Until last month, the most ancient whole genome ever sequenced from the DNA residues extracted from fossilized bone was from a polar bear. Continuously frozen in ice for about 120,000 years on Svalbard Island, Norway, this polar bear jaw helped clarify the ancient separation and recent mixing of brown bear and polar bear lineages. The most ancient human genome is widely but incorrectly reported to be an 80,000 year old Denisovan. Levels 11 and 11.1 in the Denisova cave have been radiocarbon dated to about 41,000-43,000 years of age. They have yielded four specimens – a Neanderthal toe, two Denisovan molars and a Denisovan distal phalanx – each of which has yielded a full archaic genome sequence. Preservation conditions at Denisova were thought to be almost ideal, combining annual mean temperatures near freezing with dry burial in protected cave sediments.
In contrast, the horse forelimb from Thistle Creek in the Yukon was deposited in open soil and stored between permafrost layers for more than half a million years. The remains were associated with a volcanic ash deposition reliably dated to about 735,000 years ago. The soil appears to have thawed substantially during an interglacial warming, followed by re-freezing. The endogenous DNA content of the Thistle Creek bone was only about 5% of that in Denisovan specimens, and the genome coverage was only 1.12X with an average single strand read length of about 77 base pairs. Since the majority of fossils do not spend most or any of their lifetimes under subfreezing or dehydrating conditions, obtaining more ancient genomic information will be difficult.
What genomics tells us about the horse is just as fascinating as what it tells us about humans. The ancestral horse coat color is the brownish bay/dun color that can be seen in modern-day Przewalski’s horses. This coloration is adapted to open grassland environments, and has persisted into modern horse breeds. One of the first genetic signatures of a domestication event is the release of natural constraints on coat color. Examples can be seen in dogs, cats, chickens, and other domestic animals. Likewise, the horse coat color shows a rapid fragmentation into many different patterns about 5,000 years ago, suggesting that they were domesticated in the Eurasian steppe region during the Bronze Age.
However, two additional coat color patterns in horses predate domestication. These are solid black and the spotted leopard (Lp gene) pattern re-selected in at least 3 modern breeds, including the Nez Perce Appaloosa horse. Their presence in late Pleistocene environments has been documented in the cave drawings, and the genetic signature of the Black and Lp genes have been confirmed from Paleolithic horse bones more than 25,0000 years old. It is likely that these patterns provided better adaptation to dark, shadowy boreal environments that replaced grasslands during European glaciations. I have included below a photograph of one of my own spotted horses hiding in broad daylight near the Fox Science Preserve, a local park in southeast Michigan which re-creates a post-glacial landscape.