The new African “multi-regionalism” & pan-Neanderthalism

We live in times when our understanding of the origin and diversification of modern humans is undergoing great change. More concretely, our understanding of what it means to be human is transforming. The terms are overused, but perhaps it could be called a “revolution” or “paradigm shift” between the year 2000 and today.

At the end of 2010 ancient DNA made it highly likely that people outside of Sub-Saharan Africa had non-trivial Neanderthal ancestry. That is, enough ancestry that it is detectable genomically. I should also add that I think it is highly probable that the good majority of people within Sub-Saharan Africa have Neanderthal ancestry. Some of this is due to recent attenuated Eurasian back-migration (e.g., many West Africans, Nilotic people, and KhoeSan have Holocene gene-flow signals which derive from the agricultural expansions of the past 10,000 years). But, I think once deep Pleistocene genomes of African humans are sequenced we will see evidence of some Eurasian back-migration at a very ancient date (there is already some suggestive inferential evidence of this).*

Talking with a few friends this week, I realized that the famous “We are all Africans” t-shirts, which have turned into recognizable memes, should be supplemented with “We are all Neanderthals” t-shirts. So yeah, now selling them on DNA Geeks. If the Richard Dawkins Foundation can make quid on it, why not the Razib Khan et al. Foundation?

This has all been on my mind due to a review paper in Trends in Ecology and Evolution, Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter? (OA). If you read this blog closely you’ll see there’s not much new in it. But, it is a signpost, a marker, of the times we live in. Here’s the important bit:

Together with recent archaeological and genetic lines of evidence, these data are consistent with the view that our species originated and diversified within strongly subdivided (i.e., structured) populations, probably living across Africa, that were connected by sporadic gene flow…This concept of ‘African multiregionalism’…may also include hybridization between H. sapiens and more divergent hominins (see Glossary) living in different regions…Crucially, such population subdivisions may have been shaped and sustained by shifts in ecological boundaries…challenging the view that our species was endemic to a single region or habitat, and implying an often underacknowledged complexity to our African origins.

The first person who explicitly used the term “African multi-regionalism” that I recall was Alwyn Scally, though the general framework was shaping up years before. Frankly, I was waiting for someone to use that word. If Richard Klein’s The Dawn of Human Culture, published in 2002, was the apogee of the old model, often inchoate and more crisp in popularization than within the scientific community that we are all descended from a single East African tribe, this review paper heralds the emergence of a more complex and pluralistic framework. The emergence of modern humans within Africa then may have been a polycentric gradual and interactive process; not a singular explosion against the firmament of the antique savanna landscape.

By the late 2000s, even before the 2010 Neanderthal draft genome paper, it was starting to be evident due to genome-wide analyses of contemporary populations, that the extreme bottleneck clear in non-African populations was much more modest within Africa. That opened the possibility for the existence of deep structure within the continent that pre-dated the “Out of Africa” event. A deeper look at African hunter-gatherers indicated to many researchers that these groups diverged from other modern humans in the range of ~200,000 years before the well. Recent paleontological work has confirmed this genetic insight.

Where we are today is that some people are now arguing for the overthrow of the “Out-of-Africa” idea, whether by replacing it with an “Into-Africa” model of some sort, or resurrecting a more polycentric classical multi-regionalism (“some people” as evident in the increased frequency of emails and Twitter messages I get in this vein). I don’t think we’re there yet, not by any measure. But, it is now in the realm of very unlikely, not extremely unlikely (at least the “Into-Africa” model; it is clear that strong overwhelming demographic pulses from somewhere singular dominate the genome of most modern humans).

* I don’t think it is all that implausible that some Neanderthal back-migration into Africa occurred at some point in the last ~500,000.

The Ancient Neanderthal Mariner

More recent stuff on Neanderthals of interest, Neandertals, Stone Age people may have voyaged the Mediterranean:

A decade ago, when excavators claimed to have found stone tools on the Greek island of Crete dating back at least 130,000 years, other archaeologists were stunned—and skeptical. But since then, at that site and others, researchers have quietly built up a convincing case for Stone Age seafarers—and for the even more remarkable possibility that they were Neandertals, the extinct cousins of modern humans.

But a growing inventory of stone tools and the occasional bone scattered across Eurasia tells a radically different story. (Wooden boats and paddles don’t typically survive the ages.) Early members of the human family such as Homo erectus are now known to have crossed several kilometers of deep water more than a million years ago in Indonesia, to islands such as Flores and Sulawesi. Modern humans braved treacherous waters to reach Australia by 65,000 years ago. But in both cases, some archaeologists say early seafarers might have embarked by accident, perhaps swept out to sea by tsunamis.

The effective population size of Australian people is just too large for me to imagine that it was only a few individuals swept out on driftwood. There was some sort of sea-going craft which mediated migration to Sahul from Sundaland. Just because we have only recent evidence of sea-going craft doesn’t mean that they weren’t around for tens of thousands of years before that.

I’ve been hearing about Neanderthal tools on islands like Crete, which were never connected with the European mainland, for a while now. It seems that people are finally convinced that this is the real deal, as the stratigraphy came together to confirm dates. One thing that seems obvious from this, as well as Neanderthal “art”, is that the differences between modern humans and Neanderthals were more quantitative than qualitative. Differences of degree, not of kind.

It is hard to deny that modern human expansion between 60 and 15 thousand years ago is sui generis. Hominins didn’t make it to the New World or Sahul, what later became Oceania, until our own kind. There’s also a fair amount of evidence that our lineage pushed the northern frontier of human habitation beyond what Neanderthals ever did. But in the process of marking off our distinctiveness, it seems to me that we’ve overemphasized the differences between us and Neanderthals, and dismissed or ignored evidence of “human-like” “advanced” behaviors from them.

I’ll still go with the prediction that we’ll never find a singular gene which marks us off from other human lineages.

Arabia as Africa-across-the-sea

In antiquity ostriches and lions roamed the Syrian desert. The cheetah even still clings to a tenuous existence in the fastness of the central Iranian desert. The point being that the new finding of African modern human remains on the southeast fringe of Arabia ~85,000 years ago shouldn’t be too surprising. Old modern(ish) looking humans date to 73,000 years before the present in Southeast Asia. Modern-like ancestry can be found in eastern (Altai) Neanderthals dating to ~100,000 years ago. And the earliest humans may have arrived in Australia 65,000 years ago.

These dates are important because the genetic results indicate that much of the population divergence of modern Eurasian, Amerindian, and Oceanian peoples dates to the period between 50 to 60 thousand years ago. This was the classic epoch for the emergence of “behavioral modernity,” and the older models of “Out of Africa” which posited a rapid explosive demographic growth after a punctuated speciation even in East Africa ~60,000 years ago.

Today with remains such as Ust’-Ishim man, we can peg the admixture of Neanderthal into modern Eurasians 52,000 and 58,000 years ago. About the same period that the preponderance of the ancestry of modern Eurasians and peoples of Australia and the Americas expanded across the world, as noted above.

Most peoples in Western and Southern Eurasia also have substantial ancestry from another group which doesn’t seem to have much Neanderthal ancestry at all, the “Basal Eurasians” (BEu). This population obtained its name from the fact that it was hypothesized to have diverged from the common ancestors of northern Eurasians (the Pleistocene peoples of Europe and Siberia), eastern Eurasians, the ancestors of the Amerindians, and Oceanians, before these groups moved on and then separated (i.e., proto-Melanesians are closer to Pleistocene European hunter-gatherers than they are to BEu). These facts suggest proto-BEu was a distinct population >60,000 years ago.

The maximum range of Neanderthals

 

Because of the distribution of Neanderthal admixture across so many groups relatively evenly it probably came from a single major admixture event. Geography tells us that the most likely area of this admixture would be somewhere in the northern area of West Asia.

This implies that BEu was probably resident in the southern area of West Asia, and possibly into North Africa. We do not have any samples which are “pure BEu.” Ancient agriculturalist samples from the western Near East and the eastern Near East are high in BEu ~10,000+ years ago, but these populations are still substantially mixed with a population with affinities to Mesolithic Western European hunter-gatherers (WHG). Fu et al. 2016 use a Pleistocene transect to infer that this affinity between Near Easterners and Europeans dates to the period after ~15,000 years before the present. I presume that this late Pleistocene period was when BEu was admixed away as a pure population by an expanding hunter-gatherer culture with a nexus in Southeast Europe and into Anatolia and the trans-Caucasian region.

The recent Arabian find makes sense I think in the context of BEu and other such populations, which had diverged from the Africa metapopulation ~100,000 years ago, but had not pushed further north and east, and so mixed with Neanderthals.

But what about the older modern human remains which are showing up in eastern Eurasia? I think it is entirely likely that these populations left only a little bit of an imprint in modern groups. A paper from a few years back reported having detected such an admixture in Oceanians. The first ancient genome we have from eastern Eurasia >60,000 years ago that is from a modern human will probably yield much more satisfying results.

The big dynamic looming over the likely existence of anatomically modern human range on the edge of Africa in Arabia is that for several hundred thousand years modern humans existed within Africa as a metapopulation. The proto-Out-of-Africa population can only be understood as part of this broader metapopulation. ~100,000 years before the present humans, inclusive of Neanderthals, Denisovans, and modern humans, our species was probably defined by a set of distinct metapopulations. We know that there was gene flow between these metapopulations, but the strong evidence of purifying selection of Neanderthal and Denisovan ancestry in modern human genomes tells us that this gene flow was minimal enough that biological incompatibilities were beginning to build up and the groups were on their way to speciation as defined by the biological species concept.

There is no evidence of this between any modern populations, even the most diverged (e.g., the Khoisan, who carry Eurasian and African agriculturalist genetic material). This means that within the modern human metapopulation gene flow was sufficient to prevent incompatibilities from developing due to isolation. That being said, with the oldest (proto-)modern human skull dating to ~300,000 years, and likely discernible population structure between various African lineages going beyond 200,000 years ago, there are lots of distinct modern human groups with very long histories within Africa and on its periphery.

The earliest point that you could probably say non-African humans diverged from any African (Sub-Saharan) populations is ~100,000 years ago (and this is probably a bit too generous). A conservative estimate would suggest that modern human lineages were emerging within Africa 200,000 to 300,000 years ago. So most of modern humanity’s existence has been within Africa.

The non-African populations descend from a group which underwent a period of reduced population size vis-a-vis all the African groups. But one thing I think is important to remember is that this was probably not exceptional. We know now that over the past 5,000 years African population genetic structure has been reshaped by events such as the Bantu expansion. But there were surely small and marginal groups with low effective population sizes within Africa that either went extinct or were absorbed by other populations.

The difference in the non-African population is that it was on the edge of the modern human range, and likely occupied territory that was relatively isolated from other modern humans due to the dry nature of the Sahara during most of the Pleistocene. This prevented its absorption into more numerous groups of modern humans further south and to the west. And the strong cultural and genetic barriers with the Neanderthals probably limited gene flow as well.

But even in the inclement conditions of North Africa and West Asia for most of the past 100,000 years, modern humans may have had a larger effective population size than archaic Eurasian hominins. And with this larger effective population size, one can imagine that greater cultural creativity and genetic robustness to dynamics such as population declines gave the modern humans a long-term advantage. In this context, the existence of modern human remains in a diverse array of places across warmer areas of Eurasia before 60,000 isn’t that surprising. And, the demographic wave that swallowed Neanderthals and Denisovans probably swallowed the earlier modern humans who ventured into eastern Eurasia before 60,000 years ago!

Denisovans, Neanderthals, Yetis, oh my!

An excellent open access paper is out in Cell which explores the distribution of archaic hominin, and in particular Denisovan, ancestry, Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture:

Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

Before you get caught up in the results, you should check out the methods. They’re pretty ingenious. Though with novel results like this people also really need to work their way through them as well (the authors present a lot of simulation results to validate the method, so I’m sure that will convince most; it certainly sways me).

The plots at the top of this post show the different distribution of Neanderthal and Denisovan admixture, by matching regions of the genome that they’ve identified as archaically introgressed. The ultimate logic is to look for variants which aren’t found in Africans, and are found in non-Africans, and scan over segments of the genome hoping that you can pick up the haplotypes that would slowly be chopped up over time through recombination that came in from Neanderthals or Denisovans.

At the top-left of the figure, you see “Northwest Europeans.” The segments tend to concentrate at the bottom-right of the panel. That means that they match the Neanderthal reference sequence to a high degree, but not the Denisovan. This makes sense since everything we know from earlier work indicates that Northwest Europeans don’t have Denisovan ancestry.

On the bottom-right you see Papuans. They’re very out of place because they are the only population in the list where Denisovan ancestry is greater than Neanderthal ancestry. This is visible in the match patterns.

South and East Asian populations exhibit a pattern with high (relative) levels of Neanderthal matches, but also a minor amount of Denisovan matching. This aligns with earlier work, which reported low levels of Denisovan admixture among populations with eastern Eurasian ancestry broadly.

The surprise is that the variation in matching to the Denisovan Altai genome exhibited a north-to-south cline. In particular, Northeast Asian populations seem to have a mix of two types of Denisovan. One, which is close to the Denisovan sequence that is normally used as a reference, and one which is diverged from it. The Papuans and South Asians seem to have Denisovan ancestry which is not so much like the Altai sample. This is not very shocking of course.

Finns barely miss the p-value cut-off (Bonferroni-corrected threshold), but they clearly have some Denisovan from East Asian gene flow, and some of it looks to be similar to the Altai Denisovan. Curiously, the Vietnamese (Kinh) don’t show any Altai Denisovan, but the Dai do. The Japanese have a lower proportion of the Altai Denisovan than the two Han Chinese samples. And very strangely the 1K Genomes samples from the New World, a substantial proportion of which have Amerindian admixture, show no Denisovan.

Pontus Skoglund immediately made a very interesting observation:

And Alexander Kim followed up:

In the thread to Skoglund’s original comment Africa Gomez notes that the authors suggest that high linkage disequilibrium in New World populations, due to recent admixture between diverged groups, may reduce the power to detect the Denisovan ancestry. So perhaps that’s that?

But for a moment, let’s set that aside. The best evidence right now is that the Denisovan admixture into Papuans, and therefore South Asians, occurred not too after the Neanderthal admixture event. That mixture is reasonably well dated because of ancient genomes which are closer to the period of admixture. But what about the second event with the Altai Denisovan? If what Skoglund says is true the date for that might be closer to the Last Glacial Maximum, and not when modern humans came to dominate the region. And I say dominate because there’s evidence that anatomically modern humans may have ventured quite far into eastern Eurasia before they finally swept aside more established lineages.

A few years back researchers found that one of the mutations that allow for Tibetan high altitude adaptation seems to have come in from a Denisovan genetic background. Spencer Wells, who knows a thing or two about Central Asia, has always half-seriously suggested that the legends of the Yeti derive from populations of archaic humans who persisted in the uplands of the heart of Eurasia.

But perhaps they weren’t pure Denisovans in any case. Work out of David Reich’s lab has suggested that Denisovans themselves, or at least the Alta Denisovan, harbors a deep ancient lineage diverged from modern humans, Neanderthals, and Denisovans, in low fractions. The “Altai Denisovan” admixture may have come into Northeast Asians via a mixed population, which arose when modern humans came to dominate eastern Eurasia, but only transmitted the Altai Denisovan ancestry later.

Who We Are and How We Got Here, a book worth reading

Yesterday I talked to a friend who has a review copy of Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. They gave me a preview (their overall assessment was positive).

I haven’t personally asked to get a copy because, to be honest, I thought there wouldn’t be anything new in it. If you “read the supplements” what more could there be in 368 pages? So I was waiting until the end of the month to buy the book and read it in my own sweet time as due diligence.

Well, this morning I asked a publicist to send me a copy. I will be getting it next week. The reason is that I’m told the latter portions of the book are quite challenging and candid as to what genetics may tell us in the 21st century. Who We Are and How We Got Here is a 21st-century revision and update of The History and Geography of Human Genes. But it’s apparently a lot more.

Also, I make a small cameo in the book, as does Eurogenes and Dienekes. I have always appreciated how the David Reich and Nick Patterson and their whole lab has taken people outside of the halls of the academy seriously. They didn’t need to as a matter of professional necessity but often engage as a matter of decency and seriousness.

Out of Africa to Out of Eden (well, perhaps not yet)

The recent African origins hypothesis for modern humans had several things going for it. First, most of the old fossils that look like modern humans were in Africa. Chris Stringer and others were pushing the African origins of our modern lineage before genetics came to the fore. But of course, you also have DNA. The mtDNA, Y, and autosomal DNA, which tends to show a pattern where Africans are more diverse, and non-Africans are nested within phylogenies of Africans.

In the 2000s the “Out of Africa” model got a little out of control. The stylized narrative was that a small tribe of East Africans developed some genetic mutation that allowed them to exterminate all other human lineages (e.g., language). This is best encapsulated in Richard Klein’s The Dawn of Human Culture. The British science fiction author Stephen Baxter used this idea as a frame in his novel Evolution (the innovation in this novel was religion though). In this view modern humanity was an African saltation, a great leap forward.

We’re at a different point now. The idea of admixture and/or introgression from non-African lineages into African modern humans is widely accepted. Additionally, both genomic inference and paleontology are pushing the roots of modern humanity much further than ~50,000-60,000 years before the present.

So it’s not as surprising to see a paper like this, The earliest modern humans outside Africa:

To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.

Now, the reality is that Israel is arguably part of “Greater Africa” biogeographically. So it isn’t that surprising. Or it shouldn’t be.

But, this reinforces the reality that anatomically modern humans were geographically already widespread ~200,000 years ago. I would say that this informs and updates our estimation of the plausibility of the Jebel Irhoud modern humans in Morocco, who flourished ~300,000 years ago. It also makes more sense of the reality that most of the ancestors of the Khoisan likely diverged from other modern lineages ~200,000 years ago (or more, depending on who you talk to). Finally, it makes recent archaeological finds of modern humans or their artifacts in East Asia tens of thousands of years before the great expansion of neo-African humanity50,000-60,000 years before the present much more plausible.

There has been some genetic evidence for modern(ish) human expansion before the 50,000 year date. So this isn’t resting only on paleontological evidence.

Where does this leave us? In The Guardian David Reich observes that ‘It’s important to distinguish between the migration out of Africa that’s being discussed here and the “out-of-Africa” migration that is most commonly discussed when referring to genetic data. This [Misliya] lineage contributed little if anything to present-day people.’

Obviously, this is an important point. But we know that the first modern humans to settle Europe did not leave any descendants either.  The modern human settlement of Europe was still nevertheless important. Second, these early wave humans may have given modern populations adaptive variants that are present at high frequencies in modern lineages.

Finally, there’s the issue that this may reorient our understanding about the demographic origins of human populations. Ever so slightly our priors as to an African genesis for our modern lineage are getting weaker. You have two very old modern fossils on the northwest and northeast fringe of the continent. Ten years back the arguments was between those who argued for an East African origin (most), or a minority who favored a Southern Africa one. Now the whole continent, and perhaps even Arabia, are game.

Ultimately, as always, ancient DNA is going to be the final arbiter.

Neanderthal vs us: for wont of a SNP?

Recently at a human evolution conference in England Svante Paabo (or someone in his group) was alluding to discovering how modern humans and Neanderthals differed by looking at the ~30,000 genetic positions (bases) where modern humans and Neanderthals exhibit fixed differences. That is, Neanderthals and modern humans exhibit totally disjoint frequencies.

I’ve been saying this for years, but I’ll say it again: this is probably a fool’s errand. I do think there are major differences at loci which we know about, such as at FOXP2. But, it isn’t clear that even at FOX2 Neanderthals and modern humans exhibited complete lineage sorting. That is, there’s evidence that the Altai Neanderthal had introgression from modern (or modern-related) human populations, and that those variants were sweeping. And there is still variation in modern human populations at FOXP2.

All Homo exhibit encephalization, credit Luke Jostins

It looks like Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome (also see Detecting polygenic adaptation in admixture graphs). But it may be that soft selections and recurring gene flow are common features of the broader Homo lineage for several million years.

In other words, looking for silver bullet variants which can explain why we are so special may always fail, because there are no silver bullets (for several years at ASHG I note that there were presentations which attempted to determine the locus of humanity by looking at the loci of functional interest where Neanderthals and modern humans differed). Rather, human exceptionalism is no exceptionalism, and human populations explore a wide space of phenotypes defined by a huge range of allelic variance which spans many of our extant lineages.

Khoisan may not have diverged ~300,000 years ago


A few years ago I contributed to an op-ed which defended the utility of the race concept in biology in USA Today (which by the way prompted a quite patronizing email from a famous doyen of population genetics who wished to correct my ignorance; here’s a clue: “Out of Africa again & again”).

In my initial draft, I had stated that the Khoisan diverged from other human populations ~200,000 years ago. The fact-checker came back and said that this didn’t seem to be a supportable claim. The reason I gave the ~200,000 figure is that I’d button-holed people who looked at these genomes, and they were coming to the conclusion that the divergence between Khoisan and non-Khoisan was further back than we’d presupposed. And that was the number given to me.

Ultimately I compromised and allowed them to change the divergence value to 150,000 years before the present.

Today we’re in a different landscape. The above figure is from the Science paper, Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago, which was earlier a biorxiv preprint (which I mentioned last spring). In concert with the North African find, the media is running with the idea that the origin of modern humans goes back very far indeed. This piece in ScienceNews is actually pretty good in my opinion at staying under control, though not all write-ups have been so measured.

So in a span of two years we’ve gone from me pushing and compromising on a value of ~150,000 years, to researchers suggesting that the Khoisan/non-Khoisan divergence is about two-fold older than that!

Well, I’m here to tell you that a prominent geneticist who is very conversant with these issues is simply incredulous about the likelihood of this particular value. I brought up this preprint to them over lunch and they just didn’t buy it. That is, they are skeptical that the amount of admixture would have skewed the earlier inferences to the magnitude that they seem to have in these results.

The authors in the paper used G-PhoCS and their own ingenious method to come to these inferences of split dates. The problem with these methods is that the inferences generated aren’t nearly as straightforward as an admixture estimate (which can be checked by something as simple as a PCA). I don’t want to get into the details, but I remember seeing models in the 2000s which inferred that East Asians and Europeans diverged ~25,000 years ago, or that there was no Neanderthal admixture in Europeans (to a high degree of confidence). Models can come out with a lot of values.

More importantly, look at the dates of divergence of non-Africans (Sardinians here) from their closest African relatives.

  • 115,000 years before the present (Dinka-Sardinian) for G-PhoCS
  • 76,000 years before the present for their TT-method

In light of the likelihood that the closest population to non-Africans may have been an East African population represented by Ethiopia Mota individual (along with modern Hadza), we can probably drop that estimate down a bit. But G-PhoCS in particular just gives too old an estimate. There are ways it makes sense (lots of old structure within Africa) of course. I’m just speaking in terms of possibilities.

The diversification of extant modern populations seems to have occurred around ~50,000-60,000 years before the present. This aligns with the archaeology, and the ancient genomes which we have on hand.

Of course the methods in this paper might be right. And the fossil from North Africa does add some plausibility to that. But really the whole field is somewhat unsettled now, and we should be cautious of reporting of definitive truths in the media.

Quantitative genomics, adaptation, and cognitive phenotypes

The human brain utilizes about ~20% of the calories you take in per day. It’s a large and metabolically expensive organ. Because of this fact there are lots of evolutionary models which focus on the brain. In Catching Fire: How Cooking Made Us Human Richard Wrangham suggests that our need for calories to feed our brain is one reason we started to use fire to pre-digest our food. In The Mating Mind Geoffrey Miller seems to suggest that all the things our big complex brain does allows for a signaling of mutational load. And in Grooming, Gossip, and the Evolution of Language Robin Dunbar suggests that it’s social complexity which is driving our encephalization.

These are all theories. Interesting hypotheses and models. But how do we test them? A new preprint on bioRxiv is useful because it shows how cutting-edge methods from evolutionary genomics can be used to explore questions relating to cognitive neuroscience and pyschopathology, Polygenic selection underlies evolution of human brain structure and behavioral traits:

…Leveraging publicly available data of unprecedented sample size, we studied twenty-five traits (i.e., ten neuropsychiatric disorders, three personality traits, total intracranial volume, seven subcortical brain structure volume traits, and four complex traits without neuropsychiatric associations) for evidence of several different signatures of selection over a range of evolutionary time scales. Consistent with the largely polygenic architecture of neuropsychiatric traits, we found no enrichment of trait-associated single-nucleotide polymorphisms (SNPs) in regions of the genome that underwent classical selective sweeps (i.e., events which would have driven selected alleles to near fixation). However, we discovered that SNPs associated with some, but not all, behaviors and brain structure volumes are enriched in genomic regions under selection since divergence from Neanderthals ~600,000 years ago, and show further evidence for signatures of ancient and recent polygenic adaptation. Individual subcortical brain structure volumes demonstrate genome-wide evidence in support of a mosaic theory of brain evolution while total intracranial volume and height appear to share evolutionary constraints consistent with concerted evolution…our results suggest that alleles associated with neuropsychiatric, behavioral, and brain volume phenotypes have experienced both ancient and recent polygenic adaptation in human evolution, acting through neurodevelopmental and immune-mediated pathways.

The preprint takes a kitchen-sink approach, throwing a lot of methods of selection at the phenotype of interest. Also, there is always the issue of cryptic population structure generating false positive associations, but they try to address it in the preprint. I am somewhat confused by this passage though:

Paleobiological evidence indicates that the size of the human skull has expanded massively over the last 200,000 years, likely mirroring increases in brain size.

From what I know human cranial sizes leveled off in growth ~200,000 years ago, peaked ~30,000 years ago, and have declined ever since then. That being said, they find signatures of selection around genes associated with ‘intracranial volume.’

There are loads of results using different methods in the paper, but I was curious note that schizophrenia had hits for ancient and recent adaptation. A friend who is a psychologist pointed out to me that when you look within families “unaffected” siblings of schizophrenics often exhibit deviation from the norm in various ways too; so even if they are not impacted by the disease, they are somewhere along a spectrum of ‘wild type’ to schizophrenic. In any case in this paper they found recent selection for alleles ‘protective’ of schizophrenia.

There are lots of theories one could spin out of that singular result. But I’ll just leave you with the fact that when you have a quantitative trait with lots of heritable variation it seems unlikely it’s been subject to a long period of unidirecitional selection. Various forms of balancing selection seem to be at work here, and we’re only in the early stages of understanding what’s going on. Genuine comprehension will require:

– attention to population genetic theory
– large genomic data sets from a wide array of populations
– novel methods developed by population genomicists
– and funcitonal insights which neuroscientists can bring to the table

18,000 years BC (the film)


Alpha, set 20,000 years ago in Europe, was apparently originally titled “Solutrean.” The change is probably for the best. It will come out next spring. I really hope that this movie is good and does well. It isn’t often that you have something which takes place during the Last Glacial Maximum.

The plot seems to reflect the what you might read in Pat Shipman’s The Invaders, but it’s about 20,000 years too late for her model to work. One of the major criticisms of the idea that dogs and modern humans operated as a team is that it seems way too early. But of late there have been suggestions that the date is earlier than we’d previous thought in relation to when dogs as we understand them arose: Ancient European dog genomes reveal continuity since the Early Neolithic. Here’s the relevant section: “By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000–40,000 years ago.”

Please note though that the divergence of the dog lineage from the ancestors of modern wolves is a distinct question and process from domestication as such as we understand it. Though it seems likely these events didn’t occur too far apart in time.