The present is often only a faint echo of the past. That is why ancient DNA has totally revolutionized our understanding of the evolutionary past of many branches of the trees of life. The tips of the tree that we see around us today are all that remains of diverse and chaotic brambles which have been thoroughly pruned by chance and necessity. Utilizing present genetic variation researchers have been able to make some very interesting inferences, but you can’t infer that which you lack all evidence for. When it comes to the “megafauna” (i.e., anything bigger than a rat) the past two million years have been very trying, with cold alternating with short warm spells. This has no doubt resulted in thinning every so often as populations go extinct across vast swaths of Eurasia in the face of advancing glaciers. In time the range expands, as populations are re-founded by surviving lineages. But these oscillations drive down long term genetic diversity. In addition, the rise of modern humans has resulted in a great wipe out of whole lineages due to our predatory and avaricious behavior.
Domestic animals are arguably the most extreme case of this dynamic. A recent paper on the genomics of the domestic dog highlighted just how wrongheaded previous assumptions were. The standard thinking was that modern dogs are a derived form of wolf. In other words, dogs are simply a specialized subset of wolves. A domestic wolf as it were. Using whole genome sequencing it turns out that wolves that we see around us today are a sister lineage to dogs. Using wolves as the ancestral form of the dog may not therefore be quite as obvious as we’d thought. Of course it seems likely that the ancestors of the dogs were a wolf lineage of some sort, but we can’t assume that they resemble modern Holarctic wolves.
A similar, more complicated, dynamic is being illustrated by ancient DNA for our own lineage. And now a new paper in PNAS highlights similar dynamics to dogs in horses, Prehistoric genomes reveal the genetic foundation and cost of horse domestication. The authors sequenced two horses from the Taymyr regio
n in Siberia with medium and high coverage. The horses were from 15 and 40 thousand years ago. That means they well predate domestication, which probably occurred in the 5 to 10 thousand year interval.
These results confirm that the wild Przewalski horses are not ancestral to the domestic lineages, and that rather they are simply the single wild lineage which persisted down to the modern period. The horses from Taymyr are more distantly related to modern horses than the Przewalski are, but intriguingly tests of admixture indicate that there was gene flow from lineages more closely related to the Taymyr individuals to the modern lineages. This gene flow has to be very close to the root of the origination of modern domestic horses since all breeds are equally represented in the signal of admixture. In short, the modern lineages of horse, wild and domestic, are but a fraction of the variation of the ancient populations.
They confirm this in a population genomic sense by looking at the enrichment for deleterious mutations. A major confound is that many lineages of horse are inbred, so they corrected for that. It turns out that all modern horses exhibit signs of being subject to a load due to accumulation of deleterious variants because of small population size (specifically, bottlenecks), as selection is less efficient at removing these mutations in small population because it is overwhelmed by random drift.
Finally, there is a lot in the paper on signals of selection around various causal alleles. It’s the typical laundry list. Many of the genes are associated with various pathologies and abnormalities, which shows you the cost of reshaping organisms and their behaviors which can occur due to domestication. Strong selection on major effect alleles often result in a cost due to antagonistic pleiotropy. If the selection benefit is high, then negative consequences be damned! Now, horses are notoriously dumb compared to donkeys, so I’d be curious if the cognitive/behavioral signals are found in humans and other mammals, and how they may have changed over time.
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