The state of Neanderthals in early 2019

PNAS has published a paper, Limits of long-term selection against Neandertal introgression. It’s from a preprint which I blogged this summer. What are the major takeaways here?

It’s been about 10 years since the draft Neanderthal genome was published. At around that time everyone realized that there was archaic introgression into the modern human genome. More precisely, reticulation in the human phylogeny was a major thing in the time scale of 50,000 years and earlier.

But there were a lot of details to clear up. For example:

  1. Did % Neanderthal admixture vary outside of Africa?
  2. Was there really only one single admixture?
  3. Has natural selection shaped the proportion of Neanderthal genetic material in our genomes?

The reason the new paper above is interesting is that they used differences between Neanderthal populations (of different relatedness to the source into moderns), as well as modeling different demographic scenarios through simulation, to show that:

  1. Neanderthal % is Europe is no different than Asia, rather, there is West Eurasian gene-flow into Africa
  2. Selection against Neanderthal genes seem to have occurred very early, and little later one
  3. Selection seems to be strong around regulatory elements
  4. The lack of variation due to basal Eurasian admixture indicates they may have been part of the admixture

This is not the final world. Rather, it illustrates that though the first pass result stands, a lot of details are being worked out, and that this dynamic field is sensitive to the samples available and theoretical frameworks that leverage those samples.

Neanderthals were human, say it loud and proud

The above tweet captures the essence of something that occasionally happens in science: a revelation that transforms our understanding of the possibilities of the real. 2010’s Neanderthal genome paper did that, transforming a field which was mostly skeptical or cautious of Neanderthal gene flow into modern lineages, to one that was accepting of the likelihood.

Today was a similar event. Neanderthals, the World’s First Misunderstood Artists:

The team found flowstones covering parts of the artworks and scraped away samples for dating. In three caves, it turned out, some of the art was over 64,000 years old — about 20,000 years earlier than the first evidence of modern humans in Europe.

“They must have been made by Neanderthals,” said Dr. Pike.

Wil Roebroeks, an archaeologist at Leiden University who was not involved in the new study, said the evidence was conclusive. “This constitutes a major breakthrough in the field of human evolution studies,” he said. “Neanderthal authorship of some cave art is a fact.”

The colored, pierced shells themselves are probably not much older than that. Up until about 118,000 years ago, the cave was flooded, thanks to higher sea levels.

That finding provides strong evidence that the shells were made by Neanderthals. They were definitely living in Spain 115,000 years ago, while modern humans would not arrive in Europe for another 70,000 years.

The two new studies don’t just indicate that Neanderthals could make cave art and jewelry. They also establish that Neanderthals were making these things long before modern humans — a blow to the idea that they simply copied their cousins.

Chris Stringer thinks this is real too.

What to make of this? First, a shout out to my old friend John Hawks. He’s been slowly repairing the reputation of Neanderthals for many years, and now we’re almost there. Neanderthals had large brains. Their cranial capacities were the largest of all hominins. The idea that they were brutes without language, as Richard Klein hypothesizes in Dawn of Human Culture, seems ludicrous now.

Back in the early 2000s I read Stephen Oppenheimer’s The Real Eve, and one of the arguments that I thought was ludicrous at the time is that the dominance of African humans was not due to some distinct genetic advantage (as Richard Klein posited), but accumulated cultural capital which gradually but continuously compounded over time. Though one shouldn’t discount genes, especially in the context of gene-cultural coevolution, with hindsight it seems clear that a simple causal factor of genetic innovation driving advantages vis-a-vis Neanderthals may be too simplistic.

Papers such as Genomic insights into the origin of farming in the ancient Near East illustrate that first mover advantage can result in huge demographic consequences. Small groups of farmers in the hillocks of the Fertile Crescent 10,000 years ago transitioned to agriculture just early enough that their genetic impact on West and South Eurasian populations, as well as African ones, would be enormous. Similarly, the invention of the light chariot by the Sintashta people may have resulted in the spread of haplogroup R1a-Z93.

The Neanderthal-modern human handover

We live in a time of transitions when it comes to Neanderthals. Since the 2010 discovery of strong genomic evidence for Neanderthal ancestry in most humans they’ve been…humanized. This was pretty much inevitable, but, I also think it was right. Neanderthals were a big-brained human species which dominated much of Eurasia for hundreds of thousands of years. Their culture did exhibit a certain stasis, but then so did that of our modern African ancestors ~200,000 years ago.

There has been a recent debate about how far back the divergence between Neanderthals and modern humans goes back. My own views is that it’s probably further back than 500,000 years, perhaps closer to 750,000 years, but that there may have been ancient gene flow between lineages as well.

A new paper is now out which suggests that Neanderthals persisted in southern Spain for 3,000 years after they disappeared elsewhere, Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia. Obviously, I can’t evaluate the taphonomy and all that. There have long been debates by paleoanthropologists about this region and its Neanderthal habitation (some earlier dates suggested Neanderthals persisted down to 29,000 years ago in southern Spain, but those seem to be rejected). What I can say is that it is entirely expected that the Neanderthal range as it contracted would exhibit an s-shaped trajectory, with a tail where they persisted as relic populations in areas which they were particularly well adapted to.

As paleoanthropology and genetics progress I’m rather sure that we’ll drill-down on very detailed dynamics of interaction, and local succession and replacement. Though humans leave cultural artifacts behind, as a rule the first and last fossils in paleontology usually underestimate the time span that a species flourished. I wouldn’t be surprised if the same applied to Neanderthals, and some day someone with a suspiciously high Neanderthal ancestral fraction was sequenced or genotyped who lived just before the Last Glacial Maximum.

Also, I should mention for those of you looking for a pre-Christmas gift, my company’s Neanderthal product (which does a functional analysis of a set of characteristics where modern humans segregate ancestral and derived variants from the two lineages) can be had for $29.99, as Helix is discounting the $80.00 kit cost (the same applies to the $39.99 Metabolism product, though if you bought Neanderthal earlier then Metabolism is always$39.99 since Helix has banked your data).

People keep asking us the details of the Helix-Insitome relationship and how it works. So we decided to write a blog post addressing that (it’s very short), How does Helix work?.

P.S. we’re probably the only start-up in the world where regular office conversation occurs about Neanderthals.

Basal humans in our evolutionary closet

The ancient genome from South Africa was of not because it confirmed what many had long suspected: the deep structure of modern humans in Africa goes back quite a bit further than we had been assuming. A few years ago I co-wrote an op-ed for USA Today where I initially wrote that the Khoisan divergence from other humans was around ~200,000 years ago. For various reasons I let a “fact-checker” change that to ~150,000 years ago. But as I told my co-author Alex Berezow people had access to whole genomes just leaning toward an older date than in the current literature.

Now we know that the date of divergence may be closer to ~300,000 years. Both because of the ancient DNA, and the Moroccan fossils which make it obvious that morphology associated with our own lineage was already beyond incipient before 300,000 years ago.

The past was more complicated than we think. Ancient DNA has made us toss many of our preconceptions out. For example, several years ago researchers concluded that the Out of Africa populations exhibited a different structure than we had thought. Populations of the Near East and Europe had ancestry from a group that was basal to all other non-Africans. That is, if you have a family tree then Oceanians, East Asians, Amerindians, Siberians, and European hunter-gatherers would be on one branch. On the other branch would be “Basal Eurasians” (BEu), named due to their basal position on the tree in comparison to all other non-Africans. Ancient DNA has not uncovered any population which is mostly BEu. Early Holocene Near Eastern populations, the various first farmers, invariably seem to show mixture between BEu and a West Eurasian element similar to what gave rise to the Mesolithic hunter-gatherers of Europe.

It seems possible we may never find “pure” BEu samples. We know that 10,000-15,000 years ago in Europe there was a massive expansion of a population of hunter-gatherers with stronger affinities to modern Middle Easterners than in the past. Perhaps this was part of a broader expansion of this group of hunter-gatherers across vast swaths of Western Eurasia, and in the process they absorbed the BEu populations until there were no pure populations left?

These questions were triggered by novel results which couldn’t be accommodated by current accepted models. This reminds me of a paper from over a year ago which presented some puzzling results which make much more sense now, Ancient gene flow from early modern humans into Eastern Neanderthals. The authors compared the Altai Neanderthal genome, the Denisovan genome, and those of modern humans (as well as a European Neanderthal). The stylized phylogenetic tree is one which the Neanderthal-Denisovan clade spits off from African proto-modern humans ~600,000 years ago. Then around ~400,000 years ago you see the divergence between Neanderthals and Denisovans. This gives us rough expectations as to the nature of the genetic variation in these populations, as they shared quite distinct periods of evolutionary history together and apart.

What the authors found is that a small minority of the Altai Neanderthal genome exhibited much stronger affinities to modern African populations than to the Denisovan. On the order of ~5%. Looking at the length of the haplotypes they estimated that the admixture occurred ~100,000 year ago. Curiously, at least at the time, this modern human population was basal to all modern humans. The authors estimate that the divergence from modern lineages occurred about ~200,000 year ago based on what was understood about modern human differentiation at the time.

At the time that was pushing it, though not unreasonably so. Now that number is probably comfortably defensible. One important point to note is that the modern human admixture was from a group equally related to all Africans. This implied that this group separated before the division of the Bantu and the Yoruba. So if you accept the most recent genomics then this group may date to closer to 260,000 years before the present. And in fact if the fossil record is correct they might have separated as early 350,000 years before the present. Additionally, the group which published the South African genome study posited another group, Basal Africans (BA), who diverged far earlier than the Khoisan from most African (and also non-African) groups.

Maximal Neanderthal range

The Neanderthals are a well studied group. We know what their range was. One can spit all sorts of speculative scenarios, from wide range proto-modern humans pushing deep in Eurasia during the Eemian interglacial 130,000 years ago. Or, it may have been through contact in the Near East and expansion of a somewhat admixed Neanderthal population north and east over time. Who knows? At least until there’s more ancient DNA….