The four million year odyssey of the horse

Gene ExpressionBy Razib KhanJun 29, 2013 4:31 AM


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Credit: Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Credit: Ealgdyth The horse is a beautiful animal.* That is not a trivial matter, but there is the added fact that historically it is has been of great consequence. Obviously the rise of horses as vehicles of war is preeminent in our minds, but on a more prosaic level draft horses revolutionized many societies via their effect on agricultural productivity. Dogs may be man's best friend, but horses are arguably** man's most useful friend. Or at least they were. The critical importance of the horse is probably lost on modern people, but until the rise of the automobile they were ubiquitous in many large cities (this is clear when you view early films). Today horses are perceived to be luxurious playthings (ergo, the term "horse country"), but during the heyday of the horse-powered world they served the roles of tractors, tanks, automobiles, and telegraphs. These are just some of the reasons that horse genomics may be of more than passing curiosity for those who are not to the manor born. Horses are part of our history, and as a large charismatic mammal there is a particular interest in the origins of this lineage. This is part of the reason that a new paper in Nature is important, Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. But this is not the only reason that this paper is of worthy note. It extends the time frame of ancient DNA sequencing back by an order of magnitude, from ~50,000 years before the present to ~500,000 years before the present. Obviously that is a big leap, though it is not surprising that these DNA were retrieved from remains in Canada's Yukon. Often mammalian ancient DNA breakthroughs, which entail the destruction of fossils, presage prehistoric analysis of our own lineage. But I am not quite sure that that will necessarily happen here (with the caveat that there is going to be a lot of ancient human DNA publication of more recent vintage over the next few years), as the expansion of Homo into the far north truly reached an extensive scope only with our particular lineage of sapiens sapiens.*** Nevertheless, this publication no doubt solidifies the new era in phylogenetics, where inferences of trees can be calibrated and checked against long extinct nodes and branches which had heretofore only been posited. So what did they find in this paper that was worth noting? First, we have to note that their coverage on the ancient sample was not particularly high. Only about one per site. That means that there's going to be a lot of noise in the system, but with the number of markers they have that's not as much of an issue for phylogenetic inference of population history. It does concern me more when the authors are focusing on functional regions and possible differences between the ancient sample and modern lineages. In any case, as you can see from the tree above, Przewalski's horse is an outgroup to all modern domestic horse lineages. That is not so novel a result, as domestic horses probably derive from the West Eurasian steppe, while Przewalski's_horse are localized around Mongolia. Perhaps more surprising there is no sign of admixture of domestic and Przewalski's horse in the genomes of the latter. Using the Yukon sample as a calibration, the authors estimate that the divergence between domestic horses and the wild Mongolian lineage occurred on a population wide scale ~40,000 years before the present. Some quick back of the envelope calculations suggest to me that that's about equivalent to ~150,000 humans years correcting for generation time, in the same range as the separation of Bushmen from other populations. Also, I might mention that there is a karyotype difference between Przewalski's and domestic horses (though they are inter-fertile), and apparently strong behavioral divergences. The latter is to be expected, as horses have been subject to very powerful selection on a range of phenotypes (how many animals would let another animal habitually ride them?), with skewed reproductive values between the sexes (i.e., one stallion siring many offspring) driving the dynamic. Finally, the authors note that Przewalski's_horse has relatively high genetic diversity despite a breeding bottleneck of ~15 (there are now >1,000 of them). Actually the original breeding program consciously crossed unrelated individuals, so this is confirmation of expectation. Again, this illustrates that bottlenecks in census size need not be catastrophic. I will forgo extensive discussion of possible selection events in domestic horses, using the ancient Yukon sample as an outgroup, because it seems that Przewalski's more than suffices for that. Rather, an interesting result here is that the authors push back the period of the emergence of the horse to ~4 million years, rather than ~2 million. It is implied that the horse mutation rate may be different from the human mutation rate. As you likely know, there are actually controversies about the nature of the human mutation rate and the viability of various clock estimates. With a paleontological peg the Yukon sample obviously serves as an excellent data point for purposes of calibration. Without getting into the technical guts the fact that it's so ancient, and not that far from the older putative age for the origin of the horse, means that I have rather good confidence that the results here will stand the test of time. There's no point in me commenting on the technological wizardry that went into extracting and sequencing such degraded DNA. But much of the legwork in that domain is nevertheless truly impressive to me. The fact that they managed to get that much information out of >500,000 year old DNA is incredible when you consider that less than a generation ago sequencing one individual was perceived to be a herculean task! Citation:Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse * Also, frankly, somewhat stupid. I worked on a mule farm when I was an adolescent and the dull quiescent nature of horses in comparison to the irascible and cunning donkey was always a stark contrast. ** I say arguably because one can make the case that cattle or pig and such are of greater utility as domesticated animals. But an argument can nevertheless be had on all sides. *** I am aware that archaic H. sapiens such as Neandertals were a northern subspecies, but in actuality their distribution was far more circumscribed than that of our own earliest forebears.

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