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Dog Evolution

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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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Cite: Wang, Guo-dong, et al. “The genomics of selection in dogs and the parallel evolution between dogs and humans.” Nature Communications 4 (2013): 1860.

To the left is a figure which illustrates the phylogenetic inferences from a new paper in Nature Communications, The genomics of selection in dogs and the parallel evolution between dogs and humans (see Carl Zimmer’s coverage in The New York Times). Why is this paper important? The first thing that jumped out at me is that because they’re using whole genomes (~10X coverage) of a selection of dogs and wolves the results aren’t as subject to the bias of using “chips” of polymorphisms discovered in dogs on wolves (see: Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication). The second aspect is that the coalescence of the dog vs. wolf lineage is pushed further back in time than earlier genetic work, by a factor of three. A standard model for the origin of dogs is that they arose in the Middle East ~10,000-15,000 years ago , possibly as part of the broad shift of lifestyles which culminated in the Neolithic Revolution.

This model is now in serious question. Though there have always been claims of fossils of older domestic canids (adduced as such in terms of morphology) than the ones discovered in the Middle East ~15,000 years ago, this year there has been publication of ancient mtDNA results from ~30,000 years before the present which imply the separation of putative domestic and wolf lineages at least to that date. Over the past few years I have wondered about the specific nature of the emergence of both modern humans and modern dogs, and their co-evolutionary trajectory, over the Pleistocene and into the Holocene, in light of these results.


So the preponderance of data (genomic and archaeological) leans me toward accepting the general shape and >15,000 year B.P. date for the divergence of dog and wolf lineages outlined by the authors. But there is a lot more in terms of the phylogenetics of the paper which I am not willing to agree with as so obvious and clear. In particular, the authors support a Chinese/Southeast Asian origin for the dog, rather than a Middle Eastern one. This position is backed up by the reality that the Southeast Asian dog lineages do seem quite genetically diverse, and basal to other dogs (i.e., they diverge first within the clade of domestic dogs). Additionally, in the paper itself they note that the PCA, which visualizes genetic distance, suggests that the East Asian lineages are somewhat shifted toward the wolf. Model based clustering also implies that East Asian lineages are “more wolf.”

The reason I don’t buy this conjecture is as they say in the paper itself modern distributions and relationships don’t always map onto ancient distributions and relationships. We’ve already gotten into trouble doing this for human populations of similar time depth as the new putative period of dog domestication. Ancient DNA has uncovered a great deal of discordance between the past and present. I don’t expect dogs to be any different. The authors have whole genomes of a dozen animals. When the data set is expanded to hundreds with reasonable geographic coverage let’s talk. They attempt to model some gene flow, but I suspect that this is a major problem when talking about regions of origin of a group of organisms whose divergence from the ancestral outgroup is not quite clear in its nature.

Human directed breeding. Credit: Galabwebdesign.

But, a bigger point which has less to do with the zone of origination of the dog is the mode of the origination “event.” In the paper the authors present a stark model of the classic origination event for dogs, where Ice Age hunter-gatherers adopt some puppies, and this population exhibits a sharp and punctuated divergence from the main line of the wolves. These genetic data don’t indicate that at all. Rather, the “bottleneck” as very mild, if you could call it a bottleneck (see: Vulcans through the eye of the bottleneck). Certainly some inbred modern lineages have gone through bottlenecks, but this was long subsequent to the initial separation of dog and wolf. Rather, the authors put forward an alternative hypothesis where dogs were co-existent with early man, with a subset of wolves who were happy to scavenge on the margins of human settlements. There are variations and flavors of this sort of argument, but you can bracket them as the “self domestication” model. The reality here is that I think our explicit differentiation between forms of selection is wrongheaded, the primary issue isn’t whether dogs were self-domesticated or human-domesticated, but the rate of adaptation and demographic history. It may be that the best way to think about the origin of dogs and humans isn’t that the latter domesticated the former, but that both dogs and humans changed together as their lifestyles and interactions changed. With the rise of agriculture and increased specialization of human lifestyles there occurred a concomitant diversification of dogs.

And that is where I think the second part of the paper, focusing on parallel adaptations on the genomic level, is really interesting.

If you don’t want to click the image above, it seems that genes involved in neurological function, metabolism, and cancer are enriched in terms of signals of selection in domestic dogs. This is not surprising. Dogs exhibit great life history differences from wolves (they breed more, and are not pair bonded), and famously may be able to read human faces despite being less intelligent than wolves. And of course dogs have to eat what we eat, at least to some extent.

To understand this functional aspect of the evolutionary history of dogs though one does have to nail the phylogenetics down. So there will no doubt be more coming down the pipeline in this domain, and within the next few years the natural history of man’s best friend will be of deep interest. As ancient DNA has revolutionized the understanding of the human past, I suspect there will be attempts to analyze samples from dogs as well (though I assume that the data sets will always be thinner because scholars have always been preoccupied with human remains).

Citation: Wang, Guo-dong, et al. “The genomics of selection in dogs and the parallel evolution between dogs and humans.” Nature Communications 4 (2013): 1860.

(Republished from Discover/GNXP by permission of author or representative)
 
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Wolf-to-dog transition had little to do with humans, ancient skull suggests. I think the headline here is deceptive. This is the important part:

A Canadian researcher who specializes in the biology of ancient dogs co-authored one of the most significant studies of the year in canine science: a paper detailing the world’s earliest evidence of an animal in transition from wild wolf to domesticated dog.

The “extraordinary preservation” of the creature’s 33,000-year-old skull — found in a cave in southern Siberia — has helped show that dog domestication “was, in most cases, entirely natural” and not really a “human accomplishment,” says B.C. evolutionary biologist Susan Crockford.

She was part of a six-member team of researchers from Russia, Britain, the U.S. and the Netherlands that turned the clock back on wolf-dog transformations by thousands of years and showed that the phenomenon probably happened many times in many places around the globe.


I am leaning toward this direction, because I suspect that hominins were themselves moving in an “inevitable” direction after a few initial contingent stages. The co-evolution between social canids and primates is I think not a random chance event. To some extent I think “man’s best friend” was a necessary outcome of evolutionary forces. Barring the total extermination of one lineage or the other, some sort of cooperative relationship is I suspect something that will naturally reoccur. Dogs are not simply a specific derived lineage of wolves, they’re an ecological niche created by the existence of hominins with social complexity. Humans may not have domesticated wolves per se, but human societies are the ecological niche which a certain subset of wolves naturally adapt themselves to. And, I believe humans are pre-adapted to tolerate, accept, and even extol, the presence of philo-anthropic canids. In some ways they may be a preview for what is to come with intelligent social robots, which will draw upon the same cognitive reflexes.

Image credit: Wikipedia

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Anthropology, Dog Evolution, Dogs 
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The above is a figure from a new paper in PLoS ONE, Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats. Here’s the abstract:

The Black Rat (Rattus rattus) spread out of Asia to become one of the world’s worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.


Since it is open access you can read the paper for the full details. The main result is that it looks like separate and distinction lineages of R. rattus piggybacked on the expansion of humans. The main caveat, admitted in the article, is a reliance on mtDNA and the possibility of admixture and introgression across lineages explaining the current extant variance. The authors refer to paraphyly because it may be that all the descendants of modern black rats, as we understand them, may not be identified as black rats, probably due to their lack of adaptation and coexistence with humans.

Obviously we’ll need to wait for autosomal studies which utilize many more markers. But let’s grant the robustness of this finding: that the modern black rat lineages are a compound of a recent demographic expansion from a small population in western India, as well as long standing deep rooted populations across South and Southeast Asia, which independently entered into coexistence and parasitism with humans. I find this broadly plausible. The reason is not the rat, but the dog.

A new paper just came out which established an East Asian origin for dogs. Or at least for now, as there have been multiple candidates for point of origin. Additionally there are some who argue for evidence of pre-Neolithic domestication or coexistence of dogs and humans. I am beginning to suspect that this hodgepodge of confusing results on the origin of the dog, both in location and period, indicates that in some deep way the wild ancestors of dogs were pre-adapted for coexistence with humans, and it may have occurred multiple times. This is the argument in Mark Derr’s How the Dog Became the Dog: From Wolves to Our Best Friends. My position isn’t that modern dogs aren’t the descendants of a small ancient population which crystallized in the early Neolithic. Rather, it may be that they’re just the last in a long line of dog-human co-socialization experiments.

With the radiation of the hominin clade, and its shift toward more complex social organizational structures, the evolution of parasites like rats and companion species like dogs was inevitable. Out of the set of species which exhibit a potential toward close interaction with humans you have a small number which are ideally pre-adapted. Often this pre-adaptation isn’t a universal feature of a species, but part of the quantitative range of trait value. In other words, there may have been wolves always present which would be more congenial to interaction with hominins, and rats which were optimized for living on the margins and within human settlements. When humans become numerous, these previously neutral or lower frequency morphs became strong targets of natural selection.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Dog Evolution, Evolution, Human Evolution 
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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"