Interaction and mixture: big picture and small

The traits and genes of living people have diverse histories. Mixture of ancient populations is a big part of that story, revealed more and more by studies of DNA from ancient skeletal remains. This week the Associated Press ran two great articles by Maddie Burakoff and Laura Ungar recounting how this tangled story is changing the way we understand the human past.

The old way of looking at human evolution focuses on why fossil hominins are no longer here. There must have been something wrong with the Neandertals, with Homo erectus, with other ancient groups known from fossils, the story goes, to explain why they became extinct. Today's people are survivors, and there must have been some reason, some advantage that gave our immediate ancestors the edge. The study of human evolution, in this view, amounts to testing hypotheses about why we “won” and everyone else “lost”.

My favorite paraphrase of this way of thinking is the title of a 2004 article by John Speth: “News Flash: Negative Evidence Convicts Neanderthals of Gross Mental Incompetence”.

For the last two decades, an array of evidence from DNA, archaeology, and fossils has given rise to new ways of looking at the human past. Scientists today understand that Neandertals are among the ancestors of today's people, that the vast majority of everyone's genetic heritage comes from Africa, and that those ancestors were never a small population living in any single place. They formed a reticulated tree of ancient lineages going back more than six hundred thousand years.  

Understanding that connectivity has growing importance. I provided some comments about the connections among populations to Burakoff and Ungar for their articles, and they included this line from me:

“Human evolution was not about ‘survival of the fittest and extinction,’ said John Hawks, a paleoanthropologist at the University of Wisconsin-Madison. It’s about ‘interaction and mixture.’”

Interaction and mixture. They matter to the big picture: where populations moved, how they adapted to their local circumstances, and which ones became founders of new species of hominins. They also matter to the microscopic picture: where each of our genes came from, and how variants work together with other genes to build the unique biology of everyone living today.

Every one of us holds a history within our genomes: a history of the ancient contacts across populations that brought genes together, and a history across our individual genes that builds their combined function within our biology.

Working of a Denisovan gene

A new study by Fernando Villanea and coworkers provides a great example of how the fate of a gene can transcend the fates of populations. They examined the variation of a gene called MUC19, one of many genes for glycoproteins known as mucins, which provide the gel-like consistency of mucus secretions. People today sometimes have a haplotype of this gene that is similar to the Denisova 3 genome. Villanea and collaborators found that this Denisova-like version is most common in samples with Indigenous American ancestry, common enough to suspect that some functional effect of the allele was valuable in the ancestors of these populations.

Two Neandertal genomes also had a copy of this Denisova-like haplotype: the high-coverage Chagyrskaya and Vindija genomes. Both likely reflect a history of interbreeding from one or more Denisovan groups, suggesting a very widespread impact of this introgression across time and space.

“These results point to a complex pattern of multiple introgression events, one of which may have played a unique role in the evolutionary history of Indigenous American populations.”—Fernando Villanea and colleagues

Without more knowledge of how variation in the MUC19 glycoprotein matters to function, it's hard to form testable hypotheses about how the Denisova-like allele became common in some groups. Villanea and coworkers point to the membranes of the trachea and bronchi, where the viscosity of mucus makes a difference to bacterial and viral infections. Possibly the Denisova-like allele helped to resist some ancient microbe, akin to other introgressed genes that are involved in the immune system.

Or maybe not. It could be some other of the body's mucus membranes that made this allele valuable. The evidence of its repeated introgression and increase in frequency in some populations suggests that the allele may indeed have fitted the people who carried it to their circumstances. But which circumstances? And how did it fit them?

Eddies and currents of mixture

Where genes came from is a different kind of problem than how the genes work together. Geneticists have made some great progress in tracking the connections of many genes in living people to their origins in ancient populations. It's one thing to accept that mixture happened. Following through on that knowledge requires us to question many of the assumptions that have driven research in the past.

In a new paper, Clive Finlayson and seven coauthors look critically at what we know about the connections between Late Pleistocene populations in western Eurasia. It is still a challenge to learn from a tooth or fragment of skull what the ancestry of an ancient individual may have been. True, there have been a handful of successes from the period of contact between Neandertal and modern populations where anthropologists have noted the possibility of mixture as an explanation for a fossil's morphology, and geneticists later confirmed evidence of mixture from DNA. Finlayson and coworkers mention the Oase 1 mandible; I might add the Zlatý kůň skeleton as a complementary case. Such cases may seem to increase our confidence that morphology can identify fossils accurately. But they challenge the notion that ancestors were separated as strongly as many archaeologists have assumed.

The idea of a “Neandertal trait”, or the confidence in identifying a single tooth as a Neandertal from its morphology, might be meaningful within a world where contacts between Neandertal and other populations are few and restricted in time and space. But those assumptions do not hold within the period from 50,000 to 35,000 years ago when populations with varied ancestry recurrently met. Mapping the eddies and currents of migration and mixture during this long period is beyond the resolution of the evidence.

The populations of that transitional time were like today's people: Their genes came from several ancestral populations and their morphology reflects the particular combination of genes and environment. As Finlayson and coworkers end their essay:

We must now not only accept the reality of the “Neanderthal inside us”, but also that of “us inside the Neanderthals”.—Clive Finlayson and coworkers

When it comes to practical hypothesis testing, recognizing the reality of interactions is just a first step. Most ideas about the end of the Neandertals and dispersal of modern humans have revolved around technology. There's no question that the pattern of stone artifacts changed in Europe and western Asia during the same time that the genetic heritage of populations became less and less Neandertal. Even today, it is common to suppose that any “advanced” elements in artifact assemblages must imply a presence of modern people. But is that true?

Finlayson and coworkers discuss the weakness of associations of technological patterns and genetic patterns. Even burials, which some archaeologists see as a “gold standard” of associating skeletal remains with artifacts, are actually poor evidence. Burials from the last Neandertals and earliest modern humans in Eurasia are extremely rare to begin with—only a handful are known. Finlayson and colleagues correctly emphasize that a burial is by definition intrusive into layers of sediment. In a burial, the body is covered with fill that may have been sourced from inside the hole itself. That is to say, a grave digger may have scooped dirt and old stones out of a hole, put a body into it, and then covered the body with the same dirt and old stones. Thus the potential is high that buried remains may be commingled with artifacts from a different time entirely.

What this leaves is a scattered sample of rock shelters and cave sites where well-stratified layers contain a tooth or bone fragment from an ancient individual. In these cases, the problem of identifying the genetic ancestry of the individual comes to the fore, and low-coverage DNA evidence has not typically been sufficient to answer this question. Today researchers can find DNA evidence from sediment samples that contain microscopic fragments of bone or feces. But this evidence is generally limited to mtDNA, again not sufficient to reflect mixed genetic ancestry.

“In many cases, the evidence linking a human taxon with technology is supported by a small number of sites where human remains attributed to either Neanderthals or Modern Humans have been associated with a particular stone tool technology. This is a dangerous practice which is flawed as it assumes that particular human taxa are exclusively linked to particular technologies, which they are not.”—Clive Finlayson and coworkers

We don't really know which populations made which artifacts. Worse, we don't really know which populations there were.

Without this kind of evidence, we are only starting to understand the technical flexibility of these populations and cultural interchange between them. Every historic and prehistoric case of human migration and contact has complexity. This one lasted for more than 15,000 years, vastly longer than recorded history, much less historic population contacts. It will be exciting to learn what mattered at the interfaces among these populations, ancestral and mixed.

Notes: I highly recommend Speth's article on Neandertal incompetence for readers who may not have seen it. He provides some illuminating examples where archaeologists interpret negative evidence in ways that reflect their priors.

Regarding the “Neandertal inside us”, I've previously written about evidence that Neandertals themselves got around 6% of their genomes from African populations.

References

Burakoff, Maddie & Ungar, Laura. (2023, September 25). We carry DNA from extinct cousins like Neanderthals. Science is now revealing their genetic legacy. AP News. https://apnews.com/article/neanderthals-denisovans-genetics-dna-disease-e49cb7d939cfe5d583e7ed0af8751784

Finlayson, C., Zollikofer, C., Ponce de León, M., Finlayson, G., Carrión, J., Finlayson, S., Giles Guzmán, F., & Shea, J. (2023). Close encounters vs. missed connections? A critical review of the evidence for Late Pleistocene hominin interactions in western Eurasia. Quaternary Science Reviews, 319, 108307. https://doi.org/10.1016/j.quascirev.2023.108307

Speth, J. D. (2004). News Flash: Negative Evidence Convicts Neanderthals of Gross Mental Incompetence. World Archaeology, 36(4), 519–526. https://www.jstor.org/stable/4128285

Ungar, Laura & Burakoff, Maddie. (2023, September 24). Science paints a new picture of the ancient past, when we mixed and mated with other kinds of humans. AP News. https://apnews.com/article/neanderthals-denisovans-ancient-humans-dna-e671a140b75fab3791fbd1c4b77cb6e7

Villanea, F. A., Peede, D., Kaufman, E. J., Anorve-Garibay, V., Dillon, K. E. W., Zeloni, R., Marnetto, D., Moorjani, P., Jay, F., Valdmanis, P. N., Avila-Arcos, M. C., & Huerta-Sanchez, E. (2023). The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection (p. 2023.09.25.559202). bioRxiv. https://doi.org/10.1101/2023.09.25.559202