carried out for all three genes, about which the authors are admirably candid:

‘we cannot rule out that diet-induced plasticity contributed to this difference”

In other words, it may have been that they happened to compare some particularly well-fed dogs with some very hungry wolves, and that this caused much of the difference in their levels of gene expression and their maltose:glucose ratio.  But in my opinion, given the strong evidence for selection at AMY2B and MGAM, and the difficulty in standardizing diets across all individuals measured (would you want to tell a wolf what to eat?), this weakness is not fatal to their argument.

Changes in AMY2B and MGAM were selected for during dog domestication (Creative Commons - Author: Steve Guttman)

Changes in AMY2B and MGAM were selected for during dog domestication (Creative Commons – Author: Steve Guttman)

So it appears that selection has acted on multiple stages in the starch digestion pathway.  Fascinatingly, this selection has taken different forms: at the starch-maltose stage (AMY2B) gene duplicates have been selectively retained; whereas at the maltose-glucose stage (MGAM) there have been changes in the sequence and expression of a single gene.

However, one mystery remains: did this selection on starch digestion happen before dogs were domesticated (wolves scavenging at waste dumps), or after their initial domestication (guard/hunting dogs fed starchy waste)?  Perhaps a better question is: does it matter which came first?  A far more interesting issue is how dogs adapted to this new food source, and Axelsson et al have provided a convincing exploration of the genetic basis of this adaptation.

References

Axelsson, E. et al (2013) The genomic signature of dog domestication reveals adaptation to a starch-rich diet.  Nature advance online publication

Meisler, M.H. and Ting, C-N (1993) The remarkable evolutionary history of the human amylase genes.  Critical Reviews in Oral Biology & Medicine 4: 503-509

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