Ancient Tooth Proteins Tell Tales

An analysis of six ancient Homo erectus tooth proteins from three locations in China, a Denisovan tooth protein, and some modern human and animal tooth proteins reveal some notable insights. Bernard's Blog has the story. Proteins in teeth are easier to recover than ancient DNA and can serve as a proxy for it in cases like these.

Interestingly, it implies that a tooth enamel protein found in 1% of humans in or near the former Denisovan range, and Denisovans have a tooth enamel protein also found in Chinese Homo erectus, probably due to introgression from Homo erectus to Denisovans and then from Denisovans to modern humans, in the view of the researchers.

John Hawk has a discussion of the paper, however, that interprets the data differently:

All six teeth share two derived amino acid changes, both in the sequence of an enamel matrix protein known as ameloblastin, or AMBN. One of these hasn’t before been seen in hominins: a change from alanine to glycine at position 253 of the sequence, or A253G. The other is 20 positions downstream, swapping in valine for the ancestral methionine, M273V. The DNA mutation encoding this change is shared by both the Denisova 3 and Denisova 25 genomes. The M273V amino acid change itself is in the Harbin and Penghu 1 dental proteomes—part of why they align with Denisovans. A number of genomes from modern people also share this change, possibly from Denisovan ancestors.

The hypothesis presented by Fu and coworkers is that Homo erectus was the source of M273V, and its presence in Denisovans is a result of introgression. In support of this idea of introgression, they note earlier research on the Denisova 3 and Denisova 25 genomes that suggests a contribution from a “superarchaic” source population. Many—including me—have speculated that this superarchaic ancestry came from H. erectus. Fu’s team may have just proved it.

But I don’t think these teeth are Homo erectus.

Their estimated ages, all around 400,000 years ago, are prime Denisovan time. Fu and coworkers find that all the teeth share a derived link with later Denisovan genomes. For me, the most likely hypothesis is that these teeth come from a population within the Denisovan branch of humanity.

This situation is basically the same as the Sima de los Huesos fossils. Those remains are around 430,000 years old. Those fossils look like Neanderthals in some subtle ways, but until DNA was recovered from them, many researchers considered them to be part of a different group, often called Homo heidelbergensis. DNA revised both the timeline and their identification.

It may seem heretical, but I think protein data may be about to do the same for fossils from East Asia.