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Dog domestication

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Citation: Freedman, Adam H., et al. "Genome sequencing highlights the dynamic early history of dogs." PLoS Genetics 10.1 (2014): e1004016.

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

The more we scratch beneath the surface with powerful genomic techniques, the more we see that natural history which we had presumed to have a crisp understanding of is quite a bit more muddled. Once the muddle clears what we’ll gain is the gift of accurate complexity, but in many areas right now there is little such clarity. It is a truth that a new discovery or inference does not mean that there are enough points in space to construct a new explanatory constellation when the old does not suffice. Due to the biomedical focus of modern genomics there has been a disproportionate focus on humans, but over time it is clear that this will expand out across the tree of life, and the light shall give way to a temporary fog. First up are organisms of particular human interest and/or model organisms (the latter are species which are useful for elucidating general biological phenomena, and the subjects of study of a large community of researchers). Domestic dogs have the virtue of falling into both categories.

220px-Benny-Basenji

Red Basenji

There are many theories about the origins of our “best friend.” One school of thought (though not necessarily dominant) is that dogs are relatively recent obligate companions of humanity, part of the toolkit of the Neolithic revolution. To be fair this view was rejected by many researchers on the common sense grounds that dogs arrived with the Amerindians 10,000-15,000 years ago. These were clearly hunter-gatherer populations which predated the Neolithic. But there were some genomic research which did imply that even if there were early domestication events, the preponderance of modern domestic dog ancestry dated to the Middle East ~10,000 years before the present. The newest work in genomics seems to falsify that hypothesis rather robustly. These researchers have shown how looking closely and thoroughly at whole genomes (billions of base pairs) organisms, as opposed to a subset of polymorphisms (on the order of tens or hundreds of thousands of base pairs), can yield deeper historical insight.

A new paper out in PLOS GENETICS, Genome Sequencing Highlights the Dynamic Early History of Dogs, has been out as a preprint for a while now, but it seems useful to review what it highlights we now know, and don’t know. As illustrated by the figure above a key element of the revised natural history of the domestic dog must include a minimal level of complexity in the phylogenetic origins of the species. A caricature of the simplest story about the origin of the dog is that it is a tamed wolf. Highly derived from the ancestral state (many characteristics have shifted from the last common ancestor with wolves), but a wolf nonetheless. This idea needs updating because the work in the paper above highlights that extant wolves are not perfect representatives of Pleistocene wolf populations, from which dogs derive. This was already clear with some ancient DNA, but looking at whole genomes of three wolves from disparate regions of Eurasia, a West African Basenji, and an Australian Dingo (along with the Boxer as a reference domestic dog genome and a Golden Jack as an outgroup), a major finding seems to be that modern dogs derive from a population of wolves which are not represented in the populations sampled above. This is important because many inferences about dogs are made simply by assuming that modern wolves are appropriate proxies for the last common ancestor of both lineages.

This substitution seems to be rather shakier than we’d have thought, and this comes to play most obviously in the genetic diversity and bottleneck results we’d take for granted. If modern wolves are the standard for the ancestral population from which dogs derive then the bottleneck is a relatively mild one of a few fold drop in size (wolves are more diverse, but not that much more diverse). But what the authors above found by looking at patterns of genetic diversity across the whole genomes of these wolves is that all three, sampled from Croatia, Israel, and China, also exhibit evidence of a population bottleneck. This makes more sense of the result that it looks as if modern dog lineages underwent a population bottleneck on the order of one magnitude (16 fold). The timing using different methods also definitely predates the Neolithic revolution ~10,000 years ago, and so aligns with the archaeological evidence. Wolves were the companions of hunter-gatherers first before they were associated with farmers. Any possible adaptation of dogs to a starchy diet occurred after the initial bottleneck and separation of the ancestors of this lineage from the ancestors of modern wolves (who seem to have enough variation to have had this trait as part of the ancestral range of the trait in any case). Additionally, there are dog lineages, such as the Dingo, which don’t exhibit any adaptation to starch diets, which makes historical sense as they did not coexist with agricultural populations until recently.

I do want to caution that genomics does not change everything. Many of the broad outlines of what was known before with classical genetic techniques, comparative anatomy, and paleontology, do hold up. For example the domestic dogs do seem to form a monophyletic lineage. By this one simply means that domestic dogs the world over seem to share a small set of common ancestors, rather than being instances of convergent morphological evolution from disparate wolf lineages. What is more surprising though is that these results imply reciprocal monophyly with wolves. This means that domestic dogs are not a specialized branch of a particular population of modern wolves, but a sister lineage to contemporary wolves. Though it is common to say that a dog is just a tamed wolf, one might as easily state that a wolf is a wild dog (yes, I will grant that the dog is likely more derived, but I don’t think we can just substitute modern wolves for ancient ones and call it good). Both are subsets of a wider range of canid ancestors which flourished in the Pleistocene. The tests of admixture of particular lineages suggest that the origins of dogs seem to suggest gene flow with local wolf lineages. This would confound attempts to ascertain a particular zone of domestication or adaptation, as prior genetic affinities or clines in diversity may be due to gene flow rather than patterns of descent (earlier attempts to assert that domestic dogs derive from the Middle East or China may be premised on false assumptions, as well as limitations of less dense marker sets than whole genomes).

The main drawback of this study is obviously the limited sample size. It is freely acknowledged in the paper, but that is why the authors also attempted to select individuals from populations which were highly informative, both geographically and culturally (e.g., Dingoes are outside the range of the wolf, and, not coexistent with ancient agricultural populations). I am more skeptical about assuming that the wolf samples are representative than I am about their selection of three dog lineages (Basenji, Dingo, and the Boxer reference). We know a lot more about the genetics and history of dogs than we do about wolves, and it seems more likely that there are going to be more surprising loose ends in the case of the latter than the former. But if I had to bet I’d say the authors are right, and their inferences are going to hold up (reciprocal monophyly, the bottleneck in wolves, etc.). Yet there’s no doubt going to be a lot of detail added to this model as the sample sizes increase, and ancient DNA is is included in the analysis. Though recent studies seem to establish rather clearly that domestication was a function of the later Pleistocene (and not the Holocene) in the case of dogs, the exact details of where, when, an who, are still quite woolly.

But the ultimate big picture is emphasized by the title above: the Pleistocene is going to seem like a strange country after all is said and done. Many of the organisms which are going to be sequenced in great depth (high coverage) and large sample sizes first are mammals of Palearctic origin which were shaped by the Pleistocene. The importance of this geological period for humans has long been a subject of scholarly attention, but genomics and the light it sheds upon quirks of natural history, might emphasize the ecology-wide reshaping role that Ice Ages had upon the natural history of so many familiar and charismatic species. This is where genomics will open the door to evolutionary ecology of grand scope.

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

Related: Please see a post from one of the authors at Haldane’s Sieve.

 
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Credit: PartnerHund

It’s an exciting time for those interested in the evolutionary genomics of the dog. In 2010 a big SNP-array paper came out, Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Today we’re going whole genome, which is important because many of the SNP-arrays are ascertained on domestic dogs (i.e., they are designed to pick up dog variation, and so may distort our perception of the variation in wolves). Recently I talked about an analysis of the evolutionary genomics of the dog, The genomics of selection in dogs and the parallel evolution between dogs and humans. The main interesting result of that group was to push the divergence of the dog and wolf lineages further back in time, ~30,000 years, in line with some archaeological and mtDNA finds. I did not find their arguments for the origin of the dog in East Asian convincing. Now a new preprint on arXiv, Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs, pushes this even further.

First, after reading the paper I recommend the comments at Haldane’s Sieve, where the authors engage in some back and forth. Second, one of the authors put the supplementary information on a Dropbox, so you can get that too. I highly recommend this in particular, because it has detailed methods, code, and also concise but useful explanation of concepts such as D-statistics. Overall the paper breaks down into two broad themes, the phylogenetics and analysis of adaptation and selection. There was many X coverage of an Israeli, Croatian, and Chinese wolf, and a Basenji, Boxer, and Dingo. For the primary analysis the sample sizes were N = 1, but that is not a major issue as they had extremely accurate and precise estimates as to the polymorphism across these individuals because of the repeated coerage.

A major takeaway in terms of demographics for this paper is that it’s complicated. The authors inferred that domestic dogs went through a population bottleneck in the past on the order of one to two magnitudes. Second, wolves also went through a population bottleneck, albeit milder. On the first read through I was surprised by the second finding, but after talking to a canine geneticist I was told that this wolf bottleneck had long been known. The genomics confirmed prior expectations rather than smoking out novel inferences.

Perhaps a more surprising finding is that the ancestor of dogs, and yes, there was one ancestral population, not many, derives from an extinct wolf lineage. Their inference was derived from the fact that the three wolves, sampled from putative regions of dog domestication, all exhibit equal genetic distance from the dogs. Previous work had suggested that dogs may have derived from Near Eastern wolves, while other researchers argued for an East Asian origin. The results here support the proposition that these suggestions are misinterpreting genuine gene flow between local populations of wolves and dogs. The authors detected gene flow between West Eurasian wolves and the western dogs (Basenji and Boxer) and East Eurasian wolves and eastern dogs (the Dingo).

On a minor note, these results also confirm a pre-agricultural origin for the dog, with a divergence of ~11-16 thousand years B.P. across the 95% confidence interval. This is at some discrepancy with the Chinese group, but this may just be an artifact of a different mutation rate parameter. The take home either way is that dogs pre-date agriculture.

But that doesn’t mean agriculture is irrelevant. As far as the adaptation goes there’s a lot here, and I’m not sure that this paper has anything revolutionary in that dimension. First, they confirm that just as in humans there is variation among canids in terms of copy number in the amylase gene conditional on lifestyle. Dingos and Alaskan huskies have very few copies, while ancient West Asian dogs have many. Also, the authors find normal variation in wolves for this trait, implying that amylase polymorphism is part of standing genetic variations.

I will leave it to you to survey the veritable alphabet soup of genes which have been buffeted by natural selection by evolutionary process when it comes to dogs. I’m more curious about variation within dog at this point, as there should be heritable variation there too.

Cite: arXiv:1305.7390v2 [q-bio.GN]

(Republished from Discover/GNXP by permission of author or representative)
 
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Since John Hawks already hit it I don’t have much to add about the dog-starch-adaptation-paper in Nature, The genomic signature of dog domestication reveals adaptation to a starch-rich diet. I’m impressed at the yield from the sample sizes that they had, but as John alludes to this area of study has huge possibilities. The authors suggest that agriculture catalyzed domestication. That’s fair enough, and carefully stated I’d say, because the Amerindians seem to have brought domestic dogs to the New World long before agriculture. In other words, the “domestication” event was probably a multi-layered affair. Looking through the supporting information it’s obvious that the domestics were almost all Western breeds. As the search for adaptive variants expands to other lineages we might be in for surprises in terms of the signatures of selection as they vary across the dogs.

Which brings me to humans. After all the variation in digestive abilities also applies to humans, and there’s a fair amount of evidence of recent human adaptation driven by agriculture. Is Paleolithic man to Holocene man what the wolf is to the dog? Evolutionary psychologists have long spoken of the “Paleolithic mind,” but what if the Holocene indeed has witnessed a major evolutionary change in our species? To go back to the dog analogy, imagine that wolves were extinct, and inferences were made about them based on what we know of the dog. How accurate would those inferences be? George Church might be disavowing the project of resurrecting Neandertals, but the reality is that bringing one of them back would be an incredible test of the inferences that are the bread & butter of the paleoanthropological enterprise.

Image credit: Wikimedia

(Republished from Discover/GNXP by permission of author or representative)
 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"